Deciphering complex genome rearrangements in C. elegans using short-read whole genome sequencing.
Journal
Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288
Informations de publication
Date de publication:
14 09 2021
14 09 2021
Historique:
received:
06
07
2021
accepted:
30
08
2021
entrez:
15
9
2021
pubmed:
16
9
2021
medline:
17
12
2021
Statut:
epublish
Résumé
Genomic rearrangements cause congenital disorders, cancer, and complex diseases in human. Yet, they are still understudied in rare diseases because their detection is challenging, despite the advent of whole genome sequencing (WGS) technologies. Short-read (srWGS) and long-read WGS approaches are regularly compared, and the latter is commonly recommended in studies focusing on genomic rearrangements. However, srWGS is currently the most economical, accurate, and widely supported technology. In Caenorhabditis elegans (C. elegans), such variants, induced by various mutagenesis processes, have been used for decades to balance large genomic regions by preventing chromosomal crossover events and allowing the maintenance of lethal mutations. Interestingly, those chromosomal rearrangements have rarely been characterized on a molecular level. To evaluate the ability of srWGS to detect various types of complex genomic rearrangements, we sequenced three balancer strains using short-read Illumina technology. As we experimentally validated the breakpoints uncovered by srWGS, we showed that, by combining several types of analyses, srWGS enables the detection of a reciprocal translocation (eT1), a free duplication (sDp3), a large deletion (sC4), and chromoanagenesis events. Thus, applying srWGS to decipher real complex genomic rearrangements in model organisms may help designing efficient bioinformatics pipelines with systematic detection of complex rearrangements in human genomes.
Identifiants
pubmed: 34521941
doi: 10.1038/s41598-021-97764-9
pii: 10.1038/s41598-021-97764-9
pmc: PMC8440550
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
18258Informations de copyright
© 2021. The Author(s).
Références
Bioessays. 2011 Nov;33(11):840-50
pubmed: 21959584
Hum Mutat. 2021 Apr;42(4):346-358
pubmed: 33368787
BMC Genomics. 2020 Jan 20;21(1):61
pubmed: 31959124
Nucleic Acids Res. 2017 Jan 4;45(D1):D650-D657
pubmed: 27701074
Nat Commun. 2019 Jul 19;10(1):3240
pubmed: 31324872
Int J Mol Sci. 2021 Feb 19;22(4):
pubmed: 33669700
Genome Biol. 2019 Jun 3;20(1):117
pubmed: 31159850
J Hum Genet. 2019 May;64(5):359-368
pubmed: 30760880
PLoS Genet. 2020 Dec 3;16(12):e1009213
pubmed: 33270639
Nat Methods. 2008 Feb;5(2):183-8
pubmed: 18204455
Bioinformatics. 2012 Sep 15;28(18):i333-i339
pubmed: 22962449
Genetics. 1981 Nov-Dec;99(3-4):415-28
pubmed: 6953041
PLoS Genet. 2020 Feb 24;16(2):e1008606
pubmed: 32092052
Am J Hum Genet. 2019 Apr 4;104(4):565-577
pubmed: 30951674
G3 (Bethesda). 2012 Nov;2(11):1415-25
pubmed: 23173093
Bioinformatics. 2017 Jan 15;33(2):184-191
pubmed: 27634948
Nat Genet. 2008 Jun;40(6):722-9
pubmed: 18438408
WormBook. 2006 Apr 06;:1-32
pubmed: 18050450
PLoS Genet. 2021 Feb 16;17(2):e1009386
pubmed: 33591993
F1000Res. 2017 May 10;6:664
pubmed: 28781756
J Med Genet. 1993 Sep;30(9):713-27
pubmed: 8411066
Semin Cell Dev Biol. 2021 Feb 16;:
pubmed: 33608210
Genome Res. 2014 Oct;24(10):1624-36
pubmed: 25030888
Curr Protoc Hum Genet. 2020 Sep;107(1):e103
pubmed: 32813322
J Mol Diagn. 2021 Mar;23(3):285-299
pubmed: 33346148
Genet Med. 2018 Jan;20(1):159-163
pubmed: 28640241
Nat Rev Genet. 2021 Apr;22(4):200
pubmed: 33654294
Mol Genet Genomic Med. 2020 Mar;8(3):e1114
pubmed: 31985172
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
Nature. 2020 May;581(7809):434-443
pubmed: 32461654
BMC Genomics. 2019 Jul 16;20(Suppl 8):545
pubmed: 31307387
Front Genet. 2021 Feb 04;12:550676
pubmed: 33613628
Mol Biol Evol. 2017 Sep 1;34(9):2187-2202
pubmed: 28486636
Hum Mol Genet. 2011 May 15;20(10):1916-24
pubmed: 21349919
Methods. 2017 Oct 1;129:3-7
pubmed: 28583483
Cytogenet Genome Res. 2020;160(11-12):671-679
pubmed: 33535208
Bioinformatics. 2016 Apr 15;32(8):1220-2
pubmed: 26647377
Nat Genet. 2020 Mar;52(3):331-341
pubmed: 32025003
Curr Biol. 2003 Sep 16;13(18):1641-7
pubmed: 13678597
Nat Commun. 2020 May 1;11(1):2169
pubmed: 32358516
Genome Res. 2009 Sep;19(9):1639-45
pubmed: 19541911
Genome Res. 2017 Dec;27(12):2050-2060
pubmed: 29097403
Am J Med Genet A. 2020 Nov;182(11):2533-2539
pubmed: 32841469
Cell Rep. 2018 Jan 2;22(1):232-241
pubmed: 29298424
Am J Hum Genet. 2021 Apr 1;108(4):597-607
pubmed: 33675682
Mutat Res. 2006 Oct 10;601(1-2):19-29
pubmed: 16765996
Sci Rep. 2016 Sep 21;6:33840
pubmed: 27650892
Science. 2021 Apr 2;372(6537):
pubmed: 33632895
J Pers Med. 2021 Feb 18;11(2):
pubmed: 33670576
Genome Res. 2011 Jun;21(6):974-84
pubmed: 21324876
Genet Med. 2020 Nov;22(11):1892-1897
pubmed: 32624572
G3 (Bethesda). 2015 Dec 01;6(2):351-6
pubmed: 26628482
Genes (Basel). 2019 Apr 04;10(4):
pubmed: 30987386
NPJ Genom Med. 2018 Aug 13;3:22
pubmed: 30109124
DNA Repair (Amst). 2020 Nov;95:102957
pubmed: 32980770
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
Genetics. 1941 Mar;26(2):234-82
pubmed: 17247004
J Hum Genet. 2020 Aug;65(8):667-674
pubmed: 32296131
Genetics. 2016 May;203(1):159-71
pubmed: 26944917
Curr Protoc Bioinformatics. 2014;45:15.6.1-11
pubmed: 25152801