Increased mutation and gene conversion within human segmental duplications.
Journal
Nature
ISSN: 1476-4687
Titre abrégé: Nature
Pays: England
ID NLM: 0410462
Informations de publication
Date de publication:
05 2023
05 2023
Historique:
received:
06
07
2022
accepted:
28
02
2023
medline:
12
5
2023
pubmed:
11
5
2023
entrez:
10
5
2023
Statut:
ppublish
Résumé
Single-nucleotide variants (SNVs) in segmental duplications (SDs) have not been systematically assessed because of the limitations of mapping short-read sequencing data
Identifiants
pubmed: 37165237
doi: 10.1038/s41586-023-05895-y
pii: 10.1038/s41586-023-05895-y
pmc: PMC10172114
doi:
Substances chimiques
Cytosine
8J337D1HZY
Guanine
5Z93L87A1R
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
325-334Subventions
Organisme : NIAID NIH HHS
ID : F31 AI150163
Pays : United States
Organisme : NHGRI NIH HHS
ID : U24 HG010262
Pays : United States
Organisme : NHGRI NIH HHS
ID : U01 HG010971
Pays : United States
Organisme : NHGRI NIH HHS
ID : R01 HG002385
Pays : United States
Organisme : NIGMS NIH HHS
ID : R35 GM133428
Pays : United States
Organisme : NHGRI NIH HHS
ID : R00 HG011041
Pays : United States
Organisme : NHGRI NIH HHS
ID : K99 HG011041
Pays : United States
Organisme : NIGMS NIH HHS
ID : T32 GM007454
Pays : United States
Organisme : NHGRI NIH HHS
ID : U01 HG010973
Pays : United States
Investigateurs
Haley J Abel
(HJ)
Lucinda L Antonacci-Fulton
(LL)
Gunjan Baid
(G)
Carl A Baker
(CA)
Anastasiya Belyaeva
(A)
Konstantinos Billis
(K)
Guillaume Bourque
(G)
Silvia Buonaiuto
(S)
Andrew Carroll
(A)
Mark J P Chaisson
(MJP)
Pi-Chuan Chang
(PC)
Xian H Chang
(XH)
Haoyu Cheng
(H)
Justin Chu
(J)
Sarah Cody
(S)
Vincenza Colonna
(V)
Daniel E Cook
(DE)
Robert M Cook-Deegan
(RM)
Omar E Cornejo
(OE)
Mark Diekhans
(M)
Daniel Doerr
(D)
Peter Ebert
(P)
Jana Ebler
(J)
Jordan M Eizenga
(JM)
Susan Fairley
(S)
Olivier Fedrigo
(O)
Adam L Felsenfeld
(AL)
Xiaowen Feng
(X)
Christian Fischer
(C)
Paul Flicek
(P)
Giulio Formenti
(G)
Adam Frankish
(A)
Robert S Fulton
(RS)
Yan Gao
(Y)
Shilpa Garg
(S)
Erik Garrison
(E)
Nanibaa' A Garrison
(NA)
Carlos Garcia Giron
(CG)
Richard E Green
(RE)
Cristian Groza
(C)
Andrea Guarracino
(A)
Leanne Haggerty
(L)
Ira M Hall
(IM)
Marina Haukness
(M)
David Haussler
(D)
Simon Heumos
(S)
Glenn Hickey
(G)
Thibaut Hourlier
(T)
Kerstin Howe
(K)
Miten Jain
(M)
Erich D Jarvis
(ED)
Hanlee P Ji
(HP)
Eimear E Kenny
(EE)
Barbara A Koenig
(BA)
Alexey Kolesnikov
(A)
Jan O Korbel
(JO)
Jennifer Kordosky
(J)
Sergey Koren
(S)
HoJoon Lee
(H)
Heng Li
(H)
Wen-Wei Liao
(WW)
Shuangjia Lu
(S)
Tsung-Yu Lu
(TY)
Julian K Lucas
(JK)
Hugo Magalhães
(H)
Santiago Marco-Sola
(S)
Pierre Marijon
(P)
Charles Markello
(C)
Tobias Marschall
(T)
Fergal J Martin
(FJ)
Ann McCartney
(A)
Jennifer McDaniel
(J)
Karen H Miga
(KH)
Matthew W Mitchell
(MW)
Jean Monlong
(J)
Jacquelyn Mountcastle
(J)
Moses Njagi Mwaniki
(MN)
Maria Nattestad
(M)
Adam M Novak
(AM)
Sergey Nurk
(S)
Hugh E Olsen
(HE)
Nathan D Olson
(ND)
Benedict Paten
(B)
Trevor Pesout
(T)
Adam M Phillippy
(AM)
Alice B Popejoy
(AB)
Pjotr Prins
(P)
Daniela Puiu
(D)
Mikko Rautiainen
(M)
Allison A Regier
(AA)
Arang Rhie
(A)
Samuel Sacco
(S)
Ashley D Sanders
(AD)
Valerie A Schneider
(VA)
Baergen I Schultz
(BI)
Kishwar Shafin
(K)
Jonas A Sibbesen
(JA)
Jouni Sirén
(J)
Michael W Smith
(MW)
Heidi J Sofia
(HJ)
Ahmad N Abou Tayoun
(AN)
Françoise Thibaud-Nissen
(F)
Chad Tomlinson
(C)
Francesca Floriana Tricomi
(FF)
Flavia Villani
(F)
Mitchell R Vollger
(MR)
Justin Wagner
(J)
Brian Walenz
(B)
Ting Wang
(T)
Jonathan M D Wood
(JMD)
Aleksey V Zimin
(AV)
Justin M Zook
(JM)
Commentaires et corrections
Type : CommentIn
Informations de copyright
© 2023. The Author(s).
Références
Nat Genet. 2007 Nov;39(11):1361-8
pubmed: 17922013
BMC Genomics. 2015 Jun 16;16:456
pubmed: 26077037
Science. 2002 Aug 9;297(5583):1003-7
pubmed: 12169732
Genome Biol. 2020 Sep 14;21(1):245
pubmed: 32928274
Nucleic Acids Res. 1999 Jan 15;27(2):573-80
pubmed: 9862982
Proc Natl Acad Sci U S A. 2017 Nov 28;114(48):12779-12784
pubmed: 29138319
Am J Hum Genet. 2005 Jul;77(1):78-88
pubmed: 15918152
Nat Biotechnol. 2021 Mar;39(3):302-308
pubmed: 33288906
Bioinformatics. 2023 Jan 1;39(1):
pubmed: 36321867
Nat Methods. 2018 Aug;15(8):595-597
pubmed: 30013044
Nature. 2016 Aug 11;536(7615):205-9
pubmed: 27487209
Nature. 2021 May;593(7857):101-107
pubmed: 33828295
Gigascience. 2021 Feb 16;10(2):
pubmed: 33594436
Genome Res. 2004 May;14(5):835-44
pubmed: 15123583
BMC Biol. 2018 Jun 28;16(1):64
pubmed: 29950181
Nat Med. 2013 Sep;19(9):1124-31
pubmed: 23955714
Nature. 2012 Nov 1;491(7422):56-65
pubmed: 23128226
BMC Genomics. 2009 Jan 22;10:43
pubmed: 19161616
Nature. 2022 Nov;611(7936):519-531
pubmed: 36261518
Mol Psychiatry. 2019 Sep;24(9):1329-1350
pubmed: 29467497
Science. 2022 Apr;376(6588):44-53
pubmed: 35357919
Nat Biotechnol. 2023 Oct;41(10):1474-1482
pubmed: 36797493
Nature. 2023 May;617(7960):312-324
pubmed: 37165242
Annu Rev Genomics Hum Genet. 2009;10:285-311
pubmed: 19630562
Nat Commun. 2017 Aug 21;8(1):303
pubmed: 28827725
Cell. 2018 May 31;173(6):1356-1369.e22
pubmed: 29856954
Genetics. 2012 Mar;190(3):1077-86
pubmed: 22174068
Nat Genet. 2004 Aug;36(8):861-6
pubmed: 15247918
Proc Natl Acad Sci U S A. 2015 Mar 17;112(11):3439-44
pubmed: 25733855
Curr Opin Genet Dev. 2020 Jun;62:50-57
pubmed: 32619789
Nature. 2016 Aug 17;536(7616):285-91
pubmed: 27535533
Mol Cell Biol. 1998 Jan;18(1):93-101
pubmed: 9418857
Gigascience. 2021 Feb 16;10(2):
pubmed: 33590861
Genetics. 1999 Apr;151(4):1531-45
pubmed: 10101175
Nat Genet. 2018 Apr;50(4):487-492
pubmed: 29507425
Genes (Basel). 2011 Mar 25;2(2):313-31
pubmed: 24710193
Science. 2022 Apr;376(6588):eabl4178
pubmed: 35357911
Nature. 2016 Feb 11;530(7589):177-83
pubmed: 26814963
Nature. 1980 Oct 9;287(5782):560-1
pubmed: 6999365
Science. 2022 Apr;376(6588):eabj6965
pubmed: 35357917
Genome Res. 2001 Jun;11(6):1005-17
pubmed: 11381028
Nat Methods. 2021 Feb;18(2):170-175
pubmed: 33526886
Science. 2001 Feb 16;291(5507):1304-51
pubmed: 11181995
Sci Rep. 2019 Jun 27;9(1):9354
pubmed: 31249361
Genome Res. 2003 Sep;13(9):2052-8
pubmed: 12952876
Nat Biotechnol. 2019 May;37(5):561-566
pubmed: 30936564
Mob DNA. 2021 Jan 23;12(1):4
pubmed: 33485368
Genetics. 2003 Feb;163(2):803-10
pubmed: 12618415
Elife. 2016 Aug 09;5:
pubmed: 27504805
Curr Protoc Bioinformatics. 2014 Sep 08;47:11.12.1-34
pubmed: 25199790
F1000Res. 2021 Jan 18;10:33
pubmed: 34035898
Science. 2021 Apr 2;372(6537):
pubmed: 33632895
Nature. 2001 Feb 15;409(6822):860-921
pubmed: 11237011
Genome Res. 2023 Apr;33(4):496-510
pubmed: 37164484
Nature. 2023 May;617(7960):325-334
pubmed: 37165237
Genome Res. 2003 Mar;13(3):358-68
pubmed: 12618366
Science. 2010 Oct 29;330(6004):641-6
pubmed: 21030649
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
G3 (Bethesda). 2014 Jun 06;4(8):1479-89
pubmed: 24906640
Am J Hum Genet. 2022 Apr 7;109(4):631-646
pubmed: 35290762
Bioinformatics. 2018 Sep 15;34(18):3094-3100
pubmed: 29750242
Genome Res. 2018 Oct;28(10):1566-1576
pubmed: 30228200
Proc Natl Acad Sci U S A. 2018 Jul 24;115(30):E7109-E7118
pubmed: 29987035
Proc Natl Acad Sci U S A. 2019 May 7;116(19):9491-9500
pubmed: 31019089
Am J Hum Genet. 2003 Oct;73(4):823-34
pubmed: 14505274
Elife. 2015 Mar 25;4:
pubmed: 25806687
Nature. 2003 Dec 18;426(6968):789-96
pubmed: 14685227