Diagnostics of hereditary cancer syndromes by ngs. A database creation experience

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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.

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, Moscow

Oxana 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, Moscow

Anastasiya 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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Copyright (c) 2021 Abramov I.S., Lisitsa T.S., Stroganova A.M., Ryabaya O.O., Danishevich A.M., Khakhina A.O., Zakamornaya A.I., Matsvay A.D., Shipulin G.A.

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