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1. TTR variants in patients with dilated cardiomyopathy: An investigation of the DCM Precision Medicine Study

Author

Barry H. Trachtenberg, Javier Jimenez, Alanna A. Morris, Evan Kransdorf, Anjali Owens, Daniel P. Fishbein, Elizabeth Jordan, Daniel D. Kinnamon, Jonathan O. Mead, Gordon S. Huggins, Ray E. Hershberger, Garrie Haas, Daniel Fishbein, Stephen S. Gottlieb, Matthew T. Wheeler, Mark Hofmeyer, W. H. Wilson Tang, Anjali T. Owens, Charles K. Moore, Javier Jimenez Carcamo, Barry Trachtenberg, Nancy K. Sweitzer, Palak Shah, Brian Lowes, Douglas Stoller, Frank Smart, Jane Wilcox, Stuart Katz, Gregory A. Ewald, Keith D. Aaronson, Jessica J. Wang, Salpy Pamboukian, Daniel P. Judge, Evan P. Kransdorf, Sonia Garg, Patrice Desvigne-Nickens, James Troendle, Yi-Ping Fu, and Lucia Hindorff

Subjects
Cardiomyopathy, Dilated, Amyloid Neuropathies, Familial, Humans, Exome, Genetic Testing, Precision Medicine, Genetics (clinical)
Abstract

The cardiac phenotype of hereditary transthyretin amyloidosis (hTTR) usually presents as a restrictive or hypertrophic cardiomyopathy, and, although rarely observed as dilated cardiomyopathy (DCM), TTR is routinely included in DCM genetic testing panels. However, the prevalence and phenotypes of TTR variants in patients with DCM have not been reported.Exome sequences of 729 probands with idiopathic DCM were analyzed for TTR and 35 DCM genes.Rare TTR variants were identified in 2 (0.5%; 95% CI = 0.1%-1.8%) of 404 non-Hispanic White DCM probands; neither of them had features of hTTR. In 1 proband, a TTR His110Asn variant and a variant of uncertain significance in DSP were identified, and in the other proband, a TTR Val50Met variant known to cause hTTR and a likely pathogenic variant in FLNC were identified. The TTR Val142Ile variant was identified in 8 (3.0%) non-Hispanic Black probands, comparable with African/African American Genome Aggregation Database controls (OR = 1.01; 95% CI = 0.46-1.99).Among the 729 DCM probands, 2 had rare TTR variants identified without the features of hTTR, and both had other plausible genetic causes of DCM. Moreover, the frequency of TTR Val142Ile was comparable to a control sample. These findings suggest that hTTR variants may have a limited role in patients with DCM without TTR-specific findings.

Published
2022
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2. The NHGRI-EBI GWAS Catalog: knowledgebase and deposition resource

Author

Elliot Sollis, Abayomi Mosaku, Ala Abid, Annalisa Buniello, Maria Cerezo, Laurent Gil, Tudor Groza, Osman Güneş, Peggy Hall, James Hayhurst, Arwa Ibrahim, Yue Ji, Sajo John, Elizabeth Lewis, Jacqueline A L MacArthur, Aoife McMahon, David Osumi-Sutherland, Kalliope Panoutsopoulou, Zoë Pendlington, Santhi Ramachandran, Ray Stefancsik, Jonathan Stewart, Patricia Whetzel, Robert Wilson, Lucia Hindorff, Fiona Cunningham, Samuel A Lambert, Michael Inouye, Helen Parkinson, Laura W Harris, Sollis, Elliot [0000-0003-1322-388X], Mosaku, Abayomi [0000-0002-5783-9662], Abid, Ala [0000-0002-6633-6434], Buniello, Annalisa [0000-0002-4623-8642], Cerezo, Maria [0000-0003-3073-1130], Gil, Laurent [0000-0002-9475-4502], Groza, Tudor [0000-0003-2267-8333], Güneş, Osman [0000-0002-4987-6981], Hayhurst, James [0000-0002-7460-403X], Ibrahim, Arwa [0000-0001-6757-4744], Ji, Yue [0000-0001-9844-7297], John, Sajo [0000-0003-3029-0857], Lewis, Elizabeth [0000-0002-1142-1359], MacArthur, Jacqueline AL [0000-0002-3550-9769], McMahon, Aoife [0000-0003-0978-0309], Osumi-Sutherland, David [0000-0002-7073-9172], Panoutsopoulou, Kalliope [0000-0002-5460-8025], Pendlington, Zoë [0000-0002-4071-8397], Ramachandran, Santhi [0000-0002-2376-0614], Stefancsik, Ray [0000-0001-8314-2140], Stewart, Jonathan [0000-0003-3901-9422], Whetzel, Patricia [0000-0002-3458-4839], Wilson, Robert [0000-0002-9407-5526], Hindorff, Lucia [0000-0002-4414-3236], Cunningham, Fiona [0000-0002-7445-2419], Lambert, Samuel A [0000-0001-8222-008X], Inouye, Michael [0000-0001-9413-6520], Parkinson, Helen [0000-0003-3035-4195], Harris, Laura W [0000-0003-4312-7223], and Apollo - University of Cambridge Repository

Subjects
National Human Genome Research Institute (U.S.), Mice, Phenotype, DNA Copy Number Variations, Knowledge Bases, Genetics, Animals, Humans, Polymorphism, Single Nucleotide, Software, United States, Genome-Wide Association Study
Abstract

The NHGRI-EBI GWAS Catalog (www.ebi.ac.uk/gwas) is a FAIR knowledgebase providing detailed, structured, standardised and interoperable genome-wide association study (GWAS) data to >200 000 users per year from academic research, healthcare and industry. The Catalog contains variant-trait associations and supporting metadata for >45 000 published GWAS across >5000 human traits, and >40 000 full P-value summary statistics datasets. Content is curated from publications or acquired via author submission of prepublication summary statistics through a new submission portal and validation tool. GWAS data volume has vastly increased in recent years. We have updated our software to meet this scaling challenge and to enable rapid release of submitted summary statistics. The scope of the repository has expanded to include additional data types of high interest to the community, including sequencing-based GWAS, gene-based analyses and copy number variation analyses. Community outreach has increased the number of shared datasets from under-represented traits, e.g. cancer, and we continue to contribute to awareness of the lack of population diversity in GWAS. Interoperability of the Catalog has been enhanced through links to other resources including the Polygenic Score Catalog and the International Mouse Phenotyping Consortium, refinements to GWAS trait annotation, and the development of a standard format for GWAS data.

Published
2022

3. Alaska Native genomic research: perspectives from Alaska Native leaders, federal staff, and biomedical researchers

Author

Vanessa Y. Hiratsuka, Michael J. Hahn, R. Brian Woodbury, Sara Chandros Hull, David R. Wilson, Vence L. Bonham, Denise A. Dillard, Jaedon P. Avey, Andrea C. Beckel-Mitchener, Juliana Blome, Katrina Claw, Elizabeth D. Ferucci, Francine C. Gachupin, Armen Ghazarian, Lucia Hindorff, Sonya Jooma, Susan B. Trinidad, Jennifer Troyer, and Hina Walajahi

Subjects
Biomedical Research, Genomic research, social responsibility, Review Article, 03 medical and health sciences, 0302 clinical medicine, Political science, Health care, Humans, 030212 general & internal medicine, Genetics (clinical), 030304 developmental biology, 0303 health sciences, Information Dissemination, business.industry, trust, Genomics, Public relations, Alaskan Natives, ethics, Alaska Natives, North American, Data sharing, US National Institutes of Health, General partnership, Indians, North American, Research studies, Health board, business, Social responsibility
Abstract

Meaningful engagement of Alaska Native (AN) tribes and tribal health organizations is essential in the conduct of socially responsible and ethical research. As genomics becomes increasingly important to advancements in medicine, there is a risk that populations not meaningfully included in genomic research will not benefit from the outcomes of that research. AN people have historically been underrepresented in biomedical research; AN underrepresentation in genomics research is compounded by mistrust based on past abuses, concerns about privacy and data ownership, and cultural considerations specific to this type of research. Working together, the National Human Genome Research Institute and two Alaska Native health organizations, Southcentral Foundation and the Alaska Native Health Board, cosponsored a workshop in July 2018 to engage key stakeholders in discussion, strengthen relationships, and facilitate partnership and consideration of participation of AN people in community-driven biomedical and genomic research. AN priorities related to translation of genomics research to health and health care, return of genomic results, design of research studies, and data sharing were discussed. This report summarizes the perspectives that emerged from the dialogue and offers considerations for effective and socially responsible genomic research partnerships with AN communities.

Published
2020
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4. Toward Genetics-Driven Early Intervention in Dilated Cardiomyopathy: Design and Implementation of the DCM Precision Medicine Study

Author

Daniel D. Kinnamon, Ana Morales, Deborah J. Bowen, Wylie Burke, Ray E. Hershberger, Julie M. Gastier-Foster, Deborah A. Nickerson, Michael O. Dorschner, Garrie Haas, William Abraham, Philip Binkley, Ayesha Hasan, Jennifer Host, Brent Lampert, Sakima Smith, Gordon Huggins, David DeNofrio, Michael Kiernan, Daniel Fishbein, Richard Cheng, Todd Dardas, Wayne Levy, Claudius Mahr, Sofia Masri, April Stempien-Otero, Stephen Gottlieb, Matthew Wheeler, Euan Ashley, Julia Platt, Mark Hofmeyer, Wilson Tang, Randall Starling, Rocio Moran, Anjali Owens, Kenneth Marguilies, Thomas Cappola, Lee Goldberg, Susan Brozena, J. Rame, Rhondalyn McLean, Charles Moore, Matthew deShazo, Robert Long, Francisco Jimenez Carcamo, Hakop Hrachian-Haftevani, Barry Trachtenberg, Guhu Ashrith, Arvind Bhimarahj, Jerry Estep, Nancy Sweitzer, Carlos D. Bustamante, Gail P. Jarvik, Eden R. Martin, Heidi Rehm, Patrice Desvigne-Nickens, James Troendle, Yi-Ping Fu, and Lucia Hindorff

Subjects
Cardiomyopathy, Dilated, Male, Pediatrics, medicine.medical_specialty, Genetic counseling, Disease, 030204 cardiovascular system & hematology, Article, White People, law.invention, 03 medical and health sciences, 0302 clinical medicine, Randomized controlled trial, law, Idiopathic dilated cardiomyopathy, Outcome Assessment, Health Care, Genetics, Prevalence, Medicine, Humans, 030212 general & internal medicine, Genetic Testing, Precision Medicine, Genetics (clinical), Exome sequencing, business.industry, Dilated cardiomyopathy, Hispanic or Latino, Precision medicine, medicine.disease, United States, Clinical trial, Black or African American, Cross-Sectional Studies, Female, Cardiology and Cardiovascular Medicine, business
Abstract

Background— The cause of idiopathic dilated cardiomyopathy (DCM) is unknown by definition, but its familial subtype is considered to have a genetic component. We hypothesize that most idiopathic DCM, whether familial or nonfamilial, has a genetic basis, in which case a genetics-driven approach to identifying at-risk family members for clinical screening and early intervention could reduce morbidity and mortality. Methods— On the basis of this hypothesis, we have launched the National Heart, Lung, and Blood Institute- and National Human Genome Research Institute-funded DCM Precision Medicine Study, which aims to enroll 1300 individuals (600 non-Hispanic African ancestry, 600 non-Hispanic European ancestry, and 100 Hispanic) who meet rigorous clinical criteria for idiopathic DCM along with 2600 of their relatives. Enrolled relatives will undergo clinical cardiovascular screening to identify asymptomatic disease, and all individuals with idiopathic DCM will undergo exome sequencing to identify relevant variants in genes previously implicated in DCM. Results will be returned by genetic counselors 12 to 14 months after enrollment. The data obtained will be used to describe the prevalence of familial DCM among idiopathic DCM cases and the genetic architecture of idiopathic DCM in multiple ethnicity–ancestry groups. We will also conduct a randomized controlled trial to test the effectiveness of Family Heart Talk , an intervention to aid family communication, for improving uptake of preventive screening and surveillance in at-risk first-degree relatives. Conclusions— We anticipate that this study will demonstrate that idiopathic DCM has a genetic basis and guide best practices for a genetics-driven approach to early intervention in at-risk relatives. Clinical Trial Registration— URL: http://www.clinicaltrials.gov . Unique identifier: NCT03037632.

Published
2017

5. Genome-wide physical activity interactions in adiposity ― a meta-analysis of 200,452 adults

Author

Mariaelisa Graff, Robert A Scott, Anne E Justice, Kristin L Young, Mary F Feitosa, Llilda Barata, Thomas W Winkler, Audrey Y Chu, Anubha Mahajan, David Hadley, Luting Xue, Tsegaselassie Workalemahu, Nancy L Heard-Costa, Marcel den Hoed, Tarunveer S Ahluwalia, Qibin Qi, Julius S Ngwa, Frida Renström, Lydia Quaye, John D Eicher, James E Hayes, Marilyn Cornelis, Zoltan Kutalik, Elise Lim, Jian'an Luan, Jennifer E Huffman, Weihua Zhang, Wei Zhao, Paula J Griffin, Toomas Haller, Shafqat Ahmad, Pedro M Marques-Vidal, Stephanie Bien, Loic Yengo, Alexander Teumer, Albert Vernon Smith, Meena Kumari, Marie Neergaard Harder, Johanne Marie Justesen, Marcus E Kleber, Mette Hollensted, Kurt Lohman, Natalia V Rivera, John B Whitfield, Jing Hua Zhao, Heather M Stringham, Leo-Pekka Lyytikäinen, Charlotte Huppertz, Gonneke Willemsen, Wouter J Peyrot, Ying Wu, Kati Kristiansson, Ayse Demirkan, Myriam Fornage, Maija Hassinen, Lawrence F Bielak, Gemma Cadby, Toshiko Tanaka, Reedik Mägi, Peter J van der Most, Anne U Jackson, Jennifer L Bragg-Gresham, Veronique Vitart, Jonathan Marten, Pau Navarro, Claire Bellis, Dorota Pasko, Åsa Johansson, Søren Snitker, Yu-Ching Cheng, Joel Eriksson, Unhee Lim, Mette Aadahl, Linda S Adair, Najaf Amin, Beverley Balkau, Juha Auvinen, John Beilby, Richard N Bergman, Sven Bergmann, Alain G Bertoni, John Blangero, Amélie Bonnefond, Lori L Bonnycastle, Judith B Borja, Søren Brage, Fabio Busonero, Steve Buyske, Harry Campbell, Peter S Chines, Francis S Collins, Tanguy Corre, George Davey Smith, Graciela E Delgado, Nicole Dueker, Marcus Dörr, Tapani Ebeling, Gudny Eiriksdottir, Tõnu Esko, Jessica D Faul, Mao Fu, Kristine Færch, Christian Gieger, Sven Gläser, Jian Gong, Penny Gordon-Larsen, Harald Grallert, Tanja B Grammer, Niels Grarup, Gerard van Grootheest, Kennet Harald, Nicholas D Hastie, Aki S Havulinna, Dena Hernandez, Lucia Hindorff, Lynne J Hocking, Oddgeir L Holmens, Christina Holzapfel, Jouke Jan Hottenga, Jie Huang, Tao Huang, Jennie Hui, Cornelia Huth, Nina Hutri-Kähönen, Alan L James, John-Olov Jansson, Min A Jhun, Markus Juonala, Leena Kinnunen, Heikki A Koistinen, Ivana Kolcic, Pirjo Komulainen, Johanna Kuusisto, Kirsti Kvaløy, Mika Kähönen, Timo A Lakka, Lenore J Launer, Benjamin Lehne, Cecilia M Lindgren, Mattias Lorentzon, Robert Luben, Michel Marre, Yuri Milaneschi, Keri L Monda, Grant W Montgomery, Marleen H M De Moor, Antonella Mulas, Martina Müller-Nurasyid, A W Musk, Reija Männikkö, Satu Männistö, Narisu Narisu, Matthias Nauck, Jennifer A Nettleton, Ilja M Nolte, Albertine J Oldehinkel, Matthias Olden, Ken K Ong, Sandosh Padmanabhan, Lavinia Paternoster, Jeremiah Perez, Markus Perola, Annette Peters, Ulrike Peters, Patricia A Peyser, Inga Prokopenko, Hannu Puolijoki, Olli T Raitakari, Tuomo Rankinen, Laura J Rasmussen-Torvik, Rajesh Rawal, Paul M Ridker, Lynda M Rose, Igor Rudan, Cinzia Sarti, Mark A Sarzynski, Kai Savonen, William R Scott, Serena Sanna, Alan R Shuldiner, Steve Sidney, Günther Silbernagel, Blair H Smith, Jennifer A Smith, Harold Snieder, Alena Stančáková, Barbara Sternfeld, Amy J Swift, Tuija Tammelin, Sian-Tsung Tan, Barbara Thorand, Dorothée Thuillier, Liesbeth Vandenput, Henrik Vestergaard, Jana V van Vliet-Ostaptchouk, Marie-Claude Vohl, Uwe Völker, Gérard Waeber, Mark Walker, Sarah Wild, Andrew Wong, Alan F Wright, M Carola Zillikens, Niha Zubair, Christopher A Haiman, Loic Lemarchand, Ulf Gyllensten, Claes Ohlsson, Albert Hofman, Fernando Rivadeneira, André G Uitterlinden, Louis Pérusse, James F Wilson, Caroline Hayward, Ozren Polasek, Francesco Cucca, Kristian Hveem, Catharina A Hartman, Anke Tönjes, Stefania Bandinelli, Lyle J Palmer, Sharon L R Kardia, Rainer Rauramaa, Thorkild I A Sørensen, Jaakko Tuomilehto, Veikko Salomaa, Brenda W J H Penninx, Eco J C de Geus, Dorret I Boomsma, Terho Lehtimäki, Massimo Mangino, Markku Laakso, Claude Bouchard, Nicholas G Martin, Diana Kuh, Yongmei Liu, Allan Linneberg, Winfried März, Konstantin Strauch, Mika Kivimäki, Tamara B Harris, Vilmundur Gudnason, Henry Völzke, Lu Qi, Marjo-Riitta Järvelin, John C Chambers, Jaspal S Kooner, Philippe Froguel, Charles Kooperberg, Peter Vollenweider, Göran Hallmans, Torben Hansen, Oluf Pedersen, Andres Metspalu, Nicholas J Wareham, Claudia Langenberg, David R Weir, David J Porteous, Eric Boerwinkle, Daniel I Chasman, CHARGE Consortium, EPIC-InterAct Consortium, PAGE Consortium, Gonçalo R Abecasis, Inês Barroso, Mark I McCarthy, Timothy M Frayling, Jeffrey R O'Connell, Cornelia M van Duijn, Michael Boehnke, Iris M Heid, Karen L Mohlke, David P Strachan, Caroline S Fox, Ching-Ti Liu, Joel N Hirschhorn, Robert J Klein, Andrew D Johnson, Ingrid B Borecki, Paul W Franks, Kari E North, L Adrienne Cupples, Ruth J F Loos, Tuomas O Kilpeläinen, Molecular Genetics, Epidemiology, Radiology & Nuclear Medicine, Erasmus MC other, Internal Medicine, Erasmus School of Economics, and Department of Finance

Subjects
Epigenomics, Male, 0301 basic medicine, Cancer Research, Published Erratum, lcsh:QH426-470, Genotype, Physical activity, Alpha-Ketoglutarate-Dependent Dioxygenase FTO, Computational biology, Biology, Genome, Body Mass Index, PAGE Consortium, 03 medical and health sciences, Text mining, Genetics, Humans, Genetic Predisposition to Disease, Obesity, Exercise, Molecular Biology, Genetics (clinical), Ecology, Evolution, Behavior and Systematics, Adiposity, 0604 Genetics, Waist-Hip Ratio, business.industry, Correction, lcsh:Genetics, 030104 developmental biology, Meta-analysis, CHARGE Consortium, Female, EPIC-InterAct Consortium, Waist Circumference, business, Developmental Biology, Genome-Wide Association Study
Abstract

Physical activity (PA) may modify the genetic effects that give rise to increased risk of obesity. To identify adiposity loci whose effects are modified by PA, we performed genome-wide interaction meta-analyses of BMI and BMI-adjusted waist circumference and waist-hip ratio from up to 200,452 adults of European (n = 180,423) or other ancestry (n = 20,029). We standardized PA by categorizing it into a dichotomous variable where, on average, 23% of participants were categorized as inactive and 77% as physically active. While we replicate the interaction with PA for the strongest known obesity-risk locus in the FTO gene, of which the effect is attenuated by ~30% in physically active individuals compared to inactive individuals, we do not identify additional loci that are sensitive to PA. In additional genome-wide meta-analyses adjusting for PA and interaction with PA, we identify 11 novel adiposity loci, suggesting that accounting for PA or other environmental factors that contribute to variation in adiposity may facilitate gene discovery.

Published
2017

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