Unscrambling cancer genomes via integrated analysis of structural variation and copy number.
LINX
cancer genomics
ecDNA
gene fusion
genomic rearrangement
genomic shard
homozygous disruption
mobile element insertion
reciprocal duplication
structural variation
Journal
Cell genomics
ISSN: 2666-979X
Titre abrégé: Cell Genom
Pays: United States
ID NLM: 9918284260106676
Informations de publication
Date de publication:
13 Apr 2022
13 Apr 2022
Historique:
received:
13
01
2021
revised:
29
09
2021
accepted:
25
02
2022
entrez:
13
2
2023
pubmed:
14
2
2023
medline:
14
2
2023
Statut:
epublish
Résumé
Complex somatic genomic rearrangements and copy number alterations are hallmarks of nearly all cancers. We have developed an algorithm, LINX, to aid interpretation of structural variant and copy number data derived from short-read, whole-genome sequencing. LINX classifies raw structural variant calls into distinct events and predicts their effect on the local structure of the derivative chromosome and the functional impact on affected genes. Visualizations facilitate further investigation of complex rearrangements. LINX allows insights into a diverse range of structural variation events and can reliably detect pathogenic rearrangements, including gene fusions, immunoglobulin enhancer rearrangements, intragenic deletions, and duplications. Uniquely, LINX also predicts chained fusions that we demonstrate account for 13% of clinically relevant oncogenic fusions. LINX also reports a class of inactivation events that we term homozygous disruptions that may be a driver mutation in up to 9% of tumors and may frequently affect
Identifiants
pubmed: 36776527
doi: 10.1016/j.xgen.2022.100112
pii: S2666-979X(22)00032-5
pmc: PMC9903802
doi:
Types de publication
Journal Article
Langues
eng
Pagination
100112Informations de copyright
© 2022 The Author(s).
Déclaration de conflit d'intérêts
The authors declare no competing interests.
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