HATCHet2: clone- and haplotype-specific copy number inference from bulk tumor sequencing data.
Genome Biol
; 25(1): 130, 2024 05 21.
Article
en En
| MEDLINE
| ID: mdl-38773520
ABSTRACT
Bulk DNA sequencing of multiple samples from the same tumor is becoming common, yet most methods to infer copy-number aberrations (CNAs) from this data analyze individual samples independently. We introduce HATCHet2, an algorithm to identify haplotype- and clone-specific CNAs simultaneously from multiple bulk samples. HATCHet2 extends the earlier HATCHet method by improving identification of focal CNAs and introducing a novel statistic, the minor haplotype B-allele frequency (mhBAF), that enables identification of mirrored-subclonal CNAs. We demonstrate HATCHet2's improved accuracy using simulations and a single-cell sequencing dataset. HATCHet2 analysis of 10 prostate cancer patients reveals previously unreported mirrored-subclonal CNAs affecting cancer genes.
Palabras clave
Texto completo:
1
Banco de datos:
MEDLINE
Asunto principal:
Neoplasias de la Próstata
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Algoritmos
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Haplotipos
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Variaciones en el Número de Copia de ADN
Límite:
Humans
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Male
Idioma:
En
Año:
2024
Tipo del documento:
Article