A Smoothed Version of the Lassosum Penalty for Fitting Integrated Risk Models Using Summary Statistics or Individual-Level Data

by Georg Hahn, Dmitry Prokopenko, Sharon M. Lutz, Kristina Mullin, Rudolph E. Tanzi, Michael H. Cho, Edwin K. Silverman, Christoph Lange, on the behalf of the NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium
Published 2022-01-01

GAWMerge expands GWAS sample size and diversity by combining array-based genotyping and whole-genome sequencing

by Ravi Mathur, Fang Fang, Nathan Gaddis, Dana B. Hancock, Michael H. Cho, John E. Hokanson, Laura J. Bierut, Sharon M. Lutz, Kendra Young, Albert V. Smith, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Edwin K. Silverman, Grier P. Page, Eric O. Johnson
Published 2022-08-01

Variant-specific inflation factors for assessing population stratification at the phenotypic variance level

by Tamar Sofer, Xiuwen Zheng, Cecelia A. Laurie, Stephanie M. Gogarten, Jennifer A. Brody, Matthew P. Conomos, Joshua C. Bis, Timothy A. Thornton, Adam Szpiro, Jeffrey R. O’Connell, Ethan M. Lange, Yan Gao, L. Adrienne Cupples, Bruce M. Psaty, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Kenneth M. Rice
Published 2021-06-01

Lung tissue shows divergent gene expression between chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis

by Auyon J. Ghosh, Brian D. Hobbs, Jeong H. Yun, Aabida Saferali, Matthew Moll, Zhonghui Xu, Robert P. Chase, Jarrett Morrow, John Ziniti, Frank Sciurba, Lucas Barwick, Andrew H. Limper, Kevin Flaherty, Gerard Criner, Kevin K. Brown, Robert Wise, Fernando J. Martinez, Daniel McGoldrick, Michael H. Cho, Dawn L. DeMeo, Edwin K. Silverman, Peter J. Castaldi, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Craig P. Hersh
Published 2022-04-01

Clonal hematopoiesis in sickle cell disease

by L. Alexander Liggett, Liam D. Cato, Joshua S. Weinstock, Yingze Zhang, S. Mehdi Nouraie, Mark T. Gladwin, Melanie E. Garrett, Allison Ashley-Koch, Marilyn J. Telen, Brian Custer, Shannon Kelly, Carla L. Dinardo, Ester C. Sabino, Paula Loureiro, Anna B. Carneiro-Proietti, Cláudia Maximo, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Alexander P. Reiner, Gonçalo R. Abecasis, David A. Williams, Pradeep Natarajan, Alexander G. Bick, Vijay G. Sankaran
Published 2022-02-01

Author Correction: Nasal airway transcriptome-wide association study of asthma reveals genetically driven mucus pathobiology

by Satria P. Sajuthi, Jamie L. Everman, Nathan D. Jackson, Benjamin Saef, Cydney L. Rios, Camille M. Moore, Angel C. Y. Mak, Celeste Eng, Ana Fairbanks–Mahnke, Sandra Salazar, Jennifer Elhawary, Scott Huntsman, Vivian Medina, Deborah A. Nickerson, Soren Germer, Michael C. Zody, Gonçalo Abecasis, Hyun Min Kang, Kenneth M. Rice, Rajesh Kumar, Noah A. Zaitlen, Sam Oh, NHLBI Trans–Omics for Precision Medicine (TOPMed) Consortium, José Rodríguez–Santana, Esteban G. Burchard, Max A. Seibold
Published 2022-10-01

Nasal airway transcriptome-wide association study of asthma reveals genetically driven mucus pathobiology

by Satria P. Sajuthi, Jamie L. Everman, Nathan D. Jackson, Benjamin Saef, Cydney L. Rios, Camille M. Moore, Angel C. Y. Mak, Celeste Eng, Ana Fairbanks-Mahnke, Sandra Salazar, Jennifer Elhawary, Scott Huntsman, Vivian Medina, Deborah A. Nickerson, Soren Germer, Michael C. Zody, Gonçalo Abecasis, Hyun Min Kang, Kenneth M. Rice, Rajesh Kumar, Noah A. Zaitlen, Sam Oh, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, José Rodríguez-Santana, Esteban G. Burchard, Max A. Seibold
Published 2022-03-01

Canonical correlation analysis for multi-omics: Application to cross-cohort analysis.

by Min-Zhi Jiang, François Aguet, Kristin Ardlie, Jiawen Chen, Elaine Cornell, Dan Cruz, Peter Durda, Stacey B Gabriel, Robert E Gerszten, Xiuqing Guo, Craig W Johnson, Silva Kasela, Leslie A Lange, Tuuli Lappalainen, Yongmei Liu, Alex P Reiner, Josh Smith, Tamar Sofer, Kent D Taylor, Russell P Tracy, David J VanDenBerg, James G Wilson, Stephen S Rich, Jerome I Rotter, Michael I Love, Laura M Raffield, Yun Li, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, TOPMed Analysis Working Group
Published 2023-05-01

Common α-globin variants modify hematologic and other clinical phenotypes in sickle cell trait and disease.

by Laura M Raffield, Jacob C Ulirsch, Rakhi P Naik, Samuel Lessard, Robert E Handsaker, Deepti Jain, Hyun M Kang, Nathan Pankratz, Paul L Auer, Erik L Bao, Joshua D Smith, Leslie A Lange, Ethan M Lange, Yun Li, Timothy A Thornton, Bessie A Young, Goncalo R Abecasis, Cathy C Laurie, Deborah A Nickerson, Steven A McCarroll, Adolfo Correa, James G Wilson, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Hematology & Hemostasis, Diabetes, and Structural Variation TOPMed Working Groups, Guillaume Lettre, Vijay G Sankaran, Alex P Reiner
Published 2018-03-01

Identification of novel and rare variants associated with handgrip strength using whole genome sequence data from the NHLBI Trans-Omics in Precision Medicine (TOPMed) Program.

by Chloé Sarnowski, Han Chen, Mary L Biggs, Sylvia Wassertheil-Smoller, Jan Bressler, Marguerite R Irvin, Kathleen A Ryan, David Karasik, Donna K Arnett, L Adrienne Cupples, David W Fardo, Stephanie M Gogarten, Benjamin D Heavner, Deepti Jain, Hyun Min Kang, Charles Kooperberg, Arch G Mainous, Braxton D Mitchell, Alanna C Morrison, Jeffrey R O'Connell, Bruce M Psaty, Kenneth Rice, Albert V Smith, Ramachandran S Vasan, B Gwen Windham, Douglas P Kiel, Joanne M Murabito, Kathryn L Lunetta, TOPMed Longevity and Healthy Aging Working Group, from the NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium
Published 2021-01-01

A multi-ethnic polygenic risk score is associated with hypertension prevalence and progression throughout adulthood

by Nuzulul Kurniansyah, Matthew O. Goodman, Tanika N. Kelly, Tali Elfassy, Kerri L. Wiggins, Joshua C. Bis, Xiuqing Guo, Walter Palmas, Kent D. Taylor, Henry J. Lin, Jeffrey Haessler, Yan Gao, Daichi Shimbo, Jennifer A. Smith, Bing Yu, Elena V. Feofanova, Roelof A. J. Smit, Zhe Wang, Shih-Jen Hwang, Simin Liu, Sylvia Wassertheil-Smoller, JoAnn E. Manson, Donald M. Lloyd-Jones, Stephen S. Rich, Ruth J. F. Loos, Susan Redline, Adolfo Correa, Charles Kooperberg, Myriam Fornage, Robert C. Kaplan, Bruce M. Psaty, Jerome I. Rotter, Donna K. Arnett, Alanna C. Morrison, Nora Franceschini, Daniel Levy, the NHLBI Trans-Omics in Precision Medicine (TOPMed) Consortium, Tamar Sofer
Published 2022-06-01

Whole-genome association analyses of sleep-disordered breathing phenotypes in the NHLBI TOPMed program

by Brian E. Cade, Jiwon Lee, Tamar Sofer, Heming Wang, Man Zhang, Han Chen, Sina A. Gharib, Daniel J. Gottlieb, Xiuqing Guo, Jacqueline M. Lane, Jingjing Liang, Xihong Lin, Hao Mei, Sanjay R. Patel, Shaun M. Purcell, Richa Saxena, Neomi A. Shah, Daniel S. Evans, Craig L. Hanis, David R. Hillman, Sutapa Mukherjee, Lyle J. Palmer, Katie L. Stone, Gregory J. Tranah, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Gonçalo R. Abecasis, Eric A. Boerwinkle, Adolfo Correa, L. Adrienne Cupples, Robert C. Kaplan, Deborah A. Nickerson, Kari E. North, Bruce M. Psaty, Jerome I. Rotter, Stephen S. Rich, Russell P. Tracy, Ramachandran S. Vasan, James G. Wilson, Xiaofeng Zhu, Susan Redline, TOPMed Sleep Working Group
Published 2021-08-01

Publisher Correction: Endophenotype effect sizes support variant pathogenicity in monogenic disease susceptibility genes

by Jennifer L. Halford, Valerie N. Morrill, Seung Hoan Choi, Sean J. Jurgens, Giorgio Melloni, Nicholas A. Marston, Lu-Chen Weng, Victor Nauffal, Amelia W. Hall, Sophia Gunn, Christina A. Austin-Tse, James P. Pirruccello, Shaan Khurshid, Heidi L. Rehm, Emelia J. Benjamin, Eric Boerwinkle, Jennifer A. Brody, Adolfo Correa, Brandon K. Fornwalt, Namrata Gupta, Christopher M. Haggerty, Stephanie Harris, Susan R. Heckbert, Charles C. Hong, Charles Kooperberg, Henry J. Lin, Ruth J. F. Loos, Braxton D. Mitchell, Alanna C. Morrison, Wendy Post, Bruce M. Psaty, Susan Redline, Kenneth M. Rice, Stephen S. Rich, Jerome I. Rotter, Peter F. Schnatz, Elsayed Z. Soliman, Nona Sotoodehnia, Eugene K. Wong, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Marc S. Sabatine, Christian T. Ruff, Kathryn L. Lunetta, Patrick T. Ellinor, Steven A. Lubitz
Published 2022-09-01

Endophenotype effect sizes support variant pathogenicity in monogenic disease susceptibility genes

by Jennifer L. Halford, Valerie N. Morrill, Seung Hoan Choi, Sean J. Jurgens, Giorgio Melloni, Nicholas A. Marston, Lu-Chen Weng, Victor Nauffal, Amelia W. Hall, Sophia Gunn, Christina A. Austin-Tse, James P. Pirruccello, Shaan Khurshid, Heidi L. Rehm, Emelia J. Benjamin, Eric Boerwinkle, Jennifer A. Brody, Adolfo Correa, Brandon K. Fornwalt, Namrata Gupta, Christopher M. Haggerty, Stephanie Harris, Susan R. Heckbert, Charles C. Hong, Charles Kooperberg, Henry J. Lin, Ruth J. F. Loos, Braxton D. Mitchell, Alanna C. Morrison, Wendy Post, Bruce M. Psaty, Susan Redline, Kenneth M. Rice, Stephen S. Rich, Jerome I. Rotter, Peter F. Schnatz, Elsayed Z. Soliman, Nona Sotoodehnia, Eugene K. Wong, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Marc S. Sabatine, Christian T. Ruff, Kathryn L. Lunetta, Patrick T. Ellinor, Steven A. Lubitz
Published 2022-08-01

Epigenome-wide association study of kidney function identifies trans-ethnic and ethnic-specific loci

by Charles E. Breeze, Anna Batorsky, Mi Kyeong Lee, Mindy D. Szeto, Xiaoguang Xu, Daniel L. McCartney, Rong Jiang, Amit Patki, Holly J. Kramer, James M. Eales, Laura Raffield, Leslie Lange, Ethan Lange, Peter Durda, Yongmei Liu, Russ P. Tracy, David Van Den Berg, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, TOPMed MESA Multi-Omics Working Group, Kathryn L. Evans, William E. Kraus, Svati Shah, Hermant K. Tiwari, Lifang Hou, Eric A. Whitsel, Xiao Jiang, Fadi J. Charchar, Andrea A. Baccarelli, Stephen S. Rich, Andrew P. Morris, Marguerite R. Irvin, Donna K. Arnett, Elizabeth R. Hauser, Jerome I. Rotter, Adolfo Correa, Caroline Hayward, Steve Horvath, Riccardo E. Marioni, Maciej Tomaszewski, Stephan Beck, Sonja I. Berndt, Stephanie J. London, Josyf C. Mychaleckyj, Nora Franceschini
Published 2021-04-01

Genetic and non-genetic factors affecting the expression of COVID-19-relevant genes in the large airway epithelium

by Silva Kasela, Victor E. Ortega, Molly Martorella, Suresh Garudadri, Jenna Nguyen, Elizabeth Ampleford, Anu Pasanen, Srilaxmi Nerella, Kristina L. Buschur, Igor Z. Barjaktarevic, R. Graham Barr, Eugene R. Bleecker, Russell P. Bowler, Alejandro P. Comellas, Christopher B. Cooper, David J. Couper, Gerard J. Criner, Jeffrey L. Curtis, MeiLan K. Han, Nadia N. Hansel, Eric A. Hoffman, Robert J. Kaner, Jerry A. Krishnan, Fernando J. Martinez, Merry-Lynn N. McDonald, Deborah A. Meyers, Robert Paine, Stephen P. Peters, Mario Castro, Loren C. Denlinger, Serpil C. Erzurum, John V. Fahy, Elliot Israel, Nizar N. Jarjour, Bruce D. Levy, Xingnan Li, Wendy C. Moore, Sally E. Wenzel, Joe Zein, NHLBI SubPopulations and InteRmediate Outcome Measures In COPD Study (SPIROMICS), NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Charles Langelier, Prescott G. Woodruff, Tuuli Lappalainen, Stephanie A. Christenson
Published 2021-04-01

Whole genome sequence analysis of pulmonary function and COPD in 19,996 multi-ethnic participants

by Xutong Zhao, Dandi Qiao, Chaojie Yang, Silva Kasela, Wonji Kim, Yanlin Ma, Nick Shrine, Chiara Batini, Tamar Sofer, Sarah A. Gagliano Taliun, Phuwanat Sakornsakolpat, Pallavi P. Balte, Dmitry Prokopenko, Bing Yu, Leslie A. Lange, Josée Dupuis, Brian E. Cade, Jiwon Lee, Sina A. Gharib, Michelle Daya, Cecelia A. Laurie, Ingo Ruczinski, L. Adrienne Cupples, Laura R. Loehr, Traci M. Bartz, Alanna C. Morrison, Bruce M. Psaty, Ramachandran S. Vasan, James G. Wilson, Kent D. Taylor, Peter Durda, W. Craig Johnson, Elaine Cornell, Xiuqing Guo, Yongmei Liu, Russell P. Tracy, Kristin G. Ardlie, François Aguet, David J. VanDenBerg, George J. Papanicolaou, Jerome I. Rotter, Kathleen C. Barnes, Deepti Jain, Deborah A. Nickerson, Donna M. Muzny, Ginger A. Metcalf, Harshavardhan Doddapaneni, Shannon Dugan-Perez, Namrata Gupta, Stacey Gabriel, Stephen S. Rich, George T. O’Connor, Susan Redline, Robert M. Reed, Cathy C. Laurie, Martha L. Daviglus, Liana K. Preudhomme, Kristin M. Burkart, Robert C. Kaplan, Louise V. Wain, Martin D. Tobin, Stephanie J. London, Tuuli Lappalainen, Elizabeth C. Oelsner, Goncalo R. Abecasis, Edwin K. Silverman, R. Graham Barr, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, TOPMed Lung Working Group, Michael H. Cho, Ani Manichaikul
Published 2020-10-01

Whole genome sequence analyses of eGFR in 23,732 people representing multiple ancestries in the NHLBI trans-omics for precision medicine (TOPMed) consortium

by Bridget M Lin, Kelsey E Grinde, Jennifer A Brody, Charles E Breeze, Laura M Raffield, Josyf C Mychaleckyj, Timothy A Thornton, James A Perry, Leslie J Baier, Lisa de las Fuentes, Xiuqing Guo, Benjamin D Heavner, Robert L Hanson, Yi-Jen Hung, Huijun Qian, Chao A Hsiung, Shih-Jen Hwang, Margaret R Irvin, Deepti Jain, Tanika N Kelly, Sayuko Kobes, Leslie Lange, James P Lash, Yun Li, Xiaoming Liu, Xuenan Mi, Solomon K Musani, George J Papanicolaou, Afshin Parsa, Alex P Reiner, Shabnam Salimi, Wayne H-H Sheu, Alan R Shuldiner, Kent D Taylor, Albert V Smith, Jennifer A Smith, Adrienne Tin, Dhananjay Vaidya, Robert B Wallace, Kenichi Yamamoto, Saori Sakaue, Koichi Matsuda, Yoichiro Kamatani, Yukihide Momozawa, Lisa R Yanek, Betsi A Young, Wei Zhao, Yukinori Okada, Gonzalo Abecasis, Bruce M Psaty, Donna K Arnett, Eric Boerwinkle, Jianwen Cai, Ida Yii-Der Chen, Adolfo Correa, L Adrienne Cupples, Jiang He, Sharon LR Kardia, Charles Kooperberg, Rasika A Mathias, Braxton D Mitchell, Deborah A Nickerson, Steve T Turner, Vasan S Ramachandran, Jerome I Rotter, Daniel Levy, Holly J Kramer, Anna Köttgen, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, TOPMed Kidney Working Group, Stephen S Rich, Dan-Yu Lin, Sharon R Browning, Nora Franceschini
Published 2021-01-01

Use of >100,000 NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium whole genome sequences improves imputation quality and detection of rare variant associations in admixe...

by Madeline H Kowalski, Huijun Qian, Ziyi Hou, Jonathan D Rosen, Amanda L Tapia, Yue Shan, Deepti Jain, Maria Argos, Donna K Arnett, Christy Avery, Kathleen C Barnes, Lewis C Becker, Stephanie A Bien, Joshua C Bis, John Blangero, Eric Boerwinkle, Donald W Bowden, Steve Buyske, Jianwen Cai, Michael H Cho, Seung Hoan Choi, Hélène Choquet, L Adrienne Cupples, Mary Cushman, Michelle Daya, Paul S de Vries, Patrick T Ellinor, Nauder Faraday, Myriam Fornage, Stacey Gabriel, Santhi K Ganesh, Misa Graff, Namrata Gupta, Jiang He, Susan R Heckbert, Bertha Hidalgo, Chani J Hodonsky, Marguerite R Irvin, Andrew D Johnson, Eric Jorgenson, Robert Kaplan, Sharon L R Kardia, Tanika N Kelly, Charles Kooperberg, Jessica A Lasky-Su, Ruth J F Loos, Steven A Lubitz, Rasika A Mathias, Caitlin P McHugh, Courtney Montgomery, Jee-Young Moon, Alanna C Morrison, Nicholette D Palmer, Nathan Pankratz, George J Papanicolaou, Juan M Peralta, Patricia A Peyser, Stephen S Rich, Jerome I Rotter, Edwin K Silverman, Jennifer A Smith, Nicholas L Smith, Kent D Taylor, Timothy A Thornton, Hemant K Tiwari, Russell P Tracy, Tao Wang, Scott T Weiss, Lu-Chen Weng, Kerri L Wiggins, James G Wilson, Lisa R Yanek, Sebastian Zöllner, Kari E North, Paul L Auer, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, TOPMed Hematology & Hemostasis Working Group, Laura M Raffield, Alexander P Reiner, Yun Li
Published 2019-12-01

Whole genome sequence analysis of blood lipid levels in >66,000 individuals

by Margaret Sunitha Selvaraj, Xihao Li, Zilin Li, Akhil Pampana, David Y. Zhang, Joseph Park, Stella Aslibekyan, Joshua C. Bis, Jennifer A. Brody, Brian E. Cade, Lee-Ming Chuang, Ren-Hua Chung, Joanne E. Curran, Lisa de las Fuentes, Paul S. de Vries, Ravindranath Duggirala, Barry I. Freedman, Mariaelisa Graff, Xiuqing Guo, Nancy Heard-Costa, Bertha Hidalgo, Chii-Min Hwu, Marguerite R. Irvin, Tanika N. Kelly, Brian G. Kral, Leslie Lange, Xiaohui Li, Martin Lisa, Steven A. Lubitz, Ani W. Manichaikul, Preuss Michael, May E. Montasser, Alanna C. Morrison, Take Naseri, Jeffrey R. O’Connell, Nicholette D. Palmer, Patricia A. Peyser, Muagututia S. Reupena, Jennifer A. Smith, Xiao Sun, Kent D. Taylor, Russell P. Tracy, Michael Y. Tsai, Zhe Wang, Yuxuan Wang, Wei Bao, John T. Wilkins, Lisa R. Yanek, Wei Zhao, Donna K. Arnett, John Blangero, Eric Boerwinkle, Donald W. Bowden, Yii-Der Ida Chen, Adolfo Correa, L. Adrienne Cupples, Susan K. Dutcher, Patrick T. Ellinor, Myriam Fornage, Stacey Gabriel, Soren Germer, Richard Gibbs, Jiang He, Robert C. Kaplan, Sharon L. R. Kardia, Ryan Kim, Charles Kooperberg, Ruth J. F. Loos, Karine A Viaud-Martinez, Rasika A. Mathias, Stephen T. McGarvey, Braxton D. Mitchell, Deborah Nickerson, Kari E. North, Bruce M. Psaty, Susan Redline, Alexander P. Reiner, Ramachandran S. Vasan, Stephen S. Rich, Cristen Willer, Jerome I. Rotter, Daniel J. Rader, Xihong Lin, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Gina M. Peloso, Pradeep Natarajan
Published 2022-10-01