Copy Number Variation and Allele Ratio Analysis in Candida albicans Using Whole Genome Sequencing Data.
Allele ratio
Aneuploidy
CNV
Copy number variation
RStudio
Read depth
Journal
Methods in molecular biology (Clifton, N.J.)
ISSN: 1940-6029
Titre abrégé: Methods Mol Biol
Pays: United States
ID NLM: 9214969
Informations de publication
Date de publication:
2023
2023
Historique:
medline:
10
4
2023
entrez:
6
4
2023
pubmed:
7
4
2023
Statut:
ppublish
Résumé
Whole genome sequencing of human fungal pathogens has revolutionized the speed and accuracy in which sequence variants that cause antifungal resistance can be identified. Genome rearrangements resulting in copy number variation (CNV) are a significant source of acquired antifungal drug resistance across diverse fungal species. Some CNVs are transient in nature, while other CNVs are stable and well tolerated even in the absence of antifungal drugs. By visualizing whole genome sequencing read depth as a function of genomic location, CNVs and CNV breakpoints (genomic positions where the copy number changes occur relative to the rest of the genome) are rapidly identified. A similar analysis can be used to visualize allele ratio changes that occur across the genomes of heterozygous fungal species, both in the presence and absence of CNVs. This protocol walks through the bioinformatic analysis of CNVs and allele ratios utilizing free, open-source visualization tools. We provide code to use with an example dataset (matched antifungal drug-sensitive and drug-resistant Candida albicans isolates) and notes on how to expand this protocol to other fungal genomes.
Identifiants
pubmed: 37024698
doi: 10.1007/978-1-0716-3155-3_8
pmc: PMC10676714
mid: NIHMS1940298
doi:
Substances chimiques
Antifungal Agents
0
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
105-125Subventions
Organisme : NIAID NIH HHS
ID : R01 AI143689
Pays : United States
Informations de copyright
© 2023. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.
Références
PLoS Pathog. 2010 Jun 17;6(6):e1000945
pubmed: 20585557
Fungal Genet Biol. 2014 Sep;70:68-76
pubmed: 25038494
Science. 2006 Jul 21;313(5785):367-70
pubmed: 16857942
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
Infect Genet Evol. 2004 Mar;4(1):37-43
pubmed: 15019588
Proc Natl Acad Sci U S A. 1998 Apr 28;95(9):5150-5
pubmed: 9560244
Genetics. 2021 Jun 24;218(2):
pubmed: 33837402
Proc Natl Acad Sci U S A. 2002 Dec 10;99(25):16144-9
pubmed: 12446845
Antimicrob Agents Chemother. 1997 Oct;41(10):2229-37
pubmed: 9333053
Clin Infect Dis. 1997 Oct;25(4):908-10
pubmed: 9356806
Antimicrob Agents Chemother. 2020 Dec 16;65(1):
pubmed: 33077664
G3 (Bethesda). 2016 Aug 09;6(8):2421-34
pubmed: 27317778
PLoS Biol. 2017 Jun 27;15(6):e2001333
pubmed: 28654659
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
Bioinformatics. 2009 Jul 15;25(14):1754-60
pubmed: 19451168
Microbiology (Reading). 2012 Sep;158(Pt 9):2325-2335
pubmed: 22790396
mBio. 2015 Oct 13;6(5):e01340-15
pubmed: 26463162
Genome Med. 2014 Nov 20;6(11):100
pubmed: 25505934
PLoS Biol. 2018 Dec 18;16(12):e3000069
pubmed: 30562346
Mol Microbiol. 2008 May;68(3):624-41
pubmed: 18363649
Bioinformatics. 2012 Oct 15;28(20):2678-9
pubmed: 22914218
Elife. 2019 Jun 07;8:
pubmed: 31172944
Antimicrob Agents Chemother. 1998 Oct;42(10):2584-9
pubmed: 9756759
Elife. 2020 Jul 20;9:
pubmed: 32687060
Proc Natl Acad Sci U S A. 2018 Nov 20;115(47):12040-12045
pubmed: 30389707
PLoS Genet. 2008 Dec;4(12):e1000303
pubmed: 19079573
Bioinformatics. 2011 Aug 1;27(15):2156-8
pubmed: 21653522
PLoS Biol. 2014 Mar 18;12(3):e1001815
pubmed: 24642609
PLoS Genet. 2009 Oct;5(10):e1000705
pubmed: 19876375
Curr Protoc Microbiol. 2018 Aug;50(1):e58
pubmed: 30028911
G3 (Bethesda). 2014 Mar 20;4(3):399-409
pubmed: 24368781
Curr Protoc Bioinformatics. 2013;43:11.10.1-11.10.33
pubmed: 25431634
PLoS Pathog. 2010 Jun 17;6(6):e1000953
pubmed: 20585559
Antimicrob Agents Chemother. 2001 Jan;45(1):52-9
pubmed: 11120944
BMC Genomics. 2011 Oct 27;12:526
pubmed: 22032296
PLoS Pathog. 2010 Apr 01;6(4):e1000848
pubmed: 20368972
Elife. 2015 Feb 03;4:e00662
pubmed: 25646566
Genetics. 2015 Jul;200(3):781-94
pubmed: 25991822