Inversion polymorphism in a complete human genome assembly.
Genomic structural variation
Inversion
Pathogenic copy number variant
Pericentromeric
T2T-CHM13
Journal
Genome biology
ISSN: 1474-760X
Titre abrégé: Genome Biol
Pays: England
ID NLM: 100960660
Informations de publication
Date de publication:
30 04 2023
30 04 2023
Historique:
received:
05
10
2022
accepted:
31
03
2023
medline:
2
5
2023
pubmed:
1
5
2023
entrez:
30
4
2023
Statut:
epublish
Résumé
The telomere-to-telomere (T2T) complete human reference has significantly improved our ability to characterize genome structural variation. To understand its impact on inversion polymorphisms, we remapped data from 41 genomes against the T2T reference genome and compared it to the GRCh38 reference. We find a ~ 21% increase in sensitivity improving mapping of 63 inversions on the T2T reference. We identify 26 misorientations within GRCh38 and show that the T2T reference is three times more likely to represent the correct orientation of the major human allele. Analysis of 10 additional samples reveals novel rare inversions at chromosomes 15q25.2, 16p11.2, 16q22.1-23.1, and 22q11.21.
Identifiants
pubmed: 37122002
doi: 10.1186/s13059-023-02919-8
pii: 10.1186/s13059-023-02919-8
pmc: PMC10150506
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
100Subventions
Organisme : NHGRI NIH HHS
ID : U01 HG010973
Pays : United States
Organisme : NHGRI NIH HHS
ID : R01 HG010169
Pays : United States
Organisme : NHGRI NIH HHS
ID : U24 HG010262
Pays : United States
Organisme : NHGRI NIH HHS
ID : U24 HG007497
Pays : United States
Organisme : NHGRI NIH HHS
ID : R01 HG002385
Pays : United States
Informations de copyright
© 2023. The Author(s).
Références
Bioinformatics. 2016 Jan 15;32(2):289-91
pubmed: 26424858
BMC Bioinformatics. 2015 Aug 19;16:258
pubmed: 26283514
Nature. 2004 Oct 21;431(7011):927-30
pubmed: 15496912
Nature. 2022 Apr;604(7906):437-446
pubmed: 35444317
Nat Methods. 2012 Nov;9(11):1107-12
pubmed: 23042453
Bioinformatics. 2016 Jul 15;32(14):2103-10
pubmed: 27153593
Proc Natl Acad Sci U S A. 1917 Sep;3(9):555-8
pubmed: 16586749
Nature. 2008 May 1;453(7191):56-64
pubmed: 18451855
Nat Biotechnol. 2021 Mar;39(3):302-308
pubmed: 33288906
Bioinformatics. 2015 Jun 15;31(12):2032-4
pubmed: 25697820
Genome Res. 2020 May;30(5):724-735
pubmed: 32424072
Nat Genet. 2010 Sep;42(9):745-50
pubmed: 20729854
Nature. 2022 Nov;611(7936):519-531
pubmed: 36261518
Nat Genet. 2006 Sep;38(9):999-1001
pubmed: 16906164
Science. 2022 Apr;376(6588):44-53
pubmed: 35357919
Nat Biotechnol. 2020 Mar;38(3):343-354
pubmed: 31873213
Genome Res. 2016 Nov;26(11):1453-1467
pubmed: 27803192
Cell. 2019 Jan 24;176(3):663-675.e19
pubmed: 30661756
Genome Biol. 2023 Apr 30;24(1):100
pubmed: 37122002
Hum Mutat. 2022 Nov;43(11):1576-1589
pubmed: 36047337
Bioinformatics. 2010 Mar 1;26(5):589-95
pubmed: 20080505
Nat Genet. 2008 Sep;40(9):1076-83
pubmed: 19165922
Nat Protoc. 2017 Jun;12(6):1151-1176
pubmed: 28492527
Genome Res. 2016 Nov;26(11):1575-1587
pubmed: 27472961
Nat Genet. 2012 Jul 01;44(8):872-80
pubmed: 22751100
Nucleic Acids Res. 2014 Jan;42(Database issue):D993-D1000
pubmed: 24150940
Science. 2022 Apr;376(6588):eabl4178
pubmed: 35357911
Nat Methods. 2010 May;7(5):365-71
pubmed: 20440878
Nature. 2010 Oct 28;467(7319):1099-103
pubmed: 20981099
Nat Genet. 2020 Aug;52(8):849-858
pubmed: 32541924
Cell. 2010 Nov 24;143(5):837-47
pubmed: 21111241
PLoS Genet. 2019 Mar 27;15(3):e1008075
pubmed: 30917130
Sci Rep. 2017 Jan 06;7:40031
pubmed: 28059126
Nat Genet. 2011 Aug 14;43(9):838-46
pubmed: 21841781
Science. 2022 Apr;376(6588):eabj6965
pubmed: 35357917
Science. 2021 Apr 2;372(6537):
pubmed: 33632895
Nat Commun. 2019 Apr 16;10(1):1784
pubmed: 30992455
Eur J Hum Genet. 2003 Feb;11(2):109-11
pubmed: 12634857
Proc Natl Acad Sci U S A. 2007 Nov 20;104(47):18571-6
pubmed: 18003915
Nat Biotechnol. 2023 Feb 16;:
pubmed: 36797493
Science. 2022 Apr;376(6588):eabl3533
pubmed: 35357935
Nat Genet. 2014 Oct;46(10):1063-71
pubmed: 25217958
Cell. 2022 May 26;185(11):1986-2005.e26
pubmed: 35525246
Nat Genet. 2022 Apr;54(4):518-525
pubmed: 35410384
Nat Genet. 2001 Nov;29(3):321-5
pubmed: 11685205
Int J Cancer. 1997 May 16;71(4):580-4
pubmed: 9178811
Hum Mol Genet. 1995 Dec;4(12):2199-208
pubmed: 8634688