PM Exome-seq
Exome capture was performed using the Agilent SureSelect XT HS2 kit targeting the Human Exome V7 regions. Libraries were sequenced on an Illumina NovaSeq 6000 using paired-end 100 bp reads to a target depth of approximately 100× for tumor samples and 30× for normal samples. Multiple sequencing lanes were used for some samples to achieve adequate coverage, and FASTQ files were merged prior to downstream analysis.  Sequencing data were processed using a tumor–normal variant calling workflow following Broad Institute best practices. Reads were aligned to the hg38 reference genome using BWA. Somatic variants were identified using Mutect2, and variant annotation was performed using SnpEff and SnpSift. Copy number variation, loss of heterozygosity, and tumor purity were estimated using Sequenza based on tumor and normal coverage and allele frequency information. High-confidence somatic variants were filtered to retain calls with tumor allele frequency >0.1 and minimum tumor read depth of 10.