Creating a public mutation database oncoBRCA: bioinformatic problems and solutions
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, the diagnosis of hereditary OC and BC is limited to the determination of the m...
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| Format: | Article |
| Language: | English |
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Eco-vector
2020-05-01
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| Series: | Клиническая практика |
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| Online Access: | https://journals.eco-vector.com/clinpractice/article/viewFile/25860/pdf |
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| author | A. G. Nikitin O. I. Brovkina D. S. Khodyrev Oleg Alexandrovich Gusev M. G. Gordiev |
| author_facet | A. G. Nikitin O. I. Brovkina D. S. Khodyrev Oleg Alexandrovich Gusev M. G. Gordiev |
| author_sort | A. G. Nikitin |
| collection | DOAJ |
| description | 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, the diagnosis of hereditary OC and BC is limited to the determination of the most frequent mutations (8 points) in BRCA1 and BRCA2 genes using PCR methods. However, the given mutations are frequent for Slavic population while in other populations of Russia they occur less often or do not occur at all. Aim. To reveal the landscape of hereditary pathogenic variants in the genes of the reparation system and develop methods for a fast analysis of the NGS data.
Methods. A panel of 34 genes of the reparation system was analyzed by next generation sequencing (NGS) 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 the frequencies of mutations and polymorphisms of the 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 the raw data to the final report.
Conclusions. The NGS method has created a possibility to identify rare mutations characteristic of different ethnic groups, which makes it possible to prescribe optimal chemotherapy and develop diagnostic methods of population screening for carrying gene mutations of the DNA repair system. The modern approaches to the analysis of genome sequencing data allowed reducing the time of obtaining the result to several hours after the analysis. |
| first_indexed | 2024-03-12T08:42:35Z |
| format | Article |
| id | doaj.art-1db3ad98139846e7bd0a2c37c72e31ed |
| institution | Directory Open Access Journal |
| issn | 2220-3095 2618-8627 |
| language | English |
| last_indexed | 2024-03-12T08:42:35Z |
| publishDate | 2020-05-01 |
| publisher | Eco-vector |
| record_format | Article |
| series | Клиническая практика |
| spelling | doaj.art-1db3ad98139846e7bd0a2c37c72e31ed2023-09-02T16:36:28ZengEco-vectorКлиническая практика2220-30952618-86272020-05-01111212910.17816/clinpract2586023543Creating a public mutation database oncoBRCA: bioinformatic problems and solutionsA. G. Nikitin0https://orcid.org/0000-0001-9762-3383O. I. Brovkina1https://orcid.org/0000-0002-0946-7331D. S. Khodyrev2Oleg Alexandrovich Gusev3https://orcid.org/0000-0002-6203-9758M. G. Gordiev4Federal Scientific and Clinical Center of Specialized Types of Medical Care and Medical Technologies of the Federal Medical and Biological Agency of RussiaFederal Scientific and Clinical Center of Specialized Types of Medical Care and Medical Technologies of the Federal Medical and Biological Agency of RussiaFederal Scientific and Clinical Center of Specialized Types of Medical Care and Medical Technologies of the Federal Medical and Biological Agency of RussiaKazan’ (Volga region) Federal UniversityNational BioServiceBackground. 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, the diagnosis of hereditary OC and BC is limited to the determination of the most frequent mutations (8 points) in BRCA1 and BRCA2 genes using PCR methods. However, the given mutations are frequent for Slavic population while in other populations of Russia they occur less often or do not occur at all. Aim. To reveal the landscape of hereditary pathogenic variants in the genes of the reparation system and develop methods for a fast analysis of the NGS data. Methods. A panel of 34 genes of the reparation system was analyzed by next generation sequencing (NGS) 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 the frequencies of mutations and polymorphisms of the 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 the raw data to the final report. Conclusions. The NGS method has created a possibility to identify rare mutations characteristic of different ethnic groups, which makes it possible to prescribe optimal chemotherapy and develop diagnostic methods of population screening for carrying gene mutations of the DNA repair system. The modern approaches to the analysis of genome sequencing data allowed reducing the time of obtaining the result to several hours after the analysis.https://journals.eco-vector.com/clinpractice/article/viewFile/25860/pdfcancergeneticshereditymutation |
| spellingShingle | A. G. Nikitin O. I. Brovkina D. S. Khodyrev Oleg Alexandrovich Gusev M. G. Gordiev Creating a public mutation database oncoBRCA: bioinformatic problems and solutions Клиническая практика cancer genetics heredity mutation |
| title | Creating a public mutation database oncoBRCA: bioinformatic problems and solutions |
| title_full | Creating a public mutation database oncoBRCA: bioinformatic problems and solutions |
| title_fullStr | Creating a public mutation database oncoBRCA: bioinformatic problems and solutions |
| title_full_unstemmed | Creating a public mutation database oncoBRCA: bioinformatic problems and solutions |
| title_short | Creating a public mutation database oncoBRCA: bioinformatic problems and solutions |
| title_sort | creating a public mutation database oncobrca bioinformatic problems and solutions |
| topic | cancer genetics heredity mutation |
| url | https://journals.eco-vector.com/clinpractice/article/viewFile/25860/pdf |
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