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Combining chromosome conformation capture and exome sequencing for simultaneous detection of structural and single-nucleotide variants. / Gridina, Maria; Lagunov, Timofey; Belokopytova, Polina и др.

в: Genome Medicine, Том 17, № 1, 47, 07.05.2025.

Результаты исследований: Научные публикации в периодических изданиях › статья › Рецензирование

Harvard

Gridina, M, Lagunov, T, Belokopytova, P, Torgunakov, N, Nuriddinov, M, Nurislamov, A, Nazarenko, LP, Kashevarova, AA, Lopatkina, ME, Vasilyev, S, Zuev, A, Belyaeva, EO, Salyukova, OA, Cheremnykh, AD, Sukhanova, NN, Minzhenkova, ME, Markova, ZG, Demina, NA, Stepanchuk, Y, Khabarova, A, Yan, A, Valeev, E, Koksharova, G, Grigor’eva, EV, Kokh, N, Lukjanova, T, Maximova, Y, Musatova, E, Shabanova, E, Kechin, A, Khrapov, E, Boyarskih, U, Ryzhkova, O, Suntsova, M, Matrosova, A, Karoli, M, Manakhov, A, Filipenko, M, Rogaev, E, Shilova, NV, Lebedev, IN & Fishman, V 2025, 'Combining chromosome conformation capture and exome sequencing for simultaneous detection of structural and single-nucleotide variants', Genome Medicine, Том. 17, № 1, 47. https://doi.org/10.1186/s13073-025-01471-3

APA

Gridina, M., Lagunov, T., Belokopytova, P., Torgunakov, N., Nuriddinov, M., Nurislamov, A., Nazarenko, L. P., Kashevarova, A. A., Lopatkina, M. E., Vasilyev, S., Zuev, A., Belyaeva, E. O., Salyukova, O. A., Cheremnykh, A. D., Sukhanova, N. N., Minzhenkova, M. E., Markova, Z. G., Demina, N. A., Stepanchuk, Y., ... Fishman, V. (2025). Combining chromosome conformation capture and exome sequencing for simultaneous detection of structural and single-nucleotide variants. Genome Medicine, 17(1), [47]. https://doi.org/10.1186/s13073-025-01471-3

Vancouver

Gridina M, Lagunov T, Belokopytova P, Torgunakov N, Nuriddinov M, Nurislamov A и др. Combining chromosome conformation capture and exome sequencing for simultaneous detection of structural and single-nucleotide variants. Genome Medicine. 2025 май 7;17(1):47. doi: 10.1186/s13073-025-01471-3

Author

Gridina, Maria ; Lagunov, Timofey ; Belokopytova, Polina и др. / Combining chromosome conformation capture and exome sequencing for simultaneous detection of structural and single-nucleotide variants. в: Genome Medicine. 2025 ; Том 17, № 1.

BibTeX

@article{35e2ad1e71b145438ffe7bed3d0d46ac,
title = "Combining chromosome conformation capture and exome sequencing for simultaneous detection of structural and single-nucleotide variants",
abstract = "Background: Effective molecular diagnosis of congenital diseases hinges on comprehensive genomic analysis, traditionally reliant on various methodologies specific to each variant type—whole exome or genome sequencing for single nucleotide variants (SNVs), array CGH for copy-number variants (CNVs), and microscopy for structural variants (SVs). Methods: We introduce a novel, integrative approach combining exome sequencing with chromosome conformation capture, termed Exo-C. This method enables the concurrent identification of SNVs in clinically relevant genes and SVs across the genome and allows analysis of heterozygous and mosaic carriers. Enhanced with targeted long-read sequencing, Exo-C evolves into a cost-efficient solution capable of resolving complex SVs at base-pair accuracy. Results: Applied to 66 human samples Exo-C achieved 100% recall and 73% precision in detecting chromosomal translocations and SNVs. We further benchmarked its performance for inversions and CNVs and demonstrated its utility in detecting mosaic SVs and resolving diagnostically challenging cases. Conclusions: Through several case studies, we demonstrate how Exo-C{\textquoteright}s multifaceted application can effectively uncover diverse causative variants and elucidate disease mechanisms in patients with rare disorders.",
author = "Maria Gridina and Timofey Lagunov and Polina Belokopytova and Nikita Torgunakov and Miroslav Nuriddinov and Artem Nurislamov and Nazarenko, {Lyudmila P.} and Kashevarova, {Anna A.} and Lopatkina, {Maria E.} and Stanislav Vasilyev and Andrey Zuev and Belyaeva, {Elena O.} and Salyukova, {Olga A.} and Cheremnykh, {Aleksandr D.} and Sukhanova, {Natalia N.} and Minzhenkova, {Marina E.} and Markova, {Zhanna G.} and Demina, {Nina A.} and Yana Stepanchuk and Anna Khabarova and Alexandra Yan and Emil Valeev and Galina Koksharova and Grigor{\textquoteright}eva, {Elena V.} and Natalia Kokh and Tatiana Lukjanova and Yulia Maximova and Elizaveta Musatova and Elena Shabanova and Andrey Kechin and Evgeniy Khrapov and Uliana Boyarskih and Oxana Ryzhkova and Maria Suntsova and Alina Matrosova and Mikhail Karoli and Andrey Manakhov and Maxim Filipenko and Evgeny Rogaev and Shilova, {Nadezhda V.} and Lebedev, {Igor N.} and Veniamin Fishman",
note = "The study was supported by the Russian Science Foundation (#21–65 - 00017), https://rscf.ru/project/21-65-00017/. Study of P123 and Exo-C profiling of cancer cell lines A549 and K562 was supported by the grant of the state program of the “Sirius” Federal Territory “Scientific and technological development of the “Sirius” Federal Territory” (Agreement №26–03, 27/09/2024).",
year = "2025",
month = may,
day = "7",
doi = "10.1186/s13073-025-01471-3",
language = "English",
volume = "17",
journal = "Genome Medicine",
issn = "1756-994X",
publisher = "Springer Nature",
number = "1",

}

RIS

TY - JOUR

T1 - Combining chromosome conformation capture and exome sequencing for simultaneous detection of structural and single-nucleotide variants

AU - Gridina, Maria

AU - Lagunov, Timofey

AU - Belokopytova, Polina

AU - Torgunakov, Nikita

AU - Nuriddinov, Miroslav

AU - Nurislamov, Artem

AU - Nazarenko, Lyudmila P.

AU - Kashevarova, Anna A.

AU - Lopatkina, Maria E.

AU - Vasilyev, Stanislav

AU - Zuev, Andrey

AU - Belyaeva, Elena O.

AU - Salyukova, Olga A.

AU - Cheremnykh, Aleksandr D.

AU - Sukhanova, Natalia N.

AU - Minzhenkova, Marina E.

AU - Markova, Zhanna G.

AU - Demina, Nina A.

AU - Stepanchuk, Yana

AU - Khabarova, Anna

AU - Yan, Alexandra

AU - Valeev, Emil

AU - Koksharova, Galina

AU - Grigor’eva, Elena V.

AU - Kokh, Natalia

AU - Lukjanova, Tatiana

AU - Maximova, Yulia

AU - Musatova, Elizaveta

AU - Shabanova, Elena

AU - Kechin, Andrey

AU - Khrapov, Evgeniy

AU - Boyarskih, Uliana

AU - Ryzhkova, Oxana

AU - Suntsova, Maria

AU - Matrosova, Alina

AU - Karoli, Mikhail

AU - Manakhov, Andrey

AU - Filipenko, Maxim

AU - Rogaev, Evgeny

AU - Shilova, Nadezhda V.

AU - Lebedev, Igor N.

AU - Fishman, Veniamin

N1 - The study was supported by the Russian Science Foundation (#21–65 - 00017), https://rscf.ru/project/21-65-00017/. Study of P123 and Exo-C profiling of cancer cell lines A549 and K562 was supported by the grant of the state program of the “Sirius” Federal Territory “Scientific and technological development of the “Sirius” Federal Territory” (Agreement №26–03, 27/09/2024).

PY - 2025/5/7

Y1 - 2025/5/7

N2 - Background: Effective molecular diagnosis of congenital diseases hinges on comprehensive genomic analysis, traditionally reliant on various methodologies specific to each variant type—whole exome or genome sequencing for single nucleotide variants (SNVs), array CGH for copy-number variants (CNVs), and microscopy for structural variants (SVs). Methods: We introduce a novel, integrative approach combining exome sequencing with chromosome conformation capture, termed Exo-C. This method enables the concurrent identification of SNVs in clinically relevant genes and SVs across the genome and allows analysis of heterozygous and mosaic carriers. Enhanced with targeted long-read sequencing, Exo-C evolves into a cost-efficient solution capable of resolving complex SVs at base-pair accuracy. Results: Applied to 66 human samples Exo-C achieved 100% recall and 73% precision in detecting chromosomal translocations and SNVs. We further benchmarked its performance for inversions and CNVs and demonstrated its utility in detecting mosaic SVs and resolving diagnostically challenging cases. Conclusions: Through several case studies, we demonstrate how Exo-C’s multifaceted application can effectively uncover diverse causative variants and elucidate disease mechanisms in patients with rare disorders.

AB - Background: Effective molecular diagnosis of congenital diseases hinges on comprehensive genomic analysis, traditionally reliant on various methodologies specific to each variant type—whole exome or genome sequencing for single nucleotide variants (SNVs), array CGH for copy-number variants (CNVs), and microscopy for structural variants (SVs). Methods: We introduce a novel, integrative approach combining exome sequencing with chromosome conformation capture, termed Exo-C. This method enables the concurrent identification of SNVs in clinically relevant genes and SVs across the genome and allows analysis of heterozygous and mosaic carriers. Enhanced with targeted long-read sequencing, Exo-C evolves into a cost-efficient solution capable of resolving complex SVs at base-pair accuracy. Results: Applied to 66 human samples Exo-C achieved 100% recall and 73% precision in detecting chromosomal translocations and SNVs. We further benchmarked its performance for inversions and CNVs and demonstrated its utility in detecting mosaic SVs and resolving diagnostically challenging cases. Conclusions: Through several case studies, we demonstrate how Exo-C’s multifaceted application can effectively uncover diverse causative variants and elucidate disease mechanisms in patients with rare disorders.

UR - https://www.mendeley.com/catalogue/bf4fd420-2d49-3ce3-89de-325f5ae5675a/

UR - https://www.scopus.com/record/display.uri?eid=2-s2.0-105004469904&origin=inward&txGid=8af7753f39fca68983760c40ddd11f80

U2 - 10.1186/s13073-025-01471-3

DO - 10.1186/s13073-025-01471-3

M3 - Article

C2 - 40336115

VL - 17

JO - Genome Medicine

JF - Genome Medicine

SN - 1756-994X

IS - 1

M1 - 47

ER -

ID: 66251291