TY - JOUR

T1 - Modification of the Hi-C Technology for Molecular Genetic Analysis of Formalin-Fixed Paraffin-Embedded Sections of Tumor Tissues

AU - Gridina, Maria M.

AU - Stepanchuk, Yana K.

AU - Nurridinov, Miroslav A.

AU - Lagunov, Timofey A.

AU - Torgunakov, Nikita Yu

AU - Shadsky, Artem A.

AU - Ryabova, Anastasia I.

AU - Vasiliev, Nikolay V.

AU - Vtorushin, Sergey V.

AU - Gerashchenko, Tatyana S.

AU - Denisov, Evgeny V.

AU - Travin, Mikhail A.

AU - Korolev, Maxim A.

AU - Fishman, Veniamin S.

N1 - We express our gratitude to the Ministry of Science and Higher Education of the Russian Federation (state project FWNR-2022-0019) for providing access to computing power. Access to the public resources and datasets was provided by Novosibirsk State University with the support of the Minis Ministry of Science and Higher Education of the Russian Federation (grant no. 2019-0546; FSUS-2024-0018). The research was supported by the Russian Science Foundation (project no. 22-24-00190). We express our gratitude to the Ministry of Science and Higher Education of the Russian Federation (state project FWNR-2022-0019) for providing access to computing power. Access to the public resources and datasets was provided by Novosibirsk State University with the support of the Minis Ministry of Science and Higher Education of the Russian Federation (grant no.\u00A02019-0546; FSUS-2024-0018).

PY - 2024/4

Y1 - 2024/4

N2 - Abstract: Molecular genetic analysis of tumor tissues is the most important step towards understanding the mechanisms of cancer development; it is also necessary for the choice of targeted therapy. The Hi-C (high-throughput chromatin conformation capture) technology can be used to detect various types of genomic variants, including balanced chromosomal rearrangements, such as inversions and translocations. We propose a modification of the Hi-C method for the analysis of chromatin contacts in formalin-fixed paraffin-embedded (FFPE) sections of tumor tissues. The developed protocol allows to generate high-quality Hi-C data and detect all types of chromosomal rearrangements. We have analyzed various databases to compile a comprehensive list of translocations that hold clinical importance for the targeted therapy selection. The practical value of molecular genetic testing is its ability to influence the treatment strategies and to provide prognostic insights. Detecting specific chromosomal rearrangements can guide the choice of the targeted therapies, which is a critical aspect of personalized medicine in oncology.

AB - Abstract: Molecular genetic analysis of tumor tissues is the most important step towards understanding the mechanisms of cancer development; it is also necessary for the choice of targeted therapy. The Hi-C (high-throughput chromatin conformation capture) technology can be used to detect various types of genomic variants, including balanced chromosomal rearrangements, such as inversions and translocations. We propose a modification of the Hi-C method for the analysis of chromatin contacts in formalin-fixed paraffin-embedded (FFPE) sections of tumor tissues. The developed protocol allows to generate high-quality Hi-C data and detect all types of chromosomal rearrangements. We have analyzed various databases to compile a comprehensive list of translocations that hold clinical importance for the targeted therapy selection. The practical value of molecular genetic testing is its ability to influence the treatment strategies and to provide prognostic insights. Detecting specific chromosomal rearrangements can guide the choice of the targeted therapies, which is a critical aspect of personalized medicine in oncology.

KW - FFPE sections

KW - chromosomal rearrangements

KW - oncology

KW - three-dimensional nuclear organization

UR - https://www.scopus.com/record/display.uri?eid=2-s2.0-85192188237&origin=inward&txGid=a96f525ce0db628ab23030a8fbfb41a5

UR - https://www.mendeley.com/catalogue/8099b6d1-1cfe-3517-8e6e-6ccf5fcfe03d/

U2 - 10.1134/S0006297924040047

DO - 10.1134/S0006297924040047

M3 - Article

C2 - 38831501

VL - 89

SP - 637

EP - 652

JO - Biochemistry (Moscow)

JF - Biochemistry (Moscow)

SN - 0006-2979

IS - 4

ER -