A framework for detecting noncoding rare-variant associations of large-scale whole-genome sequencing studies.
Journal
Nature methods
ISSN: 1548-7105
Titre abrégé: Nat Methods
Pays: United States
ID NLM: 101215604
Informations de publication
Date de publication:
12 2022
12 2022
Historique:
received:
06
11
2021
accepted:
06
09
2022
pubmed:
28
10
2022
medline:
7
12
2022
entrez:
27
10
2022
Statut:
ppublish
Résumé
Large-scale whole-genome sequencing studies have enabled analysis of noncoding rare-variant (RV) associations with complex human diseases and traits. Variant-set analysis is a powerful approach to study RV association. However, existing methods have limited ability in analyzing the noncoding genome. We propose a computationally efficient and robust noncoding RV association detection framework, STAARpipeline, to automatically annotate a whole-genome sequencing study and perform flexible noncoding RV association analysis, including gene-centric analysis and fixed window-based and dynamic window-based non-gene-centric analysis by incorporating variant functional annotations. In gene-centric analysis, STAARpipeline uses STAAR to group noncoding variants based on functional categories of genes and incorporate multiple functional annotations. In non-gene-centric analysis, STAARpipeline uses SCANG-STAAR to incorporate dynamic window sizes and multiple functional annotations. We apply STAARpipeline to identify noncoding RV sets associated with four lipid traits in 21,015 discovery samples from the Trans-Omics for Precision Medicine (TOPMed) program and replicate several of them in an additional 9,123 TOPMed samples. We also analyze five non-lipid TOPMed traits.
Identifiants
pubmed: 36303018
doi: 10.1038/s41592-022-01640-x
pii: 10.1038/s41592-022-01640-x
pmc: PMC10008172
mid: NIHMS1862492
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1599-1611Subventions
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Investigateurs
Namiko Abe
(N)
Gonçalo Abecasis
(G)
Francois Aguet
(F)
Christine Albert
(C)
Laura Almasy
(L)
Alvaro Alonso
(A)
Seth Ament
(S)
Peter Anderson
(P)
Pramod Anugu
(P)
Deborah Applebaum-Bowden
(D)
Kristin Ardlie
(K)
Dan Arking
(D)
Allison Ashley-Koch
(A)
Stella Aslibekyan
(S)
Tim Assimes
(T)
Dimitrios Avramopoulos
(D)
Najib Ayas
(N)
Adithya Balasubramanian
(A)
John Barnard
(J)
Kathleen Barnes
(K)
R Graham Barr
(RG)
Emily Barron-Casella
(E)
Lucas Barwick
(L)
Terri Beaty
(T)
Gerald Beck
(G)
Diane Becker
(D)
Lewis Becker
(L)
Rebecca Beer
(R)
Amber Beitelshees
(A)
Emelia Benjamin
(E)
Takis Benos
(T)
Marcos Bezerra
(M)
Nathan Blue
(N)
Russell Bowler
(R)
Ulrich Broeckel
(U)
Jai Broome
(J)
Deborah Brown
(D)
Karen Bunting
(K)
Esteban Burchard
(E)
Carlos Bustamante
(C)
Erin Buth
(E)
Jonathan Cardwell
(J)
Vincent Carey
(V)
Julie Carrier
(J)
April Carson
(A)
Cara Carty
(C)
Richard Casaburi
(R)
Juan P Casas Romero
(JP)
James Casella
(J)
Peter Castaldi
(P)
Mark Chaffin
(M)
Christy Chang
(C)
Yi-Cheng Chang
(YC)
Daniel Chasman
(D)
Sameer Chavan
(S)
Bo-Juen Chen
(BJ)
Wei-Min Chen
(WM)
Yii-Der Ida Chen
(YI)
Michael Cho
(M)
Seung Hoan Choi
(SH)
Lee-Ming Chuang
(LM)
Mina Chung
(M)
Ren-Hua Chung
(RH)
Clary Clish
(C)
Suzy Comhair
(S)
Elaine Cornell
(E)
Carolyn Crandall
(C)
James Crapo
(J)
Jeffrey Curtis
(J)
Brian Custer
(B)
Coleen Damcott
(C)
Dawood Darbar
(D)
Sean David
(S)
Colleen Davis
(C)
Michelle Daya
(M)
Mariza de Andrade
(M)
Lisa de Las Fuentes
(LL)
Michael DeBaun
(M)
Ranjan Deka
(R)
Dawn DeMeo
(D)
Scott Devine
(S)
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(H)
Harsha Doddapaneni
(H)
Qing Duan
(Q)
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(S)
Jon Peter Durda
(JP)
Susan K Dutcher
(SK)
Charles Eaton
(C)
Lynette Ekunwe
(L)
Adel El Boueiz
(A)
Patrick Ellinor
(P)
Leslie Emery
(L)
Serpil Erzurum
(S)
Charles Farber
(C)
Jesse Farek
(J)
Tasha Fingerlin
(T)
Matthew Flickinger
(M)
Myriam Fornage
(M)
Chris Frazar
(C)
Mao Fu
(M)
Stephanie M Fullerton
(SM)
Lucinda Fulton
(L)
Stacey Gabriel
(S)
Weiniu Gan
(W)
Shanshan Gao
(S)
Yan Gao
(Y)
Margery Gass
(M)
Heather Geiger
(H)
Bruce Gelb
(B)
Mark Geraci
(M)
Soren Germer
(S)
Robert Gerszten
(R)
Auyon Ghosh
(A)
Richard Gibbs
(R)
Chris Gignoux
(C)
Mark Gladwin
(M)
David Glahn
(D)
Stephanie Gogarten
(S)
Da-Wei Gong
(DW)
Sharon Graw
(S)
Kathryn J Gray
(KJ)
Daniel Grine
(D)
Colin Gross
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C Charles Gu
(CC)
Yue Guan
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Namrata Gupta
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Cathy Laurie
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None Dan Levy
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(X)
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(Y)
Henry Lin
(H)
Honghuang Lin
(H)
Simin Liu
(S)
Yongmei Liu
(Y)
Yu Liu
(Y)
Ruth J F Loos
(RJF)
Steven Lubitz
(S)
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(J)
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(U)
Michael Mahaney
(M)
Barry Make
(B)
JoAnn Manson
(J)
Melissa Marton
(M)
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Susanne May
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Patrick McArdle
(P)
Merry-Lynn McDonald
(ML)
Sean McFarland
(S)
Daniel McGoldrick
(D)
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(B)
Hao Mei
(H)
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(V)
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(L)
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(G)
Deborah A Meyers
(DA)
Emmanuel Mignot
(E)
Julie Mikulla
(J)
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(N)
Mollie Minear
(M)
Ryan L Minster
(RL)
Matt Moll
(M)
Zeineen Momin
(Z)
Courtney Montgomery
(C)
Donna Muzny
(D)
Josyf C Mychaleckyj
(JC)
Girish Nadkarni
(G)
Rakhi Naik
(R)
Sergei Nekhai
(S)
Sarah C Nelson
(SC)
Bonnie Neltner
(B)
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(C)
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(D)
Osuji Nkechinyere
(O)
Kari North
(K)
Tim O'Connor
(T)
Heather Ochs-Balcom
(H)
Geoffrey Okwuonu
(G)
Allan Pack
(A)
David T Paik
(DT)
James Pankow
(J)
George Papanicolaou
(G)
Cora Parker
(C)
Juan Manuel Peralta
(JM)
Marco Perez
(M)
James Perry
(J)
Ulrike Peters
(U)
Lawrence S Phillips
(LS)
Jacob Pleiness
(J)
Toni Pollin
(T)
Wendy Post
(W)
Julia Powers Becker
(JP)
Meher Preethi Boorgula
(MP)
Michael Preuss
(M)
Pankaj Qasba
(P)
Dandi Qiao
(D)
Zhaohui Qin
(Z)
Nicholas Rafaels
(N)
Mahitha Rajendran
(M)
D C Rao
(DC)
Laura Rasmussen-Torvik
(L)
Aakrosh Ratan
(A)
Robert Reed
(R)
Catherine Reeves
(C)
Elizabeth Regan
(E)
Rebecca Robillard
(R)
Nicolas Robine
(N)
Dan Roden
(D)
Carolina Roselli
(C)
Ingo Ruczinski
(I)
Alexi Runnels
(A)
Pamela Russell
(P)
Sarah Ruuska
(S)
Kathleen Ryan
(K)
Ester Cerdeira Sabino
(EC)
Danish Saleheen
(D)
Shabnam Salimi
(S)
Sejal Salvi
(S)
Steven Salzberg
(S)
Kevin Sandow
(K)
Vijay G Sankaran
(VG)
Jireh Santibanez
(J)
Karen Schwander
(K)
David Schwartz
(D)
Frank Sciurba
(F)
Christine Seidman
(C)
Jonathan Seidman
(J)
Frédéric Sériès
(F)
Vivien Sheehan
(V)
Stephanie L Sherman
(SL)
Amol Shetty
(A)
Aniket Shetty
(A)
Wayne Hui-Heng Sheu
(WH)
M Benjamin Shoemaker
(MB)
Brian Silver
(B)
Edwin Silverman
(E)
Robert Skomro
(R)
Albert Vernon Smith
(AV)
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