IHC analysis and WES analysis
Tumor
SOMATIC MUTATION, TUMOR, MUTATION
Tumor tissues of each patient were obtained by biopsy and embedded by paraffin. The presence of PD-L1 and PD-1 was investigated by IHC staining with corresponding primary antibody as previously.DNA in paraffin-embedded biopsy tissues from each subject was extracted. Sequencing libraries were prepared and whole-exome-sequenced according to the instructions of manufacturer. The raw data of WES have been uploaded in the OMIX, China National Center for Bioinformation/Beijing Institute of Genomics, Chinese Academy of Sciences (Mutation calling by Trimmomatic was used as quality control of FASTQ. Paired-end reads were then aligned to the human reference genome (hg19) using the Burrows–Wheeler aligner (BWA). Somatic mutations were first acquired for each sample. All single nucleotide variants (SNVs)/indels were annotated by ANNOVAR, and each SNV/indel was manually examined in the Integrative Genomics Viewer (IGV). Copy number variations (CNVs) were analyzed using in-house software. Mutations in 15 genes related to microsatellites (MS) were analyzed, and ≥30% of mutations were defined as MSI-h. Mutations in DDR-related genes were analyzed.