Analysis method based on the gene-panel sequencing data / 上海交通大学学报（医学版）

ABSTRACT

Objective· To establish an integrative method for the gene-panel sequencing data to automatically complete quality control, detection of gene mutation and visualization. Methods · Integrate several methods, e.g. FastQC, preprocessing and information of sequences (Prinseq) to develop an R package that can be used to visualize and control the quality of the raw sequencing reads and final mutations result. The sequencing reads mapped against to the reference genome using Burrows-Wheeler Alignment Tool (BWA)/Torrent Mapping Alignment Program (TMAP). Lofreq, Varscan2, the Genome Analysis Toolkit (GATK) and Torrent Variant Caller (TVC) were used to detect gene mutation and get the variant call format (VCF) format file. Annotate the gene mutation sites using Annovar. Results · Thirty-six cases of acute myeloid leukemia sequencing from Ion Torrent Personal Genome Machine (PGM) platform were passed by this analysis tool.Ten mutation sites of 2 demo data were found in DNMT3A,TET2,JAK2,PHF6,ASXL1,NPM1 and CEBPA which were validated by sanger sequencing. Conclusion · The analysis method that integrated and developed several tools for gene-panel sequencing data analysis can accomplish the gene-panel sequencing data analysis effectively. Besides, it can reduce the false positive ratio and improve the sensitivity of gene mutation detection that provides support for the analysis of gene-panel sequencing data.