Whole-exome DNA and RNA sequencing
tumor
TUMOR
DNA sequencing was performed by generating two groups of double-ended sequencing results, corresponding to the collected tumor and blood cells (normal samples), in FASTQ format in Illumina HiSeq X10 platform (paired-end run, 150 bp). Fastp (Fastp v0.16.0) was used to control the quality of the original sequencing data and filter the low-quality data. Burrows-Wheeler Aligner (BWA-MEM, v.0.7.17-r1188) was used to compare the filtered clean reads with GRCh38/hg38 human reference genome to generate the sequence alignment map (SAM) file. Two groups of BAM files were obtained by utilizing SAMtools (v1.7–2) to convert SAM files into binary alignment map (BAM) files and establish indexes. The Genome Analysis Toolkit (GATK, v.4.1.3.0) was utilized for the removal of the variations from the DNA sequencing results.For RNA sequencing, terminal sequencing results, corresponding to the collected tumor tissues, in FASTQ format were generated in Illumina HiSeq X10 platform (paired-end run, 150 bp). Fastp (Fastp v0.16.0) was utilized to control the quality of RNA sequencing data and filter low-quality data. The STAR software (2.6.0a) was utilized to compare the filtered clean reads with GRCh38/hg38 human reference genome to generate a SAM file. Based on SAMtools (V1.7), the SAM file was converted into a BAM file, and indexes were established. The Genome Analysis Toolkit (GATK, v.4.1.3.0) was utilized for detecting the variations in the RNA sequencing results.