Cancer genome analysis relies on standard human reference genomes but detecting somatic alterations in highly repetitive or individual-specific regions remains challenging. We developed the Personalized Reference genome-based Cancer Genome Analysis Pipeline (PRCGAP), to our knowledge, the first comprehensive pipeline integrating haplotype-resolved analyses of somatic point mutations, structural variants, copy number, and DNA methylation on personalized diploid reference genomes. We applied PRCGAP to eight tumor-normal cell line pairs and three pediatric B-cell acute lymphoblastic leukemia (B-ALL) clinical samples. PRCGAP detected most variants identified by GRCh38- and T2T-CHM13-based pipelines while uncovering variants in centromeric and telomeric regions. Building on PRCGAP outputs, we identified L1 retrotransposition source sites absent from standard references and showed that the IGH::DUX4 fusion in a B-ALL sample originated from an internal DUX4 pseudogene within an internal D4Z4 repeat unit, rather than the canonical full-length DUX4 gene. PRCGAP extends comprehensive cancer genome analysis from cell lines to clinical settings.
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