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1. How robust are cross-population signatures of polygenic adaptation in humans?

Author

Refoyo-Martínez, Alba, Liu, Siyang, Jørgensen, Anja Moltke, Jin, Xin, Albrechtsen, Anders, Martin, Alicia R., and Racimo, Fernando

Subjects
Archaeology, CC1-960, Science
Abstract

Over the past decade, summary statistics from genome-wide association studies (GWASs) have been used to detect and quantify polygenic adaptation in humans. Several studies have reported signatures of natural selection at sets of SNPs associated with complex traits, like height and body mass index. However, more recent studies suggest that some of these signals may be caused by biases from uncorrected population stratification in the GWAS data with which these tests are performed. Moreover, past studies have predominantly relied on SNP effect size estimates obtained from GWAS panels of European ancestries, which are known to be poor predictors of phenotypes in non-European populations. Here, we collated GWAS data from multiple anthropometric and metabolic traits that have been measured in more than one cohort around the world, including the UK Biobank, FINRISK, Chinese NIPT, Biobank Japan, APCDR and PAGE. We then evaluated how robust signals of polygenic score overdispersion (which have been interpreted as suggesting polygenic adaptation) are to the choice of GWAS cohort used to identify associated variants and their effect size estimates. We did so while using the same panel to obtain population allele frequencies (The 1000 Genomes Project). We observe many discrepancies across tests performed on the same phenotype and find that association studies performed using multiple different cohorts, like meta-analyses and mega-analyses, tend to produce polygenic scores with strong overdispersion across populations. This results in apparent signatures of polygenic adaptation which are not observed when using effect size estimates from biobank-based GWASs of homogeneous ancestries. Indeed, we were able to artificially create score overdispersion when taking the UK Biobank cohort and simulating a meta-analysis on multiple subsets of the cohort. Finally, we show that the amount of overdispersion in scores for educational attainment - a trait with strong social implications and high potential for misinterpretation - is also strongly dependent on the specific GWAS used to build them. This suggests that extreme caution should be taken in the execution and interpretation of future tests of polygenic score overdispersion based on population differentiation, especially when using summary statistics from a GWAS that combines multiple cohorts.

Published
2021
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3. A genomic mutational constraint map using variation in 76,156 human genomes

Author

Chen, Siwei, Francioli, Laurent C., Goodrich, Julia K., Collins, Ryan L., Kanai, Masahiro, Wang, Qingbo, Alföldi, Jessica, Watts, Nicholas A., Vittal, Christopher, Gauthier, Laura D., Poterba, Timothy, Wilson, Michael W., Tarasova, Yekaterina, Phu, William, Grant, Riley, Yohannes, Mary T., Koenig, Zan, Farjoun, Yossi, Banks, Eric, Donnelly, Stacey, Gabriel, Stacey, Gupta, Namrata, Ferriera, Steven, Tolonen, Charlotte, Novod, Sam, Bergelson, Louis, Roazen, David, Ruano-Rubio, Valentin, Covarrubias, Miguel, Llanwarne, Christopher, Petrillo, Nikelle, Wade, Gordon, Jeandet, Thibault, Munshi, Ruchi, Tibbetts, Kathleen, O’Donnell-Luria, Anne, Solomonson, Matthew, Seed, Cotton, Martin, Alicia R., Talkowski, Michael E., Rehm, Heidi L., Daly, Mark J., Tiao, Grace, Neale, Benjamin M., MacArthur, Daniel G., and Karczewski, Konrad J.

Published
2024
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9. The power of TOPMed imputation for the discovery of Latino-enriched rare variants associated with type 2 diabetes

Author

Huerta-Chagoya, Alicia, Schroeder, Philip, Mandla, Ravi, Deutsch, Aaron J., Zhu, Wanying, Petty, Lauren, Yi, Xiaoyan, Cole, Joanne B., Udler, Miriam S., Dornbos, Peter, Porneala, Bianca, DiCorpo, Daniel, Liu, Ching-Ti, Li, Josephine H., Szczerbiński, Lukasz, Kaur, Varinderpal, Kim, Joohyun, Lu, Yingchang, Martin, Alicia, Eizirik, Decio L., Marchetti, Piero, Marselli, Lorella, Chen, Ling, Srinivasan, Shylaja, Todd, Jennifer, Flannick, Jason, Gubitosi-Klug, Rose, Levitsky, Lynne, Shah, Rachana, Kelsey, Megan, Burke, Brian, Dabelea, Dana M., Divers, Jasmin, Marcovina, Santica, Stalbow, Lauren, Loos, Ruth J. F., Darst, Burcu F., Kooperberg, Charles, Raffield, Laura M., Haiman, Christopher, Sun, Quan, McCormick, Joseph B., Fisher-Hoch, Susan P., Ordoñez, Maria L., Meigs, James, Baier, Leslie J., González-Villalpando, Clicerio, González-Villalpando, Maria Elena, Orozco, Lorena, García-García, Lourdes, Moreno-Estrada, Andrés, Aguilar-Salinas, Carlos A., Tusié, Teresa, Dupuis, Josée, Ng, Maggie C. Y., Manning, Alisa, Highland, Heather M., Cnop, Miriam, Hanson, Robert, Below, Jennifer, Florez, Jose C., Leong, Aaron, and Mercader, Josep M.

Published
2023
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10. Novel ancestry-specific primary open-angle glaucoma loci and shared biology with vascular mechanisms and cell proliferation

Author

Lo Faro, Valeria, Bhattacharya, Arjun, Zhou, Wei, Zhou, Dan, Wang, Ying, Läll, Kristi, Kanai, Masahiro, Lopera-Maya, Esteban, Straub, Peter, Pawar, Priyanka, Tao, Ran, Zhong, Xue, Namba, Shinichi, Sanna, Serena, Nolte, Ilja M., Okada, Yukinori, Ingold, Nathan, MacGregor, Stuart, Snieder, Harold, Surakka, Ida, Shortt, Jonathan, Gignoux, Chris, Rafaels, Nicholas, Crooks, Kristy, Verma, Anurag, Verma, Shefali S., Guare, Lindsay, Rader, Daniel J., Willer, Cristen, Martin, Alicia R., Brantley, Milam A., Jr., Gamazon, Eric R., Jansonius, Nomdo M., Joos, Karen, Cox, Nancy J., and Hirbo, Jibril

Published
2024
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11. Author Correction: A genomic mutational constraint map using variation in 76,156 human genomes

Author

Chen, Siwei, Francioli, Laurent C., Goodrich, Julia K., Collins, Ryan L., Kanai, Masahiro, Wang, Qingbo, Alföldi, Jessica, Watts, Nicholas A., Vittal, Christopher, Gauthier, Laura D., Poterba, Timothy, Wilson, Michael W., Tarasova, Yekaterina, Phu, William, Grant, Riley, Yohannes, Mary T., Koenig, Zan, Farjoun, Yossi, Banks, Eric, Donnelly, Stacey, Gabriel, Stacey, Gupta, Namrata, Ferriera, Steven, Tolonen, Charlotte, Novod, Sam, Bergelson, Louis, Roazen, David, Ruano-Rubio, Valentin, Covarrubias, Miguel, Llanwarne, Christopher, Petrillo, Nikelle, Wade, Gordon, Jeandet, Thibault, Munshi, Ruchi, Tibbetts, Kathleen, O’Donnell-Luria, Anne, Solomonson, Matthew, Seed, Cotton, Martin, Alicia R., Talkowski, Michael E., Rehm, Heidi L., Daly, Mark J., Tiao, Grace, Neale, Benjamin M., MacArthur, Daniel G., and Karczewski, Konrad J.

Published
2024
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13. Problems with Using Polygenic Scores to Select Embryos

Author

Turley, Patrick, Meyer, Michelle N, Wang, Nancy, Cesarini, David, Hammonds, Evelynn, Martin, Alicia R, Neale, Benjamin M, Rehm, Heidi L, Wilkins-Haug, Louise, Benjamin, Daniel J, Hyman, Steven, Laibson, David, and Visscher, Peter M

Subjects
Reproductive Medicine, Biomedical and Clinical Sciences, Aging, Educational Status, Embryo, Mammalian, Fertilization in Vitro, Gene-Environment Interaction, Genetic Testing, Genetic Variation, Genome-Wide Association Study, Humans, Multifactorial Inheritance, Phenotype, Predictive Value of Tests, Preimplantation Diagnosis, Medical and Health Sciences, General & Internal Medicine, Biomedical and clinical sciences, Health sciences
Abstract

Companies have recently begun to sell a new service to patients considering in vitro fertilization: embryo selection based on polygenic scores (ESPS). These scores represent individualized predictions of health and other outcomes derived from genomewide association studies in adults to partially predict these outcomes. This article includes a discussion of many factors that lower the predictive power of polygenic scores in the context of embryo selection and quantifies these effects for a variety of clinical and nonclinical traits. Also discussed are potential unintended consequences of ESPS (including selecting for adverse traits, altering population demographics, exacerbating inequalities in society, and devaluing certain traits). Recommendations for the responsible communication about ESPS by practitioners are provided, and a call for a society-wide conversation about this technology is made. (Funded by the National Institute on Aging and others.).

Published
2021

14. A unified framework for estimating country-specific cumulative incidence for 18 diseases stratified by polygenic risk

Author

Jermy, Bradley, Läll, Kristi, Wolford, Brooke N., Wang, Ying, Zguro, Kristina, Cheng, Yipeng, Kanai, Masahiro, Kanoni, Stavroula, Yang, Zhiyu, Hartonen, Tuomo, Monti, Remo, Wanner, Julian, Youssef, Omar, Lippert, Christoph, van Heel, David, Okada, Yukinori, McCartney, Daniel L., Hayward, Caroline, Marioni, Riccardo E., Furini, Simone, Renieri, Alessandra, Martin, Alicia R., Neale, Benjamin M., Hveem, Kristian, Mägi, Reedik, Palotie, Aarno, Heyne, Henrike, Mars, Nina, Ganna, Andrea, and Ripatti, Samuli

Published
2024
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19. Population History and Gene Divergence in Native Mexicans Inferred from 76 Human Exomes.

Author

Ávila-Arcos, María C, McManus, Kimberly F, Sandoval, Karla, Rodríguez-Rodríguez, Juan Esteban, Villa-Islas, Viridiana, Martin, Alicia R, Luisi, Pierre, Peñaloza-Espinosa, Rosenda I, Eng, Celeste, Huntsman, Scott, Burchard, Esteban G, Gignoux, Christopher R, Bustamante, Carlos D, and Moreno-Estrada, Andrés

Subjects
Native Americans, adaptive evolution, demographic inference, exome sequencing, Biochemistry and Cell Biology, Evolutionary Biology, Genetics
Abstract

Native American genetic variation remains underrepresented in most catalogs of human genome sequencing data. Previous genotyping efforts have revealed that Mexico's Indigenous population is highly differentiated and substructured, thus potentially harboring higher proportions of private genetic variants of functional and biomedical relevance. Here we have targeted the coding fraction of the genome and characterized its full site frequency spectrum by sequencing 76 exomes from five Indigenous populations across Mexico. Using diffusion approximations, we modeled the demographic history of Indigenous populations from Mexico with northern and southern ethnic groups splitting 7.2 KYA and subsequently diverging locally 6.5 and 5.7 KYA, respectively. Selection scans for positive selection revealed BCL2L13 and KBTBD8 genes as potential candidates for adaptive evolution in Rarámuris and Triquis, respectively. BCL2L13 is highly expressed in skeletal muscle and could be related to physical endurance, a well-known phenotype of the northern Mexico Rarámuri. The KBTBD8 gene has been associated with idiopathic short stature and we found it to be highly differentiated in Triqui, a southern Indigenous group from Oaxaca whose height is extremely low compared to other Native populations.

Published
2020

20. Genomic Relationships, Novel Loci, and Pleiotropic Mechanisms across Eight Psychiatric Disorders

Author

Consortium, Cross-Disorder Group of the Psychiatric Genomics, Lee, Phil H, Anttila, Verneri, Won, Hyejung, Feng, Yen-Chen A, Rosenthal, Jacob, Zhu, Zhaozhong, Tucker-Drob, Elliot M, Nivard, Michel G, Grotzinger, Andrew D, Posthuma, Danielle, Wang, Meg M-J, Yu, Dongmei, Stahl, Eli A, Walters, Raymond K, Anney, Richard JL, Duncan, Laramie E, Ge, Tian, Adolfsson, Rolf, Banaschewski, Tobias, Belangero, Sintia, Cook, Edwin H, Coppola, Giovanni, Derks, Eske M, Hoekstra, Pieter J, Kaprio, Jaakko, Keski-Rahkonen, Anna, Kirov, George, Kranzler, Henry R, Luykx, Jurjen J, Rohde, Luis A, Zai, Clement C, Agerbo, Esben, Arranz, MJ, Asherson, Philip, Bækvad-Hansen, Marie, Baldursson, Gísli, Bellgrove, Mark, Belliveau, Richard A, Buitelaar, Jan, Burton, Christie L, Bybjerg-Grauholm, Jonas, Casas, Miquel, Cerrato, Felecia, Chambert, Kimberly, Churchhouse, Claire, Cormand, Bru, Crosbie, Jennifer, Dalsgaard, Søren, Demontis, Ditte, Doyle, Alysa E, Dumont, Ashley, Elia, Josephine, Grove, Jakob, Gudmundsson, Olafur O, Haavik, Jan, Hakonarson, Hakon, Hansen, Christine S, Hartman, Catharina A, Hawi, Ziarih, Hervás, Amaia, Hougaard, David M, Howrigan, Daniel P, Huang, Hailiang, Kuntsi, Jonna, Langley, Kate, Lesch, Klaus-Peter, Leung, Patrick WL, Loo, Sandra K, Martin, Joanna, Martin, Alicia R, McGough, James J, Medland, Sarah E, Moran, Jennifer L, Mors, Ole, Mortensen, Preben B, Oades, Robert D, Palmer, Duncan S, Pedersen, Carsten B, Pedersen, Marianne G, Peters, Triinu, Poterba, Timothy, Poulsen, Jesper B, Ramos-Quiroga, Josep Antoni, Reif, Andreas, Ribasés, Marta, Rothenberger, Aribert, Rovira, Paula, Sánchez-Mora, Cristina, Satterstrom, F Kyle, Schachar, Russell, Artigas, Maria Soler, Steinberg, Stacy, Stefansson, Hreinn, Turley, Patrick, Walters, G Bragi, Team, 23andMe Research, Werge, Thomas, Zayats, Tetyana, and Arking, Dan E

Subjects
Neurosciences, Serious Mental Illness, Human Genome, Schizophrenia, Intellectual and Developmental Disabilities (IDD), Brain Disorders, Genetics, Pediatric, Mental Health, Aetiology, 2.1 Biological and endogenous factors, Mental health, Genetic Pleiotropy, Genetic Predisposition to Disease, Genome-Wide Association Study, Humans, Mental Disorders, Neurogenesis, Quantitative Trait Loci, Cross-Disorder Group of the Psychiatric Genomics Consortium. Electronic address: plee0@mgh.harvard.edu, Cross-Disorder Group of the Psychiatric Genomics Consortium, GWAS, Psychiatric genetics, cross-disorder genetics, functional genomics, gene expression, genetic architecture, genetic correlation, neurodevelopment, pleiotropy, psychiatric disorders, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

Genetic influences on psychiatric disorders transcend diagnostic boundaries, suggesting substantial pleiotropy of contributing loci. However, the nature and mechanisms of these pleiotropic effects remain unclear. We performed analyses of 232,964 cases and 494,162 controls from genome-wide studies of anorexia nervosa, attention-deficit/hyperactivity disorder, autism spectrum disorder, bipolar disorder, major depression, obsessive-compulsive disorder, schizophrenia, and Tourette syndrome. Genetic correlation analyses revealed a meaningful structure within the eight disorders, identifying three groups of inter-related disorders. Meta-analysis across these eight disorders detected 109 loci associated with at least two psychiatric disorders, including 23 loci with pleiotropic effects on four or more disorders and 11 loci with antagonistic effects on multiple disorders. The pleiotropic loci are located within genes that show heightened expression in the brain throughout the lifespan, beginning prenatally in the second trimester, and play prominent roles in neurodevelopmental processes. These findings have important implications for psychiatric nosology, drug development, and risk prediction.

Published
2019

21. Comparative genetic architectures of schizophrenia in East Asian and European populations

Author

Lam, Max, Chen, Chia-Yen, Li, Zhiqiang, Martin, Alicia R, Bryois, Julien, Ma, Xixian, Gaspar, Helena, Ikeda, Masashi, Benyamin, Beben, Brown, Brielin C, Liu, Ruize, Zhou, Wei, Guan, Lili, Kamatani, Yoichiro, Kim, Sung-Wan, Kubo, Michiaki, Kusumawardhani, Agung AAA, Liu, Chih-Min, Ma, Hong, Periyasamy, Sathish, Takahashi, Atsushi, Xu, Zhida, Yu, Hao, Zhu, Feng, Chen, Wei J, Faraone, Stephen, Glatt, Stephen J, He, Lin, Hyman, Steven E, Hwu, Hai-Gwo, McCarroll, Steven A, Neale, Benjamin M, Sklar, Pamela, Wildenauer, Dieter B, Yu, Xin, Zhang, Dai, Mowry, Bryan J, Lee, Jimmy, Holmans, Peter, Xu, Shuhua, Sullivan, Patrick F, Ripke, Stephan, O’Donovan, Michael C, Daly, Mark J, Qin, Shengying, Sham, Pak, Iwata, Nakao, Hong, Kyung S, Schwab, Sibylle G, Yue, Weihua, Tsuang, Ming, Liu, Jianjun, Ma, Xiancang, Kahn, René S, Shi, Yongyong, and Huang, Hailiang

Subjects
Genetics, Human Genome, Serious Mental Illness, Schizophrenia, Brain Disorders, Mental Health, Prevention, Aetiology, 2.1 Biological and endogenous factors, Mental health, Good Health and Well Being, Asian People, Case-Control Studies, Asia, Eastern, Genetics, Population, Genome-Wide Association Study, Humans, Polymorphism, Single Nucleotide, White People, Schizophrenia Working Group of the Psychiatric Genomics Consortium, Indonesia Schizophrenia Consortium, Genetic REsearch on schizophreniA neTwork-China and the Netherlands, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

Schizophrenia is a debilitating psychiatric disorder with approximately 1% lifetime risk globally. Large-scale schizophrenia genetic studies have reported primarily on European ancestry samples, potentially missing important biological insights. Here, we report the largest study to date of East Asian participants (22,778 schizophrenia cases and 35,362 controls), identifying 21 genome-wide-significant associations in 19 genetic loci. Common genetic variants that confer risk for schizophrenia have highly similar effects between East Asian and European ancestries (genetic correlation = 0.98 ± 0.03), indicating that the genetic basis of schizophrenia and its biology are broadly shared across populations. A fixed-effect meta-analysis including individuals from East Asian and European ancestries identified 208 significant associations in 176 genetic loci (53 novel). Trans-ancestry fine-mapping reduced the sets of candidate causal variants in 44 loci. Polygenic risk scores had reduced performance when transferred across ancestries, highlighting the importance of including sufficient samples of major ancestral groups to ensure their generalizability across populations.

Published
2019

22. International meta-analysis of PTSD genome-wide association studies identifies sex- and ancestry-specific genetic risk loci.

Author

Nievergelt, Caroline M, Maihofer, Adam X, Klengel, Torsten, Atkinson, Elizabeth G, Chen, Chia-Yen, Choi, Karmel W, Coleman, Jonathan RI, Dalvie, Shareefa, Duncan, Laramie E, Gelernter, Joel, Levey, Daniel F, Logue, Mark W, Polimanti, Renato, Provost, Allison C, Ratanatharathorn, Andrew, Stein, Murray B, Torres, Katy, Aiello, Allison E, Almli, Lynn M, Amstadter, Ananda B, Andersen, Søren B, Andreassen, Ole A, Arbisi, Paul A, Ashley-Koch, Allison E, Austin, S Bryn, Avdibegovic, Esmina, Babić, Dragan, Bækvad-Hansen, Marie, Baker, Dewleen G, Beckham, Jean C, Bierut, Laura J, Bisson, Jonathan I, Boks, Marco P, Bolger, Elizabeth A, Børglum, Anders D, Bradley, Bekh, Brashear, Megan, Breen, Gerome, Bryant, Richard A, Bustamante, Angela C, Bybjerg-Grauholm, Jonas, Calabrese, Joseph R, Caldas-de-Almeida, José M, Dale, Anders M, Daly, Mark J, Daskalakis, Nikolaos P, Deckert, Jürgen, Delahanty, Douglas L, Dennis, Michelle F, Disner, Seth G, Domschke, Katharina, Dzubur-Kulenovic, Alma, Erbes, Christopher R, Evans, Alexandra, Farrer, Lindsay A, Feeny, Norah C, Flory, Janine D, Forbes, David, Franz, Carol E, Galea, Sandro, Garrett, Melanie E, Gelaye, Bizu, Geuze, Elbert, Gillespie, Charles, Uka, Aferdita Goci, Gordon, Scott D, Guffanti, Guia, Hammamieh, Rasha, Harnal, Supriya, Hauser, Michael A, Heath, Andrew C, Hemmings, Sian MJ, Hougaard, David Michael, Jakovljevic, Miro, Jett, Marti, Johnson, Eric Otto, Jones, Ian, Jovanovic, Tanja, Qin, Xue-Jun, Junglen, Angela G, Karstoft, Karen-Inge, Kaufman, Milissa L, Kessler, Ronald C, Khan, Alaptagin, Kimbrel, Nathan A, King, Anthony P, Koen, Nastassja, Kranzler, Henry R, Kremen, William S, Lawford, Bruce R, Lebois, Lauren AM, Lewis, Catrin E, Linnstaedt, Sarah D, Lori, Adriana, Lugonja, Bozo, Luykx, Jurjen J, Lyons, Michael J, Maples-Keller, Jessica, Marmar, Charles, and Martin, Alicia R

Subjects
Humans, Genetic Predisposition to Disease, Ubiquitin-Protein Ligases, Stress Disorders, Post-Traumatic, Sex Factors, African Continental Ancestry Group, European Continental Ancestry Group, Veterans, Female, Male, Genome-Wide Association Study, Genetic Loci, Datasets as Topic, Human Genome, Mental Health, Biotechnology, Clinical Research, Post-Traumatic Stress Disorder (PTSD), Anxiety Disorders, Prevention, Genetics
Abstract

The risk of posttraumatic stress disorder (PTSD) following trauma is heritable, but robust common variants have yet to be identified. In a multi-ethnic cohort including over 30,000 PTSD cases and 170,000 controls we conduct a genome-wide association study of PTSD. We demonstrate SNP-based heritability estimates of 5-20%, varying by sex. Three genome-wide significant loci are identified, 2 in European and 1 in African-ancestry analyses. Analyses stratified by sex implicate 3 additional loci in men. Along with other novel genes and non-coding RNAs, a Parkinson's disease gene involved in dopamine regulation, PARK2, is associated with PTSD. Finally, we demonstrate that polygenic risk for PTSD is significantly predictive of re-experiencing symptoms in the Million Veteran Program dataset, although specific loci did not replicate. These results demonstrate the role of genetic variation in the biology of risk for PTSD and highlight the necessity of conducting sex-stratified analyses and expanding GWAS beyond European ancestry populations.

Published
2019

23. Global Biobank analyses provide lessons for developing polygenic risk scores across diverse cohorts

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, Chapman, Sinéad B., Karjalainen, Juha, Kurki, Mitja, Mutaamba, Maasha, Partanen, Juulia J., Brumpton, Ben M., Chavan, Sameer, Chen, Tzu-Ting, Daya, Michelle, Ding, Yi, Feng, Yen-Chen A., Gignoux, Christopher R., Graham, Sarah E., Hornsby, Whitney E., Ingold, Nathan, Johnson, Ruth, Laisk, Triin, Lin, Kuang, Lv, Jun, Millwood, Iona Y., Palta, Priit, Pandit, Anita, Preuss, Michael H., Thorsteinsdottir, Unnur, Uzunovic, Jasmina, Zawistowski, Matthew, Zhong, Xue, Campbell, Archie, Crooks, Kristy, de Bock, Geertruida H., Douville, Nicholas J., Finer, Sarah, Fritsche, Lars G., Griffiths, Christopher J., Guo, Yu, Hunt, Karen A., Konuma, Takahiro, Marioni, Riccardo E., Nomdo, Jansonius, Patil, Snehal, Rafaels, Nicholas, Richmond, Anne, Shortt, Jonathan A., Straub, Peter, Tao, Ran, Vanderwerff, Brett, 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, Koskela, Jukka T., Lajonchere, Clara, Law, Matthew H., Li, Liming, Lindgren, Cecilia M., Loos, Ruth J.F., MacGregor, Stuart, Matsuda, Koichi, Olsen, Catherine M., Porteous, David J., Shavit, Jordan A., Snieder, Harold, Trembath, Richard C., Vonk, Judith M., Whiteman, David, Wicks, Stephen J., Wijmenga, Cisca, Wright, John, Zheng, Jie, Zhou, Xiang, Awadalla, Philip, Boehnke, Michael, Cox, Nancy J., Geschwind, Daniel H., Hayward, Caroline, Hveem, Kristian, Kenny, Eimear E., Lin, Yen-Feng, Mägi, Reedik, Martin, Hilary C., Medland, Sarah E., Okada, Yukinori, Palotie, Aarno V., Pasaniuc, Bogdan, Sanna, Serena, Smoller, Jordan W., Stefansson, Kari, van Heel, David A., Walters, Robin G., Zöllner, Sebastian, Martin, Alicia R., Willer, Cristen J., Daly, Mark J., Neale, Benjamin M., Lopera, Esteban, Kerminen, Sini, Wu, Kuan-Han, Bhatta, Laxmi, Brumpton, Ben, Deelen, Patrick, Murakami, Yoshinori, Willer, Cristen, and Hirbo, Jibril

Published
2023
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24. Increasing diversity in genomics requires investment in equitable partnerships and capacity building

Author

Martin, Alicia R., Stroud, II, Rocky E., Abebe, Tamrat, Akena, Dickens, Alemayehu, Melkam, Atwoli, Lukoye, Chapman, Sinéad B., Flowers, Katelyn, Gelaye, Bizu, Gichuru, Stella, Kariuki, Symon M., Kinyanjui, Sam, Korte, Kristina J., Koen, Nastassja, Koenen, Karestan C., Newton, Charles R. J. C., Olivares, Ana Maria, Pollock, Sam, Post, Kristianna, Singh, Ilina, Stein, Dan J., Teferra, Solomon, Zingela, Zukiswa, and Chibnik, Lori B.

Published
2022
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26. Meta-analysis fine-mapping is often miscalibrated at single-variant resolution

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, Michael Lee, Ming Ta, 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 J.F., 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, The Qskin Sun and Health Study, Taiwan Biobank, The Hunt Study, Ucla Atlas Community Health Initiative, Uganda Genome Resource, Uk Biobank, Martin, Alicia R., Willer, Cristen J., Daly, Mark J., Neale, Benjamin M., and Elzur, Roy

Published
2022
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29. Pan-UK Biobank GWAS improves discovery, analysis of genetic architecture, and resolution into ancestry-enriched effects

Author

Karczewski, Konrad J, primary, Gupta, Rahul, additional, Kanai, Masahiro, additional, Lu, Wenhan, additional, Tsuo, Kristin, additional, Wang, Ying, additional, Walters, Raymond K, additional, Turley, Patrick, additional, Callier, Shawneequa, additional, Baya, Nikolas, additional, Palmer, Duncan S, additional, Goldstein, Jacqueline I, additional, Sarma, Gopal, additional, Solomonson, Matthew, additional, Cheng, Nathan, additional, Bryant, Sam, additional, Churchhouse, Claire, additional, Cusick, Caroline M, additional, Poterba, Timothy, additional, Compitello, John, additional, King, Daniel, additional, Zhou, Wei, additional, Seed, Cotton, additional, Finucane, Hilary K, additional, Daly, Mark J, additional, Neale, Benjamin M, additional, Atkinson, Elizabeth G, additional, and Martin, Alicia R, additional

Published
2024
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32. Mapping genomic loci implicates genes and synaptic biology in schizophrenia

Author

Trubetskoy, Vassily, Pardiñas, Antonio F., Qi, Ting, Panagiotaropoulou, Georgia, Awasthi, Swapnil, Bigdeli, Tim B., Bryois, Julien, Chen, Chia-Yen, Dennison, Charlotte A., Hall, Lynsey S., Lam, Max, Watanabe, Kyoko, Frei, Oleksandr, Ge, Tian, Harwood, Janet C., Koopmans, Frank, Magnusson, Sigurdur, Richards, Alexander L., Sidorenko, Julia, Wu, Yang, Zeng, Jian, Grove, Jakob, Kim, Minsoo, Li, Zhiqiang, Voloudakis, Georgios, Zhang, Wen, Adams, Mark, Agartz, Ingrid, Atkinson, Elizabeth G., Agerbo, Esben, Al Eissa, Mariam, Albus, Margot, Alexander, Madeline, Alizadeh, Behrooz Z., Alptekin, Köksal, Als, Thomas D., Amin, Farooq, Arolt, Volker, Arrojo, Manuel, Athanasiu, Lavinia, Azevedo, Maria Helena, Bacanu, Silviu A., Bass, Nicholas J., Begemann, Martin, Belliveau, Richard A., Bene, Judit, Benyamin, Beben, Bergen, Sarah E., Blasi, Giuseppe, Bobes, Julio, Bonassi, Stefano, Braun, Alice, Bressan, Rodrigo Affonseca, Bromet, Evelyn J., Bruggeman, Richard, Buckley, Peter F., Buckner, Randy L., Bybjerg-Grauholm, Jonas, Cahn, Wiepke, Cairns, Murray J., Calkins, Monica E., Carr, Vaughan J., Castle, David, Catts, Stanley V., Chambert, Kimberley D., Chan, Raymond C. K., Chaumette, Boris, Cheng, Wei, Cheung, Eric F. C., Chong, Siow Ann, Cohen, David, Consoli, Angèle, Cordeiro, Quirino, Costas, Javier, Curtis, Charles, Davidson, Michael, Davis, Kenneth L., de Haan, Lieuwe, Degenhardt, Franziska, DeLisi, Lynn E., Demontis, Ditte, Dickerson, Faith, Dikeos, Dimitris, Dinan, Timothy, Djurovic, Srdjan, Duan, Jubao, Ducci, Giuseppe, Dudbridge, Frank, Eriksson, Johan G., Fañanás, Lourdes, Faraone, Stephen V., Fiorentino, Alessia, Forstner, Andreas, Frank, Josef, Freimer, Nelson B., Fromer, Menachem, Frustaci, Alessandra, Gadelha, Ary, Genovese, Giulio, Gershon, Elliot S., Giannitelli, Marianna, Giegling, Ina, Giusti-Rodríguez, Paola, Godard, Stephanie, Goldstein, Jacqueline I., González Peñas, Javier, González-Pinto, Ana, Gopal, Srihari, Gratten, Jacob, Green, Michael F., Greenwood, Tiffany A., Guillin, Olivier, Gülöksüz, Sinan, Gur, Raquel E., Gur, Ruben C., Gutiérrez, Blanca, Hahn, Eric, Hakonarson, Hakon, Haroutunian, Vahram, Hartmann, Annette M., Harvey, Carol, Hayward, Caroline, Henskens, Frans A., Herms, Stefan, Hoffmann, Per, Howrigan, Daniel P., Ikeda, Masashi, Iyegbe, Conrad, Joa, Inge, Julià, Antonio, Kähler, Anna K., Kam-Thong, Tony, Kamatani, Yoichiro, Karachanak-Yankova, Sena, Kebir, Oussama, Keller, Matthew C., Kelly, Brian J., Khrunin, Andrey, Kim, Sung-Wan, Klovins, Janis, Kondratiev, Nikolay, Konte, Bettina, Kraft, Julia, Kubo, Michiaki, Kučinskas, Vaidutis, Kučinskiene, Zita Ausrele, Kusumawardhani, Agung, Kuzelova-Ptackova, Hana, Landi, Stefano, Lazzeroni, Laura C., Lee, Phil H., Legge, Sophie E., Lehrer, Douglas S., Lencer, Rebecca, Lerer, Bernard, Li, Miaoxin, Lieberman, Jeffrey, Light, Gregory A., Limborska, Svetlana, Liu, Chih-Min, Lönnqvist, Jouko, Loughland, Carmel M., Lubinski, Jan, Luykx, Jurjen J., Lynham, Amy, Macek, Jr, Milan, Mackinnon, Andrew, Magnusson, Patrik K. E., Maher, Brion S., Maier, Wolfgang, Malaspina, Dolores, Mallet, Jacques, Marder, Stephen R., Marsal, Sara, Martin, Alicia R., Martorell, Lourdes, Mattheisen, Manuel, McCarley, Robert W., McDonald, Colm, McGrath, John J., Medeiros, Helena, Meier, Sandra, Melegh, Bela, Melle, Ingrid, Mesholam-Gately, Raquelle I., Metspalu, Andres, Michie, Patricia T., Milani, Lili, Milanova, Vihra, Mitjans, Marina, Molden, Espen, Molina, Esther, Molto, María Dolores, Mondelli, Valeria, Moreno, Carmen, Morley, Christopher P., Muntané, Gerard, Murphy, Kieran C., Myin-Germeys, Inez, Nenadić, Igor, Nestadt, Gerald, Nikitina-Zake, Liene, Noto, Cristiano, Nuechterlein, Keith H., O’Brien, Niamh Louise, O’Neill, F. Anthony, Oh, Sang-Yun, Olincy, Ann, Ota, Vanessa Kiyomi, Pantelis, Christos, Papadimitriou, George N., Parellada, Mara, Paunio, Tiina, Pellegrino, Renata, Periyasamy, Sathish, Perkins, Diana O., Pfuhlmann, Bruno, Pietiläinen, Olli, Pimm, Jonathan, Porteous, David, Powell, John, Quattrone, Diego, Quested, Digby, Radant, Allen D., Rampino, Antonio, Rapaport, Mark H., Rautanen, Anna, Reichenberg, Abraham, Roe, Cheryl, Roffman, Joshua L., Roth, Julian, Rothermundt, Matthias, Rutten, Bart P. F., Saker-Delye, Safaa, Salomaa, Veikko, Sanjuan, Julio, Santoro, Marcos Leite, Savitz, Adam, Schall, Ulrich, Scott, Rodney J., Seidman, Larry J., Sharp, Sally Isabel, Shi, Jianxin, Siever, Larry J., Sigurdsson, Engilbert, Sim, Kang, Skarabis, Nora, Slominsky, Petr, So, Hon-Cheong, Sobell, Janet L., Söderman, Erik, Stain, Helen J., Steen, Nils Eiel, Steixner-Kumar, Agnes A., Stögmann, Elisabeth, Stone, William S., Straub, Richard E., Streit, Fabian, Strengman, Eric, Stroup, T. Scott, Subramaniam, Mythily, Sugar, Catherine A., Suvisaari, Jaana, Svrakic, Dragan M., Swerdlow, Neal R., Szatkiewicz, Jin P., Ta, Thi Minh Tam, Takahashi, Atsushi, Terao, Chikashi, Thibaut, Florence, Toncheva, Draga, Tooney, Paul A., Torretta, Silvia, Tosato, Sarah, Tura, Gian Battista, Turetsky, Bruce I., Üçok, Alp, Vaaler, Arne, van Amelsvoort, Therese, van Winkel, Ruud, Veijola, Juha, Waddington, John, Walter, Henrik, Waterreus, Anna, Webb, Bradley T., Weiser, Mark, Williams, Nigel M., Witt, Stephanie H., Wormley, Brandon K., Wu, Jing Qin, Xu, Zhida, Yolken, Robert, Zai, Clement C., Zhou, Wei, Zhu, Feng, Zimprich, Fritz, Atbaşoğlu, Eşref Cem, Ayub, Muhammad, Benner, Christian, Bertolino, Alessandro, Black, Donald W., Bray, Nicholas J., Breen, Gerome, Buccola, Nancy G., Byerley, William F., Chen, Wei J., Cloninger, C. Robert, Crespo-Facorro, Benedicto, Donohoe, Gary, Freedman, Robert, Galletly, Cherrie, Gandal, Michael J., Gennarelli, Massimo, Hougaard, David M., Hwu, Hai-Gwo, Jablensky, Assen V., McCarroll, Steven A., Moran, Jennifer L., Mors, Ole, Mortensen, Preben B., Müller-Myhsok, Bertram, Neil, Amanda L., Nordentoft, Merete, Pato, Michele T., Petryshen, Tracey L., Pirinen, Matti, Pulver, Ann E., Schulze, Thomas G., Silverman, Jeremy M., Smoller, Jordan W., Stahl, Eli A., Tsuang, Debby W., Vilella, Elisabet, Wang, Shi-Heng, Xu, Shuhua, Adolfsson, Rolf, Arango, Celso, Baune, Bernhard T., Belangero, Sintia Iole, Børglum, Anders D., Braff, David, Bramon, Elvira, Buxbaum, Joseph D., Campion, Dominique, Cervilla, Jorge A., Cichon, Sven, Collier, David A., Corvin, Aiden, Curtis, David, Forti, Marta Di, Domenici, Enrico, Ehrenreich, Hannelore, Escott-Price, Valentina, Esko, Tõnu, Fanous, Ayman H., Gareeva, Anna, Gawlik, Micha, Gejman, Pablo V., Gill, Michael, Glatt, Stephen J., Golimbet, Vera, Hong, Kyung Sue, Hultman, Christina M., Hyman, Steven E., Iwata, Nakao, Jönsson, Erik G., Kahn, René S., Kennedy, James L., Khusnutdinova, Elza, Kirov, George, Knowles, James A., Krebs, Marie-Odile, Laurent-Levinson, Claudine, Lee, Jimmy, Lencz, Todd, Levinson, Douglas F., Li, Qingqin S., Liu, Jianjun, Malhotra, Anil K., Malhotra, Dheeraj, McIntosh, Andrew, McQuillin, Andrew, Menezes, Paulo R., Morgan, Vera A., Morris, Derek W., Mowry, Bryan J., Murray, Robin M., Nimgaonkar, Vishwajit, Nöthen, Markus M., Ophoff, Roel A., Paciga, Sara A., Palotie, Aarno, Pato, Carlos N., Qin, Shengying, Rietschel, Marcella, Riley, Brien P., Rivera, Margarita, Rujescu, Dan, Saka, Meram C., Sanders, Alan R., Schwab, Sibylle G., Serretti, Alessandro, Sham, Pak C., Shi, Yongyong, St Clair, David, Stefánsson, Hreinn, Stefansson, Kari, Tsuang, Ming T., van Os, Jim, Vawter, Marquis P., Weinberger, Daniel R., Werge, Thomas, Wildenauer, Dieter B., Yu, Xin, Yue, Weihua, Holmans, Peter A., Pocklington, Andrew J., Roussos, Panos, Vassos, Evangelos, Verhage, Matthijs, Visscher, Peter M., Yang, Jian, Posthuma, Danielle, Andreassen, Ole A., Kendler, Kenneth S., Owen, Michael J., Wray, Naomi R., Daly, Mark J., Huang, Hailiang, Neale, Benjamin M., Sullivan, Patrick F., Ripke, Stephan, Walters, James T. R., and O’Donovan, Michael C.

Published
2022
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34. 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 J.F., 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, Martin, Alicia R., Willer, Cristen J., Daly, Mark J., and Neale, Benjamin M.

Published
2022
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35. Identification of common genetic risk variants for autism spectrum disorder

Author

Grove, Jakob, Ripke, Stephan, Als, Thomas D, Mattheisen, Manuel, Walters, Raymond K, Won, Hyejung, Pallesen, Jonatan, Agerbo, Esben, Andreassen, Ole A, Anney, Richard, Awashti, Swapnil, Belliveau, Rich, Bettella, Francesco, Buxbaum, Joseph D, Bybjerg-Grauholm, Jonas, Bækvad-Hansen, Marie, Cerrato, Felecia, Chambert, Kimberly, Christensen, Jane H, Churchhouse, Claire, Dellenvall, Karin, Demontis, Ditte, De Rubeis, Silvia, Devlin, Bernie, Djurovic, Srdjan, Dumont, Ashley L, Goldstein, Jacqueline I, Hansen, Christine S, Hauberg, Mads Engel, Hollegaard, Mads V, Hope, Sigrun, Howrigan, Daniel P, Huang, Hailiang, Hultman, Christina M, Klei, Lambertus, Maller, Julian, Martin, Joanna, Martin, Alicia R, Moran, Jennifer L, Nyegaard, Mette, Nærland, Terje, Palmer, Duncan S, Palotie, Aarno, Pedersen, Carsten Bøcker, Pedersen, Marianne Giørtz, dPoterba, Timothy, Poulsen, Jesper Buchhave, Pourcain, Beate St, Qvist, Per, Rehnström, Karola, Reichenberg, Abraham, Reichert, Jennifer, Robinson, Elise B, Roeder, Kathryn, Roussos, Panos, Saemundsen, Evald, Sandin, Sven, Satterstrom, F Kyle, Davey Smith, George, Stefansson, Hreinn, Steinberg, Stacy, Stevens, Christine R, Sullivan, Patrick F, Turley, Patrick, Walters, G Bragi, Xu, Xinyi, Stefansson, Kari, Geschwind, Daniel H, Nordentoft, Merete, Hougaard, David M, Werge, Thomas, Mors, Ole, Mortensen, Preben Bo, Neale, Benjamin M, Daly, Mark J, and Børglum, Anders D

Subjects
Intellectual and Developmental Disabilities (IDD), Human Genome, Pediatric, Brain Disorders, Autism, Biotechnology, Genetics, Mental Health, Prevention, 2.3 Psychological, social and economic factors, Aetiology, 2.1 Biological and endogenous factors, Mental health, Adolescent, Autism Spectrum Disorder, Case-Control Studies, Child, Child, Preschool, Denmark, Female, Genetic Predisposition to Disease, Genome-Wide Association Study, Humans, Male, Multifactorial Inheritance, Phenotype, Polymorphism, Single Nucleotide, Risk Factors, Autism Spectrum Disorder Working Group of the Psychiatric Genomics Consortium, BUPGEN, Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium, 23andMe Research Team, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

Autism spectrum disorder (ASD) is a highly heritable and heterogeneous group of neurodevelopmental phenotypes diagnosed in more than 1% of children. Common genetic variants contribute substantially to ASD susceptibility, but to date no individual variants have been robustly associated with ASD. With a marked sample-size increase from a unique Danish population resource, we report a genome-wide association meta-analysis of 18,381 individuals with ASD and 27,969 controls that identified five genome-wide-significant loci. Leveraging GWAS results from three phenotypes with significantly overlapping genetic architectures (schizophrenia, major depression, and educational attainment), we identified seven additional loci shared with other traits at equally strict significance levels. Dissecting the polygenic architecture, we found both quantitative and qualitative polygenic heterogeneity across ASD subtypes. These results highlight biological insights, particularly relating to neuronal function and corticogenesis, and establish that GWAS performed at scale will be much more productive in the near term in ASD.

Published
2019

36. Discovery of the first genome-wide significant risk loci for attention deficit/hyperactivity disorder.

Author

Demontis, Ditte, Walters, Raymond K, Martin, Joanna, Mattheisen, Manuel, Als, Thomas D, Agerbo, Esben, Baldursson, Gísli, Belliveau, Rich, Bybjerg-Grauholm, Jonas, Bækvad-Hansen, Marie, Cerrato, Felecia, Chambert, Kimberly, Churchhouse, Claire, Dumont, Ashley, Eriksson, Nicholas, Gandal, Michael, Goldstein, Jacqueline I, Grasby, Katrina L, Grove, Jakob, Gudmundsson, Olafur O, Hansen, Christine S, Hauberg, Mads Engel, Hollegaard, Mads V, Howrigan, Daniel P, Huang, Hailiang, Maller, Julian B, Martin, Alicia R, Martin, Nicholas G, Moran, Jennifer, Pallesen, Jonatan, Palmer, Duncan S, Pedersen, Carsten Bøcker, Pedersen, Marianne Giørtz, Poterba, Timothy, Poulsen, Jesper Buchhave, Ripke, Stephan, Robinson, Elise B, Satterstrom, F Kyle, Stefansson, Hreinn, Stevens, Christine, Turley, Patrick, Walters, G Bragi, Won, Hyejung, Wright, Margaret J, ADHD Working Group of the Psychiatric Genomics Consortium (PGC), Early Lifecourse & Genetic Epidemiology (EAGLE) Consortium, 23andMe Research Team, Andreassen, Ole A, Asherson, Philip, Burton, Christie L, Boomsma, Dorret I, Cormand, Bru, Dalsgaard, Søren, Franke, Barbara, Gelernter, Joel, Geschwind, Daniel, Hakonarson, Hakon, Haavik, Jan, Kranzler, Henry R, Kuntsi, Jonna, Langley, Kate, Lesch, Klaus-Peter, Middeldorp, Christel, Reif, Andreas, Rohde, Luis Augusto, Roussos, Panos, Schachar, Russell, Sklar, Pamela, Sonuga-Barke, Edmund JS, Sullivan, Patrick F, Thapar, Anita, Tung, Joyce Y, Waldman, Irwin D, Medland, Sarah E, Stefansson, Kari, Nordentoft, Merete, Hougaard, David M, Werge, Thomas, Mors, Ole, Mortensen, Preben Bo, Daly, Mark J, Faraone, Stephen V, Børglum, Anders D, and Neale, Benjamin M

Subjects
ADHD Working Group of the Psychiatric Genomics Consortium, Early Lifecourse & Genetic Epidemiology (EAGLE) Consortium, 23andMe Research Team, Brain, Humans, Genetic Predisposition to Disease, Risk, Cohort Studies, Attention Deficit Disorder with Hyperactivity, Gene Expression Regulation, Polymorphism, Single Nucleotide, Adolescent, Child, Child, Preschool, Female, Male, Genome-Wide Association Study, Genetic Loci, Clinical Research, Mental Health, Human Genome, Pediatric, Prevention, Genetics, Brain Disorders, Attention Deficit Hyperactivity Disorder (ADHD), Behavioral and Social Science, Aetiology, 2.1 Biological and endogenous factors, Mental health, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

Attention deficit/hyperactivity disorder (ADHD) is a highly heritable childhood behavioral disorder affecting 5% of children and 2.5% of adults. Common genetic variants contribute substantially to ADHD susceptibility, but no variants have been robustly associated with ADHD. We report a genome-wide association meta-analysis of 20,183 individuals diagnosed with ADHD and 35,191 controls that identifies variants surpassing genome-wide significance in 12 independent loci, finding important new information about the underlying biology of ADHD. Associations are enriched in evolutionarily constrained genomic regions and loss-of-function intolerant genes and around brain-expressed regulatory marks. Analyses of three replication studies: a cohort of individuals diagnosed with ADHD, a self-reported ADHD sample and a meta-analysis of quantitative measures of ADHD symptoms in the population, support these findings while highlighting study-specific differences on genetic overlap with educational attainment. Strong concordance with GWAS of quantitative population measures of ADHD symptoms supports that clinical diagnosis of ADHD is an extreme expression of continuous heritable traits.

Published
2019

37. Rapid evolution of a skin-lightening allele in southern African KhoeSan.

Author

Lin, Meng, Siford, Rebecca, Martin, Alicia, Nakagome, Shigeki, Möller, Marlo, Hoal, Eileen, Bustamante, Carlos, Gignoux, Christopher, and Henn, Brenna

Subjects
Africa, KhoeSan, SLC24A5, adaptation, pigmentation, Adult, Africa, Southern, Alleles, Antiporters, Asian People, Black People, Demography, Evolution, Molecular, Female, Gene Flow, Genetic Variation, Genetics, Population, Genotype, Haplotypes, Humans, Male, Phenotype, Phylogeny, Polymorphism, Single Nucleotide, Skin Pigmentation, White People
Abstract

Skin pigmentation is under strong directional selection in northern European and Asian populations. The indigenous KhoeSan populations of far southern Africa have lighter skin than other sub-Saharan African populations, potentially reflecting local adaptation to a region of Africa with reduced UV radiation. Here, we demonstrate that a canonical Eurasian skin pigmentation gene, SLC24A5, was introduced to southern Africa via recent migration and experienced strong adaptive evolution in the KhoeSan. To reconstruct the evolution of skin pigmentation, we collected phenotypes from over 400 ≠Khomani San and Nama individuals and high-throughput sequenced candidate pigmentation genes. The derived causal allele in SLC24A5, p.Ala111Thr, significantly lightens basal skin pigmentation in the KhoeSan and explains 8 to 15% of phenotypic variance in these populations. The frequency of this allele (33 to 53%) is far greater than expected from colonial period European gene flow; however, the most common derived haplotype is identical among European, eastern African, and KhoeSan individuals. Using four-population demographic simulations with selection, we show that the allele was introduced into the KhoeSan only 2,000 y ago via a back-to-Africa migration and then experienced a selective sweep (s = 0.04 to 0.05 in ≠Khomani and Nama). The SLC24A5 locus is both a rare example of intense, ongoing adaptation in very recent human history, as well as an adaptive gene flow at a pigmentation locus in humans.

Published
2018

41. A new class of metric f-manifolds

Author

Alegre, Pablo, FernÁndez, Luis M., and Prieto-MartÍn, Alicia

Subjects
Mathematics - Differential Geometry, 53C15, 53C25, 53C99
Abstract

We introduce a new general class of metric f-manifolds which we call (nearly) trans-S-manifolds and includes S- manifolds, C-manifolds, s-th Sasakian manifolds and generalized Kenmotsu manifold studied previously. We prove their main properties and we present many examples which justify their study., Comment: 15 pages

Published
2016

42. Shared molecular neuropathology across major psychiatric disorders parallels polygenic overlap

Author

Gandal, Michael J, Haney, Jillian R, Parikshak, Neelroop N, Leppa, Virpi, Ramaswami, Gokul, Hartl, Chris, Schork, Andrew J, Appadurai, Vivek, Buil, Alfonso, Werge, Thomas M, Liu, Chunyu, White, Kevin P, Horvath, Steve, Geschwind, Daniel H, Sestan, Nenad, Vaccarino, Flora, Gerstein, Mark, Weissman, Sherman, Pochareddy, Sirisha, State, Matthew, Knowles, James, Farnham, Peggy, Akbarian, Schahram, Pinto, Dalila, Van Baekl, Harm, Dracheva, Stella, Jaffe, Andrew, Hyde, Thomas, Zandi, Peter, Crawford, Gregory, Sullivan, Pat, Thompson, Wesley Kurt, Mortensen, Preben Bo, Agerbo, Esben, Pedersen, Marianne Giørtz, Pedersen, Carsten Bøcker, Mors, Ole, Børglum, Anders D, Nordentoft, Merete, Hougaard, David M, Bybjerg-Grauholm, Jonas, Bækvad-Hansen, Marie, Martin, Alicia R, Dumont, Ashley, Stevens, Christine, Churchhouse, Claire, Howrigan, Daniel P, Palmer, Duncan S, Robinson, Elise B, Satterstrom, Kyle F, Cerrato, Felecia, Huang, Hailiang, Goldstein, Jacqueline, Moran, Jennifer, Julian, Joanna Martin, Kimberly, Maller, Patrick, Chambert, Turley, Patrick, Walters, Raymond, Belliveau, Rich, Ripke, Stephan, Poterba, Timothy, Daly, Mark J, Neale, Benjamin, Fromer, Menachem, Roussos, Panos, Johnson, Jessica S, Shah, Hardik R, Mahajan, Milind C, Schadt, Eric, Haroutunian, Vahram, Ruderfer, Douglas M, Buxbaum, Joseph D, Sieberts, Solveig K, Dang, Kristen, Logsdon, Ben, Mangravite, Lara M, Peters, Mette, Gur, Raquel E, Hahn, Chang-Gyu, Devlin, Bernie, Klei, Lambertus L, Lewis, David, Lipska, Barbara, Hirai, Keisuke, Toyoshiba, Hiroyoshi, and Domenici, Enrico

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Biological Psychology, Psychology, Pharmacology and Pharmaceutical Sciences, Serious Mental Illness, Brain Disorders, Human Genome, Mental Health, Schizophrenia, Neurosciences, Bipolar Disorder, Depression, Mental Illness, 2.1 Biological and endogenous factors, Aetiology, Mental health, Good Health and Well Being, Cerebral Cortex, Gene Expression Profiling, Gene Expression Regulation, Genetic Predisposition to Disease, Humans, Mental Disorders, Multifactorial Inheritance, Nervous System Diseases, Polymorphism, Single Nucleotide, Transcription, Genetic, CommonMind Consortium, PsychENCODE Consortium, iPSYCH-BROAD Working Group, General Science & Technology
Abstract

The predisposition to neuropsychiatric disease involves a complex, polygenic, and pleiotropic genetic architecture. However, little is known about how genetic variants impart brain dysfunction or pathology. We used transcriptomic profiling as a quantitative readout of molecular brain-based phenotypes across five major psychiatric disorders-autism, schizophrenia, bipolar disorder, depression, and alcoholism-compared with matched controls. We identified patterns of shared and distinct gene-expression perturbations across these conditions. The degree of sharing of transcriptional dysregulation is related to polygenic (single-nucleotide polymorphism-based) overlap across disorders, suggesting a substantial causal genetic component. This comprehensive systems-level view of the neurobiological architecture of major neuropsychiatric illness demonstrates pathways of molecular convergence and specificity.

Published
2018

43. An Unexpectedly Complex Architecture for Skin Pigmentation in Africans

Author

Martin, Alicia R, Lin, Meng, Granka, Julie M, Myrick, Justin W, Liu, Xiaomin, Sockell, Alexandra, Atkinson, Elizabeth G, Werely, Cedric J, Möller, Marlo, Sandhu, Manjinder S, Kingsley, David M, Hoal, Eileen G, Liu, Xiao, Daly, Mark J, Feldman, Marcus W, Gignoux, Christopher R, Bustamante, Carlos D, and Henn, Brenna M

Subjects
Biological Sciences, Genetics, Human Genome, Skin, Africa, Black People, Humans, Polymorphism, Single Nucleotide, Skin Pigmentation, heritability, human evolution, pigmentation, population genetics, Medical and Health Sciences, Developmental Biology, Biological sciences, Biomedical and clinical sciences
Abstract

Approximately 15 genes have been directly associated with skin pigmentation variation in humans, leading to its characterization as a relatively simple trait. However, by assembling a global survey of quantitative skin pigmentation phenotypes, we demonstrate that pigmentation is more complex than previously assumed, with genetic architecture varying by latitude. We investigate polygenicity in the KhoeSan populations indigenous to southern Africa who have considerably lighter skin than equatorial Africans. We demonstrate that skin pigmentation is highly heritable, but known pigmentation loci explain only a small fraction of the variance. Rather, baseline skin pigmentation is a complex, polygenic trait in the KhoeSan. Despite this, we identify canonical and non-canonical skin pigmentation loci, including near SLC24A5, TYRP1, SMARCA2/VLDLR, and SNX13, using a genome-wide association approach complemented by targeted resequencing. By considering diverse, under-studied African populations, we show how the architecture of skin pigmentation can vary across humans subject to different local evolutionary pressures.

Published
2017

45. Fine-Scale Human Population Structure in Southern Africa Reflects Ecogeographic Boundaries.

Author

Uren, Caitlin, Kim, Minju, Martin, Alicia, Bobo, Dean, Gignoux, Christopher, van Helden, Paul, Möller, Marlo, Hoal, Eileen, and Henn, Brenna

Subjects
KhoeSan, ancestry, pastoralism, population structure, Africa, Southern, Black People, DNA, Mitochondrial, Ethnicity, Gene Flow, Genetics, Population, Genotype, Haplotypes, Humans, Phylogeny, Phylogeography, Polymorphism, Single Nucleotide
Abstract

Recent genetic studies have established that the KhoeSan populations of southern Africa are distinct from all other African populations and have remained largely isolated during human prehistory until ∼2000 years ago. Dozens of different KhoeSan groups exist, belonging to three different language families, but very little is known about their population history. We examine new genome-wide polymorphism data and whole mitochondrial genomes for >100 South Africans from the ≠Khomani San and Nama populations of the Northern Cape, analyzed in conjunction with 19 additional southern African populations. Our analyses reveal fine-scale population structure in and around the Kalahari Desert. Surprisingly, this structure does not always correspond to linguistic or subsistence categories as previously suggested, but rather reflects the role of geographic barriers and the ecology of the greater Kalahari Basin. Regardless of subsistence strategy, the indigenous Khoe-speaking Nama pastoralists and the N|u-speaking ≠Khomani (formerly hunter-gatherers) share ancestry with other Khoe-speaking forager populations that form a rim around the Kalahari Desert. We reconstruct earlier migration patterns and estimate that the southern Kalahari populations were among the last to experience gene flow from Bantu speakers, ∼14 generations ago. We conclude that local adoption of pastoralism, at least by the Nama, appears to have been primarily a cultural process with limited genetic impact from eastern Africa.

Published
2016

47. Admix-kit: an integrated toolkit and pipeline for genetic analyses of admixed populations.

Author

Hou, Kangcheng, Gogarten, Stephanie, Kim, Joohyun, Hua, Xing, Dias, Julie-Alexia, Sun, Quan, Wang, Ying, Tan, Taotao, Group, Polygenic Risk Methods in Diverse Populations (PRIMED) Consortium Methods Working, Atkinson, Elizabeth G, Martin, Alicia, Shortt, Jonathan, Hirbo, Jibril, Li, Yun, Pasaniuc, Bogdan, and Zhang, Haoyu

Subjects
HEALTH equity, PHENOTYPES, GENOTYPES
Abstract

Summary Admixed populations, with their unique and diverse genetic backgrounds, are often underrepresented in genetic studies. This oversight not only limits our understanding but also exacerbates existing health disparities. One major barrier has been the lack of efficient tools tailored for the special challenges of genetic studies of admixed populations. Here, we present admix-kit, an integrated toolkit and pipeline for genetic analyses of admixed populations. Admix-kit implements a suite of methods to facilitate genotype and phenotype simulation, association testing, genetic architecture inference, and polygenic scoring in admixed populations. Availability and implementation Admix-kit package is open-source and available at https://github.com/KangchengHou/admix-kit. Additionally, users can use the pipeline designed for admixed genotype simulation available at https://github.com/UW-GAC/admix-kit_workflow. [ABSTRACT FROM AUTHOR]

Published
2024
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48. Genome-wide association studies

Author

Uffelmann, Emil, Huang, Qin Qin, Munung, Nchangwi Syntia, de Vries, Jantina, Okada, Yukinori, Martin, Alicia R., Martin, Hilary C., Lappalainen, Tuuli, and Posthuma, Danielle

Published
2021
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49. Effect of obstructive sleep apnoea and its treatment with continuous positive airway pressure on the prevalence of cardiovascular events in patients with acute coronary syndrome (ISAACC study): a randomised controlled trial

Author

Abad, Laura, Muñoz, Aida, Zamora, Elisabet, Vicente, Ignacio, Inglés, Sandra, Egea, Carlos, Marcos, Jaime, Fernández, Almudena, Ullate, Jorge, Durán Carro, Joaquín, Rodríguez, Jose L, Mendoza, María J, Labeaga, Raul, Diez, David, Muria, Berenice, Amibilia, Chechu, Urrutia, Amaia, Castro, Sonia, Serrano, Leyre, Salinas, Idoia, Diez, Ruth, Martínez, Ana, Florés, Marina, Galera, Estefanía, Mas, Anna, Martínez, Montserrat, Arbonés, Maricel, Ortega, Silvia, Martín, Alicia, Román-Sánchez, Jose M, Valiente-Diaz, M<ce:sup loc='post">a</ce:sup> Isabel, Viejo-Ayuso, M<ce:sup loc='post">a</ce:sup> Esther, Rodríguez-García, Concepción, Sánchez-Rodríguez, Noelia, Mayoral, Nieves, Rubio, Francisco J, Anta-Mejias, Yunelsy, Romera-Peralta, Sofía, Resano, Pilar, Arroyo-Espilguero, Ramón, Bienvenido-Villalba, María, Vigil, Laura, Ramírez, Enriqueta, Piñar, María, Martínez, Elisabet, Múñoz, Carmen, Ordax, Estrella, Surname, Name, Corral, Jaime, Gómez de Terreros Caro, Francisco J, García-Ledesma, Estefanía, Gallego, Rocío, Cabrero, Jose L, Pereira, Ricardo, Giménez, Paloma, Carrera, Miguel, Pierola, Javier, Villena, Cristina, Campaner, Magdalena, Fortuna, Ana M, Peñacoba, Patricia, Martínez García, Abel J, García Castillo, Sergio, Navas, Lara, Garmendia, Onintza, Suárez, Monique, Sancho, José, Farre, Nuria, Bonet, Gil, Bardaji, Alfredo, Villares, Anna, Vázquez, M<ce:sup loc='post">a</ce:sup> José, Sánchez-de-la-Torre, Manuel, Sánchez-de-la-Torre, Alicia, Bertran, Sandra, Abad, Jorge, Duran-Cantolla, Joaquín, Cabriada, Valentín, Mediano, Olga, Masdeu, María José, Alonso, Mari Luz, Masa, Juan Fernando, Barceló, Antonia, de la Peña, Mónica, Mayos, Mercè, Coloma, Ramón, Montserrat, Josep M, Chiner, Eusebi, Perelló, Salvador, Rubinós, Gemma, Mínguez, Olga, Pascual, Lydia, Cortijo, Anunciación, Martínez, Dolores, Aldomà, Albina, Dalmases, Mireia, McEvoy, R Doug, and Barbé, Ferran

Published
2020
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