Creating a public mutation database oncoBRCA: bioinformatic problems and solutions

Abstract

Background: the development of hereditary cancer syndromes is caused by genetic disorders in the DNA repair system, which consists of more than 100 genes. However, at present, in the majority of medical centers in Russia, diagnosis of hereditary OC and BC is to determine the most frequent mutations (8 points) in BRCA1 and BRCA2 genes using PCR methods. Thus the given mutations are frequent for Slavic population while in other populations of Russia they occur less often or do not occur at all. Aims: to reveal the landscape of hereditary pathogenic variants in the genes of reparation system and develop methods of quick analysis of the NGS data. Materials and methods: by next generation sequencing (NGS) a panel of 34 genes of the reparation system was analyzed in 1644 samples of patients with inherited cancer syndromes. Results: the NGS analysis revealed 119 pathogenic mutations of BRCA1/BRCA2 genes in 374 patients, with a marked difference in mutation frequencies between different ethnic groups - Slavs, Tatars, Bashkirs and Chuvash. A public database of frequencies of mutations and polymorphisms of genes of the DNA reparation system in different ethnoses was created at https://oncobrca.ru. Methods were created for automatic parallel processing of any number of samples from raw data to the final report. Conclusions: with the NGS method it became possible to identify rare mutations characteristic of different ethnic groups, which makes it possible to prescribe optimal chemotherapy and develop diagnostic methods of population screening of gene mutation carrier of DNA repair system. Modern approaches to the analysis of genome sequencing data allowed reducing the time of obtaining the result to several hours after the analysis.