Personalized reference genome-based pipeline reveals comprehensive haplotype-resolved views of cancer genomes.

PRCGAP: first pipeline integrating haplotype-resolved analysis of somatic point mutations, SV, CNV, and DNA methylation on a personalized diploid reference genome

PRCGAP (Personalized Reference genome-based Cancer Genome Analysis Pipeline) is the first pipeline integrating comprehensive haplotype-resolved analysis — somatic point mutations, structural variants, copy number, and DNA methylation — on personalized diploid reference genomes. Applied to 8 tumor-normal pairs and 3 pediatric B-ALL clinical samples, it detects variants missed by GRCh38 or T2T-CHM13 pipelines in repetitive or individual-specific regions.

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Using a personalized reference genome represents the next level of analytical sophistication beyond T2T-CHM13. PRCGAP demonstrates that regions unresolved by standard references harbor clinically relevant variants — particularly in pediatric oncology. An ambitious pipeline to monitor for larger-scale validation and potential integration into genomic medicine centers.

Clinical impact: 2/3 · Evidence strength: 2/3 · Novelty: 2/2 · Sample size: 1/1 · Publication status: -1/1 → Total: 6/10