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1. Whole genome sequence analysis of platelet traits in the NHLBI Trans-Omics for Precision Medicine (TOPMed) initiative

Author

Nauder Faraday, Brian D. Hobbs, Quan Sun, Michael Preuss, Ani Manichaikul, Eric Jorgenson, Ming-Huei Chen, Eric Boerwinkle, Florian Thibord, Arunoday Bhan, Alanna C. Morrison, Ramachandran S. Vasan, Nathan Pankratz, Charles Kooperberg, Deborah A. Nickerson, Joshua P. Lewis, Hélène Choquet, Jee-Young Moon, Jeffrey R. O'Connell, Marsha M. Wheeler, Albert V. Smith, Russell P. Tracy, Nathalie Chami, Ruth J. F. Loos, Alexander P. Reiner, Nicholas L. Smith, Gonçalo R. Abecasis, Laura M. Raffield, Amarise Little, Nancy L. Heard-Costa, Andrew D. Johnson, David C. Glahn, Rasika A. Mathias, Adam S. Butterworth, John Blangero, Joanne E. Curran, Timothy A. Thornton, Laura Almasy, Jerome I. Rotter, Nancy Min, Lisa R. Yanek, Donald M. Lloyd-Jones, Zhe Wang, Matthew P. Conomos, Myriam Fornage, Hua Tang, Lewis C. Becker, Lynette Ekunwe, Cecelia A. Laurie, Adolfo Correa, Jai G. Broome, Terri H. Beaty, Jennifer A. Brody, Caitlin P. McHugh, Yao Hu, Braxton D. Mitchell, Lifang Hou, Yun Li, Kathleen A. Ryan, Paul L. Auer, Stephen S. Rich, Kari E. North, Thomas W. Blackwell, Bruce M. Psaty, Deepti Jain, Paul S Vries, Praveen Surendran, Butterworth, Adam [0000-0002-6915-9015], and Apollo - University of Cambridge Repository

Subjects
Blood Platelets, Platelet disorder, Population, Genome-wide association study, Biology, Quantitative trait locus, Polymorphism, Single Nucleotide, Medical and Health Sciences, Genome, 03 medical and health sciences, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, 0302 clinical medicine, Clinical Research, and Blood Institute (U.S.), Genetics, Humans, 2.1 Biological and endogenous factors, Polymorphism, Precision Medicine, Aetiology, Mean platelet volume, education, Hemostatic function, Lung, Molecular Biology, Genetics (clinical), 030304 developmental biology, Blood Platelet Disorders, Genetics & Heredity, 0303 health sciences, education.field_of_study, Human Genome, Single Nucleotide, National Heart, Hematology, General Medicine, Biological Sciences, United States, 3. Good health, Phenotype, Good Health and Well Being, 030220 oncology & carcinogenesis, General Article, National Heart, Lung, and Blood Institute (U.S.), Genome-Wide Association Study, Biotechnology
Abstract

Platelets play a key role in thrombosis and hemostasis. Platelet count (PLT) and mean platelet volume (MPV) are highly heritable quantitative traits, with hundreds of genetic signals previously identified, mostly in European ancestry populations. We here utilize whole genome sequencing (WGS) from NHLBI’s Trans-Omics for Precision Medicine initiative (TOPMed) in a large multi-ethnic sample to further explore common and rare variation contributing to PLT (n = 61 200) and MPV (n = 23 485). We identified and replicated secondary signals at MPL (rs532784633) and PECAM1 (rs73345162), both more common in African ancestry populations. We also observed rare variation in Mendelian platelet-related disorder genes influencing variation in platelet traits in TOPMed cohorts (not enriched for blood disorders). For example, association of GP9 with lower PLT and higher MPV was partly driven by a pathogenic Bernard-Soulier syndrome variant (rs5030764, p.Asn61Ser), and the signals at TUBB1 and CD36 were partly driven by loss of function variants not annotated as pathogenic in ClinVar (rs199948010 and rs571975065). However, residual signal remained for these gene-based signals after adjusting for lead variants, suggesting that additional variants in Mendelian genes with impacts in general population cohorts remain to be identified. Gene-based signals were also identified at several genome-wide association study identified loci for genes not annotated for Mendelian platelet disorders (PTPRH, TET2, CHEK2), with somatic variation driving the result at TET2. These results highlight the value of WGS in populations of diverse genetic ancestry to identify novel regulatory and coding signals, even for well-studied traits like platelet traits.

Published
2021
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2. Mendelian randomization supports bidirectional causality between telomere length and clonal hematopoiesis of indeterminate potential

Author

Tetsushi, Nakao, Alexander G, Bick, Margaret A, Taub, Seyedeh M, Zekavat, Md M, Uddin, Abhishek, Niroula, Cara L, Carty, John, Lane, Michael C, Honigberg, Joshua S, Weinstock, Akhil, Pampana, Christopher J, Gibson, Gabriel K, Griffin, Shoa L, Clarke, Romit, Bhattacharya, Themistocles L, Assimes, Leslie S, Emery, Adrienne M, Stilp, Quenna, Wong, Jai, Broome, Cecelia A, Laurie, Alyna T, Khan, Albert V, Smith, Thomas W, Blackwell, Veryan, Codd, Christopher P, Nelson, Zachary T, Yoneda, Juan M, Peralta, Donald W, Bowden, Marguerite R, Irvin, Meher, Boorgula, Wei, Zhao, Lisa R, Yanek, Kerri L, Wiggins, James E, Hixson, C Charles, Gu, Gina M, Peloso, Dan M, Roden, Muagututi'a S, Reupena, Chii-Min, Hwu, Dawn L, DeMeo, Kari E, North, Shannon, Kelly, Solomon K, Musani, Joshua C, Bis, Donald M, Lloyd-Jones, Jill M, Johnsen, Michael, Preuss, Russell P, Tracy, Patricia A, Peyser, Dandi, Qiao, Pinkal, Desai, Joanne E, Curran, Barry I, Freedman, Hemant K, Tiwari, Sameer, Chavan, Jennifer A, Smith, Nicholas L, Smith, Tanika N, Kelly, Bertha, Hidalgo, L Adrienne, Cupples, Daniel E, Weeks, Nicola L, Hawley, Ryan L, Minster, Ranjan, Deka, Take T, Naseri, Lisa, de Las Fuentes, Laura M, Raffield, Alanna C, Morrison, Paul S, Vries, Christie M, Ballantyne, Eimear E, Kenny, Stephen S, Rich, Eric A, Whitsel, Michael H, Cho, M Benjamin, Shoemaker, Betty S, Pace, John, Blangero, Nicholette D, Palmer, Braxton D, Mitchell, Alan R, Shuldiner, Kathleen C, Barnes, Susan, Redline, Sharon L R, Kardia, Gonçalo R, Abecasis, Lewis C, Becker, Susan R, Heckbert, Jiang, He, Wendy, Post, Donna K, Arnett, Ramachandran S, Vasan, Dawood, Darbar, Scott T, Weiss, Stephen T, McGarvey, Mariza, de Andrade, Yii-Der Ida, Chen, Robert C, Kaplan, Deborah A, Meyers, Brian S, Custer, Adolfo, Correa, Bruce M, Psaty, Myriam, Fornage, JoAnn E, Manson, Eric, Boerwinkle, Barbara A, Konkle, Ruth J F, Loos, Jerome I, Rotter, Edwin K, Silverman, Charles, Kooperberg, John, Danesh, Nilesh J, Samani, Siddhartha, Jaiswal, Peter, Libby, Patrick T, Ellinor, Nathan, Pankratz, Benjamin L, Ebert, Alexander P, Reiner, Rasika A, Mathias, Ron, Do, and Pradeep, Natarajan

Subjects
Multidisciplinary
Abstract

Human genetic studies support an inverse causal relationship between leukocyte telomere length (LTL) and coronary artery disease (CAD), but directionally mixed effects for LTL and diverse malignancies. Clonal hematopoiesis of indeterminate potential (CHIP), characterized by expansion of hematopoietic cells bearing leukemogenic mutations, predisposes both hematologic malignancy and CAD. TERT (which encodes telomerase reverse transcriptase) is the most significantly associated germline locus for CHIP in genome-wide association studies. Here, we investigated the relationship between CHIP, LTL, and CAD in the Trans-Omics for Precision Medicine (TOPMed) program ( n = 63,302) and UK Biobank ( n = 47,080). Bidirectional Mendelian randomization studies were consistent with longer genetically imputed LTL increasing propensity to develop CHIP, but CHIP then, in turn, hastens to shorten measured LTL (mLTL). We also demonstrated evidence of modest mediation between CHIP and CAD by mLTL. Our data promote an understanding of potential causal relationships across CHIP and LTL toward prevention of CAD.

Published
2022
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3. Bidirectional Mendelian randomization supports bidirectional causality between telomere length and clonal hematopoiesis of intermediate potential

Author

Dan M. Roden, John Blangero, Myriam Fornage, Kerri L. Wiggins, Benjamin L. Ebert, Gina M. Peloso, Tetsushi Nakao, John Lane, Russell P. Tracy, Lisa de las Fuentes, Ryan L. Minster, Donna K. Arnett, Seyedeh M. Zekavat, Laura M. Raffield, Akhil Pampana, Stephen S. Rich, Kathleen C. Barnes, R. Mathias, Alyna T. Khan, Lewis C. Becker, James E. Hixson, Gabriel K. Griffin, Nicholas L. Smith, JoAnn E. Manson, Robert C. Kaplan, Gonçalo R. Abecasis, Nathan Pankratz, Alexander P. Reiner, Donald M. Lloyd-Jones, Sharon L.R. Kardia, C. Charles Gu, Wendy Post, Lisa R. Yanek, Tanika N. Kelly, Hemant K. Tiwari, Jennifer A. Smith, Shoa L. Clarke, Ramachandran S. Vasan, Themistocles L. Assimes, Betty S. Pace, Jill M. Johnsen, Cara L. Carty, Pinkal Desai, Barry I. Freedman, Pradeep Natarajan, Margaret A. Taub, S Redline, Adrienne M. Stilp, Ranjan Deka, Alexander G. Bick, Donald W. Bowden, Mariza de Andrade, Abhishek Niroula, Joanne E. Curran, Quenna Wong, Siddhartha Jaiswal, Chii-Min Hwu, Michael Preuss, Christie M. Ballantyne, Shannon Kelly, Patrick T. Ellinor, Sameer Chavan, Dandi Qiao, Nicola L. Hawley, Charles Kooperberg, Juan M. Peralta, Braxton D. Mitchell, Solomon K. Musani, Jerome I. Rotter, Ruth J.F. Loos, Zachary T. Yoneda, Bruce M. Psaty, Christopher J. Gibson, Ron Do, Barbara A. Konkle, Marguerite R. Irvin, Jai G. Broome, Take Naseri, Alanna C. Morrison, L. Adrienne Cupples, Bertha A. Hildalgo, Jiang He, Mesbah Uddin, Dawood Darbar, Cecelia A. Laurie, Eric A. Whitsel, Patricia A. Peyser, Brian Custer, Michael H. Cho, Scott T. Weiss, Peter Libby, Susan R. Heckbert, Albert V. Smith, Joshua S. Weinstock, Meher Preethi Boorgula, M. Benjamin Shoemaker, Muagututi’a S. Reupena, Michael C. Honigberg, Nicholette D. Palmer, Wei Zhao, Paul S. Vries, Edwin K. Silverman, Daniel E. Weeks, Romit Bhattacharya, Joshua C. Bis, Kari E. North, Thomas W. Blackwell, Dawn L. DeMeo, Stephen T. McGarvey, Leslie S. Emery, A. R. Shuldiner, Yii-Der Ida Chen, Eric Boerwinkle, Adolfo Correa, Deborah A. Meyers, and Eimear E. Kenny

Subjects
Mendelian randomization, Locus (genetics), Telomerase reverse transcriptase, CAD, Computational biology, Biology, Causality, Germline, Telomere, Genetic association
Abstract

Human genetic studies support an inverse causal relationship between leukocyte telomere length (LTL) and coronary artery disease (CAD), but directionally mixed effects for LTL and diverse malignancies. Clonal hematopoiesis of indeterminate potential (CHIP), characterized by expansion of hematopoietic cells bearing leukemogenic mutations, predisposes both hematologic malignancy and CAD. TERT (which encodes telomerase reverse transcriptase) is the most significantly associated germline locus for CHIP in genome-wide association studies. Here, we investigated the relationship between CHIP, LTL, and CAD in Trans-Omics for Precision Medicine (TOPMed) program (N=63,302) and UK Biobank (N=48,658). Bidirectional Mendelian randomization studies were consistent with LTL lengthening increasing propensity to develop CHIP, but CHIP then in turn hastening LTL shortening. We also demonstrated evidence of modest mediation between CHIP and CAD by LTL. Our data promote an understanding of potential causal relationships across CHIP and LTL toward prevention of CAD.

Published
2021
Full Text
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