LongPhase-S: purity estimation and variant recalibration with somatic haplotying for long-read sequencing

Abstract

Accurate detection of somatic variants is crucial for precision oncology, and long-read sequencing offers unprecedented advantages in resolving complex cancer genomes. However, most long-read somatic callers rely on phasing built for a diploid genome, an assumption violated by various contamination, subclonal heterogeneity, and aneuploidy in tumors. We present LongPhase-S, a novel method that jointly reconstructs somatic haplotypes, infers tumor purity, and recalibrates somatic variants in a purity-aware manner for paired tumor-normal long-read sequencing. By anchoring each somatic read to a parental germline lin-eage, LongPhase-S provides a phase-resolved view in which germline and somatic reads are disentangled across the genome. Building on somatic haplotyping, LongPhase-S trains a phase-aware purity estimator that outperformed existing methods. Using eight benchmark datasets comprising six cancer cell lines, including breast, melanoma, and lung cancers, LongPhase-S boosted the accuracy of state-of-the-art somatic callers wuth the estimated purity and somatic haplotypes. Specifically, mean F1 scores increased by 4.5% and 7.1% for single-nucleotide variants and insertions and deletions with ClairS, and by 1.2% and 0.5% with DeepSomatic. Collectively, these results showed that somatic haplotyping is a critical yet missing piece in existing somatic callers, which enables purity-aware and phase-resolved variant interpretation in heterogneous tumors.