WHOLE GENOME SEQUENCING DATA PROCESSING SYSTEM Russian patent published in 2023 - IPC G16B50/30 

FIELD: biotechnology.

SUBSTANCE: data processing system (pipeline) for whole-genome sequencing and is intended for automatic analysis of germinal samples with an average coverage of 30x from a set of raw reads to results ready for analysis by a clinical interpreter. The whole-genome sequencing data processing system includes interconnected modules: the SNP/INDELS module, designed for mapping reads to the reference genome and genotyping vcf and INDELS and consisting of blocks, one of which provides mapping of the original reads submitted in pairs in .fastq.gz format to the reference human genome (hg19 or hg38, as selected) with obtaining a file in bam format, the second one carries out SNP/INDELS collating and generates vcf and, optionally gvcf, files containing information on polymorphisms of the analysed sample, the third one collects statistics on the completion of each step of the SNP/INDELS module and generates a separate report in html format for quality control of analysed samples; the cohort collating module takes as input a set of .gvcf files obtained after running the SNP/INDELS search module on several samples and returns a single .vcf file containing the resulting SNP/INDELS set for all samples; the SNP/INDELS annotation module is launched separately for each received .vcf file, and for each variant recorded in the .vcf file, the module matches information from various databases containing clinically relevant information about the variants, and also aggregates it into ACMG rank; module for determining Mt and Y haplogroups.

EFFECT: expanded functionality for analysing data from the complete human genome while reducing the time to obtain genetic analysis results ready for interpretation.

6 cl, 7 dwg, 2 tbl