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1. Global Biobank Meta-analysis Initiative: Powering genetic discovery across human disease

Author: Zhou, Wei, Kanai, Masahiro, Wu, Kuan-Han H, Rasheed, Humaira, Tsuo, Kristin, Hirbo, Jibril B, Wang, Ying, Bhattacharya, Arjun, Zhao, Huiling, Namba, Shinichi, Surakka, Ida, Wolford, Brooke N, Lo Faro, Valeria, Lopera-Maya, Esteban A, Läll, Kristi, Favé, Marie-Julie, Partanen, Juulia J, Chapman, Sinéad B, Karjalainen, Juha, Kurki, Mitja, Maasha, Mutaamba, Brumpton, Ben M, Chavan, Sameer, Chen, Tzu-Ting, Daya, Michelle, Ding, Yi, Feng, Yen-Chen A, Guare, Lindsay A, Gignoux, Christopher R, Graham, Sarah E, Hornsby, Whitney E, Ingold, Nathan, Ismail, Said I, Johnson, Ruth, Laisk, Triin, Lin, Kuang, Lv, Jun, Millwood, Iona Y, Moreno-Grau, Sonia, Nam, Kisung, Palta, Priit, Pandit, Anita, Preuss, Michael H, Saad, Chadi, Setia-Verma, Shefali, Thorsteinsdottir, Unnur, Uzunovic, Jasmina, Verma, Anurag, Zawistowski, Matthew, Zhong, Xue, Afifi, Nahla, Al-Dabhani, Kawthar M, Al Thani, Asma, Bradford, Yuki, Campbell, Archie, Crooks, Kristy, De Bock, Geertruida H, Damrauer, Scott M, Douville, Nicholas J, Finer, Sarah, Fritsche, Lars G, Fthenou, Eleni, Gonzalez-Arroyo, Gilberto, Griffiths, Christopher J, Guo, Yu, Hunt, Karen A, Ioannidis, Alexander, Jansonius, Nomdo M, Konuma, Takahiro, Lee, Ming Ta Michael, Lopez-Pineda, Arturo, Matsuda, Yuta, Marioni, Riccardo E, Moatamed, Babak, Nava-Aguilar, Marco A, Numakura, Kensuke, Patil, Snehal, Rafaels, Nicholas, Richmond, Anne, Rojas-Muñoz, Agustin, Shortt, Jonathan A, Straub, Peter, Tao, Ran, Vanderwerff, Brett, Vernekar, Manvi, Veturi, Yogasudha, Barnes, Kathleen C, Boezen, Marike, Chen, Zhengming, Chen, Chia-Yen, Cho, Judy, Smith, George Davey, Finucane, Hilary K, Franke, Lude, Gamazon, Eric R, Ganna, Andrea, Gaunt, Tom R, Ge, Tian, Huang, Hailiang, Huffman, Jennifer, Katsanis, Nicholas, Koskela, Jukka T, Lajonchere, Clara, Law, Matthew H, Li, Liming, Lindgren, Cecilia M, Loos, Ruth JF, MacGregor, Stuart, Matsuda, Koichi, Olsen, Catherine M, Porteous, David J, Shavit, Jordan A, Snieder, Harold, Takano, Tomohiro, Trembath, Richard C, Vonk, Judith M, Whiteman, David C, Wicks, Stephen J, Wijmenga, Cisca, Wright, John, Zheng, Jie, Zhou, Xiang, Awadalla, Philip, Boehnke, Michael, Bustamante, Carlos D, Cox, Nancy J, Fatumo, Segun, Geschwind, Daniel H, Hayward, Caroline, Hveem, Kristian, Kenny, Eimear E, Lee, Seunggeun, Lin, Yen-Feng, Mbarek, Hamdi, Mägi, Reedik, Martin, Hilary C, Medland, Sarah E, Okada, Yukinori, Palotie, Aarno V, Pasaniuc, Bogdan, Rader, Daniel J, Ritchie, Marylyn D, Sanna, Serena, Smoller, Jordan W, Stefansson, Kari, Van Heel, David A, Walters, Robin G, Zöllner, Sebastian, Biobank Of The Americas, Biobank Japan Project, BioMe, BioVU, CanPath-Ontario Health Study, China Kadoorie Biobank Collaborative Group, Colorado Center For Personalized Medicine, DeCODE Genetics, Estonian Biobank, FinnGen, Generation Scotland, Genes & Health Research Team, LifeLines, Mass General Brigham Biobank, Michigan Genomics Initiative, National Biobank Of Korea, Penn Medicine BioBank, Qatar Biobank, QSkin Sun And Health Study, Taiwan Biobank, HUNT Study, UCLA ATLAS Community Health Initiative, Uganda Genome Resource, UK Biobank, Martin, Alicia R, Willer, Cristen J, Daly, Mark J, Neale, Benjamin M, Namba, Shinichi [0000-0002-7486-3146], Guare, Lindsay A [0000-0001-6988-5319], Palta, Priit [0000-0001-9320-7008], de Bock, Geertruida H [0000-0003-3104-4471], Finer, Sarah [0000-0002-2684-4653], Jansonius, Nomdo M [0000-0002-6495-6568], Rojas-Muñoz, Agustin [0000-0001-7594-0599], Gamazon, Eric R [0000-0003-4204-8734], Ganna, Andrea [0000-0002-8147-240X], Koskela, Jukka T [0000-0002-0154-7222], MacGregor, Stuart [0000-0001-6731-8142], Palotie, Aarno V [0000-0002-2527-5874], and Apollo - University of Cambridge Repository
Subjects: biobank, meta-analysis, genetic association studies, GWAS, ancestry diversity, phenotype harmonization
Abstract: Funder: Biogen, Biobanks facilitate genome-wide association studies (GWASs), which have mapped genomic loci across a range of human diseases and traits. However, most biobanks are primarily composed of individuals of European ancestry. We introduce the Global Biobank Meta-analysis Initiative (GBMI)-a collaborative network of 23 biobanks from 4 continents representing more than 2.2 million consented individuals with genetic data linked to electronic health records. GBMI meta-analyzes summary statistics from GWASs generated using harmonized genotypes and phenotypes from member biobanks for 14 exemplar diseases and endpoints. This strategy validates that GWASs conducted in diverse biobanks can be integrated despite heterogeneity in case definitions, recruitment strategies, and baseline characteristics. This collaborative effort improves GWAS power for diseases, benefits understudied diseases, and improves risk prediction while also enabling the nomination of disease genes and drug candidates by incorporating gene and protein expression data and providing insight into the underlying biology of human diseases and traits.
Published: 2023
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2. Association of Novel Loci With Keratoconus Susceptibility in a Multitrait Genome-Wide Association Study of the UK Biobank Database and Canadian Longitudinal Study on Aging

Author: He, Weixiong, Han, Xikun, Ong, Jue-Sheng, Hewitt, Alex W., Mackey, David A., Gharahkhani, Puya, MacGregor, Stuart, Clinical Genetics, Ophthalmology, and Epidemiology
Subjects: Male, Aging, Canada, Glaucoma, Middle Aged, Keratoconus, United Kingdom, Cornea, Ophthalmology, Young Adult, Humans, Female, Longitudinal Studies, Original Investigation, Biological Specimen Banks, Genome-Wide Association Study
Abstract: IMPORTANCE: Keratoconus can be a debilitating corneal ectasia in which the cornea thins, bulges, and steepens into a conical shape. Early features of keratoconus include myopia and irregular astigmatism, which affect vision and can be treated with contact lenses, collagen cross-linking, or, in advanced cases, corneal transplant. Recent estimates of the prevalence of keratoconus based on results of Scheimpflug imaging in young adults are as high as 1.2%. However, obtaining very large keratoconus data sets for a genome-wide association study (GWAS) is problematic because few population studies include Scheimpflug imaging and because severe keratoconus is relatively rare. OBJECTIVE: To identify novel keratoconus loci using corneal resistance factor (CRF) and central corneal thickness (CCT). DESIGN, SETTING, AND PARTICIPANTS: This multitrait GWAS used European ancestry CRF data from UK Biobank (UKB) (n = 105 427) and the Canadian Longitudinal Study on Aging (CLSA) (n = 18 307) and European ancestry CCT data from the International Glaucoma Genetics Consortium (IGGC) (n = 17 803). The CRF and CCT variants in published keratoconus data sets (4669 cases and 116 547 controls) were compared. The data set from UKB was compiled March 24, 2020; data were released from the CLSA in July 2020; and IGGC data were available from May 1, 2018. MAIN OUTCOMES AND MEASURES: Association of CRF and CCT variants with keratoconus risk. RESULTS: The GWAS included 4 cohorts: 105 427 UKB European ancestry (56 134 women [53.2%] and 49 293 men [46.7%]; mean [SD] age, 57 [8] years), 5029 UKB South Asian ancestry (2368 women [47.1%] and 2661 men [52.9%]; mean [SD] age, 54 [8] years), 902 UKB East Asian ancestry (622 women [68.9%] and 280 men [31.0%]; mean [SD] age, 53 [8] years), and 18 307 CLSA European ancestry (9260 women [50.6%] and 9047 men [49.4%]; mean [SD] age, 63 [10] years) participants. A total of 369 CRF and 233 CCT loci were identified, including 36 novel CRF loci and 114 novel CCT loci. Twenty-nine CRF loci and 24 CCT loci were associated with keratoconus. Polygenic risk scores (PRS) were constructed using CRF- and CCT-associated variants and published keratoconus variants. The PRS result showed that adding a CRF- or CCT-based PRS to the keratoconus PRS from previously published variants improved the prediction area under the receiver operating characteristic curve (from 0.705 to 0.756 for CRF and from 0.715 to 0.755 for CCT). CONCLUSIONS AND RELEVANCE: These findings support the use of multitrait modeling of corneal parameters in a relatively large data set to identify new keratoconus risk loci and enhance polygenic risk score models.
Published: 2022

3. The genetic basis of endometriosis and comorbidity with other pain and inflammatory conditions

Author: Rahmioglu, Nilufer, Mortlock, Sally, Ghiasi, Marzieh, Møller, Peter L, Stefansdottir, Lilja, Galarneau, Geneviève, Turman, Constance, Danning, Rebecca, Law, Matthew H, Sapkota, Yadav, Christofidou, Paraskevi, Skarp, Sini, Giri, Ayush, Banasik, Karina, Krassowski, Michal, Lepamets, Maarja, Marciniak, Błażej, Nõukas, Margit, Perro, Danielle, Sliz, Eeva, Sobalska-Kwapis, Marta, Thorleifsson, Gudmar, Topbas-Selcuki, Nura F, Vitonis, Allison, Westergaard, David, Arnadottir, Ragnheidur, Burgdorf, Kristoffer S, Campbell, Archie, Cheuk, Cecilia SK, Clementi, Caterina, Cook, James, De Vivo, Immaculata, DiVasta, Amy, Dorien, O, Donoghue, Jacqueline F, Edwards, Todd, Fontanillas, Pierre, Fung, Jenny N, Geirsson, Reynir T, Girling, Jane E, Harkki, Paivi, Harris, Holly R, Healey, Martin, Heikinheimo, Oskari, Holdsworth-Carson, Sarah, Hostettler, Isabel C, Houlden, Henry, Houshdaran, Sahar, Irwin, Juan C, Jarvelin, Marjo-Riitta, Kamatani, Yoichiro, Kennedy, Stephen H, Kepka, Ewa, Kettunen, Johannes, Kubo, Michiaki, Kulig, Bartosz, Kurra, Venla, Laivuori, Hannele, Laufer, Marc R, Lindgren, Cecilia M, MacGregor, Stuart, Mangino, Massimo, Martin, Nicholas G, Matalliotaki, Charoula, Matalliotakis, Michail, Murray, Alison D, Ndungu, Anne, Nezhat, Camran, Olsen, Catherine M, Opoku-Anane, Jessica, Padmanabhan, Sandosh, Paranjpe, Manish, Peters, Maire, Polak, Grzegorz, Porteous, David J, Rabban, Joseph, Rexrode, Kathyrn M, Romanowicz, Hanna, Saare, Merli, Saavalainen, Liisu, Schork, Andrew J, Sen, Sushmita, Shafrir, Amy L, Siewierska-Górska, Anna, Słomka, Marcin, Smith, Blair H, Smolarz, Beata, Szaflik, Tomasz, Szyłło, Krzysztof, Takahashi, Atsushi, Terry, Kathryn L, Tomassetti, Carla, Treloar, Susan A, Vanhie, Arne, Vincent, Katy, Vo, Kim C, Werring, David J, Zeggini, Eleftheria, Zervou, Maria I, and DBDS Genomic Consortium
Subjects: Prevention, Contraception/Reproduction, Pain Research, Endometriosis, DBDS Genomic Consortium, Pain, FinnGen Study, Comorbidity, Biological Sciences, 23andMe Research Team, Medical and Health Sciences, Clinical Research, Infertility, Genetics, Humans, 2.1 Biological and endogenous factors, Genetic Predisposition to Disease, Female, Celmatix Research Team, Chronic Pain, Aetiology, FinnGen Endometriosis Taskforce, Genome-Wide Association Study, Developmental Biology
Abstract: Endometriosis is a common condition associated with debilitating pelvic pain and infertility. A genome-wide association study meta-analysis, including 60,674 cases and 701,926 controls of European and East Asian descent, identified 42 genome-wide significant loci comprising 49 distinct association signals. Effect sizes were largest for stage 3/4 disease, driven by ovarian endometriosis. Identified signals explained up to 5.01% of disease variance and regulated expression or methylation of genes in endometrium and blood, many of which were associated with pain perception/maintenance (SRP14/BMF, GDAP1, MLLT10, BSN and NGF). We observed significant genetic correlations between endometriosis and 11 pain conditions, including migraine, back and multisite chronic pain (MCP), as well as inflammatory conditions, including asthma and osteoarthritis. Multitrait genetic analyses identified substantial sharing of variants associated with endometriosis and MCP/migraine. Targeted investigations of genetically regulated mechanisms shared between endometriosis and other pain conditions are needed to aid the development of new treatments and facilitate early symptomatic intervention.
Published: 2023

4. The genetic basis of endometriosis and comorbidity with other pain and inflammatory conditions

Author: Rahmioglu, Nilufer, Mortlock, Sally, Ghiasi, Marzieh, Møller, Peter L., Stefansdottir, Lilja, Galarneau, Geneviève, Turman, Constance, Danning, Rebecca, Law, Matthew H., Sapkota, Yadav, Christofidou, Paraskevi, Skarp, Sini, Giri, Ayush, Banasik, Karina, Krassowski, Michal, Lepamets, Maarja, Marciniak, Błażej, Nõukas, Margit, Perro, Danielle, Sliz, Eeva, Sobalska-Kwapis, Marta, Thorleifsson, Gudmar, Topbas-Selcuki, Nura F., Vitonis, Allison, Westergaard, David, Arnadottir, Ragnheidur, Burgdorf, Kristoffer S., Campbell, Archie, Cheuk, Cecilia S. K., Clementi, Caterina, Cook, James, De Vivo, Immaculata, DiVasta, Amy, Dorien, O., Donoghue, Jacqueline F., Edwards, Todd, Fontanillas, Pierre, Fung, Jenny N., Geirsson, Reynir T., Girling, Jane E., Harkki, Paivi, Harris, Holly R., Healey, Martin, Heikinheimo, Oskari, Holdsworth-Carson, Sarah, Hostettler, Isabel C., Houlden, Henry, Houshdaran, Sahar, Irwin, Juan C., Jarvelin, Marjo-Riitta, Kamatani, Yoichiro, Kennedy, Stephen H., Kepka, Ewa, Kettunen, Johannes, Kubo, Michiaki, Kulig, Bartosz, Kurra, Venla, Laivuori, Hannele, Laufer, Marc R., Lindgren, Cecilia M., MacGregor, Stuart, Mangino, Massimo, Martin, Nicholas G., Matalliotaki, Charoula, Matalliotakis, Michail, Murray, Alison D., Ndungu, Anne, Nezhat, Camran, Olsen, Catherine M., Opoku-Anane, Jessica, Padmanabhan, Sandosh, Paranjpe, Manish, Peters, Maire, Polak, Grzegorz, Porteous, David J., Rabban, Joseph, Rexrode, Kathyrn M., Romanowicz, Hanna, Saare, Merli, Saavalainen, Liisu, Schork, Andrew J., Sen, Sushmita, Shafrir, Amy L., Siewierska-Górska, Anna, Słomka, Marcin, Smith, Blair H., Smolarz, Beata, Szaflik, Tomasz, Szyłło, Krzysztof, Takahashi, Atsushi, Terry, Kathryn L., Tomassetti, Carla, Treloar, Susan A., Vanhie, Arne, Vincent, Katy, Vo, Kim C., Werring, David J., Zeggini, Eleftheria, Zervou, Maria I., Stefansson, Kari, Nyegaard, Mette, Uimari, Outi, Yurttas-Beim, Piraye, Tung, Joyce Y., Adachi, Sosuke, Buring, Julie E., Ridker, Paul M., D’Hooghe, Thomas, Goulielmos, George N., Hapangama, Dharani K., Hayward, Caroline, Horne, Andrew W., Low, Siew-Kee, Martikainen, Hannu, Chasman, Daniel I., Rogers, Peter A. W., Saunders, Philippa T., Sirota, Marina, Spector, Tim, Strapagiel, Dominik, Whiteman, David C., Giudice, Linda C., Velez-Edwards, Digna R., Kraft, Peter, Salumets, Andres, Nyholt, Dale R., Mägi, Reedik, Becker, Christian M., Steinthorsdottir, Valgerdur, Missmer, Stacey A., Montgomery, Grant W., Morris, Andrew P., and Zondervan, Krina T.
Subjects: genome-wide association studies, gene expression, genomics, Genetics, Humans, Pain, Female, Genetic Predisposition to Disease, Comorbidity, reproductive disorders, Article, Endometriosis/genetics, Genome-Wide Association Study
Abstract: Endometriosis is a common condition associated with debilitating pelvic pain and infertility. A genome-wide association study meta-analysis, including 60,674 cases and 701,926 controls of European and East Asian descent, identified 42 genome-wide significant loci comprising 49 distinct association signals. Effect sizes were largest for stage 3/4 disease, driven by ovarian endometriosis. Identified signals explained up to 5.01% of disease variance and regulated expression or methylation of genes in endometrium and blood, many of which were associated with pain perception/maintenance (SRP14/BMF, GDAP1, MLLT10, BSN and NGF). We observed significant genetic correlations between endometriosis and 11 pain conditions, including migraine, back and multisite chronic pain (MCP), as well as inflammatory conditions, including asthma and osteoarthritis. Multitrait genetic analyses identified substantial sharing of variants associated with endometriosis and MCP/migraine. Targeted investigations of genetically regulated mechanisms shared between endometriosis and other pain conditions are needed to aid the development of new treatments and facilitate early symptomatic intervention.
Published: 2023

5. No Strong Association between the Apolipoprotein E E4 Allele and Glaucoma: A Multicohort Study

Author: Mullany, Sean, Diaz-Torres, Santiago, Schmidt, Joshua M., Thomson, Daniel, Qassim, Ayub, Marshall, Henry N., Knight, Lachlan S.W., Berry, Ella C., Kolovos, Antonia, Dimasi, David, Lake, Stewart, Mills, Richard A., Landers, John, Mitchell, Paul, Healey, Paul R., Commerford, Toby, Klebe, Sonja, Souzeau, Emmanuelle, Hassall, Mark M., MacGregor, Stuart, Gharahkhani, Puya, Siggs, Owen M., and Craig, Jamie E.
Subjects: Original Article
Abstract: PURPOSE: To elucidate a potential association between the apolipoprotein E (APOE) E4 allele and glaucoma prevalence in large cohorts. DESIGN: A cross-sectional analysis of baseline and prospectively collected cohort data. PARTICIPANTS: UK Biobank (UKBB) participants of genetically determined European ancestry (n = 438 711). Replication analyses were performed using clinical and genotyping data collected from European participants recruited to the Canadian Longitudinal Study of Aging (CLSA; n = 18 199), the Australian and New Zealand Registry of Advanced Glaucoma (ANZRAG; n = 1970), and the Blue Mountains Eye Study (BMES; n = 2440). METHODS: Apolipoprotein E alleles and genotypes were determined, and their distributions were compared on the basis of glaucoma status. Similar analyses were performed using positive control outcomes associated with the APOE E4 allele (death, dementia, age-related macular degeneration) and negative control outcomes not associated with the APOE E4 allele (cataract, diabetic eye disease). Outcome phenotypes were also correlated with Alzheimer’s dementia (AD), a clinical outcome highly associated with the APOE E4 allele. MAIN OUTCOME MEASURES: Results of APOE E4 genotype-phenotype comparisons were reported as odds ratios (ORs) with 95% confidence intervals (CIs). Replication analyses investigated APOE E4 associations in 2 replication cohorts (CLSA and ANZRAG/BMES). RESULTS: The APOE E4 allele was inversely associated with glaucoma (OR, 0.96; 95% CI, 0.93–0.99; P = 0.016) and both negative controls (cataract: OR, 0.98; 95% CI, 0.96–0.99; P = 0.015; diabetic eye disease: OR, 0.92; 95% CI, 0.87–0.97; P = 0.003) in the UKBB cohort. A paradoxical positive association was observed between AD and both glaucoma (OR, 1.30; 95% CI, 1.08–1.54; P < 0.01) and cataract (OR, 1.15; 1.04–1.28; P = 0.018). No association between the APOE E4 allele and glaucoma was observed in either replication cohort (CLSA: OR, 1.03; 95% CI, 0.89–1.19; P = 0.66; ANZRAG/BMES: OR, 0.97; 95% CI, 0.84–1.12; P = 0.65). CONCLUSIONS: A small negative association observed between APOE E4 and glaucoma within the UKBB was not evident in either replication cohort and may represent an artifact of glaucoma underdiagnosis in APOE E4 carriers. FINANCIAL DISCLOSURE(S): The author(s) have no proprietary or commercial interest in any materials discussed in this article.
Published: 2023

6. Rare variant analyses across multiethnic cohorts identify novel genes for refractive error

Author: Musolf, Anthony M., Haarman, Annechien E. G., Luben, Robert N., Ong, Jue-Sheng, Patasova, Karina, Trapero, Rolando Hernandez, Marsh, Joseph, Jain, Ishika, Jain, Riya, Wang, Paul Zhiping, Lewis, Deyana D., Tedja, Milly S., Iglesias, Adriana I., Li, Hengtong, Cowan, Cameron S., Baird, Paul Nigel, Veluchamy, Amutha Barathi, Burdon, Kathryn P., Campbell, Harry, Chen, Li Jia, Cheng, Ching-Yu, Chew, Emily Y., Craig, Jamie E., Cumberland, Phillippa M., Deangelis, Margaret M., Delcourt, Cécile, Ding, Xiaohu, Evans, David M., Fan, Qiao, Fossarello, Maurizio, Foster, Paul J., Gharahkhani, Puya, Guggenheim, Jeremy A., Guo, Xiaobo, Han, Xikun, He, Mingguang, Hewitt, Alex W., Hoang, Quan V., Iyengar, Sudha K., Jonas, Jost B., Kähönen, Mika, Kaprio, Jaakko, Klein, Barbara E., Lass, Jonathan H., Lee, Kris, Lehtimäki, Terho, Lewis, Deyana, Li, Qing, Li, Shi-Ming, Lyytikäinen, Leo-Pekka, MacGregor, Stuart, Mackey, David A., Martin, Nicholas G., Meguro, Akira, Middlebrooks, Candace, Miyake, Masahiro, Mizuki, Nobuhisa, Musolf, Anthony, Nickels, Stefan, Oexle, Konrad, Pang, Chi Pui, Paterson, Andrew D., Pennell, Craig, Pfeiffer, Norbert, Polasek, Ozren, Rahi, Jugnoo S., Raitakari, Olli, Rudan, Igor, Sahebjada, Srujana, Simpson, Claire L., Tai, E-Shyong, Tideman, J. Willem L., Tsujikawa, Akitaka, Wang, Ningli, Bin, Wei Wen, Williams, Cathy, Williams, Katie M., Wilson, James F., Wojciechowski, Robert, Wang, Ya Xing, Yamashiro, Kenji, Yam, Jason C. S., Yap, Maurice K. H., Yazar, Seyhan, Yip, Shea Ping, Young, Terri L., Zhou, Xiangtian, Biino, Ginevra, Klein, Alison P., Duggal, Priya, Hayward, Caroline, Haller, Toomas, Metspalu, Andres, Wedenoja, Juho, Pärssinen, Olavi, Saw, Seang-Mei, Stambolian, Dwight, Hysi, Pirro G., Khawaja, Anthony P., Vitart, Veronique, Hammond, Christopher J., van Duijn, Cornelia M., Verhoeven, Virginie J. M., Klaver, Caroline C. W., and Bailey-Wilson, Joan E.
Subjects: genetic predisposition to disease, perinnölliset taudit, ympäristötekijät, taittovirheet, perinnöllisyyslääketiede, riskitekijät, quantitative trait, periytyvyys, genome-wide association studies, quantitative trait loci, perimä, silmätaudit, microarrays, perinnöllisyys
Abstract: Refractive error, measured here as mean spherical equivalent (SER), is a complex eye condition caused by both genetic and environmental factors. Individuals with strong positive or negative values of SER require spectacles or other approaches for vision correction. Common genetic risk factors have been identified by genome-wide association studies (GWAS), but a great part of the refractive error heritability is still missing. Some of this heritability may be explained by rare variants (minor allele frequency [MAF] ≤ 0.01.). We performed multiple gene-based association tests of mean Spherical Equivalent with rare variants in exome array data from the Consortium for Refractive Error and Myopia (CREAM). The dataset consisted of over 27,000 total subjects from five cohorts of Indo-European and Eastern Asian ethnicity. We identified 129 unique genes associated with refractive error, many of which were replicated in multiple cohorts. Our best novel candidates included the retina expressed PDCD6IP, the circadian rhythm gene PER3, and P4HTM, which affects eye morphology. Future work will include functional studies and validation. Identification of genes contributing to refractive error and future understanding of their function may lead to better treatment and prevention of refractive errors, which themselves are important risk factors for various blinding conditions. peerReviewed
Published: 2023

7. GWAS meta-analysis of 16 790 patients with Barrett’s oesophagus and oesophageal adenocarcinoma identifies 16 novel genetic risk loci and provides insights into disease aetiology beyond the single marker level

Author: Schröder, Julia, Chegwidden, Laura, Maj, Carlo, Gehlen, Jan, Speller, Jan, Böhmer, Anne C., Borisov, Oleg, Hess, Timo, Kreuser, Nicole, Venerito, Marino, Alakus, Hakan, May, Andrea, Gerges, Christian, Schmidt, Thomas, Thieme, Rene, Heider, Dominik, Hillmer, Axel M., Reingruber, Julian, Lyros, Orestis, Dietrich, Arne, Hoffmeister, Albrecht, Mehdorn, Matthias, Lordick, Florian, Stocker, Gertraud, Hohaus, Michael, Reim, Daniel, Kandler, Jennis, Müller, Michaela, Ebigbo, Alanna, Fuchs, Claudia, Bruns, Christiane J., Hölscher, Arnulf H., Lang, Hauke, Grimminger, Peter P., Dakkak, Dani, Vashist, Yogesh, May, Sandra, Görg, Siegfried, Franke, Andre, Ellinghaus, David, Galavotti, Sara, Veits, Lothar, Weismüller, Josef, Dommermuth, Jens, Benner, Udo, Rösch, Thomas, Messmann, Helmut, Schumacher, Brigitte, Neuhaus, Horst, Schmidt, Carsten, Wissinowski, Thaddäus T., Nöthen, Markus M., Dong, Jing, Ong, Jue-Sheng, Buas, Matthew F., Thrift, Aaron P., Vaughan, Thomas L., Tomlinson, Ian, Whiteman, David C., Fitzgerald, Rebecca Claire, Jankowski, Janusz, Vieth, Michael, Mayr, Andreas, Gharahkhani, Puya, MacGregor, Stuart, Gockel, Ines, Palles, Claire, Schumacher, Johannes, Prenen, Hans, Wellcome Trust Case Control Consortium 2 (WTCCC2), Esophageal Adenocarcinoma Genetics Consortium (EAGLE), Barrett's and Esophageal Adenocarcinoma Consortium (BEACON), Wellcome Trust Case Control Consortium 2 (WTCCC2), Esophageal Adenocarcinoma Genetics Consortium (EAGLE), and Barrett's and Esophageal Adenocarcinoma Consortium (BEACON)
Subjects: Gastroenterology, Human medicine, Biology
Abstract: ObjectiveOesophageal cancer (EC) is the sixth leading cause of cancer-related deaths. Oesophageal adenocarcinoma (EA), with Barrett’s oesophagus (BE) as a precursor lesion, is the most prevalent EC subtype in the Western world. This study aims to contribute to better understand the genetic causes of BE/EA by leveraging genome wide association studies (GWAS), genetic correlation analyses and polygenic risk modelling.DesignWe combined data from previous GWAS with new cohorts, increasing the sample size to 16 790 BE/EA cases and 32 476 controls. We also carried out a transcriptome wide association study (TWAS) using expression data from disease-relevant tissues to identify BE/EA candidate genes. To investigate the relationship with reported BE/EA risk factors, a linkage disequilibrium score regression (LDSR) analysis was performed. BE/EA risk models were developed combining clinical/lifestyle risk factors with polygenic risk scores (PRS) derived from the GWAS meta-analysis.ResultsThe GWAS meta-analysis identified 27 BE and/or EA risk loci, 11 of which were novel. The TWAS identified promising BE/EA candidate genes at seven GWAS loci and at five additional risk loci. The LDSR analysis led to the identification of novel genetic correlations and pointed to differences in BE and EA aetiology. Gastro-oesophageal reflux disease appeared to contribute stronger to the metaplastic BE transformation than to EA development. Finally, combining PRS with BE/EA risk factors improved the performance of the risk models.ConclusionOur findings provide further insights into BE/EA aetiology and its relationship to risk factors. The results lay the foundation for future follow-up studies to identify underlying disease mechanisms and improving risk prediction.
Published: 2023

8. MicroED Characterization of a Robust Cationic -Alkane Complex Stabilized by the [B(3,5-(SF5)2C6H3)4]– Anion, via On-Grid Solid/Gas Single-Crystal to Single-Crystal Reactivity

Author: Weller, Andrew, Doyle, Laurence Robertson, Thompson, Emily, Burnage, Arron L., Whitwood, Adrian C., Jenkins, Huw Thomas, and Macgregor, Stuart A.
Abstract: Microcrystalline (~1 m) [Rh(Cy2PCH2CH2PCy2)(norbornadiene)][S-BArF4], [S-BArF4] = [B(3,5-(SF5)2C6H3)4]–, reacts with H2 in a single-crystal to single-crystal transformation to form the -alkane complex [Rh(Cy2PCH2CH2PCy2)(norbornane)][S-BArF4], for which the structure was determined by microcrystal Electron Diffraction (microED), to 0.95 Å resolution, via an on-grid hydrogenation, and a complementary single-crystal X-ray diffraction study on larger, but challenging to isolate, crystals. Comparison with the [BArF4]– analogue [ArF = 3,5-(CF3)2C5H3)] shows that the [S-BArF4]– anion makes the -alkane complex robust towards decomposition both thermally and when suspended in pentane. Subsequent reactivity with dissolved ethene in a pentane slurry, forms [Rh(Cy2PCH2CH2PCy2)(ethene)2][S-BArF4], and the catalytic dimerisation/isomerisation of ethene to 2-butenes. The increased stability of [S-BArF4]– salts is identified as being due to increased non-covalent interactions in the lattice, resulting in a solid-state molecular organometallic material with desirable stability characteristics.
Published: 2022

9. eQTL Set-Based Association Analysis Identifies Novel Susceptibility Loci for Barrett Esophagus and Esophageal Adenocarcinoma

Author: Wang, Xiaoyu, Gharahkhani, Puya, Levine, David M., Fitzgerald, Rebecca C., Gockel, Ines, Corley, Douglas A., Risch, Harvey A., Bernstein, Leslie, Chow, Wong-Ho, Onstad, Lynn, Shaheen, Nicholas J., Lagergren, Jesper, Hardie, Laura J., Wu, Anna H., Pharoah, Paul D.P., Liu, Geoffrey, Anderson, Lesley A., Iyer, Prasad G., Gammon, Marilie D., Caldas, Carlos, Ye, Weimin, Barr, Hugh, Moayyedi, Paul, Harrison, Rebecca, Watson, R.G. Peter, Attwood, Stephen, Chegwidden, Laura, Love, Sharon B., MacDonald, David, deCaestecker, John, Prenen, Hans, Ott, Katja, Moebus, Susanne, Venerito, Marino, Lang, Hauke, Mayershofer, Rupert, Knapp, Michael, Veits, Lothar, Gerges, Christian, Weismüller, Josef, Reeh, Matthias, Nöthen, Markus, Izbicki, Jakob R., Manner, Hendrik, Neuhaus, Horst, Rösch, Thomas, Böhmer, Anne C., Hölscher, Arnulf H., Anders, Mario, Pech, Oliver, Schumacher, Brigitte, Schmidt, Claudia, Schmidt, Thomas, Noder, Tania, Lorenz, Dietmar, Vieth, Michael, May, Andrea, Hess, Timo, Kreuser, Nicole, Becker, Jessica, Ell, Christian, Tomlinson, Ian, Palles, Claire, Jankowski, Janusz A., Whiteman, David C., MacGregor, Stuart, Schumacher, Johannes, Vaughan, Thomas L., Buas, Matthew F., Dai, James Y., DeCaestecker, John, Weismueller, Josef, Noethen, Markus M., Roesch, Thomas, Boehmer, Anne C., and Hoelscher, Arnulf H.
Subjects: Barrett Esophagus, Renal disorders Radboud Institute for Molecular Life Sciences [Radboudumc 11], Oncology, Esophageal Neoplasms, Epidemiology, Quantitative Trait Loci, Medizin, Humans, Genetic Predisposition to Disease, Human medicine, Adenocarcinoma, Biology, Article
Abstract: Background: Over 20 susceptibility single-nucleotide polymorphisms (SNP) have been identified for esophageal adenocarcinoma (EAC) and its precursor, Barrett esophagus (BE), explaining a small portion of heritability. Methods: Using genetic data from 4,323 BE and 4,116 EAC patients aggregated by international consortia including the Barrett's and Esophageal Adenocarcinoma Consortium (BEACON), we conducted a comprehensive transcriptome-wide association study (TWAS) for BE/EAC, leveraging Genotype Tissue Expression (GTEx) gene-expression data from six tissue types of plausible relevance to EAC etiology: mucosa and muscularis from the esophagus, gastroesophageal (GE) junction, stomach, whole blood, and visceral adipose. Two analytical approaches were taken: standard TWAS using the predicted gene expression from local expression quantitative trait loci (eQTL), and set-based SKAT association using selected eQTLs that predict the gene expression. Results: Although the standard approach did not identify significant signals, the eQTL set–based approach identified eight novel associations, three of which were validated in independent external data (eQTL SNP sets for EXOC3, ZNF641, and HSP90AA1). Conclusions: This study identified novel genetic susceptibility loci for EAC and BE using an eQTL set–based genetic association approach. Impact: This study expanded the pool of genetic susceptibility loci for EAC and BE, suggesting the potential of the eQTL set–based genetic association approach as an alternative method for TWAS analysis.
Published: 2022

10. Additional file 1 of Higher polygenic risk for melanoma is associated with improved survival in a high ultraviolet radiation setting

Author: Seviiri, Mathias, Scolyer, Richard A., Bishop, D. Timothy, Newton-Bishop, Julia A., Iles, Mark M., Lo, Serigne N., Stretch, Johnathan R., Saw, Robyn P. M., Nieweg, Omgo E., Shannon, Kerwin F., Spillane, Andrew J., Gordon, Scott D., Olsen, Catherine M., Whiteman, David C., Landi, Maria Teresa, Thompson, John F., Long, Georgina V., MacGregor, Stuart, and Law, Matthew H.
Abstract: Additional file 1: Figure 1. Manhattan plot for the MSS GWAS meta-analysis between MIA and UKB cohorts. Figure 2. Skin colour polygenic risk score model performance in the validation cohort (QSkin). The x-axis represents the different melanoma polygenic risk score (PRS) models of varying fractions of causal SNPs (i.e. 1 (F0), 0.1 (F1), 0.01 (F2),0.001(F3),0.0001 (F4) and 0.00002 (F5)) at the different radii of the linkage disequilibrium (LD) (i.e. 2 megabase (mb) and 5 mb). The y-axis represents Nagelkerke’s R2 (%) for each of the 12 PRS models. The horizontal dashed black line highlights the optimal model (F1-2mb) (i.e. with the highest Nagelkerke’s R2). Figure 3. The association between polygenic risk scores and the risk of melanoma in QSkin. Figure 4. The association by quartile of polygenic risk for melanoma susceptibility and melanoma specific survival in the MIA cohort. Figure 5. Association of standalone skin colour and naevus PRSs and melanoma specific survival in MIA and UKB.
Published: 2022
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11. Genome-wide meta-analysis identifies 127 open-angle glaucoma loci with consistent effect across ancestries

Author: Gharahkhani, Puya, Jorgenson, Eric, Hysi, Pirro, Khawaja, Anthony P, Pendergrass, Sarah, Han, Xikun, Ong, Jue Sheng, Hewitt, Alex W, Segrè, Ayellet V, Rouhana, John M, Hamel, Andrew R, Igo, Robert P, Choquet, Helene, Qassim, Ayub, Josyula, Navya S, Cooke Bailey, Jessica N, Bonnemaijer, Pieter WM, Iglesias, Adriana, Siggs, Owen M, Young, Terri L, Vitart, Veronique, Thiadens, Alberta AHJ, Karjalainen, Juha, Uebe, Steffen, Melles, Ronald B, Nair, K Saidas, Luben, Robert, Simcoe, Mark, Amersinghe, Nishani, Cree, Angela J, Hohn, Rene, Poplawski, Alicia, Chen, Li Jia, Rong, Shi-Song, Aung, Tin, Vithana, Eranga Nishanthie, NEIGHBORHOOD consortium, ANZRAG consortium, Biobank Japan project, FinnGen study, UK Biobank Eye and Vision Consortium, GIGA study group, 23 and Me Research Team, Tamiya, Gen, Shiga, Yukihiro, Yamamoto, Masayuki, Nakazawa, Toru, Currant, Hannah, Birney, Ewan, Wang, Xin, Auton, Adam, Lupton, Michelle K, Martin, Nicholas G, Ashaye, Adeyinka, Olawoye, Olusola, Williams, Susan E, Akafo, Stephen, Ramsay, Michele, Hashimoto, Kazuki, Kamatani, Yoichiro, Akiyama, Masato, Momozawa, Yukihide, Foster, Paul J, Khaw, Peng T, Morgan, James E, Strouthidis, Nicholas G, Kraft, Peter, Kang, Jae H, Pang, Chi Pui, Pasutto, Francesca, Mitchell, Paul, Lotery, Andrew J, Palotie, Aarno, van Duijn, Cornelia, Haines, Jonathan L, Hammond, Chris, Pasquale, Louis R, Klaver, Caroline CW, Hauser, Michael, Khor, Chiea Chuen, Mackey, David A, Kubo, Michiaki, Cheng, Ching-Yu, Craig, Jamie E, MacGregor, Stuart, Wiggs, Janey L, Epidemiology, Ophthalmology, Clinical Genetics, Gharahkhani, Puya [0000-0002-4203-5952], Jorgenson, Eric [0000-0002-5829-8191], Hysi, Pirro [0000-0001-5752-2510], Khawaja, Anthony P [0000-0001-6802-8585], Han, Xikun [0000-0002-3823-7308], Ong, Jue Sheng [0000-0002-6062-710X], Hewitt, Alex W [0000-0002-5123-5999], Rouhana, John M [0000-0002-8599-0271], Igo, Robert P [0000-0002-0024-1993], Choquet, Helene [0000-0001-9839-8667], Josyula, Navya S [0000-0003-2782-8812], Cooke Bailey, Jessica N [0000-0002-4001-8702], Bonnemaijer, Pieter WM [0000-0001-5154-6765], Iglesias, Adriana [0000-0001-5532-764X], Siggs, Owen M [0000-0003-2840-4851], Young, Terri L [0000-0001-6994-9941], Vitart, Veronique [0000-0002-4991-3797], Thiadens, Alberta AHJ [0000-0002-4911-9462], Luben, Robert [0000-0002-5088-6343], Simcoe, Mark [0000-0003-2432-0810], Cree, Angela J [0000-0002-1987-8900], Poplawski, Alicia [0000-0003-2527-0763], Rong, Shi-Song [0000-0001-8352-6363], Vithana, Eranga Nishanthie [0000-0002-8898-0095], Yamamoto, Masayuki [0000-0002-9073-9436], Currant, Hannah [0000-0003-2764-6787], Birney, Ewan [0000-0001-8314-8497], Wang, Xin [0000-0001-7242-357X], Martin, Nicholas G [0000-0003-4069-8020], Olawoye, Olusola [0000-0003-2357-8924], Williams, Susan E [0000-0002-4479-8638], Ramsay, Michele [0000-0002-4156-4801], Kamatani, Yoichiro [0000-0001-8748-5597], Foster, Paul J [0000-0002-4755-177X], Khaw, Peng T [0000-0002-8087-2268], Kraft, Peter [0000-0002-4472-8103], Kang, Jae H [0000-0003-4812-0557], Pasutto, Francesca [0000-0002-0026-5362], Lotery, Andrew J [0000-0001-5541-4305], Haines, Jonathan L [0000-0002-4351-4728], Hammond, Chris [0000-0002-3227-2620], Pasquale, Louis R [0000-0002-5835-3496], Klaver, Caroline CW [0000-0002-2355-5258], Khor, Chiea Chuen [0000-0002-1128-4729], Cheng, Ching-Yu [0000-0003-0655-885X], MacGregor, Stuart [0000-0001-6731-8142], Wiggs, Janey L [0000-0003-1890-3278], Apollo - University of Cambridge Repository, Institute for Molecular Medicine Finland, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Centre of Excellence in Complex Disease Genetics, Aarno Palotie / Principal Investigator, Genomics of Neurological and Neuropsychiatric Disorders, HUSLAB, HUS Helsinki and Uusimaa Hospital District, APH - Mental Health, APH - Methodology, and Amsterdam Neuroscience - Neuroinfection & -inflammation
Subjects: 0301 basic medicine, Aging, genetic structures, General Physics and Astronomy, Glaucoma, PROTEIN, Genome-wide association study, Neurodegenerative, Genome, ANNOTATION, Genome-wide association studies, Sensory disorders Donders Center for Medical Neuroscience [Radboudumc 12], 0302 clinical medicine, Polymorphism (computer science), Genotype, 2.1 Biological and endogenous factors, ANZRAG consortium, Aetiology, GENE-EXPRESSION, Genetics, HUMAN-DISEASES, RISK, Multidisciplinary, and Me Research Team, Single Nucleotide, ASSOCIATION, GIGA study group, Biobank Japan project, 3. Good health, PREVALENCE, Open-Angle, Meta-analysis, NEIGHBORHOOD consortium, Optic nerve diseases, Glaucoma, Open-Angle, Asian Continental Ancestry Group, Open angle glaucoma, Science, European Continental Ancestry Group, FinnGen study, Biology, GENOTYPE IMPUTATION, Polymorphism, Single Nucleotide, General Biochemistry, Genetics and Molecular Biology, UK Biobank Eye and Vision Consortium, Article, White People, 03 medical and health sciences, Asian People, medicine, Humans, Genetic Predisposition to Disease, 3125 Otorhinolaryngology, ophthalmology, Polymorphism, Eye Disease and Disorders of Vision, Genetic association, MUTATIONS, Human Genome, General Chemistry, medicine.disease, eye diseases, 030104 developmental biology, Genetic Loci, DIFFERENTIAL EXPRESSION ANALYSIS, 030221 ophthalmology & optometry, sense organs, Genome-Wide Association Study
Abstract: Primary open-angle glaucoma (POAG), is a heritable common cause of blindness world-wide. To identify risk loci, we conduct a large multi-ethnic meta-analysis of genome-wide association studies on a total of 34,179 cases and 349,321 controls, identifying 44 previously unreported risk loci and confirming 83 loci that were previously known. The majority of loci have broadly consistent effects across European, Asian and African ancestries. Cross-ancestry data improve fine-mapping of causal variants for several loci. Integration of multiple lines of genetic evidence support the functional relevance of the identified POAG risk loci and highlight potential contributions of several genes to POAG pathogenesis, including SVEP1, RERE, VCAM1, ZNF638, CLIC5, SLC2A12, YAP1, MXRA5, and SMAD6. Several drug compounds targeting POAG risk genes may be potential glaucoma therapeutic candidates., Primary open-angle glaucoma (POAG) is highly heritable, yet not well understood from a genetic perspective. Here, the authors perform a meta-analysis of genome-wide association studies in 34,179 POAG cases, identifying 44 previously unreported risk loci and mapping effects across multiple ethnicities.
Published: 2021

12. Genome-wide association meta-analysis of corneal curvature identifies novel loci and shared genetic influences across axial length and refractive error

Author: Fan, Qiao, Pozarickij, Alfred, Tan, Nicholas Y. Q., Guo, Xiaobo, Verhoeven, Virginie J. M., Vitart, Veronique, Guggenheim, Jeremy A., Miyake, Masahiro, Tideman, J. Willem L., Khawaja, Anthony P., Zhang, Liang, MacGregor, Stuart, Höhn, René, Chen, Peng, Biino, Ginevra, Wedenoja, Juho, Saffari, Seyed Ehsan, Tedja, Milly S., Xie, Jing, Lanca, Carla, Wang, Ya Xing, Sahebjada, Srujana, Mazur, Johanna, Mirshahi, Alireza, Martin, Nicholas G., Yazar, Seyhan, Pennell, Craig E., Yap, Maurice, Haarman, Annechien E. G., Enthoven, Clair A., Polling, JanRoelof, Hewitt, Alex W., Jaddoe, Vincent W. V., Van Duijn, Cornelia M., Hayward, Caroline, Polasek, Ozren, Tai, E-Shyong, Yoshikatsu, Hosoda, Hysi, Pirro G., Young, Terri L., Tsujikawa, Akitaka, Wang, Jie Jing, Mitchell, Paul, Pfeiffer, Norbert, Pärssinen, Olavi, Foster, Paul J., Fossarello, Maurizio, Yip, Shea Ping, Williams, Cathy, Hammond, Christopher J., Jonas, Jost B., He, Mingguang, Mackey, David A., Wong, Tien-Yin, Klaver, Caroline C. W., Saw, Seang-Mei, Baird, Paul N., Cheng, Ching-Yu, Bailey-Wilson, Joan E., Veluchamy, Amutha Barathi, Burdon, Kathryn P., Campbell, Harry, Chen, Li Jia, Chew, Emily Y., Craig, Jamie E., Cumberland, Phillippa M., Deangelis, Margaret M., Delcourt, Cécile, Ding, Xiaohu, Evans, David M., Gharahkhani, Puya, Iglesias, Adriana I., Haller, Toomas, Han, Xikun, Hoang, Quan, Igo, Robert P., Iyengar, Sudha K., Kähönen, Mika, Kaprio, Jaakko, Klein, Barbara E., Klein, Ronald, Lass, Jonathan H., Lee, Kris, Lehtimäki, Terho, Lewis, Deyana D., Li, Qing, Li, Shi-Ming, Lyytikäinen, Leo-Pekka, Meguro, Akira, Metspalu, Andres, Middlebrooks, Candace D., Mizuki, Nobuhisa, Musolf, Anthony M., Nickels, Stefan, Oexle, Konrad, Pang, Chi Pui, Paterson, Andrew D., Rahi, Jugnoo S., Raitakari, Olli, Rudan, Igor, Stambolian, Dwight, Simpson, Claire L., Wang, Ningli, Bin Wei, Wen, Williams, Katie M., Wilson, James F., Wojciechowski, Robert, Yamashiro, Kenji, Yam, Jason C. S., Zhou, Xiangtian, Aslam, Tariq, Barman, Sarah A., Barrett, Jenny H., Bishop, Paul, Blows, Peter, Bunce, Catey, Carare, Roxana O., Chakravarthy, Usha, Chan, Michelle, Chua, Sharon Y. L., Crabb, David P., Cumberland, Philippa M., Day, Alexander, Desai, Parul, Dhillon, Bal, Dick, Andrew D., Egan, Cathy, Ennis, Sarah, Fruttiger, Marcus, Gallacher, John E. J., Garway-Heath, David F., Gibson, Jane, Gore, Dan, Hardcastle, Alison, Harding, Simon P., Hogg, Ruth E., Keane, Pearse A., Khaw, Sir Peng T., Lascaratos, Gerassimos, Lotery, Andrew J., Macgillivray, Tom, Mackie, Sarah, Martin, Keith, McGaughey, Michelle, McGuinness, Bernadette, McKay, Gareth J., McKibbin, Martin, Mitry, Danny, Moore, Tony, Morgan, James E., Muthy, Zaynah A., O’Sullivan, Eoin, Owen, Chris G., Patel, Praveen, Paterson, Euan, Peto, Tunde, Petzold, Axel, Rudnikca, Alicja R., Self, Jay, Sivaprasad, Sobha, Steel, David, Stratton, Irene, Strouthidis, Nicholas, Sudlow, Cathie, Thomas, Dhanes, Trucco, Emanuele, Tufail, Adnan, Vernon, Stephen A., Viswanathan, Ananth C., Williams, Katie, Woodside, Jayne V., Yates, Max M., Yip, Jennifer, Zheng, Yalin, Verhoeven, Virginie J. M. [0000-0001-7359-7862], Vitart, Veronique [0000-0002-4991-3797], Guggenheim, Jeremy A. [0000-0001-5164-340X], Khawaja, Anthony P. [0000-0001-6802-8585], Zhang, Liang [0000-0001-9264-170X], MacGregor, Stuart [0000-0001-6731-8142], Wedenoja, Juho [0000-0002-6155-0378], Saffari, Seyed Ehsan [0000-0002-6473-4375], Tedja, Milly S. [0000-0003-0356-9684], Lanca, Carla [0000-0001-9918-787X], Wang, Ya Xing [0000-0003-2749-7793], Martin, Nicholas G. [0000-0003-4069-8020], Yap, Maurice [0000-0003-4687-4101], Hewitt, Alex W. [0000-0002-5123-5999], Jaddoe, Vincent W. V. [0000-0003-2939-0041], Hayward, Caroline [0000-0002-9405-9550], Hysi, Pirro G. [0000-0001-5752-2510], Young, Terri L. [0000-0001-6994-9941], Wang, Jie Jing [0000-0001-9491-4898], Pfeiffer, Norbert [0000-0002-5766-2617], Foster, Paul J. [0000-0002-4755-177X], Hammond, Christopher J. [0000-0002-3227-2620], Jonas, Jost B. [0000-0003-2972-5227], Klaver, Caroline C. W. [0000-0002-2355-5258], Baird, Paul N. [0000-0002-1305-3502], and Apollo - University of Cambridge Repository
Subjects: genetic structures, 45, 692/699/3161/3163, 631/208/727/2000, 631/208/205/2138, 45/43, article, sense organs, eye diseases
Abstract: Corneal curvature, a highly heritable trait, is a key clinical endophenotype for myopia - a major cause of visual impairment and blindness in the world. Here we present a trans-ethnic meta-analysis of corneal curvature GWAS in 44,042 individuals of Caucasian and Asian with replication in 88,218 UK Biobank data. We identified 47 loci (of which 26 are novel), with population-specific signals as well as shared signals across ethnicities. Some identified variants showed precise scaling in corneal curvature and eye elongation (i.e. axial length) to maintain eyes in emmetropia (i.e. HDAC11/FBLN2 rs2630445, RBP3 rs11204213); others exhibited association with myopia with little pleiotropic effects on eye elongation. Implicated genes are involved in extracellular matrix organization, developmental process for body and eye, connective tissue cartilage and glycosylation protein activities. Our study provides insights into population-specific novel genes for corneal curvature, and their pleiotropic effect in regulating eye size or conferring susceptibility to myopia.
Published: 2021
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13. Meta-analysis of 542,934 subjects of European ancestry identifies new genes and mechanisms predisposing to refractive error and myopia

Author: Hysi, Pirro G, Choquet, Hélène, Khawaja, Anthony P, Wojciechowski, Robert, Tedja, Milly S, Yin, Jie, Simcoe, Mark J, Patasova, Karina, Mahroo, Omar A, Thai, Khanh K, Cumberland, Phillippa M, Melles, Ronald B, Verhoeven, Virginie JM, Vitart, Veronique, Segre, Ayellet, Stone, Richard A, Wareham, Nicholas, Hewitt, Alex W, Mackey, David A, Klaver, Caroline CW, MacGregor, Stuart, Error, Consortium For Refractive, Khaw, Peng T, Foster, Paul J, Eye, UK, Guggenheim, Jeremy A, 23andMe Inc., Rahi, Jugnoo S, Jorgenson, Eric, Hammond, Christopher J, Apollo-University Of Cambridge Repository, Hysi, Pirro G [0000-0001-5752-2510], Choquet, Hélène [0000-0001-9839-8667], Khawaja, Anthony P [0000-0001-6802-8585], Wojciechowski, Robert [0000-0002-9593-4652], Tedja, Milly S [0000-0003-0356-9684], Simcoe, Mark J [0000-0003-2432-0810], Verhoeven, Virginie JM [0000-0001-7359-7862], Vitart, Veronique [0000-0002-4991-3797], Hewitt, Alex W [0000-0002-5123-5999], Klaver, Caroline CW [0000-0002-2355-5258], MacGregor, Stuart [0000-0001-6731-8142], Khaw, Peng T [0000-0002-8087-2268], Foster, Paul J [0000-0002-4755-177X], Guggenheim, Jeremy A [0000-0001-5164-340X], Jorgenson, Eric [0000-0002-5829-8191], Hammond, Christopher J [0000-0002-3227-2620], and Apollo - University of Cambridge Repository
Subjects: Adult, Male, genetic structures, Consortium for Refractive Error and Myopia, European Continental Ancestry Group, Middle Aged, Refractive Errors, Polymorphism, Single Nucleotide, eye diseases, White People, 23andMe Inc, UK Eye and Vision Consortium, Myopia, Humans, Genetic Predisposition to Disease, Female, Aged, Genome-Wide Association Study
Abstract: Refractive errors, in particular myopia, are a leading cause of morbidity and disability worldwide. Genetic investigation can improve understanding of the molecular mechanisms that underlie abnormal eye development and impaired vision. We conducted a meta-analysis of genome-wide association studies (GWAS) that involved 542,934 European participants and identified 336 novel genetic loci associated with refractive error. Collectively, all associated genetic variants explain 18.4% of heritability and improve the accuracy of myopia prediction (area under the curve (AUC) = 0.75). Our results suggest that refractive error is genetically heterogeneous, driven by genes that participate in the development of every anatomical component of the eye. In addition, our analyses suggest that genetic factors controlling circadian rhythm and pigmentation are also involved in the development of myopia and refractive error. These results may enable the prediction of refractive error and the development of personalized myopia prevention strategies in the future.
Published: 2021

14. A comprehensive re-assessment of the association between vitamin D and cancer susceptibility using Mendelian randomization

Author: Ong, Jue-Sheng, Dixon-Suen, Suzanne C., Han, Xikun, An, Jiyuan, Liyanage, Upekha, Dusingize, Jean-Cluade, Schumacher, Johannes, Gockel, Ines, Böhmer, Anne, Jankowski, Janusz, Palles, Claire, O’Mara, Tracy, Spurdle, Amanda, Law, Matthew H., Iles, Mark M., Pharoah, Paul, Berchuck, Andrew, Zheng, Wei, Thrift, Aaron P., Olsen, Catherine, Neale, Rachel E., Gharahkhani, Puya, Webb, Penelope M., MacGregor, Stuart, Fitzgerald, Rebecca, Buas, Matt, Gammon, Marilie D., Corley, Douglas A., Shaheen, Nicholas J., Hardie, Laura J., Bird, Nigel C., Reid, Brian J., Chow, Wong-Ho, Risch, Harvey A., Ye, Weimin, Liu, Geoffrey, Romero, Yvonne, Bernstein, Leslie, Wu, Anna H., Whiteman, David E., Vaughan, Thomas, Agee, M., Alipanahi, B., Auton, A., Bell, R. K., Bryc, K., Elson, S. L., Fontanillas, P., Furlotte, N. A., Hinds, D. A., Huber, K. E., Kleinman, A., Litterman, N. K., McIntyre, M. H., Mountain, J. L., Noblin, E. S., Northover, C. A. M., Pitts, S. J., Sathirapongsasuti, J. Fah, Sazonova, O. V., Shelton, J. F., Shringarpure, S., Tian, C., Tung, J. Y., Vacic, V., Wilson, C. H., Ong, Jue-Sheng [0000-0002-6062-710X], Dixon-Suen, Suzanne C. [0000-0003-3714-8386], Han, Xikun [0000-0002-3823-7308], Gockel, Ines [0000-0001-7423-713X], Böhmer, Anne [0000-0002-5716-786X], O’Mara, Tracy [0000-0002-5436-3232], Spurdle, Amanda [0000-0003-1337-7897], Law, Matthew H. [0000-0002-4303-8821], Iles, Mark M. [0000-0002-2603-6509], Pharoah, Paul [0000-0001-8494-732X], Zheng, Wei [0000-0003-1226-070X], Thrift, Aaron P. [0000-0002-0084-5308], Olsen, Catherine [0000-0003-4483-1888], Gharahkhani, Puya [0000-0002-4203-5952], Webb, Penelope M. [0000-0003-0733-5930], MacGregor, Stuart [0000-0001-6731-8142], and Apollo - University of Cambridge Repository
Subjects: 631/67/68, 45/43, article, 692/699/67/2195, 692/4028/67/2324
Abstract: Previous Mendelian randomization (MR) studies on 25-hydroxyvitamin D (25(OH)D) and cancer have typically adopted a handful of variants and found no relationship between 25(OH)D and cancer; however, issues of horizontal pleiotropy cannot be reliably addressed. Using a larger set of variants associated with 25(OH)D (74 SNPs, up from 6 previously), we perform a unified MR analysis to re-evaluate the relationship between 25(OH)D and ten cancers. Our findings are broadly consistent with previous MR studies indicating no relationship, apart from ovarian cancers (OR 0.89; 95% C.I: 0.82 to 0.96 per 1 SD change in 25(OH)D concentration) and basal cell carcinoma (OR 1.16; 95% C.I.: 1.04 to 1.28). However, after adjustment for pigmentation related variables in a multivariable MR framework, the BCC findings were attenuated. Here we report that lower 25(OH)D is unlikely to be a causal risk factor for most cancers, with our study providing more precise confidence intervals than previously possible.
Published: 2021
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15. Computational Studies of the Solid-State Molecular Organometallic (SMOM) Chemistry of Rh σ-Alkane Complexes

Author: Algarra, Andrés G, Burnage, Arron L, Iannuzzi, Marcella, Krämer, Tobias, Macgregor, Stuart A, Pirie, Rachael E M, Tegner, Bengt, Weller, Andrew S, University of Zurich, Mingos, D Michael P, Raithby, Paul R, and Macgregor, Stuart A
Subjects: 10120 Department of Chemistry, 1604 Inorganic Chemistry, 540 Chemistry, 1607 Spectroscopy, 1606 Physical and Theoretical Chemistry
Published: 2020

16. Multi-trait genome-wide association study identifies new loci associated with optic disc parameters

Author: Bonnemaijer, Pieter WM, van Leeuwen, Elisabeth M, Iglesias, Adriana I, Gharahkhani, Puya, Vitart, Veronique, Khawaja, Anthony P, Simcoe, Mark, Hoehn, Rene, Cree, Angela J, Igo, Rob P, Burdon, Kathryn P, Craig, Jamie E, Hewitt, Alex W, Jonas, Jost, Khor, Chiea-Cheun, Pasutto, Francesca, Mackey, David A, Mitchell, Paul, Mishra, Aniket, Pang, Calvin, Pasquale, Louis R, Springelkamp, Henriette, Thorleifsson, Gudmar, Thorsteinsdottir, Unnur, Viswanathan, Ananth C, Wojciechowski, Robert, Wong, Tien, Young, Terrri L, Zeller, Tanja, Atan, Denize, Aslam, Tariq, Barman, Sarah A, Barrett, Jenny H, Bishop, Paul, Blows, Peter, Bunce, Catey, Carare, Roxana O, Chakravarthy, Usha, Chan, Michelle, Chua, Sharon YL, Crabb, David P, Cumberland, Philippa M, Day, Alexander, Desai, Parul, Dhillon, Bal, Dick, Andrew D, Egan, Cathy, Ennis, Sarah, Foster, Paul, Fruttiger, Marcus, Gallacher, John EJ, Garway, David F, Gibson, Jane, Gore, Dan, Guggenheim, Jeremy A, Hardcastle, Alison, Harding, Simon P, Hogg, Ruth E, Keane, Pearse A, Khaw, Peng T, Lascaratos, Gerassimos, Macgillivray, Tom, Mackie, Sarah, Martin, Keith, McGaughey, Michelle, McGuinness, Bernadette, Mckay, Gareth J, McKibbin, Martin, Mitry, Danny, Moore, Tony, Morgan, James E, Muthy, Zaynah A, O'Sullivan, Eoin, Owen, Chris G, Patel, Praveen, Paterson, Euan, Peto, Tunde, Petzold, Axel, Rahi, Jugnoo S, Rudnikca, Alicja R, Self, Jay, Sivaprasad, Sobha, Steel, David, Stratton, Irene, Strouthidis, Nicholas, Sudlow, Cathie, Thomas, Dhanes, Trucco, Emanuele, Tufail, Adnan, Vernon, Stephen A, Williams, Cathy, Williams, Katie, Woodside, Jayne V, Yates, Max M, Yip, Jennifer, Zheng, Yalin, Allingham, Rand, Budenz, Don, Bailey, Jessica Cooke, Fingert, John, Gaasterland, Douglas, Gaasterland, Teresa, Haines, Jonathan L, Hark, Lisa, Hauser, Michael, Kang, Jae Hee, Kraft, Peter, Lee, Richard, Lichter, Paul, Liu, Yutao, Moroi, Syoko, Pericak, Margaret, Realini, Anthony, Rhee, Doug, Richards, Julia R, Ritch, Robert, Scott, William K, Singh, Kuldev, Sit, Arthur, Vollrath, Douglas, Weinreb, Robert, Wollstein, Gadi, Wilmer, Don Zack, Gerhold-Ay, Aslihan, Nickels, Stefan, Wilson, James F, Hayward, Caroline, Boutin, Thibaud S, Polasek, Ozren, Aung, Tin, Khor, Chiea Chuen, Amin, Najaf, Lotery, Andrew J, Wiggs, Janey L, Cheng, Ching-Yu, Hysi, Pirro G, Hammond, Christopher J, Thiadens, Alberta AHJ, MacGregor, Stuart, Klaver, Caroline CW, van Duijn, Cornelia M, Consortium, Int Glaucoma Genetics, Consortium, Uk Biobank Eye Vision, Consortium, NEIGHBORHOOD, Epidemiology, Ophthalmology, Clinical Genetics, Bonnemaijer, Pieter WM [0000-0001-5154-6765], Iglesias, Adriana I [0000-0001-5532-764X], Gharahkhani, Puya [0000-0002-4203-5952], Vitart, Veronique [0000-0002-4991-3797], Khawaja, Anthony P [0000-0001-6802-8585], Simcoe, Mark [0000-0003-2432-0810], Nickels, Stefan [0000-0003-0415-2354], Wilson, James F [0000-0001-5751-9178], Hayward, Caroline [0000-0002-9405-9550], Boutin, Thibaud S [0000-0003-4754-1675], Khor, Chiea Chuen [0000-0002-1128-4729], Lotery, Andrew J [0000-0001-5541-4305], Wiggs, Janey L [0000-0003-1890-3278], Cheng, Ching-Yu [0000-0003-0655-885X], Hysi, Pirro G [0000-0001-5752-2510], Hammond, Christopher J [0000-0002-3227-2620], MacGregor, Stuart [0000-0001-6731-8142], Klaver, Caroline CW [0000-0002-2355-5258], and Apollo - University of Cambridge Repository
Subjects: genetic structures, Optic disk, Medicine (miscellaneous), Genome-wide association study, Neurodegenerative, Genome-wide association studies, Sensory disorders Donders Center for Medical Neuroscience [Radboudumc 12], 0302 clinical medicine, Optic Nerve Diseases, 2.1 Biological and endogenous factors, Aetiology, 610 Medicine & health, lcsh:QH301-705.5, 0303 health sciences, Agricultural and Biological Sciences(all), Single Nucleotide, medicine.anatomical_structure, NEIGHBORHOOD consortium, General Agricultural and Biological Sciences, Optic disc, Signal Transduction, Optic Disk, Quantitative Trait Loci, International Glaucoma Genetics Consortium, Quantitative trait locus, Biology, Genetic correlation, Polymorphism, Single Nucleotide, General Biochemistry, Genetics and Molecular Biology, Article, UK Biobank Eye and Vision Consortium, 03 medical and health sciences, Quantitative Trait, Quantitative Trait, Heritable, medicine, Genetics, Humans, Genetic Predisposition to Disease, 1000 Genomes Project, Polymorphism, Heritable, Eye Disease and Disorders of Vision, Genetic Association Studies, 030304 developmental biology, Genetic association, CENTRAL CORNEAL THICKNESS, METAANALYSIS, GLAUCOMA, EXPRESSION, HERITABILITY, PREVALENCE, STATISTICS, PANEL, Biochemistry, Genetics and Molecular Biology(all), Gene Expression Profiling, Haplotype, Human Genome, Computational Biology, Glaucoma, Molecular Sequence Annotation, eye diseases, lcsh:Biology (General), Evolutionary biology, Case-Control Studies, RE, sense organs, 030217 neurology & neurosurgery, Genome-Wide Association Study
Abstract: A new avenue of mining published genome-wide association studies includes the joint analysis of related traits. The power of this approach depends on the genetic correlation of traits, which reflects the number of pleiotropic loci, i.e. genetic loci influencing multiple traits. Here, we applied new meta-analyses of optic nerve head (ONH) related traits implicated in primary open-angle glaucoma (POAG); intraocular pressure and central corneal thickness using Haplotype reference consortium imputations. We performed a multi-trait analysis of ONH parameters cup area, disc area and vertical cup-disc ratio. We uncover new variants; rs11158547 in PPP1R36-PLEKHG3 and rs1028727 near SERPINE3 at genome-wide significance that replicate in independent Asian cohorts imputed to 1000 Genomes. At this point, validation of these variants in POAG cohorts is hampered by the high degree of heterogeneity. Our results show that multi-trait analysis is a valid approach to identify novel pleiotropic variants for ONH., The International Glaucoma Genetics Consortium reports a genome-wide association study meta-analysis of optic disc parameters relevant to primary open-angle glaucoma. They identify two novel variants in PPP1R36-PLEKHG3 and SERPINE3 by multi-trait analysis in European-ancestry cohorts that were replicated in independent Asian cohorts.
Published: 2019

17. Genome-wide meta-analysis identifies 127 open-angle glaucoma loci with consistent effect across ancestries

Author: Gharahkhani, Puya, Jorgenson, Eric, Hysi, Pirro, Khawaja, Anthony P., Pendergrass, Sarah, Han, Xikun, Ong, Jue Sheng, Hewitt, Alex W., Segrè, Ayellet V., Rouhana, John M., Hamel, Andrew R., Igo Jr, Robert P., Choquet, Helene, Qassim, Ayub, Josyula, Navya S., Cooke Bailey, Jessica N., Bonnemaijer, Pieter W. M., Iglesias, Adriana, Siggs, Owen M., Young, Terri L., Vitart, Veronique, Thiadens, Alberta A. H. J., Karjalainen, Juha, Uebe, Steffen, Melles, Ronald B., Nair, K. Saidas, Luben, Robert, Simcoe, Mark, Amersinghe, Nishani, Cree, Angela J., Hohn, Rene, Poplawski, Alicia, Chen, Li Jia, Rong, Shi-Song, Aung, Tin, Vithana, Eranga Nishanthie, NEIGHBORHOOD consortium, ANZRAG consortium, Biobank Japan project, FinnGen study, UK Biobank Eye and Vision Consortium, Barman, Sarah A., GIGA study group, 23 and Me Research Team, Tamiya, Gen, Shiga, Yukihiro, Yamamoto, Masayuki, Nakazawa, Toru, Currant, Hannah, Birney, Ewan, Wang, Xin, Auton, Adam, Lupton, Michelle K., Martin, Nicholas G., Ashaye, Adeyinka, Olawoye, Olusola, Williams, Susan E., Akafo, Stephen, Ramsay, Michele, Hashimoto, Kazuki, Kamatani, Yoichiro, Akiyama, Masato, Momozawa, Yukihide, Foster, Paul J., Khaw, Peng T., Morgan, James E., Strouthidis, Nicholas G., Kraft, Peter, Kang, Jae H., Pang, Chi Pui, Pasutto, Francesca, Mitchell, Paul, Lotery, Andrew J., Palotie, Aarno, van Duijn, Cornelia, Haines, Jonathan L., Hammond, Chris, Pasquale, Louis R., Klaver, Caroline C. W., Hauser, Michael, Khor, Chiea Chuen, Mackey, David A., Kubo, Michiaki, Cheng, Ching-Yu, Craig, Jamie E., MacGregor, Stuart, and Wiggs, Janey L.
Subjects: biological
Published: 2021

18. Selective C–H Activation at a Molecular Rhodium Sigma-Alkane Complex by Solid/Gas Single-Crystal to Single-Crystal H/D Exchange

Author: Chadwick, F. Mark, Krämer, Tobias, Gutmann, Torsten, Rees, Nicholas H., Thompson, Amber L., Edwards, Alison J., Buntkowsky, Gerd, Macgregor, Stuart A., and Weller, Andrew S.
Subjects: METAL OXIDE CLUSTERS, Science & Technology, TRANSITION-METALS, Chemistry, Multidisciplinary, General Chemistry, CATALYTIC-HYDROGENATION, DEHYDROGENATION-OLEFIN-METATHESIS, ORGANOMETALLIC CHEMISTRY, ETHANE COMPLEXES, Chemistry, NEUTRON-DIFFRACTION, STATE NMR, Physical Sciences, X-RAY, 03 Chemical Sciences, TIME-RESOLVED IR
Abstract: The controlled catalytic functionalization of alkanes via the activation of C-H bonds is a significant challenge. Although C-H activation by transition metal catalysts is often suggested to operate via intermediate σ-alkane complexes, such transient species are difficult to observe due to their instability in solution. This instability may be controlled by use of solid/gas synthetic techniques that enable the isolation of single-crystals of well-defined σ-alkane complexes. Here we show that, using this unique platform, selective alkane C-H activation occurs, as probed by H/D exchange using D2, and that five different isotopomers/isotopologues of the σ-alkane complex result, as characterized by single-crystal neutron diffraction studies for three examples. Low-energy fluxional processes associated with the σ-alkane ligand are identified using variable-temperature X-ray diffraction, solid-state NMR spectroscopy, and periodic DFT calculations. These observations connect σ-alkane complexes with their C-H activated products, and demonstrate that alkane-ligand mobility, and selective C-H activation, are possible when these processes occur in the constrained environment of the solid-state.
Published: 2021

19. Additional file 1 of Associations of sleep apnoea with glaucoma and age-related macular degeneration: an analysis in the United Kingdom Biobank and the Canadian Longitudinal Study on Aging

Author: Han, Xikun, Lee, Samantha Sze-Yee, Ingold, Nathan, McArdle, Nigel, Khawaja, Anthony P., MacGregor, Stuart, and Mackey, David A.
Subjects: genetic structures, sense organs, eye diseases
Abstract: Additional file 1: Figure S1. Flowchart of Canadian Longitudinal Study on Ageing cohort participants. Figure S2. Venn diagram of sleep apnoea, glaucoma and age-related macular degeneration cases ascertained from different sources in UK Biobank. Table S1. Data coding list in UK Biobank. Table S2. Data coding list in the Canadian Longitudinal Study on Ageing (CLSA) cohort. Table S3. Characteristics of Canadian Longitudinal Study on Ageing cohort samples included in analysis versus participants excluded. Table S4. Univariate and multivariable regression models for the incidence risk of glaucoma and AMD in the UK Biobank. Table S5. Sensitivity analysis of the associations between sleep apnoea with the risk of age-related macular degeneration and glaucoma without imputation of covariates in UK Biobank. Table S6. The number of samples with missing covariates in UK Biobank. Table S7. Sensitivity analysis of the associations between sleep apnoea with the risk of age-related macular degeneration and glaucoma after removing participants who developed sleep apnoea after baseline visit in UK Biobank. Table S8. Univariate and multivariable regression models for the incidence risk of glaucoma and AMD in the Canadian Longitudinal Study on Aging (CLSA). Table S9. Reverse association analysis between age-related macular degeneration, glaucoma and the risk of sleep apnoea in UK biobank. Table S10. Reverse association analysis between age-related macular degeneration, glaucoma and the risk of sleep apnoea in CLSA. Table S11. Sensitivity analysis of the associations between sleep apnoea with the risk of age-related macular degeneration and glaucoma restricting to participants having hospital inpatient records in UK Biobank.
Published: 2021
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20. Computational Studies of the Solid-State Molecular Organometallic (SMOM) Chemistry of Rh !-Alkane Complexes

Author: Algarra, Andrés G., Burnage, Arron L., Iannuzzi, Marcella, Krämer, Tobias, Macgregor, Stuart A., Pirie, Rachael E.M., Tegner, Bengt, and Weller, Andrew S.
Abstract: A review of computational studies on the structures, bonding and reactivity of rhodium σ-alkane complexes in the solid state is presented. These complexes of the general form [(R2P(CH2)nPR2)Rh(alkane)][BArF 4] (where ArF = 3,5-(CF3)2C6H3) are formed via solid/gas hydrogenation of alkene precursors, often in single-crystal-to-single-crystal (SC-SC) transformations. Molecular and periodic density functional theory (DFT) calculations complement experimental characterisation techniques (X-ray, solid-state NMR) to provide a detailed picture of the structure and bonding in these species. These σ-alkane complexes exhibit reactivity in the solid state, undergoing fluxional processes, and access different alkane binding modes that link to C-H activation and H/D exchange. The mechanisms of several of these processes have been defined using periodic DFT calculations which provide excellent quantitative agreement with the available experimental activation barriers. A comparison of computed results derived from periodic DFT calculations, where the full solid-state environment is taken into account, with simple model calculations using the isolated molecular cations highlights the importance of modelling the solid state to reproduce the structures of these alkane complexes. The solid-state environment can also have a significant impact on the computed reaction energetics.
Published: 2020

21. Gastroesophageal reflux GWAS identifies risk loci that also associate with subsequent severe esophageal diseases

Author: An, Jiyuan, Gharahkhani, Puya, Law, Matthew H., Ong, Jue-Sheng, Han, Xikun, Olsen, Catherine M., Neale, Rachel E., Lai, John, Vaughan, Tom L., Gockel, Ines, Thieme, René, Böhmer, Anne C., Jankowski, Janusz, Fitzgerald, Rebecca C., Schumacher, Johannes, Palles, Claire, Whiteman, David C., MacGregor, Stuart, Gammon, Marilie D., Corley, Douglas A., Shaheen, Nicholas J., Bird, Nigel C., Hardie, Laura J., Murray, Liam J., Reid, Brian J., Chow, Wong-Ho, Risch, Harvey A., Ye, Weimin, Liu, Geoffrey, Romero, Yvonne, Bernstein, Leslie, Wu, Anna H., Agee, M., Alipanahi, B., Auton, A., Bell, R. K., Bryc, K., Elson, S. L., Fontanillas, P., Furlotte, N. A., Hinds, D. A., Huber, K. E., Kleinman, A., Litterman, N. K., McIntyre, M. H., Mountain, J. L., Noblin, E. S., Northover, C. A. M., Pitts, S. J., Sathirapongsasuti, J. Fah, Sazonova, O. V., Shelton, J. F., Shringarpure, S., Tian, C., Tung, J. Y., Vacic, V., Wilson, C. H., Gharahkhani, Puya [0000-0002-4203-5952], Law, Matthew H. [0000-0002-4303-8821], Ong, Jue-Sheng [0000-0002-6062-710X], Han, Xikun [0000-0002-3823-7308], Olsen, Catherine M. [0000-0003-4483-1888], Böhmer, Anne C. [0000-0002-5716-786X], Fitzgerald, Rebecca C. [0000-0002-3434-3568], MacGregor, Stuart [0000-0001-6731-8142], and Apollo - University of Cambridge Repository
Subjects: 631/67/1504/1477, 631/208/205/2138, 45/43, article, 38/39, 631/208/68, 692/699/1503/1476/196, health care economics and organizations, humanities, digestive system diseases
Abstract: Funder: The Swedish Esophageal Cancer Study was funded by grants (R01 CA57947-03) from the National Cancer Institute he California Tobacco Related Research Program (3RT-0122; and; 10RT-0251) Marit Peterson Fund for Melanoma Research. CIDR is supported by contract HHSN268200782096C, Gastroesophageal reflux disease (GERD) is caused by gastric acid entering the esophagus. GERD has high prevalence and is the major risk factor for Barrett’s esophagus (BE) and esophageal adenocarcinoma (EA). We conduct a large GERD GWAS meta-analysis (80,265 cases, 305,011 controls), identifying 25 independent genome-wide significant loci for GERD. Several of the implicated genes are existing or putative drug targets. Loci discovery is greatest with a broad GERD definition (including cases defined by self-report or medication data). Further, 91% of the GERD risk-increasing alleles also increase BE and/or EA risk, greatly expanding gene discovery for these traits. Our results map genes for GERD and related traits and uncover potential new drug targets for these conditions.
Published: 2019

22. Assessment of polygenic architecture and risk prediction based on common variants across fourteen cancers

Author: Zhang, Yan Dora, Hurson, Amber N, Zhang, Haoyu, Choudhury, Parichoy Pal, Easton, Douglas F, Milne, Roger L, Simard, Jacques, Hall, Per, Michailidou, Kyriaki, Dennis, Joe, Schmidt, Marjanka K, Chang-Claude, Jenny, Gharahkhani, Puya, Whiteman, David, Campbell, Peter T, Hoffmeister, Michael, Jenkins, Mark, Peters, Ulrike, Hsu, Li, Gruber, Stephen B, Casey, Graham, Schmit, Stephanie L, O'Mara, Tracy A, Spurdle, Amanda B, Thompson, Deborah J, Tomlinson, Ian, De Vivo, Immaculata, Landi, Maria Teresa, Law, Matthew H, Iles, Mark M, Demenais, Florence, Kumar, Rajiv, MacGregor, Stuart, Bishop, D Timothy, Ward, Sarah V, Bondy, Melissa L, Houlston, Richard, Wiencke, John K, Melin, Beatrice, Barnholtz-Sloan, Jill, Kinnersley, Ben, Wrensch, Margaret R, Amos, Christopher I, Hung, Rayjean J, Brennan, Paul, McKay, James, Caporaso, Neil E, Berndt, Sonja I, Birmann, Brenda M, Camp, Nicola J, Kraft, Peter, Rothman, Nathaniel, Slager, Susan L, Berchuck, Andrew, Pharoah, Paul DP, Sellers, Thomas A, Gayther, Simon A, Pearce, Celeste L, Goode, Ellen L, Schildkraut, Joellen M, Moysich, Kirsten B, Amundadottir, Laufey T, Jacobs, Eric J, Klein, Alison P, Petersen, Gloria M, Risch, Harvey A, Stolzenberg-Solomon, Rachel Z, Wolpin, Brian M, Li, Donghui, Eeles, Rosalind A, Haiman, Christopher A, Kote-Jarai, Zsofia, Schumacher, Fredrick R, Al Olama, Ali Amin, Purdue, Mark P, Scelo, Ghislaine, Dalgaard, Marlene D, Greene, Mark H, Grotmol, Tom, Kanetsky, Peter A, McGlynn, Katherine A, Nathanson, Katherine L, Turnbull, Clare, Wiklund, Fredrik, Breast Cancer Association Consortium (BCAC), Barrett’s and Esophageal Adenocarcinoma Consortium (BEACON), Colon Cancer Family Registry (CCFR), Transdisciplinary Studies of Genetic Variation in Colorectal Cancer (CORECT), Endometrial Cancer Association Consortium (ECAC), Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO), Melanoma Genetics Consortium (GenoMEL), Glioma International Case-Control Study (GICC), International Lung Cancer Consortium (ILCCO), Integrative Analysis of Lung Cancer Etiology and Risk (INTEGRAL) Consortium, International Consortium of Investigators Working on Non-Hodgkin’s Lymphoma Epidemiologic Studies (InterLymph), Ovarian Cancer Association Consortium (OCAC), Oral Cancer GWAS, Pancreatic Cancer Case-Control Consortium (PanC4), Pancreatic Cancer Cohort Consortium (PanScan), and Prostate Cancer Association Group to Investigate Cancer Associated Alterations in the Genome (PRACTICAL)
Subjects: Male, Urologic Diseases, Multifactorial Inheritance, Ovarian Cancer Association Consortium, Risk Assessment, Transdisciplinary Studies of Genetic Variation in Colorectal Cancer, Genetic, Risk Factors, Models, Neoplasms, Genetics, Animals, Humans, 2.1 Biological and endogenous factors, Genetic Predisposition to Disease, Endometrial Cancer Association Consortium, Aetiology, Polymorphism, International Consortium of Investigators Working on Non-Hodgkin’s Lymphoma Epidemiologic Studies, Cancer, Renal Cancer GWAS, Incidence, Prevention, Prostate Cancer, International Lung Cancer Consortium, Human Genome, Melanoma Genetics Consortium, Single Nucleotide, Barrett’s and Esophageal Adenocarcinoma Consortium, Prostate Cancer Association Group to Investigate Cancer Associated Alterations in the Genome, Genetics and Epidemiology of Colorectal Cancer Consortium, Pancreatic Cancer Case-Control Consortium, Testicular Cancer Consortium, Breast Cancer Association Consortium, Oral Cancer GWAS, Female, Integrative Analysis of Lung Cancer Etiology and Risk (INTEGRAL) Consortium, Colon Cancer Family Registry, Glioma International Case-Control Study, Pancreatic Cancer Cohort Consortium, Genome-Wide Association Study
Abstract: Genome-wide association studies (GWAS) have led to the identification of hundreds of susceptibility loci across cancers, but the impact of further studies remains uncertain. Here we analyse summary-level data from GWAS of European ancestry across fourteen cancer sites to estimate the number of common susceptibility variants (polygenicity) and underlying effect-size distribution. All cancers show a high degree of polygenicity, involving at a minimum of thousands of loci. We project that sample sizes required to explain 80% of GWAS heritability vary from 60,000 cases for testicular to over 1,000,000 cases for lung cancer. The maximum relative risk achievable for subjects at the 99th risk percentile of underlying polygenic risk scores (PRS), compared to average risk, ranges from 12 for testicular to 2.5 for ovarian cancer. We show that PRS have potential for risk stratification for cancers of breast, colon and prostate, but less so for others because of modest heritability and lower incidence.
Published: 2020

23. A Structurally Characterized Cobalt(I) σ-Alkane Complex

Author: Boyd, Timothy M, Tegner, Bengt, Tizzard, Graham, Martinez-Martinez, Antonio, Neale, Samuel, Hayward, Michael, Coles, Simon, Macgregor, Stuart, and Weller, Andrew S
Abstract: The synthesis, and x-ray structure, of a cobalt s -alkane complex, [Co(Cy 2 P(CH 2 ) 4 PCy 2 )( norbornane )][BAr F 4 ], is achieved by a single-crystal to single-crystal solid/gas hydrogenation from a norbornadiene precursor. Magnetic data show this complex to be a triplet. Periodic DFT and electronic structure analyses identify weak C-H ··· Co σ -interactions, augmented by dispersive stabilisation between the alkane ligand and the anion-microenvironment. The calculations are most consistent with a η 1 : η 1 -alkane binding mode.
Published: 2020

24. Genome-wide association meta-analysis of corneal curvature identifies novel loci and shared genetic influences across axial length and refractive error

Author: Fan, Qiao, Pozarickij, Alfred, Tan, Nicholas Y. Q., Guo, Xiaobo, Verhoeven, Virginie J. M., Vitart, Veronique, Guggenheim, Jeremy A., Miyake, Masahiro, Tideman, J. Willem L., Khawaja, Anthony P., Zhang, Liang, MacGregor, Stuart, Höhn, René, Chen, Peng, Biino, Ginevra, Wedenoja, Juho, Saffari, Seyed Ehsan, Tedja, Milly S., Xie, Jing, Lanca, Carla, Wang, Ya Xing, Sahebjada, Srujana, Mazur, Johanna, Mirshahi, Alireza, Martin, Nicholas G., Yazar, Seyhan, Pennell, Craig E., Yap, Maurice, Haarman, Annechien E. G., Enthoven, Clair A., Polling, JanRoelof, Consortium for Refractive Error and Myopia (CREAM), UK Biobank Eye and Vision Consortium, Barman, Sarah A., Hewitt, Alex W., Jaddoe, Vincent W. V., van Duijn, Cornelia M., Hayward, Caroline, Polasek, Ozren, Tai, E-Shyong, Yoshikatsu, Hosoda, Hysi, Pirro G., Young, Terri L., Tsujikawa, Akitaka, Wang, Jie Jing, Mitchell, Paul, Pfeiffer, Norbert, Pärssinen, Olavi, Foster, Paul J., Fossarello, Maurizio, Yip, Shea Ping, Williams, Cathy, Hammond, Christopher J., Jonas, Jost B., He, Mingguang, Mackey, David A., Wong, Tien-Yin, Klaver, Caroline C. W., Saw, Seang-Mei, Baird, Paul N., and Cheng, Ching-Yu
Subjects: genetic structures, sense organs, eye diseases, biological
Abstract: Corneal curvature, a highly heritable trait, is a key clinical endophenotype for myopia - a major cause of visual impairment and blindness in the world. Here we present a trans-ethnic meta-analysis of corneal curvature GWAS in 44,042 individuals of Caucasian and Asian with replication in 88,218 UK Biobank data. We identified 47 loci (of which 26 are novel), with population-specific signals as well as shared signals across ethnicities. Some identified variants showed precise scaling in corneal curvature and eye elongation (i.e. axial length) to maintain eyes in emmetropia (i.e. HDAC11/FBLN2 rs2630445, RBP3 rs11204213); others exhibited association with myopia with little pleiotropic effects on eye elongation. Implicated genes are involved in extracellular matrix organization, developmental process for body and eye, connective tissue cartilage and glycosylation protein activities. Our study provides insights into population-specific novel genes for corneal curvature, and their pleiotropic effect in regulating eye size or conferring susceptibility to myopia.
Published: 2020

25. Genome-wide association meta-analysis of corneal curvature identifies novel loci and shared genetic influences across axial length and refractive error

Author: Fan, Qiao, Pozarickij, Alfred, Tan, Nicholas Y. Q., Guo, Xiaobo, Verhoeven, Virginie J. M., Vitart, Veronique, Guggenheim, Jeremy A., Miyake, Masahiro, Tideman, J. Willem L., Khawaja, Anthony P., Zhang, Liang, MacGregor, Stuart, Höhn, René, Chen, Peng, Biino, Ginevra, Wedenoja, Juho, Saffari, Seyed Ehsan, Tedja, Milly S., Xie, Jing, Lanca, Carla, Wang, Ya Xing, Sahebjada, Srujana, Mazur, Johanna, Mirshahi, Alireza, Martin, Nicholas G., Yazar, Seyhan, Pennell, Craig E., Yap, Maurice, Haarman, Annechien E. G., Enthoven, Clair A., Polling, JanRoelof, Bailey-Wilson, Joan E., Veluchamy, Amutha Barathi, Burdon, Kathryn P., Campbell, Harry, Chen, Li Jia, Chew, Emily Y., Craig, Jamie E., Cumberland, Phillippa M., Deangelis, Margaret M., Delcourt, Cécile, Ding, Xiaohu, Evans, David M., Gharahkhani, Puya, Iglesias, Adriana I., Haller, Toomas, Han, Xikun, Hoang, Quan, Igo, Robert P., Iyengar, Sudha K., Kähönen, Mika, Kaprio, Jaakko, Klein, Barbara E., Klein, Ronald, Lass, Jonathan H., Lee, Kris, Lehtimäki, Terho, Lewis, Deyana D., Li, Qing, Li, Shi-Ming, Lyytikäinen, Leo-Pekka, Meguro, Akira, Metspalu, Andres, Middlebrooks, Candace D., Mizuki, Nobuhisa, Musolf, Anthony M., Nickels, Stefan, Oexle, Konrad, Pang, Chi Pui, Paterson, Andrew D., Rahi, Jugnoo S., Raitakari, Olli, Rudan, Igor, Stambolian, Dwight, Simpson, Claire L., Wang, Ningli, Bin Wei, Wen, Williams, Katie M., Wilson, James F., Wojciechowski, Robert, Yamashiro, Kenji, Yam, Jason C. S., Zhou, Xiangtian, Aslam, Tariq, Barman, Sarah A., Barrett, Jenny H., Bishop, Paul, Blows, Peter, Bunce, Catey, Carare, Roxana O., Chakravarthy, Usha, Chan, Michelle, Chua, Sharon Y. L., Crabb, David P., Cumberland, Philippa M., Day, Alexander, Desai, Parul, Dhillon, Bal, Dick, Andrew D., Egan, Cathy, Ennis, Sarah, Fruttiger, Marcus, Gallacher, John E. J., Garway-Heath, David F., Gibson, Jane, Gore, Dan, Hardcastle, Alison, Harding, Simon P., Hogg, Ruth E., Keane, Pearse A., Khaw, Sir Peng T., Lascaratos, Gerassimos, Lotery, Andrew J., Macgillivray, Tom, Mackie, Sarah, Martin, Keith, McGaughey, Michelle, McGuinness, Bernadette, McKay, Gareth J., McKibbin, Martin, Mitry, Danny, Moore, Tony, Morgan, James E., Muthy, Zaynah A., O’Sullivan, Eoin, Owen, Chris G., Patel, Praveen, Paterson, Euan, Peto, Tunde, Petzold, Axel, Rudnikca, Alicja R., Self, Jay, Sivaprasad, Sobha, Steel, David, Stratton, Irene, Strouthidis, Nicholas, Sudlow, Cathie, Thomas, Dhanes, Trucco, Emanuele, Tufail, Adnan, Vernon, Stephen A., Viswanathan, Ananth C., Williams, Katie, Woodside, Jayne V., Yates, Max M., Yip, Jennifer, Zheng, Yalin, Hewitt, Alex W., Jaddoe, Vincent W. V., van Duijn, Cornelia M., Hayward, Caroline, Polasek, Ozren, Tai, E-Shyong, Yoshikatsu, Hosoda, Hysi, Pirro G., Young, Terri L., Tsujikawa, Akitaka, Wang, Jie Jing, Mitchell, Paul, Pfeiffer, Norbert, Pärssinen, Olavi, Foster, Paul J., Fossarello, Maurizio, Yip, Shea Ping, Williams, Cathy, Hammond, Christopher J., Jonas, Jost B., He, Mingguang, Mackey, David A., Wong, Tien-Yin, Klaver, Caroline C. W., Saw, Seang-Mei, Baird, Paul N., and Cheng, Ching-Yu
Subjects: genetic structures, likinäköisyys, sense organs, geneettiset tekijät, eye diseases
Abstract: Corneal curvature, a highly heritable trait, is a key clinical endophenotype for myopia - a major cause of visual impairment and blindness in the world. Here we present a trans-ethnic meta-analysis of corneal curvature GWAS in 44,042 individuals of Caucasian and Asian with replication in 88,218 UK Biobank data. We identified 47 loci (of which 26 are novel), with population-specific signals as well as shared signals across ethnicities. Some identified variants showed precise scaling in corneal curvature and eye elongation (i.e. axial length) to maintain eyes in emmetropia (i.e. HDAC11/FBLN2 rs2630445, RBP3 rs11204213); others exhibited association with myopia with little pleiotropic effects on eye elongation. Implicated genes are involved in extracellular matrix organization, developmental process for body and eye, connective tissue cartilage and glycosylation protein activities. Our study provides insights into population-specific novel genes for corneal curvature, and their pleiotropic effect in regulating eye size or conferring susceptibility to myopia. peerReviewed
Published: 2020

26. Multi-trait genome-wide association study identifies new loci associated with optic disc parameters

Author: Bonnemaijer, Pieter W. M., Leeuwen, Elisabeth M. van, Iglesias, Adriana I., Gharahkhani, Puya, Vitart, Veronique, Khawaja, Anthony P., Simcoe, Mark, Hohn, Rene, Cree, Angela J., Igo, Rob P., International Glaucoma Genetics Consortium, NEIGHBORHOOD consortium, UK Biobank Eye and Vision Consortium, Barman, Sarah A., Gerhold-Ay, Aslihan, Nickels, Stefan, Wilson, James F., Hayward, Caroline, Boutin, Thibaud S., Polasek, Ozren, Aung, Tin, Khor, Chiea Chuen, Amin, Najaf, Lotery, Andrew J., Wiggs, Janey L., Cheng, Ching-Yu, Hysi, Pirro G., Hammond, Christopher J., Thiadens, Alberta A. H. J., MacGregor, Stuart, Klaver, Caroline C. W., and Duijn, Cornelia M. van
Subjects: genetic structures, sense organs, eye diseases, biological
Abstract: A new avenue of mining published genome-wide association studies includes the joint analysis of related traits. The power of this approach depends on the genetic correlation of traits, which reflects the number of pleiotropic loci, i.e. genetic loci influencing multiple traits. Here, we applied new meta-analyses of optic nerve head (ONH) related traits implicated in primary open-angle glaucoma (POAG); intraocular pressure and central corneal thickness using Haplotype reference consortium imputations. We performed a multi-trait analysis of ONH parameters cup area, disc area and vertical cup-disc ratio. We uncover new variants; rs11158547 in PPP1R36-PLEKHG3 and rs1028727 near SERPINE3 at genome-wide significance that replicate in independent Asian cohorts imputed to 1000 Genomes. At this point, validation of these variants in POAG cohorts is hampered by the high degree of heterogeneity. Our results show that multi-trait analysis is a valid approach to identify novel pleiotropic variants for ONH.
Published: 2019

27. No Association Between Vitamin D Status and Risk of Barrett's Esophagus or Esophageal Adenocarcinoma: A Mendelian Randomization Study

Author: Dong, Jing, Gharahkhani, Puya, Chow, Wong-Ho, Gammon, Marilie D, Liu, Geoffrey, Caldas, Carlos, Wu, Anna H, Ye, Weimin, Onstad, Lynn, Anderson, Lesley A, Bernstein, Leslie, Pharoah, Paul D, Risch, Harvey A, Corley, Douglas A, Fitzgerald, Rebecca C, Stomach And Esophageal Cancer Study Consortium, Iyer, Prasad G, Reid, Brian J, Lagergren, Jesper, Shaheen, Nicholas J, Vaughan, Thomas L, MacGregor, Stuart, Love, Sharon, Palles, Claire, Tomlinson, Ian, Gockel, Ines, May, Andrea, Gerges, Christian, Anders, Mario, Böhmer, Anne C, Becker, Jessica, Kreuser, Nicole, Thieme, Rene, Noder, Tania, Venerito, Marino, Veits, Lothar, Schmidt, Thomas, Schmidt, Claudia, Izbicki, Jakob R, Hölscher, Arnulf H, Lang, Hauke, Lorenz, Dietmar, Schumacher, Brigitte, Mayershofer, Rupert, Vashist, Yogesh, Ott, Katja, Vieth, Michael, Weismüller, Josef, Nöthen, Markus M, Moebus, Susanne, Knapp, Michael, Peters, Wilbert HM, Neuhaus, Horst, Rösch, Thomas, Ell, Christian, Jankowski, Janusz, Schumacher, Johannes, Neale, Rachel E, Whiteman, David C, Thrift, Aaron P, Caldas, Carlos [0000-0003-3547-1489], Pharoah, Paul [0000-0001-8494-732X], Fitzgerald, Rebecca [0000-0002-3434-3568], and Apollo - University of Cambridge Repository
Subjects: Esophageal Cancer, Etiology, Risk Factors, Chemoprevention, BEACON
Abstract: BACKGROUND & AIMS: Epidemiology studies of circulating concentrations of 25 hydroxy vitamin D (25(OH)D) and risk of esophageal adenocarcinoma (EAC) have produced conflicting results. We conducted a Mendelian randomization study to determine the associations between circulating concentrations of 25(OH)D and risks of EAC and its precursor, Barrett's esophagus (BE). METHODS: We conducted a Mendelian randomization study using a 2-sample (summary data) approach. Six single-nucleotide polymorphisms (SNPs; rs3755967, rs10741657, rs12785878, rs10745742, rs8018720, and rs17216707) associated with circulating concentrations of 25(OH)D were used as instrumental variables. We collected data from 6167 patients with BE, 4112 patients with EAC, and 17,159 individuals without BE or EAC (controls) participating in the Barrett's and Esophageal Adenocarcinoma Consortium, as well as studies from Bonn, Germany, and Cambridge and Oxford, United Kingdom. Analyses were performed separately for BE and EAC. RESULTS: Overall, we found no evidence for an association between genetically estimated 25(OH)D concentration and risk of BE or EAC. The odds ratio per 20 nmol/L increase in genetically estimated 25(OH)D concentration for BE risk estimated by combining the individual SNP association using inverse variance weighting was 1.21 (95% CI, 0.77-1.92; P = .41). The odds ratio for EAC risk, estimated by combining the individual SNP association using inverse variance weighting, was 0.68 (95% CI, 0.39-1.19; P = .18). CONCLUSIONS: In a Mendelian randomization study, we found that low genetically estimated 25(OH)D concentrations were not associated with risk of BE or EAC.
Published: 2019
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28. Exome-Derived Adiponectin-Associated Variants Implicate Obesity and Lipid Biology

Author: Spracklen, Cassandra N, Karaderi, Tugce, Yaghootkar, Hanieh, Schurmann, Claudia, Fine, Rebecca S, Kutalik, Zoltan, Preuss, Michael H, Lu, Yingchang, Wittemans, Laura BL, Adair, Linda S, Allison, Matthew, Amin, Najaf, Auer, Paul L, Bartz, Traci M, Blüher, Matthias, Boehnke, Michael, Borja, Judith B, Bork-Jensen, Jette, Broer, Linda, Chasman, Daniel I, Chen, Yii-Der Ida, Chirstofidou, Paraskevi, Demirkan, Ayse, van Duijn, Cornelia M, Feitosa, Mary F, Garcia, Melissa E, Graff, Mariaelisa, Grallert, Harald, Grarup, Niels, Guo, Xiuqing, Haesser, Jeffrey, Hansen, Torben, Harris, Tamara B, Highland, Heather M, Hong, Jaeyoung, Ikram, M Arfan, Ingelsson, Erik, Jackson, Rebecca, Jousilahti, Pekka, Kähönen, Mika, Kizer, Jorge R, Kovacs, Peter, Kriebel, Jennifer, Laakso, Markku, Lange, Leslie A, Lehtimäki, Terho, Li, Jin, Li-Gao, Ruifang, Lind, Lars, Luan, Jian'an, Lyytikäinen, Leo-Pekka, MacGregor, Stuart, Mackey, David A, Mahajan, Anubha, Mangino, Massimo, Männistö, Satu, McCarthy, Mark I, McKnight, Barbara, Medina-Gomez, Carolina, Meigs, James B, Molnos, Sophie, Mook-Kanamori, Dennis, Morris, Andrew P, de Mutsert, Renee, Nalls, Mike A, Nedeljkovic, Ivana, North, Kari E, Pennell, Craig E, Pradhan, Aruna D, Province, Michael A, Raitakari, Olli T, Raulerson, Chelsea K, Reiner, Alex P, Ridker, Paul M, Ripatti, Samuli, Roberston, Neil, Rotter, Jerome I, Salomaa, Veikko, Sandoval-Zárate, America A, Sitlani, Colleen M, Spector, Tim D, Strauch, Konstantin, Stumvoll, Michael, Taylor, Kent D, Thuesen, Betina, Tönjes, Anke, Uitterlinden, Andre G, Venturini, Cristina, Walker, Mark, Wang, Carol A, Wang, Shuai, Wareham, Nicholas J, Willems, Sara M, Willems van Dijk, Ko, Wilson, James G, Wu, Ying, Yao, Jie, Young, Kristin L, Langenberg, Claudia, and Frayling, Timothy M
Subjects: Adult, Male, obesity, Adolescent, Quantitative Trait Loci, Cardiovascular, Medical and Health Sciences, White People, lipids, Young Adult, 80 and over, Genetics, Humans, 2.1 Biological and endogenous factors, Genetic Predisposition to Disease, Exome, Polymorphism, Aetiology, Metabolic and endocrine, Aged, Nutrition, African Americans, Genetics & Heredity, genome-wide association study, adiponectin, Whites, Human Genome, Single Nucleotide, Hispanic or Latino, Middle Aged, Biological Sciences, cardio metabolic traits, Black or African American, Phenotype, Adipose Tissue, Female
Abstract: Circulating levels of adiponectin, an adipocyte-secreted protein associated with cardiovascular and metabolic risk, are highly heritable. To gain insights into the biology that regulates adiponectin levels, we performed an exome array meta-analysis of 265,780 genetic variants in 67,739 individuals of European, Hispanic, African American, and East Asian ancestry. We identified 20 loci associated with adiponectin, including 11 that had been reported previously (p < 2× 10-7). Comparison of exome array variants to regional linkage disequilibrium (LD) patterns and prior genome-wide association study (GWAS) results detected candidate variants (r2 > .60) spanning as much as 900 kb. To identify potential genes and mechanisms through which the previously unreported association signals act to affect adiponectin levels, we assessed cross-trait associations, expression quantitative trait loci in subcutaneous adipose, and biological pathways of nearby genes. Eight of the nine loci were also associated (p < 1× 10-4) with at least one obesity or lipid trait. Candidate genes include PRKAR2A, PTH1R, and HDAC9, which have been suggested to play roles in adipocyte differentiation or bone marrow adipose tissue. Taken together, these findings provide further insights into the processes that influence circulating adiponectin levels.
Published: 2019

29. Author Correction: GWAS of lifetime cannabis use reveals new risk loci, genetic overlap with psychiatric traits, and a causal effect of schizophrenia liability (Nature Neuroscience, (2018), 21, 9, (1161-1170), 10.1038/s41593-018-0206-1)

Author: Pasman, Joëlle A., Verweij, Karin J. H., Gerring, Zachary, Stringer, Sven, Sanchez-Roige, Sandra, Treur, Jorien L., Abdellaoui, Abdel, Nivard, Michel G., Baselmans, Bart M. L., Ong, Jue-Sheng, Ip, Hill F., van der Zee, Matthijs D., Bartels, Meike, Day, Felix R., Fontanillas, Pierre, Elson, Sarah L., de Wit, Harriet, Davis, Lea K., MacKillop, James, Derringer, Jaime L., Branje, Susan J. T., Hartman, Catharina A., Heath, Andrew C., van Lier, Pol A. C., Madden, Pamela A. F., Mägi, Reedik, Meeus, Wim, Montgomery, Grant W., Oldehinkel, A. J., Pausova, Zdenka, Ramos-Quiroga, Josep A., Paus, Tomas, Ribases, Marta, Kaprio, Jaakko, Boks, Marco P. M., Bell, Jordana T., Spector, Tim D., Gelernter, Joel, Boomsma, Dorret I., Martin, Nicholas G., MacGregor, Stuart, Perry, John R. B., Palmer, Abraham A., Posthuma, Danielle, Munafò, Marcus R., Gillespie, Nathan A., Derks, Eske M., and Vink, Jacqueline M.
Subjects: mental disorders, behavioral disciplines and activities
Abstract: Several occurrences of the word ‘schizophrenia’ have been re-worded as ‘liability to schizophrenia’ or ‘schizophrenia risk’, including in the title, which should have been “GWAS of lifetime cannabis use reveals new risk loci, genetic overlap with psychiatric traits, and a causal effect of schizophrenia liability,” as well as in Supplementary Figures 1–10 and Supplementary Tables 7–10, to more accurately reflect the findings of the work.
Published: 2019

30. Publisher Correction: Novel pleiotropic risk loci for melanoma and nevus density implicate multiple biological pathways

Author: Duffy, David L., Zhu, Gu, Li, Xin, Sanna, Marianna, Jacobs, Leonie C., Evans, David M., Yazar, Seyhan, Beesley, Jonathan, Lawrence, Matthew H., Kraft, Peter, Visconti, Alessia, Taylor, John C., Lui, Fan, Wright, Margaret J., Henders, Anjali K., Bowdler, Lisa, Glass, Dan, Ikram, Arfan M., Uitterlinden, André G., Madden, Pamela A., Heath, Andrew C., Nelson, Elliot C., Green, Adele C., Chanock, Stephen, Barrett, Jennifer H., Brown, Matthew A., Hayward, Nicholas K., MacGregor, Stuart, Sturm, Richard A., Hewitt, Alex W., Leenhardt, Jeffrey E., Brossard, Myriam, Moses, Eric K., Song, Fengju, Kumar, Rajiv, Easton, Douglas F., Pharoah, Paul D. P., Swerdlow, Anthony J., Kypreou, Katerina P., Harland, Mark, Randerson-Moor, Juliette, Akslen, Lars A., Andresen, Per A., Avril, Marie-Françoise, Azizi, Esther, Scarrà, Giovanna Bianchi, Brown, Kevin M., Dębniak, Tadeusz, Elder, David E., Fang, Shenying, Friedman, Eitan, Galan, Pilar, Ghiorzo, Paola, Gillanders, Elizabeth M., Goldstein, Alisa M., Gruis, Nelleke A., Hansson, Johan, Helsing, Per, Hočevar, Marko, Höiom, Veronica, Ingvar, Christian, Kanetsky, Peter A., Chen, Wei V., Landi, Maria Teresa, Lang, Julie, Lathrop, G. Mark, Lubiński, Jan, Mackie, Rona M., Mann, Graham J., Molven, Anders, Novaković, Srdjan, Olsson, Håkan, Puig, Susana, Puig-Butille, Joan Anton, Radford-Smith, Graham L., van Doorn, Remco, Whiteman, David C., Craig, Jamie E., Schadendorf, Dirk, Simms, Lisa A., Burdon, Kathryn P., Nyholt, Dale R., Pooley, Karen A., Orr, Nicholas, Stratigos, Alexander J., Cust, Anne E., Ward, Sarah V., Schulze, Hans-Joachim, Dunning, Alison M., Demenais, Florence, Amos, Christopher I., Kayser, Manfred, Hunter, David J., Newton Bishop, Julia A., Spector, Timothy D., Montgomery, Grant W., Mackey, David A., Smith, George Davey, Nijsten, Tamar E., Bishop, D. Timothy, Bataille, Veronique, Falchi, Mario, Han, Jiali, and Martin, Nicholas G.
Subjects: 0301 basic medicine, Skin Neoplasms, Medizin, General Physics and Astronomy, 02 engineering and technology, Receptors, G-Protein-Coupled, Guanine Nucleotide Exchange Factors, skin and connective tissue diseases, lcsh:Science, Melanoma, Telomerase, Nevus, Pigmented, Stem Cell Factor, Multidisciplinary, Microfilament Proteins, Nuclear Proteins, RNA-Binding Proteins, Genetic Pleiotropy, 021001 nanoscience & nanotechnology, Publisher Correction, Spelling, Cytochrome P-450 CYP1B1, Interferon Regulatory Factors, 0210 nano-technology, Science, Telomere-Binding Proteins, Nerve Tissue Proteins, Computational biology, Biology, Polymorphism, Single Nucleotide, General Biochemistry, Genetics and Molecular Biology, Article, Histone Deacetylases, White People, Group VI Phospholipases A2, 03 medical and health sciences, medicine, Nevus, Humans, Genetic Predisposition to Disease, General Chemistry, medicine.disease, Repressor Proteins, MicroRNAs, 030104 developmental biology, RNA, lcsh:Q, Carrier Proteins, Genome-Wide Association Study
Abstract: The total number of acquired melanocytic nevi on the skin is strongly correlated with melanoma risk. Here we report a meta-analysis of 11 nevus GWAS from Australia, Netherlands, UK, and USA comprising 52,506 individuals. We confirm known loci including MTAP, PLA2G6, and IRF4, and detect novel SNPs in KITLG and a region of 9q32. In a bivariate analysis combining the nevus results with a recent melanoma GWAS meta-analysis (12,874 cases, 23,203 controls), SNPs near GPRC5A, CYP1B1, PPARGC1B, HDAC4, FAM208B, DOCK8, and SYNE2 reached global significance, and other loci, including MIR146A and OBFC1, reached a suggestive level. Overall, we conclude that most nevus genes affect melanoma risk (KITLG an exception), while many melanoma risk loci do not alter nevus count. For example, variants in TERC and OBFC1 affect both traits, but other telomere length maintenance genes seem to affect melanoma risk only. Our findings implicate multiple pathways in nevogenesis., Melanocytic nevus count is associated with melanoma risk. In this study, a meta-analysis of 11 nevus GWAS studies identifies novel SNPs in KITLG and 9q32, and bivariate analysis with melanoma GWAS meta-analysis reveals that most nevus genes affect melanoma risk, while melanoma risk loci do not alter the nevus count.
Published: 2019

31. Publisher Correction::Novel pleiotropic risk loci for melanoma and nevus density implicate multiple biological pathways (Nature Communications, (2018), 9, 1, (4774), 10.1038/s41467-018-06649-5)

Author: Duffy, David L., Zhu, Gu, Li, Xin, Sanna, Marianna, Iles, Mark M., Jacobs, Leonie C., Evans, David M., Yazar, Seyhan, Beesley, Jonathan, Law, Matthew H., Kraft, Peter, Visconti, Alessia, Taylor, John C., Liu, Fan, Wright, Margaret J., Henders, Anjali K., Bowdler, Lisa, Glass, Dan, Ikram, M. Arfan, Uitterlinden, André G., Madden, Pamela A., Heath, Andrew C., Nelson, Elliot C., Green, Adele C., Chanock, Stephen, Barrett, Jennifer H., Brown, Matthew A., Hayward, Nicholas K., MacGregor, Stuart, Sturm, Richard A., Hewitt, Alex W., Lee, Jeffrey E., Brossard, Myriam, Moses, Eric K., Song, Fengju, Kumar, Rajiv, Easton, Douglas F., Pharoah, Paul D.P., Swerdlow, Anthony J., Kypreou, Katerina P., Harland, Mark, Randerson-Moor, Juliette, Akslen, Lars A., Andresen, Per A., Avril, Marie Françoise, Azizi, Esther, Scarrà, Giovanna Bianchi, Brown, Kevin M., Dębniak, Tadeusz, and Smith, George Davey
Abstract: The original version of this Article contained errors in the spelling of the authors Fan Liu and M. Arfan Ikram, which were incorrectly given as Fan Lui and Arfan M. Ikram. In addition, the original version of this Article also contained errors in the author affiliations which are detailed in the associated Publisher Correction.
Published: 2019

32. Correction: Exome-Derived Adiponectin-Associated Variants Implicate Obesity and Lipid Biology

Author: Spracklen, Cassandra N., Karaderi, Tugce, Yaghootkar, Hanieh, Schurmann, Claudia, Fine, Rebecca S., Kutalik, Zoltan, Preuss, Michael H., Lu, Yingchang, Wittemans, Laura B. L., Adair, Linda S., Allison, Matthew, Amin, Najaf, Auer, Paul L., Bartz, Traci M., Blüher, Matthias, Boehnke, Michael, Borja, Judith B., Bork-Jensen, Jette, Broer, Linda, Chasman, Daniel I., Chen, Yii-Der Ida, Chirstofidou, Paraskevi, Demirkan, Ayse, van Duijn, Cornelia M., Feitosa, Mary F., Garcia, Melissa E., Graff, Mariaelisa, Grallert, Harald, Grarup, Niels, Guo, Xiuqing, Haesser, Jeffrey, Hansen, Torben, Harris, Tamara B., Highland, Heather M., Hong, Jaeyoung, Ikram, M. Arfan, Ingelsson, Erik, Jackson, Rebecca, Jousilahti, Pekka, Kähönen, Mika, Kizer, Jorge R., Kovacs, Peter, Kriebel, Jennifer, Laakso, Markku, Lange, Leslie A., Lehtimäki, Terho, Li, Jin, Li-Gao, Ruifang, Lind, Lars, Luan, Jian'an, Lyytikäinen, Leo-Pekka, MacGregor, Stuart, Mackey, David A., Mahajan, Anubha, Mangino, Massimo, Männistö, Satu, McCarthy, Mark I., McKnight, Barbara, Medina-Gomez, Carolina, Meigs, James B., Molnos, Sophie, Mook-Kanamori, Dennis, Morris, Andrew P., de Mutsert, Renee, Nalls, Mike A., Nedeljkovic, Ivana, North, Kari E., Pennell, Craig E., Pradhan, Aruna D., Province, Michael A., Raitakari, Olli T., Raulerson, Chelsea K., Reiner, Alex P., Ridker, Paul M., Ripatti, Samuli, Roberston, Neil, Rotter, Jerome I., Salomaa, Veikko, Sandoval-Zárate, America A., Sitlani, Colleen M., Spector, Tim D., Strauch, Konstantin, Stumvoll, Michael, Taylor, Kent D., Thuesen, Betina, Tönjes, Anke, Uitterlinden, Andre G., Venturini, Cristina, Walker, Mark, Wang, Carol A., Wang, Shuai, Wareham, Nicholas J., Willems, Sara M., Willems van Dijk, Ko, Wilson, James G., Wu, Ying, Yao, Jie, Young, Kristin L., Langenberg, Claudia, Frayling, Timothy M., Kilpeläinen, Tuomas O., Lindgren, Cecilia M., Loos, Ruth J. F., and Mohlke, Karen L.
Subjects: SDG 3 - Good Health and Well-being
Published: 2019

33. Investigating Genetic Heterogeneity in Major Depression Through Item-level Genetic Analyses of the PHQ-9

Author: Thorp, Jackson G, Marees, Andries T, Ong, Jue-Sheng, An, Jiyuan, MacGregor, Stuart, Derks, Eske M, Economics, and Biological Psychology
Subjects: SDG 3 - Good Health and Well-being, mental disorders, behavioral disciplines and activities
Abstract: 26 Background: Major Depressive Disorder (MDD) is a clinically heterogeneous disorder. Previous 27
Published: 2019

34. Novel pleiotropic risk loci for melanoma and nevus density implicate multiple biological pathways (vol 9, 4774, 2018)

Author: Duffy, David L. Zhu, Gu Li, Xin Sanna, Marianna Iles, Mark M. Jacobs, Leonie C. Evans, David M. Yazar, Seyhan and Beesley, Jonathan Law, Matthew H. Kraft, Peter Visconti, Alessia Taylor, John C. Liu, Fan Wright, Margaret J. and Henders, Anjali K. Bowdler, Lisa Glass, Dan Ikram, M. Arfan and Uitterlinden, Andre G. Madden, Pamela A. Heath, Andrew C. and Nelson, Elliot C. Green, Adele C. Chanock, Stephen and Barrett, Jennifer H. Brown, Matthew A. Hayward, Nicholas K. and MacGregor, Stuart Sturm, Richard A. Hewitt, Alex W. Kayser, Manfred Hunter, David J. Bishop, Julia A. Newton Spector, Timothy D. Montgomery, Grant W. Mackey, David A. Smith, George Davey Nijsten, Tamar E. Bishop, D. Timothy Bataille, Veronique Falchi, Mario Han, Jiali Martin, Nicholas G. and Lee, Jeffrey E. Brossard, Myriam Moses, Eric K. Song, Fengju and Kumar, Rajiv Easton, Douglas F. Pharoah, Paul D. P. and Swerdlow, Anthony J. Kypreou, Katerina P. Harland, Mark and Randerson-Moor, Juliette Akslen, Lars A. Andresen, Per A. and Avril, Marie-Francoise Azizi, Esther Scarra, Giovanna Bianchi and Brown, Kevin M. Debniak, Tadeusz Elder, David E. Fang, Shenying Friedman, Eitan Galan, Pilar Ghiorzo, Paola and Gillanders, Elizabeth M. Goldstein, Alisa M. Gruis, Nelleke A. and Hansson, Johan Helsing, Per Hocevar, Marko Hoiom, Veronica Ingvar, Christian Kanetsky, Peter A. Chen, Wei V. and Landi, Maria Teresa Lang, Julie Lathrop, G. Mark and Lubinski, Jan Mackie, Rona M. Mann, Graham J. Molven, Anders and Novakovic, Srdjan Olsson, Hakan Puig, Susana and Puig-Butille, Joan Anton Radford-Smith, Graham L. van der Stoep, Nienke van Doorn, Remco Whiteman, David C. Craig, Jamie E. and Schadendorf, Dirk Simms, Lisa A. Burdon, Kathryn P. and Nyholt, Dale R. Pooley, Karen A. Orr, Nicholas Stratigos, Alexander J. Cust, Anne E. Ward, Sarah V. Schulze, Hans-Joachim Dunning, Alison M. Demenais, Florence Amos, Christopher I. Melanoma GWAS Consortium
Published: 2019

35. Novel pleiotropic risk loci for melanoma and nevus density implicate multiple biological pathways

Author: Duffy, David L, Zhu, Gu, Xin, Li, Sanna, Marianna, Iles, Mark M, Jacobs, Leonie C, Evans, David M, Yazar, Seyhan, Beesley, Jonathan, Law, Matthew H, Kraft, Peter, Visconti, Alessia, Taylor, John C, Lui, Fan, Wright, Margaret J, Henders, Anjali K, Bowdler, Lisa, Glass, Dan, Ikram, Arfan M, Uitterlinden, André G, Madden, Pamela A, Heath, Andrew C, Nelson, Elliot C, Green, Adele C, Chanock, Stephen, Barrett, Jennifer H, Brown, Matthew A, Hayward, Nicholas K, Macgregor, Stuart, Sturm, Richard A, Hewitt, Alex W, Kayser, Manfred, Hunter, David J, Newton Bishop, Julia A, Spector, Timothy D, Montgomery, Grant W, Mackey, David A, Smith, George Davey, Nijsten, Tamar E, Bishop, D Timothy, Bataille, Veronique, Falchi, Mario, Han, Jiali, Martin, Nicholas, G, Lee, Je, Brossard, M, Moses, Ek, Song, F, Kumar, R, Easton, Df, Pharoah, Pdp, Swerdlow, Aj, Kypreou, Kp, Harland, M, Randerson-Moor, J, Akslen, La, Andresen, Pa, Avril, Mf, Azizi, E, Scarrà, Gb, Brown, Km, Dębniak, T, Elder, De, Fang, S, Friedman, E, Galan, P, Ghiorzo, P, Gillanders, Em, Goldstein, Am, Gruis, Na, Hansson, J, Helsing, P, Hočevar, M, Höiom, V, Ingvar, C, Kanetsky, Pa, Chen, Wv, Landi, Mt, Lang, J, Lathrop, Gm, Lubiński, J, Mackie, Rm, Mann, Gj, Molven, A, Novaković, S, Olsson, H, Puig, S, Puig-Butille, Ja, Radford-Smith, Gl, van der Stoep, N, van Doorn, R, Whiteman, Dc, Craig, Je, Schadendorf, D, Simms, La, Burdon, Kp, Nyholt, Dr, Pooley, Ka, Orr, N, Stratigos, Aj, Cust, Ae, Ward, Sv, Schulze, Hj, Dunning, Am, Demenais, F, Amos, Ci., Apollo - University of Cambridge Repository, Dermatology, Genetic Identification, Epidemiology, Internal Medicine, and Consortium, Melanoma Gwas
Subjects: 0301 basic medicine, Skin Neoplasms, Medizin, General Physics and Astronomy, Genome-wide association study, Receptors, G-Protein-Coupled, 0302 clinical medicine, Guanine Nucleotide Exchange Factors, lcsh:Science, skin and connective tissue diseases, Melanoma, Telomerase, Genetics, 0303 health sciences, Nevus, Pigmented, Stem Cell Factor, Multidisciplinary, Microfilament Proteins, Nuclear Proteins, RNA-Binding Proteins, Genetic Pleiotropy, Microphthalmia-associated transcription factor, 3. Good health, 030220 oncology & carcinogenesis, Cytochrome P-450 CYP1B1, Interferon Regulatory Factors, Medical genetics, PPARGC1B, Dock8, medicine.medical_specialty, Science, Telomere-Binding Proteins, Single-nucleotide polymorphism, Nerve Tissue Proteins, Biology, Polymorphism, Single Nucleotide, General Biochemistry, Genetics and Molecular Biology, Histone Deacetylases, White People, Group VI Phospholipases A2, 03 medical and health sciences, Genetic predisposition, Pigmented Nevus, medicine, Nevus, Humans, Genetic Predisposition to Disease, neoplasms, 030304 developmental biology, General Chemistry, medicine.disease, Repressor Proteins, MicroRNAs, 030104 developmental biology, Cutaneous melanoma, RNA, lcsh:Q, Carrier Proteins, IRF4, Genome-Wide Association Study
Abstract: The total number of acquired melanocytic nevi on the skin is strongly correlated with melanoma risk. Here we report a meta-analysis of 11 nevus GWAS from Australia, Netherlands, United Kingdom, and United States, comprising a total of 52,506 phenotyped individuals. We confirm known loci including MTAP, PLA2G6, and IRF4, and detect novel SNPs at a genome-wide level of significance in KITLG, DOCK8, and a broad region of 9q32. In a bivariate analysis combining the nevus results with those from a recent melanoma GWAS meta-analysis (12,874 cases, 23,203 controls), SNPs near GPRC5A, CYP1B1, PPARGC1B, HDAC4, FAM208B and SYNE2 reached global significance, and other loci, including MIR146A and OBFC1, reached a suggestive level of significance. Overall, we conclude that most nevus genes affect melanoma risk (KITLG an exception), while many melanoma risk loci do not alter nevus count. For example, variants in TERC and OBFC1 affect both traits, but other telomere length maintenance genes seem to affect melanoma risk only. Our findings implicate multiple pathways in nevogenesis via genes we can show to be expressed under control of the MITF melanocytic cell lineage regulator.
Published: 2018

36. Modulation of σ-Alkane interactions in [Rh(L2)(alkane)]+ solid-state organometallic (SMOM) systems by variation of the chelating phosphine and alkane: Access to η2,η2-σ-alkane Rh(I), η1-σ-alkane Rh(III) complexes, and alkane encapsulation

Author: Martínez-Martínez, Antonio J., Tegner, Bengt E., McKay, Alasdair I., Bukvic, Alexander J., Rees, Nicholas H., Tizzard, Graham J., Coles, Simon J., Warren, Mark R., Macgregor, Stuart A., and Weller, Andrew S.
Abstract: Solid/gas single-crystal to single-crystal (SC–SC) hydrogenation of appropriate diene precursors forms the corresponding σ-alkane complexes [Rh(Cy2P(CH2)nPCy2)(L)][BArF4] (n = 3, 4) and [tiebar above startRhH(Cy2P(CH2)2(tiebar above endCH)(CH2)2PCy2)(L)][BArF4] (n = 5, L = norbornane, NBA; cyclooctane, COA). Their structures, as determined by single-crystal X-ray diffraction, have cations exhibiting Rh···H–C σ-interactions which are modulated by both the chelating ligand and the identity of the alkane, while all sit in an octahedral anion microenvironment. These range from chelating η2,η2 Rh···H–C (e.g., [Rh(Cy2P(CH2)nPCy2)(η2η2-NBA)][BArF4], n = 3 and 4), through to more weakly bound η1 Rh···H–C in which C–H activation of the chelate backbone has also occurred (e.g., [tiebar above startRhH(Cy2P(CH2)2(tiebar above endCH)(CH2)2PCy2)(η1-COA)][BArF4]) and ultimately to systems where the alkane is not ligated with the metal center, but sits encapsulated in the supporting anion microenvironment, [Rh(Cy2P(CH2)3PCy2)][COA⊂BArF4], in which the metal center instead forms two intramolecular agostic η1 Rh···H–C interactions with the phosphine cyclohexyl groups. CH2Cl2 adducts formed by displacement of the η1-alkanes in solution (n = 5; L = NBA, COA), [tiebar above startRhH(Cy2P(CH2)2(tiebar above endCH)(CH2)2PCy2)(κ1-ClCH2Cl)][BArF4], are characterized crystallographically. Analyses via periodic DFT, QTAIM, NBO, and NCI calculations, alongside variable temperature solid-state NMR spectroscopy, provide snapshots marking the onset of Rh···alkane interactions along a C–H activation trajectory. These are negligible in [Rh(Cy2P(CH2)3PCy2)][COA⊂BArF4]; in [tiebar above startRhH(Cy2P(CH2)2(tiebar above endCH)(CH2)2PCy2)(η1-COA)][BArF4], σC–H → Rh σ-donation is supported by Rh → σ*C–H “pregostic” donation, and in [Rh(Cy2P(CH2)nPCy2)(η2η2-NBA)][BArF4] (n = 2–4), σ-donation dominates, supported by classical Rh(dπ) → σ*C–H π-back-donation. Dispersive interactions with the [BArF4]− anions and Cy substituents further stabilize the alkanes within the binding pocket.
Published: 2018

37. Cell-type–specific eQTL of primary melanocytes facilitates identification of melanoma susceptibility genes

Author: Zhang, Tongwu, Choi, Jiyeon, Kovacs, Michael A., Shi, Jianxin, Mai, Xu, Goldstein, Alisa M., Trower, Adam J., Bishop, D. Timothy, Iles, Mark M., Duffy, David L., Macgregor, Stuart, Amundadottir, Laufey T., Law, Matthew H., Loftus, Stacie K., Pavan, William J., Brown, Kevin M., Lee, Je, Brossard, M, Martin, Ng, Moses, Ek, Song, F, Barrett, Jh, Kumar, R, Easton, Df, Pharoah, Pdp, Swerdlow, Aj, Kypreou, Kp, Taylor, Jc, Harland, M, Randerson-Moor, J, Akslen, La, Andresen, Pa, Avril, Mf, Azizi, E, Bianchi Scarrà, G, Dȩbniak, T, Duffy, Dl, Elder, De, Fang, S, Friedman, E, Galan, P, Ghiorzo, P, Gillanders, Em, Goldstein, Am, Gruis, Na, Hansson, J, Helsing, P, Hočevar, M, Höiom, V, Ingvar, C, Kanetsky, Pa, Chen, Wv, Landi, Mt, Lang, J, Lathrop, Gm, Lubiński, J, Mackie, Rm, Mann, Gj, Molven, A, Montgomery, Gw, Novaković, S, Olsson, H, Puig, S, Puig-Butille, Ja, Wu, W, Qureshi, Aa, Radford-Smith, Gl, van der Stoep, N, van Doorn, R, Whiteman, Dc, Craig, Je, Schadendorf, D, Simms, La, Burdon, Kp, Nyholt, Dr, Pooley, Ka, Orr, N, Stratigos, Aj, Cust, Ae, Ward, Sv, Hayward, Nk, Han, J, Schulze, Hj, Dunning, Am, Bishop, Jan, Demenais, F, Amos, Ci, Macgregor, S, Iles, Mm, Barnabas, Bb, Bouffard, Gg, Brooks, Sy, Coleman, H, Dekhtyar, L, Guan, X, Ho, Sl, Legaspi, R, Maduro, Ql, Masiello, Ca, Mcdowell, Jc, Montemayor, C, Mullikin, Jc, Park, M, Riebow, Nl, Schandler, K, Schmidt, B, Sison, C, Smith, R, Stantripop, S, Thomas, Jw, Thomas, Pj, Vemulapalli, M, and Young, Ac.
Subjects: 0301 basic medicine, Hemeproteins, Linkage disequilibrium, Quantitative Trait Loci, Single-nucleotide polymorphism, Genome-wide association study, Biology, Quantitative trait locus, Melanocyte, Polymorphism, Single Nucleotide, Linkage Disequilibrium, 03 medical and health sciences, Heme-Binding Proteins, 0302 clinical medicine, Genetics, medicine, Basic Helix-Loop-Helix Transcription Factors, Humans, Genetic Predisposition to Disease, Melanoma, Genetics (clinical), Cells, Cultured, Genetic association, Research, medicine.disease, Repressor Proteins, 030104 developmental biology, medicine.anatomical_structure, 030220 oncology & carcinogenesis, Expression quantitative trait loci, Interferon Regulatory Factors, Melanocytes, Carrier Proteins
Abstract: Most expression quantitative trait locus (eQTL) studies to date have been performed in heterogeneous tissues as opposed to specific cell types. To better understand the cell-type–specific regulatory landscape of human melanocytes, which give rise to melanoma but account for cis-eQTL SNPs prior to linkage disequilibrium (LD) pruning and 4997 eGenes (FDR < 0.05). Melanocyte eQTLs differed considerably from those identified in the 44 GTEx tissue types, including skin. Over a third of melanocyte eGenes, including key genes in melanin synthesis pathways, were unique to melanocytes compared to those of GTEx skin tissues or TCGA melanomas. The melanocyte data set also identified trans-eQTLs, including those connecting a pigmentation-associated functional SNP with four genes, likely through cis-regulation of IRF4. Melanocyte eQTLs are enriched in cis-regulatory signatures found in melanocytes as well as in melanoma-associated variants identified through genome-wide association studies. Melanocyte eQTLs also colocalized with melanoma GWAS variants in five known loci. Finally, a transcriptome-wide association study using melanocyte eQTLs uncovered four novel susceptibility loci, where imputed expression levels of five genes (ZFP90, HEBP1, MSC, CBWD1, and RP11-383H13.1) were associated with melanoma at genome-wide significant P-values. Our data highlight the utility of lineage-specific eQTL resources for annotating GWAS findings, and present a robust database for genomic research of melanoma risk and melanocyte biology.
Published: 2018

38. Isothiourea-catalysed enantioselective pyrrolizine synthesis: synthetic and computational studies† †Electronic supplementary information (ESI) available: NMR spectra, HPLC analysis and computational co-ordinates. Data available.12 CCDC 1483759. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c6ob01557c Click here for additional data file. Click here for additional data file. Click here for additional data file

Author: Stark, Daniel G., Williamson, Patrick, Gayner, Emma R., Musolino, Stefania F., Kerr, Ryan W. F., Taylor, James E., Slawin, Alexandra M. Z., O'Riordan, Timothy J. C., Macgregor, Stuart A., and Smith, Andrew D.
Subjects: Chemistry
Abstract: The isothiourea-catalysed enantioselective synthesis of cis-pyrrolizines is explored synthetically and computationally., The catalytic enantioselective synthesis of a range of cis-pyrrolizine carboxylate derivatives with outstanding stereocontrol (14 examples, >95 : 5 dr, >98 : 2 er) through an isothiourea-catalyzed intramolecular Michael addition-lactonisation and ring-opening approach from the corresponding enone acid is reported. An optimised and straightforward three-step synthetic route to the enone acid starting materials from readily available pyrrole-2-carboxaldehydes is delineated, with benzotetramisole (5 mol%) proving the optimal catalyst for the enantioselective process. Ring-opening of the pyrrolizine dihydropyranone products with either MeOH or a range of amines leads to the desired products in excellent yield and enantioselectivity. Computation has been used to probe the factors leading to high stereocontrol, with the formation of the observed cis-steroisomer predicted to be kinetically and thermodynamically favoured.
Published: 2016

39. GWAS of lifetime cannabis use reveals new risk loci, genetic overlap with psychiatric traits, and a causal influence of schizophrenia

Author: Pasman, Joëlle A, Verweij, Karin JH, Gerring, Zachary, Stringer, Sven, Sanchez-Roige, Sandra, Treur, Jorien L, Abdellaoui, Abdel, Nivard, Michel G, Baselmans, Bart ML, Ong, Jue-Sheng, Ip, Hill F, van der Zee, Matthijs D, Bartels, Meike, Day, Felix R, Fontanillas, Pierre, Elson, Sarah L, 23andMe Research Team, de Wit, Harriet, Davis, Lea K, MacKillop, James, Substance Use Disorders Working Group of the Psychiatric Genomics Consortium, International Cannabis Consortium, Derringer, Jaime L, Branje, Susan JT, Hartman, Catharina A, Heath, Andrew C, van Lier, Pol AC, Madden, Pamela AF, Mägi, Reedik, Meeus, Wim, Montgomery, Grant W, Oldehinkel, AJ, Pausova, Zdenka, Ramos-Quiroga, Josep A, Paus, Tomas, Ribases, Marta, Kaprio, Jaakko, Boks, Marco PM, Bell, Jordana T, Spector, Tim D, Gelernter, Joel, Boomsma, Dorret I, Martin, Nicholas G, MacGregor, Stuart, Perry, John RB, Palmer, Abraham A, Posthuma, Danielle, Munafò, Marcus R, Gillespie, Nathan A, Derks, Eske M, and Vink, Jacqueline M
Subjects: Adult, Male, Marijuana Abuse, Genotype, Adolescent, and over, Cardiovascular, 23andMe Research Team, Drug Abuse, Substance Misuse, Databases, Young Adult, Risk-Taking, Genetic, Clinical Research, 80 and over, Genetics, International Cannabis Consortium, Humans, 2.1 Biological and endogenous factors, Psychology, Genetic Predisposition to Disease, Aetiology, Polymorphism, Aged, Neurology & Neurosurgery, Prevention, Human Genome, Substance Abuse, Neurosciences, Single Nucleotide, Middle Aged, Mendelian Randomization Analysis, Brain Disorders, Good Health and Well Being, Mental Health, Gene Expression Regulation, Schizophrenia, Substance Use Disorders Working Group of the Psychiatric Genomics Consortium, Female, Cognitive Sciences, Drug Abuse (NIDA only), Cell Adhesion Molecules, Genome-Wide Association Study
Abstract: Cannabis use is a heritable trait that has been associated with adverse mental health outcomes. In the largest genome-wide association study (GWAS) for lifetime cannabis use to date (N = 184,765), we identified eight genome-wide significant independent single nucleotide polymorphisms in six regions. All measured genetic variants combined explained 11% of the variance. Gene-based tests revealed 35 significant genes in 16 regions, and S-PrediXcan analyses showed that 21 genes had different expression levels for cannabis users versus nonusers. The strongest finding across the different analyses was CADM2, which has been associated with substance use and risk-taking. Significant genetic correlations were found with 14 of 25 tested substance use and mental health-related traits, including smoking, alcohol use, schizophrenia and risk-taking. Mendelian randomization analysis showed evidence for a causal positive influence of schizophrenia risk on cannabis use. Overall, our study provides new insights into the etiology of cannabis use and its relation with mental health.
Published: 2018

40. GWAS of lifetime cannabis use reveals new risk loci, genetic overlap with psychiatric traits, and a causal influence of schizophrenia

Author: Pasman, Joëlle A., Verweij, Karin J. H., Gerring, Zachary, Stringer, Sven, Sanchez-roige, Sandra, Treur, Jorien L., Abdellaoui, Abdel, Nivard, Michel G., Baselmans, Bart M. L., Ong, Jue-sheng, Ip, Hill F., Van Der Zee, Matthijs D., Bartels, Meike, Day, Felix R., Fontanillas, Pierre, Elson, Sarah L., De Wit, Harriet, Davis, Lea K., Mackillop, James, Derringer, Jaime L., Branje, Susan J. T., Hartman, Catharina A., Heath, Andrew C., Van Lier, Pol A. C., Madden, Pamela A. F., Mägi, Reedik, Meeus, Wim, Montgomery, Grant W., Oldehinkel, A. J., Pausova, Zdenka, Ramos-quiroga, Josep A., Paus, Tomas, Ribases, Marta, Kaprio, Jaakko, Boks, Marco P. M., Bell, Jordana T., Spector, Tim D., Gelernter, Joel, Boomsma, Dorret I., Martin, Nicholas G., Macgregor, Stuart, Perry, John R. B., Palmer, Abraham A., Posthuma, Danielle, Munafò, Marcus R., Gillespie, Nathan A., Derks, Eske M., Vink, Jacqueline M., Leerstoel Branje, and Adolescent development: Characteristics and determinants
Subjects: Taverne
Abstract: Cannabis use is a heritable trait that has been associated with adverse mental health outcomes. In the largest genome-wide association study (GWAS) for lifetime cannabis use to date (N = 184,765), we identified eight genome-wide significant independent single nucleotide polymorphisms in six regions. All measured genetic variants combined explained 11% of the variance. Gene-based tests revealed 35 significant genes in 16 regions, and S-PrediXcan analyses showed that 21 genes had different expression levels for cannabis users versus nonusers. The strongest finding across the different analyses was CADM2, which has been associated with substance use and risk-taking. Significant genetic correlations were found with 14 of 25 tested substance use and mental health–related traits, including smoking, alcohol use, schizophrenia and risk-taking. Mendelian randomization analysis showed evidence for a causal positive influence of schizophrenia risk on cannabis use. Overall, our study provides new insights into the etiology of cannabis use and its relation with mental health.
Published: 2018

41. GWAS of lifetime cannabis use reveals new risk loci, genetic overlap with psychiatric traits, and a causal influence of schizophrenia

Author: Pasman, Joëlle A., Verweij, Karin J.H., Gerring, Zachary, Stringer, Sven, Sanchez-Roige, Sandra, Treur, Jorien L., Abdellaoui, Abdel, Nivard, Michel G., Baselmans, Bart M.L., Ong, Jue-Sheng, Ip, Hill F., van der Zee, Matthijs D., Bartels, Meike, Day, Felix R., Fontanillas, Pierre, Elson, Sarah L., de Wit, Harriet, Davis, Lea K., MacKillop, James, Derringer, Jaime L., Branje, Susan J.T., Hartman, Catharina A., Heath, Andrew C., van Lier, Pol A.C., Madden, Pamela A.F., Mägi, Reedik, Meeus, Wim, Montgomery, Grant W., Oldehinkel, A.J., Pausova, Zdenka, Ramos-Quiroga, Josep A., Paus, Tomas, Ribases, Marta, Kaprio, Jaakko, Boks, Marco P.M., Bell, Jordana T., Spector, Tim D., Gelernter, Joel, Boomsma, Dorret I., Martin, Nicholas G., MacGregor, Stuart, Perry, John R.B., Palmer, Abraham A., Posthuma, Danielle, Munafò, Marcus R., Gillespie, Nathan A., Derks, Eske M., Vink, Jacqueline M., Leerstoel Branje, Adolescent development: Characteristics and determinants, and Interdisciplinary Centre Psychopathology and Emotion regulation (ICPE)
Subjects: Adult, Male, Marijuana Abuse, Adolescent, Genotype, Gene Expression Regulation/genetics, Polymorphism, Single Nucleotide, 23andMe Research Team, Article, Schizophrenia/chemically induced, Marijuana Abuse/genetics, Young Adult, Risk-Taking, Databases, Genetic, Taverne, Humans, International Cannabis Consortium, Genetic Predisposition to Disease, Aged, Aged, 80 and over, Mendelian Randomization Analysis, Middle Aged, Mental Health, Gene Expression Regulation, Schizophrenia, Substance Use Disorders Working Group of the Psychiatric Genomics Consortium, Female, Cell Adhesion Molecules/genetics, Cell Adhesion Molecules, Genome-Wide Association Study
Abstract: © 2018, The Author(s). Cannabis use is a heritable trait that has been associated with adverse mental health outcomes. In the largest genome-wide association study (GWAS) for lifetime cannabis use to date (N = 184,765), we identified eight genome-wide significant independent single nucleotide polymorphisms in six regions. All measured genetic variants combined explained 11% of the variance. Gene-based tests revealed 35 significant genes in 16 regions, and S-PrediXcan analyses showed that 21 genes had different expression levels for cannabis users versus nonusers. The strongest finding across the different analyses was CADM2, which has been associated with substance use and risk-taking. Significant genetic correlations were found with 14 of 25 tested substance use and mental health–related traits, including smoking, alcohol use, schizophrenia and risk-taking. Mendelian randomization analysis showed evidence for a causal positive influence of schizophrenia risk on cannabis use. Overall, our study provides new insights into the etiology of cannabis use and its relation with mental health.
Published: 2018

42. Cross-ancestry genome-wide association analysis of corneal thickness strengthens link between complex and Mendelian eye diseases

Author: Iglesias, Adriana I, Mishra, Aniket, Vitart, Veronique, Bykhovskaya, Yelena, Höhn, René, Springelkamp, Henriët, Cuellar-Partida, Gabriel, Gharahkhani, Puya, Bailey, Jessica N Cooke, Willoughby, Colin E, Li, Xiaohui, Yazar, Seyhan, Nag, Abhishek, Khawaja, Anthony P, Polašek, Ozren, Siscovick, David, Mitchell, Paul, Tham, Yih Chung, Haines, Jonathan L, Kearns, Lisa S, Hayward, Caroline, Shi, Yuan, van Leeuwen, Elisabeth M, Taylor, Kent D, Blue Mountains Eye Study—GWAS group, Bonnemaijer, Pieter, Rotter, Jerome I, Martin, Nicholas G, Zeller, Tanja, Mills, Richard A, Souzeau, Emmanuelle, Staffieri, Sandra E, Jonas, Jost B, Schmidtmann, Irene, Boutin, Thibaud, Kang, Jae H, Lucas, Sionne EM, Wong, Tien Yin, Beutel, Manfred E, Wilson, James F, NEIGHBORHOOD Consortium, Wellcome Trust Case Control Consortium 2 (WTCCC2), Uitterlinden, André G, Vithana, Eranga N, Foster, Paul J, Hysi, Pirro G, Hewitt, Alex W, Khor, Chiea Chuen, Pasquale, Louis R, Montgomery, Grant W, Klaver, Caroline CW, Aung, Tin, Pfeiffer, Norbert, Mackey, David A, Hammond, Christopher J, Cheng, Ching-Yu, Craig, Jamie E, Rabinowitz, Yaron S, Wiggs, Janey L, Burdon, Kathryn P, van Duijn, Cornelia M, and MacGregor, Stuart
Subjects: Asian Continental Ancestry Group, Lumican, genetic structures, Corneal Dystrophies, Eye Diseases, Fibrillin-1, 1.1 Normal biological development and functioning, European Continental Ancestry Group, Quantitative Trait Loci, Gene Expression, Keratoconus, Eye, White People, Marfan Syndrome, Corneal Diseases, Cornea, Quantitative Trait, Transforming Growth Factor beta2, ADAMTS Proteins, Rare Diseases, Asian People, Underpinning research, Blue Mountains Eye Study—GWAS group, Myopia, Genetics, Humans, Polymorphism, Heritable, Eye Disease and Disorders of Vision, Loeys-Dietz Syndrome, Genome, NEIGHBORHOOD Consortium, Wellcome Trust Case Control Consortium 2, Human Genome, Glaucoma, Single Nucleotide, Mendelian Randomization Analysis, eye diseases, Hereditary, Open-Angle, Ehlers-Danlos Syndrome, Proteoglycans, sense organs, Decorin, Human, Genome-Wide Association Study
Abstract: Central corneal thickness (CCT) is a highly heritable trait associated with complex eye diseases such as keratoconus and glaucoma. We perform a genome-wide association meta-analysis of CCT and identify 19 novel regions. In addition to adding support for known connective tissue-related pathways, pathway analyses uncover previously unreported gene sets. Remarkably, >20% of the CCT-loci are near or within Mendelian disorder genes. These included FBN1, ADAMTS2 and TGFB2 which associate with connective tissue disorders (Marfan, Ehlers-Danlos and Loeys-Dietz syndromes), and the LUM-DCN-KERA gene complex involved in myopia, corneal dystrophies and cornea plana. Using index CCT-increasing variants, we find a significant inverse correlation in effect sizes between CCT and keratoconus (r = -0.62, P = 5.30 × 10-5) but not between CCT and primary open-angle glaucoma (r = -0.17, P = 0.2). Our findings provide evidence for shared genetic influences between CCT and keratoconus, and implicate candidate genes acting in collagen and extracellular matrix regulation.
Published: 2018

43. Genomic locus modulating corneal thickness in the mouse identifies POU6F2 as a potential risk of developing glaucoma

Author: King, Rebecca, Struebing, Felix L., Li, Ying, Wang, Jiaxing, Koch, Allison Ashley, Cooke Bailey, Jessica N., Gharahkhani, Puya, MacGregor, Stuart, Allingham, Rand, Hauser, Michael, Wiggs, Janey L., Geisert, Eldon E., Brilliant, Murray, Budenz, Don, Bailey, Jessica N.Cooke, Fingert, John, Gaasterland, Douglas, Gaasterland, Teresa, Haines, Jonathan L., Hark, Lisa, Igo, Rob, Kang, Jae Hee, Kraft, Peter, Lee, Richard, Lichter, Paul, Liu, Yutao, Moroi, Syoko, Pasquale, Louis R., Pericak-Vance, Margaret, Realini, Anthony, Rhee, Doug, Richards, Julia R., Ritch, Robert, Schuman, Joel, Scott, William K., Singh, Kuldev, Sit, Arthur, Vollrath, Douglas, Weinreb, Robert N., Wollstein, Gadi, Zack, Don, Aung, Tin, Burdon, Kathryn P., Cheng, Ching Yu, Craig, Jamie E., Cree, Angela J., Hammond, Christopher J., Psychiatry, Epidemiology, Ophthalmology, Obstetrics & Gynecology, and Anderson, Michael G
Subjects: 0301 basic medicine, Retinal Ganglion Cells, Male, Cancer Research, Candidate gene, Aging, Eye Diseases, Corneal Pachymetry, genetic structures, Genome-wide association study, Apoptosis, QH426-470, Inbred C57BL, Eye, Transgenic, Cornea, Mice, 0302 clinical medicine, Animal Cells, Risk Factors, Pregnancy, Medicine and Health Sciences, 2.1 Biological and endogenous factors, Aetiology, Genetics (clinical), Cells, Cultured, 2. Zero hunger, Genetics, Neurons, 0303 health sciences, Mammalian Genomics, Cultured, NEIGHBORHOOD Consortium, Chromosome Mapping, Genomics, Single Nucleotide, Phenotype, Mice, Inbred DBA, Embryo, Female, Anatomy, Cellular Types, Research Article, Biotechnology, Ganglion Cells, Ocular Anatomy, Cells, Locus (genetics), Mice, Transgenic, International Glaucoma Genetics Consortium, Biology, Quantitative trait locus, Retinal ganglion, Polymorphism, Single Nucleotide, Retina, 03 medical and health sciences, SDG 3 - Good Health and Well-being, Ocular System, SNP, Animals, Inbred DBA, Humans, Genetic Predisposition to Disease, Polymorphism, Molecular Biology, Gene, Eye Disease and Disorders of Vision, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Animal, Mammalian, Prevention, Human Genome, Neurosciences, Biology and Life Sciences, Afferent Neurons, Glaucoma, Cell Biology, Embryo, Mammalian, eye diseases, Mice, Inbred C57BL, Ophthalmology, Disease Models, Animal, 030104 developmental biology, Animal Genomics, Genetic Loci, Cellular Neuroscience, Disease Models, POU Domain Factors, 030221 ophthalmology & optometry, Eyes, sense organs, Head, Neuroscience, Genome-Wide Association Study, Developmental Biology
Abstract: Central corneal thickness (CCT) is one of the most heritable ocular traits and it is also a phenotypic risk factor for primary open angle glaucoma (POAG). The present study uses the BXD Recombinant Inbred (RI) strains to identify novel quantitative trait loci (QTLs) modulating CCT in the mouse with the potential of identifying a molecular link between CCT and risk of developing POAG. The BXD RI strain set was used to define mammalian genomic loci modulating CCT, with a total of 818 corneas measured from 61 BXD RI strains (between 60–100 days of age). The mice were anesthetized and the eyes were positioned in front of the lens of the Phoenix Micron IV Image-Guided OCT system or the Bioptigen OCT system. CCT data for each strain was averaged and used to QTLs modulating this phenotype using the bioinformatics tools on GeneNetwork (www.genenetwork.org). The candidate genes and genomic loci identified in the mouse were then directly compared with the summary data from a human POAG genome wide association study (NEIGHBORHOOD) to determine if any genomic elements modulating mouse CCT are also risk factors for POAG.This analysis revealed one significant QTL on Chr 13 and a suggestive QTL on Chr 7. The significant locus on Chr 13 (13 to 19 Mb) was examined further to define candidate genes modulating this eye phenotype. For the Chr 13 QTL in the mouse, only one gene in the region (Pou6f2) contained nonsynonymous SNPs. Of these five nonsynonymous SNPs in Pou6f2, two resulted in changes in the amino acid proline which could result in altered secondary structure affecting protein function. The 7 Mb region under the mouse Chr 13 peak distributes over 2 chromosomes in the human: Chr 1 and Chr 7. These genomic loci were examined in the NEIGHBORHOOD database to determine if they are potential risk factors for human glaucoma identified using meta-data from human GWAS. The top 50 hits all resided within one gene (POU6F2), with the highest significance level of p = 10−6 for SNP rs76319873. POU6F2 is found in retinal ganglion cells and in corneal limbal stem cells. To test the effect of POU6F2 on CCT we examined the corneas of a Pou6f2-null mice and the corneas were thinner than those of wild-type littermates. In addition, these POU6F2 RGCs die early in the DBA/2J model of glaucoma than most RGCs. Using a mouse genetic reference panel, we identified a transcription factor, Pou6f2, that modulates CCT in the mouse. POU6F2 is also found in a subset of retinal ganglion cells and these RGCs are sensitive to injury., Author summary Glaucoma is a complex group of diseases with several known causal mutations and many known risk factors. One well-known risk factor for developing primary open angle glaucoma is the thickness of the central cornea. The present study leverages a unique blend of systems biology methods using BXD recombinant inbred mice and genome-wide association studies from humans to define a putative molecular link between a phenotypic risk factor (central corneal thickness) and glaucoma. We identified a transcription factor, POU6F2, that is found in the developing retinal ganglion cells and cornea. POU6F2 is also present in a subpopulation of retinal ganglion cells and in stem cells of the cornea. Functional studies reveal that POU6F2 is associated with the central corneal thickness and susceptibility of retinal ganglion cells to injury.
Published: 2018

44. Benzoate cyclometallation enables oxidative addition of haloarenes at a Ru(II) center

Author: Simonetti, Marco, Kuniyil, Rositha, Macgregor, Stuart A., and Larrosa, Igor
Abstract: The first Ru(II)-catalyzed arylation of substrates without a directing group was recently developed. Remarkably, this process only worked in the presence of a benzoate additive, found to be crucial for the oxidative addition step at Ru(II). However, the exact mode of action of the benzoate was unknown. Herein, we disclose a mechanistic study that elucidates the key role of the benzoate salt in the C–H arylation of fluoroarenes with aryl halides. Through a combination of rationally designed stoichiometric experiments and DFT studies, we demonstrate that the aryl–Ru(II) species arising from initial C–H activation of the fluoroarene undergoes cyclometalation with the benzoate to generate an anionic Ru(II) intermediate. The enhanced lability of this intermediate, coupled with the electron-rich anionic Ru(II) metal center renders the oxidative addition of the aryl halide accessible. The role of an additional (NMe4)OC(CF3)3 additive in facilitating the overall arylation process is also shown to be linked to a shift in the C–H pre-equilibrium associated with benzoate cyclometalation.
Published: 2018

45. Benzoate Cyclometalation Enables Oxidative Addition of Haloarenes at a Ru(II) Center

Author: Simonetti, Marco, Kuniyil, Rositha, Macgregor, Stuart A., and Larrosa, Igor
Subjects: Article
Abstract: The first Ru(II)-catalyzed arylation of substrates without a directing group was recently developed. Remarkably, this process only worked in the presence of a benzoate additive, found to be crucial for the oxidative addition step at Ru(II). However, the exact mode of action of the benzoate was unknown. Herein, we disclose a mechanistic study that elucidates the key role of the benzoate salt in the C–H arylation of fluoroarenes with aryl halides. Through a combination of rationally designed stoichiometric experiments and DFT studies, we demonstrate that the aryl–Ru(II) species arising from initial C–H activation of the fluoroarene undergoes cyclometalation with the benzoate to generate an anionic Ru(II) intermediate. The enhanced lability of this intermediate, coupled with the electron-rich anionic Ru(II) metal center renders the oxidative addition of the aryl halide accessible. The role of an additional (NMe4)OC(CF3)3 additive in facilitating the overall arylation process is also shown to be linked to a shift in the C–H pre-equilibrium associated with benzoate cyclometalation.
Published: 2018

46. Isomerisation of nido-[C2B10H12]2– dianions: unprecedented rearrangements and new structural motifs in carborane cluster chemistry† †Electronic supplementary information (ESI) available: Movies of the 1,7 to 7,9 isomerisation (17-79_isom.avi), ortho-carborane reduction (ortho-carborane_RED.avi) and meta-carborane reduction (meta-carborane_RED.avi); alternative reaction profiles; computed Cartesian coordinates and energies for all structures. See DOI: 10.1039/c5sc00726g Click here for additional data file. Click here for additional data file. Click here for additional data file. Click here for additional data file

Author: McKay, David, Macgregor, Stuart A., and Welch, Alan J.
Subjects: Chemistry
Abstract: The formation and isomerisation of nido-[C2B10H12]2– species is investigated through DFT calculations, which reveal novel basket and inverted nido intermediates and unusual inverconversion pathways, including basket collapse and pivoting triangles and diamonds., Dianionic nido-[C2B10]2– species are key intermediates in the polyhedral expansion from 12- to 13-vertex carboranes and metallacarboranes, and the isomer adopted by these nido intermediates dictates the isomeric form of the 13-vertex product. Upon reduction and metallation of para-carborane up to five MC2B10 metallacarboranes can be produced (Angew. Chem., Int. Ed., 2007, 46, 6706), the structures of which imply the intermediacy of 1,7-, 3,7-, 4,7-, 7,9- and 7,10-isomers of the nido-[C2B10]2– species. In this paper we use density functional theory (DFT) calculations to characterise the reduction of closo-C2B10H12 carboranes and the subsequent isomerisations of the nido-[C2B10H12]2– dianions. Upon reduction para-carborane initially opens to [1,7-nido-C2B10H12]2– (abbreviated to 1,7) and [4,7-nido-C2B10H12]2– (4,7) and isomerisation pathways connecting 1,7 to 7,9, 4,7 to 7,10 and 1,7 to 3,7 have been characterised. For ortho- and meta-carborane the experimental reduction produces 7,9 in both cases and computed pathways for both processes are also defined; with ortho-carborane rearrangement occurs via 7,8, whereas with meta-carborane 7,9 is formed directly. The 7,9 isomer is the global minimum nido-structure. The characterisation of these isomerisation processes uncovers intermediates that adopt new structural motifs that we term basket and inverted nido. Basket intermediates feature a two-vertex basket handle bridging the remaining 10 vertices; inverted nido intermediates are related to known nido species, in that they have 5- and 6-membered belts, but where the latter, rather than the former, is capped, leaving a 5-membered open face. These new intermediates exhibit similar stability to the nido species, which is attributed to their relation to the 13-vertex docosahedron through the removal of 5-connected vertices. Isomerisation pathways starting from nido geometries are most often initiated by destabilisation of the cluster through a DSD process causing the 3-connected C7 vertex to move into a 4-connected site and a neighbouring B vertex to become 3-connected. The ensuing rearrangement of the cluster involves processes such as the pivoting of a 4-vertex diamond about its long diagonal, the pivoting of two 3-vertex triangles about a shared vertex and DSD processes. These processes are all ultimately driven by the preference for carbon to occupy low-connected vertices on the open 6-membered face of the resulting nido species.
Published: 2015

47. Fluoroarene Complexes with Small Bite Angle Bisphosphines : Routes to Amine–Borane and Aminoborylene Complexes

Author: Colebatch, Annie L., McKay, Alasdair I., Beattie, Nicholas A., Macgregor, Stuart A., and Weller, Andrew S.
Abstract: Fluoroarene complexes of the small bite angle bisphosphine Cy2PCH2PCy2 (dcpm) have been prepared: [Rh(dcpm)(η6-1,2-F2C6H4)][Al{OC(CF3)3}4] and [Rh(dcpm)(η6-1,2,3-F3C6H3)][Al{OC(CF3)3}4]. These complexes act as precursors to a previously inaccessible σ-amine–borane complex [Rh(dcpm)(η2-H3B·NMe3)][Al{OC(CF3)3}4] of a small bite-angle phosphine. This complex is a poor catalyst for the dehydrocoupling of H3B·NMe2H. Instead, formation of the bridging borylene complex [{RhH(µ-dcpm)}2(µ-H)(µ-BNMe2)][Al{OC(CF3)3}4] occurs, which has been studied by NMR, mass spectrometry, crystallographic and DFT techniques. This represents a new route to bridging borylene complexes.
Published: 2017

48. Genome-Wide Association Reveals Pigmentation Genes Play a Role in Skin Aging

Author: Law, Matthew H., Medland, Sarah E., Zhu, Gu, Yazar, Seyhan, Viñuela, Ana, Wallace, Leanne, Shekar, Sri Niranjan, Duffy, David L., Bataille, Veronique, Glass, Dan, Spector, Tim D., Wood, Diane, Gordon, Scott D., Barbour, Julie M., Henders, Anjali K., Hewitt, Alex W., Montgomery, Grant W., Sturm, Richard A., Mackey, David A., Green, Adèle C., Martin, Nicholas G., and MacGregor, Stuart
Subjects: Photoaging, Skin aging, integumentary system, Pigmentation, GWAS, Gene
Abstract: Loss of fine skin patterning is a sign of both aging and photoaging. Studies investigating the genetic contribution to skin patterning offer an opportunity to better understand a trait that influences both physical appearance and risk of keratinocyte skin cancer. We undertook a meta-analysis of genome-wide association studies (GWAS) of a measure of skin pattern (microtopography score) damage in 1,671 twin pairs and 1,745 singletons (N = 5,087) drawn from three independent cohorts. We identified that rs185146 near SLC45A2 is associated with a skin aging trait (p = 4.1 × 10-9); to our knowledge this is previously unreported. We also confirm previously identified loci, rs12203592 near IRF4 (p = 8.8 × 10-13), and rs4268748 near MC1R (p = 1.2 × 10-15). At all three loci we highlight putative functionally relevant SNPs. There are a number of red hair/low pigmentation alleles of MC1R; we found that together these MC1R alleles explained 4.1% of variance in skin pattern damage. We also show that skin aging and reported experience of sunburns was proportional to the degree of penetrance for red hair of alleles of MC1R. Our work has uncovered genetic contributions to skin aging and confirmed previous findings, showing that pigmentation is a critical determinate of skin aging.
Published: 2017

49. Computation provides chemical insight into the diverse hydride NMR chemical shifts of [Ru(NHC)4(L)H]0/+ species (NHC = N-heterocyclic carbene; L = vacant, H2, N2, CO, MeCN, O2, P4, SO2, H−, F− and Cl−) and their [Ru(R2PCH2CH2PR2)2(L)H]+ congeners

Author: Häller, L. jonas l., Mas-marzá, Elena, Cybulski, Mateusz k., Sanguramath, Rajashekharayya a., Macgregor, Stuart a, Mahon, Mary F., Raynaud, Christophe, Russell, Christopher a., Whittlesey, Michael k., Heriot-Watt University [Edinburgh] (HWU), Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK, Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, University of Bristol [Bristol], Institut Charles Gerhardt Montpellier - Institut de Chimie Moléculaire et des Matériaux de Montpellier (ICGM ICMMM), and Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut de Chimie du CNRS (INC)
Subjects: [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, [CHIM.COOR]Chemical Sciences/Coordination chemistry, [CHIM.INOR]Chemical Sciences/Inorganic chemistry
Abstract: International audience; Relativistic density functional theory calculations, both with and without the effects of spin–orbit coupling, have been employed to model hydride NMR chemical shifts for a series of [Ru(NHC)4(L)H]0/+ species (NHC = N-heterocyclic carbene; L = vacant, H2, N2, CO, MeCN, O2, P4, SO2, H−, F− and Cl−), as well as selected phosphine analogues [Ru(R2PCH2CH2PR2)2(L)H]+ (R = iPr, Cy; L = vacant, O2). Inclusion of spin–orbit coupling provides good agreement with the experimental data. For the NHC systems large variations in hydride chemical shift are shown to arise from the paramagnetic term, with high net shielding (L = vacant, Cl−, F−) being reinforced by the contribution from spin–orbit coupling. Natural chemical shift analysis highlights the major orbital contributions to the paramagnetic term and rationalizes trends via changes in the energies of the occupied Ru dπ orbitals and the unoccupied σ*Ru–H orbital. In [Ru(NHC)4(η2-O2)H]+ a δ-interaction with the O2 ligand results in a low-lying LUMO of dπ character. As a result this orbital can no longer contribute to the paramagnetic shielding, but instead provides additional deshielding via overlap with the remaining (occupied) dπ orbital under the Lz angular momentum operator. These two effects account for the unusual hydride chemical shift of +4.8 ppm observed experimentally for this species. Calculations reproduce hydride chemical shift data observed for [Ru(iPr2PCH2CH2PiPr2)2(η2-O2)H]+ (δ = −6.2 ppm) and [Ru(R2PCH2CH2PR2)2H]+ (ca. −32 ppm, R = iPr, Cy). For the latter, the presence of a weak agostic interaction trans to the hydride ligand is significant, as in its absence (R = Me) calculations predict a chemical shift of −41 ppm, similar to the [Ru(NHC)4H]+ analogues. Depending on the strength of the agostic interaction a variation of up to 18 ppm in hydride chemical shift is possible and this factor (that is not necessarily readily detected experimentally) can aid in the interpretation of hydride chemical shift data for nominally unsaturated hydride-containing species. The synthesis and crystallographic characterization of the BArF4− salts of [Ru(IMe4)4(L)H]+ (IMe4 = 1,3,4,5-tetramethylimidazol-2-ylidene; L = P4, SO2; ArF = 3,5-(CF3)2C6H3) and [Ru(IMe4)4(Cl)H] are also reported.
Published: 2017

50. Room Temperature Regioselective Catalytic Hydrodefluorination of Fluoroarenes with trans-[Ru(NHC)4H2] Via a Converted Nucleophlic Ru-H Attack Pathway

Author: Cybulski, Mateusz, McKay, David, Macgregor, Stuart, Mahon, Mary, and Whittlesey, Michael
Subjects: integumentary system
Abstract: The efficient and highly selective room temperature hydrodefluorination (HDF) of fluoroarenes by the trans-[Ru(IMe4)4H2] catalyst, 3, is reported. Mechanistic studies show 3 acts directly in catalysis without any ligand dissociation and DFT calculations indicate a concerted nucleophilic attack mechanism. The calculations fully account for the observed selectivities which corroborate earlier predictions regarding the selectivity of HDF.
Published: 2017

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