GRIDSS2: comprehensive characterisation of somatic structural variation using single breakend variants and structural variant phasing.
Journal
Genome biology
ISSN: 1474-760X
Titre abrégé: Genome Biol
Pays: England
ID NLM: 100960660
Informations de publication
Date de publication:
12 07 2021
12 07 2021
Historique:
received:
21
01
2021
accepted:
30
06
2021
entrez:
13
7
2021
pubmed:
14
7
2021
medline:
22
1
2022
Statut:
epublish
Résumé
GRIDSS2 is the first structural variant caller to explicitly report single breakends-breakpoints in which only one side can be unambiguously determined. By treating single breakends as a fundamental genomic rearrangement signal on par with breakpoints, GRIDSS2 can explain 47% of somatic centromere copy number changes using single breakends to non-centromere sequence. On a cohort of 3782 deeply sequenced metastatic cancers, GRIDSS2 achieves an unprecedented 3.1% false negative rate and 3.3% false discovery rate and identifies a novel 32-100 bp duplication signature. GRIDSS2 simplifies complex rearrangement interpretation through phasing of structural variants with 16% of somatic calls phasable using paired-end sequencing.
Identifiants
pubmed: 34253237
doi: 10.1186/s13059-021-02423-x
pii: 10.1186/s13059-021-02423-x
pmc: PMC8274009
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
202Informations de copyright
© 2021. The Author(s).
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