GWAS using low-pass whole genome sequence reveals a novel locus in canine congenital idiopathic megaesophagus.
Journal
Mammalian genome : official journal of the International Mammalian Genome Society
ISSN: 1432-1777
Titre abrégé: Mamm Genome
Pays: United States
ID NLM: 9100916
Informations de publication
Date de publication:
09 2023
09 2023
Historique:
received:
08
02
2023
accepted:
29
03
2023
pmc-release:
01
09
2024
medline:
31
7
2023
pubmed:
12
4
2023
entrez:
11
4
2023
Statut:
ppublish
Résumé
Congenital idiopathic megaesophagus (CIM) is a gastrointestinal disorder of dogs wherein the esophagus is dilated and swallowing activity is reduced, causing regurgitation of ingesta. Affected individuals experience weight loss and malnourishment and are at risk for aspiration pneumonia, intussusception, and euthanasia. Great Danes have among the highest incidences of CIM across dog breeds, suggesting a genetic predisposition. We generated low-pass sequencing data for 83 Great Danes and used variant calls to impute missing whole genome single-nucleotide variants (SNVs) for each individual based on haplotypes phased from 624 high-coverage dog genomes, including 21 Great Danes. We validated the utility of our imputed data set for genome-wide association studies (GWASs) by mapping loci known to underlie coat phenotypes with simple and complex inheritance patterns. We conducted a GWAS for CIM with 2,010,300 SNVs, identifying a novel locus on canine chromosome 1 (P-val = 2.76 × 10
Identifiants
pubmed: 37041421
doi: 10.1007/s00335-023-09991-2
pii: 10.1007/s00335-023-09991-2
pmc: PMC10600401
mid: NIHMS1937006
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
464-472Subventions
Organisme : NIH HHS
ID : K01 OD027058
Pays : United States
Informations de copyright
© 2023. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.
Références
Heliyon. 2021 Jun 15;7(6):e07308
pubmed: 34195419
Gastroenterology. 2021 Jan;160(1):99-114.e3
pubmed: 32294476
J Am Vet Med Assoc. 2008 Dec 1;233(11):1748-55
pubmed: 19046034
BMC Genomics. 2021 Mar 20;22(1):197
pubmed: 33743587
Genome Res. 2011 Jun;21(6):940-51
pubmed: 21460063
J Cell Mol Med. 2021 Oct;25(20):9609-9616
pubmed: 34545688
Neural Regen Res. 2023 Mar;18(3):541-542
pubmed: 36018168
Brief Bioinform. 2013 Mar;14(2):178-92
pubmed: 22517427
J Hered. 2007;98(5):468-73
pubmed: 17519392
Bioinformatics. 2009 Jul 15;25(14):1754-60
pubmed: 19451168
Vet Med Small Anim Clin. 1968 Jun;63(6):574-6
pubmed: 4385116
Am J Hum Genet. 2007 Nov;81(5):1084-97
pubmed: 17924348
J Am Vet Med Assoc. 2011 Jun 15;238(12):1622-8
pubmed: 21671818
BMC Genomics. 2020 Apr 16;21(1):307
pubmed: 32299354
Science. 2022 Apr 29;376(6592):eabk0639
pubmed: 35482869
PLoS Genet. 2018 Dec 6;14(12):e1007850
pubmed: 30521570
PLoS Genet. 2019 Sep 16;15(9):e1008003
pubmed: 31525180
PLoS Genet. 2017 Feb 3;13(2):e1006604
pubmed: 28158183
J Am Vet Med Assoc. 2020 Apr 15;256(8):914-920
pubmed: 32223709
Curr Biol. 2022 Feb 28;32(4):889-897.e9
pubmed: 35090588
Proc Natl Acad Sci U S A. 2020 Oct 6;117(40):24929-24935
pubmed: 32958658
J Am Vet Med Assoc. 1974 Sep 1;165(5):443-6
pubmed: 4420331
Proc Natl Acad Sci U S A. 2006 Jan 31;103(5):1376-81
pubmed: 16407134
J Vet Emerg Crit Care (San Antonio). 2016 Mar-Apr;26(2):234-53
pubmed: 26822390
BMC Biol. 2010 Jun 18;8:86
pubmed: 20565848
Parkinsons Dis. 2016;2016:6762528
pubmed: 28050310
Mob DNA. 2018 Aug 03;9:26
pubmed: 30123327
Nat Commun. 2019 Apr 2;10(1):1489
pubmed: 30940804
J Am Anim Hosp Assoc. 2019 Jul/Aug;55(4):167-177
pubmed: 31099601
Mol Psychiatry. 2021 May;26(5):1442-1444
pubmed: 32461615
Cell Mol Life Sci. 2021 Jan;78(2):513-529
pubmed: 32748156
Front Genet. 2020 Nov 30;11:527484
pubmed: 33329688
Bioinformatics. 2011 Nov 1;27(21):2987-93
pubmed: 21903627
Gastroenterology. 2022 Jan;162(1):179-192.e11
pubmed: 34425092
PLoS One. 2015 Oct 27;10(10):e0141514
pubmed: 26506231
Genes (Basel). 2020 Nov 05;11(11):
pubmed: 33167491
Mamm Genome. 2016 Oct;27(9-10):485-94
pubmed: 27129452
Curr Gastroenterol Rep. 2014 Dec;16(12):420
pubmed: 25543338
World J Pediatr. 2017 Oct;13(5):489-495
pubmed: 28965333
Am J Hum Genet. 2021 Apr 1;108(4):656-668
pubmed: 33770507
Semin Vet Med Surg Small Anim. 1990 Feb;5(1):37-45
pubmed: 2191392
Transl Psychiatry. 2020 May 28;10(1):169
pubmed: 32467585
eNeuro. 2017 May 16;4(3):
pubmed: 28512649
Am J Vet Res. 1980 Mar;41(3):326-30
pubmed: 7189391
Mamm Genome. 2022 Mar;33(1):213-229
pubmed: 34498136
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
Natl Sci Rev. 2019 Jul;6(4):810-824
pubmed: 31598383
Immunogenetics. 2013 Jul;65(7):501-9
pubmed: 23604463
PLoS Genet. 2022 Mar 10;18(3):e1010044
pubmed: 35271580
Dev Dyn. 2005 Jan;232(1):200-8
pubmed: 15580626
Genes (Basel). 2022 Jul 26;13(8):
pubmed: 35893065
Acta Endocrinol (Buchar). 2019 Oct-Dec;15(4):497-504
pubmed: 32377248
Commun Biol. 2021 Feb 10;4(1):185
pubmed: 33568770
Proc Natl Acad Sci U S A. 2016 May 31;113(22):E3091-100
pubmed: 27185954
Annu Rev Anim Biosci. 2019 Feb 15;7:449-472
pubmed: 30418802
Can Vet J. 1998 Nov;39(11):709-11
pubmed: 9818138