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HATCHet2: clone- and haplotype-specific copy number inference from bulk tumor sequencing data.

ABSTRACT: Multi-region DNA sequencing of primary tumors and metastases from individual patients helps identify somatic aberrations driving cancer development. However, most methods to infer copy-number aberrations (CNAs) analyze individual samples. We introduce HATCHet2 to identify haplotype- and clone-specific CNAs simultaneously from multiple bulk samples. HATCHet2 introduces a novel statistic, the mirrored haplotype B-allele frequency (mhBAF), to identify mirrored-subclonal CNAs having different numbers of copies of parental haplotypes in different tumor clones. HATCHet2 also has high accuracy in identifying focal CNAs and extends the earlier HATCHet method in several directions. We demonstrate HATCHet2's improved accuracy using simulations and a single-cell sequencing dataset. HATCHet2 analysis of 50 prostate cancer samples from 10 patients reveals previously-unreported mirrored-subclonal CNAs affecting cancer genes.

SUBMITTER: Myers MA 

PROVIDER: S-EPMC10370020 | biostudies-literature | 2023 Jul

REPOSITORIES: biostudies-literature

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HATCHet2: clone- and haplotype-specific copy number inference from bulk tumor sequencing data.

Myers Matthew A MA   Arnold Brian J BJ   Bansal Vineet V   Mullen Katelyn M KM   Zaccaria Simone S   Raphael Benjamin J BJ  

bioRxiv : the preprint server for biology 20230715

Multi-region DNA sequencing of primary tumors and metastases from individual patients helps identify somatic aberrations driving cancer development. However, most methods to infer copy-number aberrations (CNAs) analyze individual samples. We introduce HATCHet2 to identify haplotype- and clone-specific CNAs simultaneously from multiple bulk samples. HATCHet2 introduces a novel statistic, the mirrored haplotype B-allele frequency (mhBAF), to identify mirrored-subclonal CNAs having different number  ...[more]

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