<p>Large-scale whole-genome sequencing (WGS) studies have improved our understanding of the contributions of coding and noncoding rare variants to complex human traits. Leveraging association effect sizes across multiple traits in WGS rare variant association analysis can improve statistical power over single-trait analysis, and also detect pleiotropic genes and regions. Existing multi-trait methods have limited ability to perform rare variant analysis of large-scale WGS data. We propose MultiSTAAR, a statistical framework and computationally scalable analytical pipeline for functionally informed multi-trait rare variant analysis in large-scale WGS studies. MultiSTAAR accounts for relatedness, population structure and correlation among phenotypes by jointly analyzing multiple traits, and further empowers rare variant association analysis by incorporating multiple functional annotations. We applied MultiSTAAR to jointly analyze three lipid traits in 61,838 multi-ethnic samples from the Trans-Omics for Precision Medicine (TOPMed) Program. We discovered and replicated new associations with lipid traits missed by single-trait analysis.</p>

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A statistical framework for multi-trait rare variant analysis in large-scale whole-genome sequencing studies

  • Xihao Li,
  • Han Chen,
  • Margaret Sunitha Selvaraj,
  • Eric Van Buren,
  • Hufeng Zhou,
  • Yuxuan Wang,
  • Ryan Sun,
  • Zachary R. McCaw,
  • Zhi Yu,
  • Min-Zhi Jiang,
  • Daniel DiCorpo,
  • Sheila M. Gaynor,
  • Rounak Dey,
  • Donna K. Arnett,
  • Emelia J. Benjamin,
  • Joshua C. Bis,
  • John Blangero,
  • Eric Boerwinkle,
  • Donald W. Bowden,
  • Jennifer A. Brody,
  • Brian E. Cade,
  • April P. Carson,
  • Jenna C. Carlson,
  • Nathalie Chami,
  • Yii-Der Ida Chen,
  • Joanne E. Curran,
  • Paul S. de Vries,
  • Myriam Fornage,
  • Nora Franceschini,
  • Barry I. Freedman,
  • Charles Gu,
  • Nancy L. Heard-Costa,
  • Jiang He,
  • Lifang Hou,
  • Yi-Jen Hung,
  • Marguerite R. Irvin,
  • Robert C. Kaplan,
  • Sharon L. R. Kardia,
  • Tanika N. Kelly,
  • Iain Konigsberg,
  • Charles Kooperberg,
  • Brian G. Kral,
  • Changwei Li,
  • Yun Li,
  • Honghuang Lin,
  • Ching-Ti Liu,
  • Ruth J. F. Loos,
  • Michael C. Mahaney,
  • Lisa W. Martin,
  • Rasika A. Mathias,
  • Braxton D. Mitchell,
  • May E. Montasser,
  • Alanna C. Morrison,
  • Take Naseri,
  • Kari E. North,
  • Nicholette D. Palmer,
  • Patricia A. Peyser,
  • Bruce M. Psaty,
  • Susan Redline,
  • Alexander P. Reiner,
  • Stephen S. Rich,
  • Colleen M. Sitlani,
  • Jennifer A. Smith,
  • Kent D. Taylor,
  • Hemant K. Tiwari,
  • Ramachandran S. Vasan,
  • Satupa’itea Viali,
  • Zhe Wang,
  • Jennifer Wessel,
  • Lisa R. Yanek,
  • Bing Yu,
  • Namiko Abe,
  • Gonçalo Abecasis,
  • Francois Aguet,
  • Christine Albert,
  • Laura Almasy,
  • Alvaro Alonso,
  • Seth Ament,
  • Peter Anderson,
  • Pramod Anugu,
  • Deborah Applebaum-Bowden,
  • Kristin Ardlie,
  • Dan Arking,
  • Allison Ashley-Koch,
  • Stella Aslibekyan,
  • Tim Assimes,
  • Dimitrios Avramopoulos,
  • Najib Ayas,
  • Adithya Balasubramanian,
  • John Barnard,
  • Kathleen Barnes,
  • R. Graham Barr,
  • Emily Barron-Casella,
  • Lucas Barwick,
  • Terri Beaty,
  • Gerald Beck,
  • Diane Becker,
  • Lewis Becker,
  • Rebecca Beer,
  • Amber Beitelshees,
  • Takis Benos,
  • Marcos Bezerra,
  • Larry Bielak,
  • Thomas Blackwell,
  • Nathan Blue,
  • Russell Bowler,
  • Ulrich Broeckel,
  • Jai Broome,
  • Deborah Brown,
  • Karen Bunting,
  • Esteban Burchard,
  • Carlos Bustamante,
  • Erin Buth,
  • Jonathan Cardwell,
  • Vincent Carey,
  • Julie Carrier,
  • Cara Carty,
  • Richard Casaburi,
  • Juan P. Casas Romero,
  • James Casella,
  • Peter Castaldi,
  • Mark Chaffin,
  • Christy Chang,
  • Yi-Cheng Chang,
  • Daniel Chasman,
  • Sameer Chavan,
  • Bo-Juen Chen,
  • Wei-Min Chen,
  • Michael Cho,
  • Seung Hoan Choi,
  • Lee-Ming Chuang,
  • Mina Chung,
  • Ren-Hua Chung,
  • Clary Clish,
  • Suzy Comhair,
  • Matthew Conomos,
  • Elaine Cornell,
  • Adolfo Correa,
  • Carolyn Crandall,
  • James Crapo,
  • L. Adrienne Cupples,
  • Jeffrey Curtis,
  • Brian Custer,
  • Coleen Damcott,
  • Dawood Darbar,
  • Sean David,
  • Colleen Davis,
  • Michelle Daya,
  • Michael DeBaun,
  • Dawn DeMeo,
  • Ranjan Deka,
  • Scott Devine,
  • Huyen Dinh,
  • Harsha Doddapaneni,
  • Qing Duan,
  • Shannon Dugan-Perez,
  • Ravi Duggirala,
  • Jon Peter Durda,
  • Susan K. Dutcher,
  • Charles Eaton,
  • Lynette Ekunwe,
  • Adel El Boueiz,
  • Patrick T. Ellinor,
  • Leslie Emery,
  • Serpil Erzurum,
  • Charles Farber,
  • Jesse Farek,
  • Tasha Fingerlin,
  • Matthew Flickinger,
  • Chris Frazar,
  • Mao Fu,
  • Stephanie M. Fullerton,
  • Lucinda Fulton,
  • Stacey Gabriel,
  • Weiniu Gan,
  • Shanshan Gao,
  • Yan Gao,
  • Margery Gass,
  • Heather Geiger,
  • Bruce Gelb,
  • Mark Geraci,
  • Soren Germer,
  • Robert Gerszten,
  • Auyon Ghosh,
  • Richard Gibbs,
  • Chris Gignoux,
  • Mark Gladwin,
  • David Glahn,
  • Stephanie Gogarten,
  • Da-Wei Gong,
  • Harald Goring,
  • Sharon Graw,
  • Kathryn J. Gray,
  • Daniel Grine,
  • Colin Gross,
  • Yue Guan,
  • Xiuqing Guo,
  • Namrata Gupta,
  • Jeff Haessler,
  • Michael Hall,
  • Yi Han,
  • Patrick Hanly,
  • Daniel Harris,
  • Nicola L. Hawley,
  • Ben Heavner,
  • Susan Heckbert,
  • Ryan Hernandez,
  • David Herrington,
  • Craig Hersh,
  • Bertha Hidalgo,
  • James Hixson,
  • Brian Hobbs,
  • John Hokanson,
  • Elliott Hong,
  • Karin Hoth,
  • Chao Agnes Hsiung,
  • Jianhong Hu,
  • Haley Huston,
  • Chii Min Hwu,
  • Rebecca Jackson,
  • Deepti Jain,
  • Cashell Jaquish,
  • Jill Johnsen,
  • Andrew Johnson,
  • Craig Johnson,
  • Rich Johnston,
  • Kimberly Jones,
  • Hyun Min Kang,
  • Shannon Kelly,
  • Eimear Kenny,
  • Michael Kessler,
  • Alyna Khan,
  • Ziad Khan,
  • Wonji Kim,
  • John Kimoff,
  • Greg Kinney,
  • Barbara Konkle,
  • Holly Kramer,
  • Christoph Lange,
  • Ethan Lange,
  • Leslie Lange,
  • Cathy Laurie,
  • Cecelia Laurie,
  • Meryl LeBoff,
  • Jonathon LeFaive,
  • Jiwon Lee,
  • Sandra Lee,
  • Wen-Jane Lee,
  • David Levine,
  • Daniel Levy,
  • Joshua Lewis,
  • Xiaohui Li,
  • Henry Lin,
  • Simin Liu,
  • Yongmei Liu,
  • Yu Liu,
  • Steven A. Lubitz,
  • Kathryn L. Lunetta,
  • James Luo,
  • Ulysses Magalang,
  • Barry Make,
  • Ani Manichaikul,
  • JoAnn Manson,
  • Melissa Marton,
  • Susan Mathai,
  • Susanne May,
  • Patrick McArdle,
  • Merry-Lynn McDonald,
  • Sean McFarland,
  • Stephen McGarvey,
  • Daniel McGoldrick,
  • Caitlin McHugh,
  • Becky McNeil,
  • Hao Mei,
  • Vipin Menon,
  • Luisa Mestroni,
  • Ginger Metcalf,
  • Deborah A. Meyers,
  • Emmanuel Mignot,
  • Julie Mikulla,
  • Nancy Min,
  • Mollie Minear,
  • Ryan L. Minster,
  • Matt Moll,
  • Zeineen Momin,
  • Courtney Montgomery,
  • Donna Muzny,
  • Josyf C. Mychaleckyj,
  • Girish Nadkarni,
  • Rakhi Naik,
  • Sergei Nekhai,
  • Sarah C. Nelson,
  • Bonnie Neltner,
  • Caitlin Nessner,
  • Deborah Nickerson,
  • Osuji Nkechinyere,
  • Jeff O’Connell,
  • Tim O’Connor,
  • Heather Ochs-Balcom,
  • Geoffrey Okwuonu,
  • Allan Pack,
  • David T. Paik,
  • James Pankow,
  • George Papanicolaou,
  • Cora Parker,
  • Juan Manuel Peralta,
  • Marco Perez,
  • James Perry,
  • Ulrike Peters,
  • Lawrence S. Phillips,
  • Jacob Pleiness,
  • Toni Pollin,
  • Wendy Post,
  • Julia Powers Becker,
  • Meher Preethi Boorgula,
  • Michael Preuss,
  • Pankaj Qasba,
  • Dandi Qiao,
  • Zhaohui Qin,
  • Nicholas Rafaels,
  • Mahitha Rajendran,
  • D. C. Rao,
  • Laura Rasmussen-Torvik,
  • Aakrosh Ratan,
  • Robert Reed,
  • Catherine Reeves,
  • Elizabeth Regan,
  • Muagututi’a Sefuiva Reupena,
  • Rebecca Robillard,
  • Nicolas Robine,
  • Dan Roden,
  • Carolina Roselli,
  • Ingo Ruczinski,
  • Alexi Runnels,
  • Pamela Russell,
  • Sarah Ruuska,
  • Kathleen Ryan,
  • Ester Cerdeira Sabino,
  • Danish Saleheen,
  • Shabnam Salimi,
  • Sejal Salvi,
  • Steven Salzberg,
  • Kevin Sandow,
  • Vijay G. Sankaran,
  • Jireh Santibanez,
  • Karen Schwander,
  • David Schwartz,
  • Frank Sciurba,
  • Christine Seidman,
  • Jonathan Seidman,
  • Vivien Sheehan,
  • Stephanie L. Sherman,
  • Amol Shetty,
  • Aniket Shetty,
  • Wayne Hui-Heng Sheu,
  • M. Benjamin Shoemaker,
  • Brian Silver,
  • Edwin Silverman,
  • Robert Skomro,
  • Albert Vernon Smith,
  • Josh Smith,
  • Nicholas Smith,
  • Tanja Smith,
  • Sylvia Smoller,
  • Beverly Snively,
  • Michael Snyder,
  • Tamar Sofer,
  • Nona Sotoodehnia,
  • Adrienne M. Stilp,
  • Garrett Storm,
  • Elizabeth Streeten,
  • Jessica Lasky Su,
  • Yun Ju Sung,
  • Jody Sylvia,
  • Adam Szpiro,
  • Frédéric Sériès,
  • Daniel Taliun,
  • Hua Tang,
  • Margaret Taub,
  • Matthew Taylor,
  • Simeon Taylor,
  • Marilyn Telen,
  • Timothy A. Thornton,
  • Machiko Threlkeld,
  • Lesley Tinker,
  • David Tirschwell,
  • Sarah Tishkoff,
  • Catherine Tong,
  • Russell Tracy,
  • Michael Tsai,
  • Dhananjay Vaidya,
  • David Van Den Berg,
  • Peter VandeHaar,
  • Scott Vrieze,
  • Tarik Walker,
  • Robert Wallace,
  • Avram Walts,
  • Fei Fei Wang,
  • Heming Wang,
  • Jiongming Wang,
  • Karol Watson,
  • Jennifer Watt,
  • Daniel E. Weeks,
  • Joshua Weinstock,
  • Bruce Weir,
  • Scott T. Weiss,
  • Lu-Chen Weng,
  • Cristen Willer,
  • Kayleen Williams,
  • L. Keoki Williams,
  • Scott Williams,
  • Carla Wilson,
  • James Wilson,
  • Lara Winterkorn,
  • Quenna Wong,
  • Baojun Wu,
  • Joseph Wu,
  • Huichun Xu,
  • Ivana Yang,
  • Ketian Yu,
  • Seyedeh Maryam Zekavat,
  • Yingze Zhang,
  • Snow Xueyan Zhao,
  • Wei Zhao,
  • Xiaofeng Zhu,
  • Elad Ziv,
  • Michael Zody,
  • Sebastian Zoellner,
  • Mariza de Andrade,
  • Lisa de las Fuentes,
  • Josée Dupuis,
  • James B. Meigs,
  • Paul L. Auer,
  • Laura M. Raffield,
  • Alisa K. Manning,
  • Kenneth M. Rice,
  • Jerome I. Rotter,
  • Gina M. Peloso,
  • Pradeep Natarajan,
  • Zilin Li,
  • Zhonghua Liu,
  • Xihong Lin

摘要

Large-scale whole-genome sequencing (WGS) studies have improved our understanding of the contributions of coding and noncoding rare variants to complex human traits. Leveraging association effect sizes across multiple traits in WGS rare variant association analysis can improve statistical power over single-trait analysis, and also detect pleiotropic genes and regions. Existing multi-trait methods have limited ability to perform rare variant analysis of large-scale WGS data. We propose MultiSTAAR, a statistical framework and computationally scalable analytical pipeline for functionally informed multi-trait rare variant analysis in large-scale WGS studies. MultiSTAAR accounts for relatedness, population structure and correlation among phenotypes by jointly analyzing multiple traits, and further empowers rare variant association analysis by incorporating multiple functional annotations. We applied MultiSTAAR to jointly analyze three lipid traits in 61,838 multi-ethnic samples from the Trans-Omics for Precision Medicine (TOPMed) Program. We discovered and replicated new associations with lipid traits missed by single-trait analysis.