%0 Journal Article
%T HATCHet2: clone- and haplotype-specific copy number inference from bulk tumor sequencing data.
%A Myers MA
%A Arnold BJ
%A Bansal V
%A Balaban M
%A Mullen KM
%A Zaccaria S
%A Raphael BJ
%J Genome Biol
%V 25
%N 1
%D 2024 05 21
%M 38773520
暂无%R 10.1186/s13059-024-03267-x
%X 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.