Diagnostics of hereditary cancer syndromes by ngs. A database creation experience
- Authors: Abramov I.S.1, Lisitsa T.S.1, Stroganova A.M.2, Ryabaya O.O.2, Danishevich A.M.3, Khakhina A.O.1, Zakamornaya A.I.1, Matsvay A.D.1, Shipulin G.A.1
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Affiliations:
- Centre for Strategic Planning and Management of Biomedical Health Risks of the Federal Medical Biological Agency
- N.N. Blokhin National Medical Research Center of Oncology
- Moscow Clinical Scientific Center
- Issue: Vol 12, No 3 (2021)
- Pages: 36-42
- Section: Original Study Articles
- URL: https://journals.rcsi.science/clinpractice/article/view/76383
- DOI: https://doi.org/10.17816/clinpract76383
- ID: 76383
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Abstract
Background: More than 500 thousand new cases of malignant neoplasms are registered annually in the Russian Federation, of which more than 50 thousand new cases are due to hereditary forms. Improving the diagnosis of these diseases will make it possible to detect tumors at the early stages and take timely preventive and therapeutic measures.
Aims: Creation of a database and development of a software for the NGS data analysis for the prevention and early diagnosis of hereditary forms of oncological diseases.
Methods: The present study used 636 DNA samples obtained from cancer patients with a high hereditary risk or a burdened family history. DNA was isolated from blood lymphocytes. DNA libraries were prepared with a KAPA Target Enrichment Panel (Roche). The panel included probes for targeted enrichment of the coding region of 44 genes. NGS was performed on the MiSeq platform (Illumina).
Results: We identified 65 pathogenic/ probably pathogenic nucleotide sequence variants in 96 patients in the ATM, BLM, BRCA1, BRCA2, CHEK2, EPCAM, MEN1, MLH1, MSH2, MSH3, MSH6, MUTYH, PALB2, TP53 genes. We also identified 2858 nucleotide sequence variants of unknown clinical significance. Conclusions: We have created a local database that contains both genetic variants and clinical and anamnestic data. The database contains 4763 nucleotide sequence variants at the moment, among which 2522 are unique variants identified in a single patient.
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##article.viewOnOriginalSite##About the authors
Ivan S. Abramov
Centre for Strategic Planning and Management of Biomedical Health Risks of the Federal Medical Biological Agency
Author for correspondence.
Email: IAbramov@cspmz.ru
ORCID iD: 0000-0002-6954-1564
SPIN-code: 1436-3601
Russian Federation, 10 bild. 1, Pogodinskaya street, 119121, Moscow
Tatyana S. Lisitsa
Centre for Strategic Planning and Management of Biomedical Health Risks of the Federal Medical Biological Agency
Email: Tlisitsa@cspmz.ru
ORCID iD: 0000-0002-6212-7627
SPIN-code: 2289-4331
Russian Federation, 10 bild. 1, Pogodinskaya street, 119121, Moscow
Anna M. Stroganova
N.N. Blokhin National Medical Research Center of Oncology
Email: stroganova_am@mail.ru
ORCID iD: 0000-0002-7297-5240
SPIN-code: 5295-3338
MD, Cand. Sci. (Med.)
Russian Federation, MoscowOxana O. Ryabaya
N.N. Blokhin National Medical Research Center of Oncology
Email: oxa2601@yandex.ru
ORCID iD: 0000-0001-6295-3497
SPIN-code: 4865-5850
Cand. Sci. (Biol.)
Russian Federation, MoscowAnastasiya M. Danishevich
Moscow Clinical Scientific Center
Email: danisham7@gmail.com
ORCID iD: 0000-0002-3573-8342
SPIN-code: 3195-1760
Russian Federation, Moscow
Anastasia O. Khakhina
Centre for Strategic Planning and Management of Biomedical Health Risks of the Federal Medical Biological Agency
Email: AKhakhina@cspmz.ru
ORCID iD: 0000-0002-0723-9765
SPIN-code: 2922-9674
Russian Federation, 10 bild. 1, Pogodinskaya street, 119121, Moscow
Anastasiya I. Zakamornaya
Centre for Strategic Planning and Management of Biomedical Health Risks of the Federal Medical Biological Agency
Email: AZakamornaya@cspmz.ru
ORCID iD: 0000-0001-5151-0236
SPIN-code: 6263-9686
Russian Federation, 10 bild. 1, Pogodinskaya street, 119121, Moscow
Alina D. Matsvay
Centre for Strategic Planning and Management of Biomedical Health Risks of the Federal Medical Biological Agency
Email: AMatsvay@cspmz.ru
ORCID iD: 0000-0002-6301-9169
SPIN-code: 2679-3183
Russian Federation, 10 bild. 1, Pogodinskaya street, 119121, Moscow
German A. Shipulin
Centre for Strategic Planning and Management of Biomedical Health Risks of the Federal Medical Biological Agency
Email: shipulin@cspmz.ru
ORCID iD: 0000-0002-3668-6601
SPIN-code: 1908-9098
Russian Federation, 10 bild. 1, Pogodinskaya street, 119121, Moscow
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