Evidence map›Paper›PMID 40336115›Full record

ArticleGenome medicine2025

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

Maria Gridina, Timofey Lagunov, Polina Belokopytova, Nikita Torgunakov, Miroslav Nuriddinov, Artem Nurislamov, Lyudmila P Nazarenko, Anna A Kashevarova, Maria E Lopatkina, Stanislav Vasilyev and 32 more

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Article in Genome medicine, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

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2citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

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3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

  1. Article
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4 · The record

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PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

42 authors.

Maria GridinaInstitute of Cytology and Genetics, 10, Prospekt Akademika Lavrent'yeva, Novosibirsk, 630090, Russia. gridinam@gmail.com.ORCID 0000-0002-7972-5949
Timofey LagunovInstitute of Cytology and Genetics, 10, Prospekt Akademika Lavrent'yeva, Novosibirsk, 630090, Russia.
Polina BelokopytovaInstitute of Cytology and Genetics, 10, Prospekt Akademika Lavrent'yeva, Novosibirsk, 630090, Russia.
Nikita TorgunakovInstitute of Cytology and Genetics, 10, Prospekt Akademika Lavrent'yeva, Novosibirsk, 630090, Russia.
Miroslav NuriddinovInstitute of Cytology and Genetics, 10, Prospekt Akademika Lavrent'yeva, Novosibirsk, 630090, Russia.
Artem NurislamovInstitute of Cytology and Genetics, 10, Prospekt Akademika Lavrent'yeva, Novosibirsk, 630090, Russia.
Lyudmila P NazarenkoResearch Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, 10, Nab. Ushaiki, Tomsk, 634050, Russia.
Anna A KashevarovaResearch Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, 10, Nab. Ushaiki, Tomsk, 634050, Russia.
Maria E LopatkinaResearch Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, 10, Nab. Ushaiki, Tomsk, 634050, Russia.
Stanislav VasilyevResearch Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, 10, Nab. Ushaiki, Tomsk, 634050, Russia.
Andrey ZuevResearch Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, 10, Nab. Ushaiki, Tomsk, 634050, Russia.
Elena O BelyaevaResearch Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, 10, Nab. Ushaiki, Tomsk, 634050, Russia.
Olga A SalyukovaResearch Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, 10, Nab. Ushaiki, Tomsk, 634050, Russia.
Aleksandr D CheremnykhResearch Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, 10, Nab. Ushaiki, Tomsk, 634050, Russia.
Natalia N SukhanovaResearch Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, 10, Nab. Ushaiki, Tomsk, 634050, Russia.
Marina E MinzhenkovaResearch Centre for Medical Genetics, Moscow, 115522, Russia.
Zhanna G MarkovaResearch Centre for Medical Genetics, Moscow, 115522, Russia.
Nina A DeminaResearch Centre for Medical Genetics, Moscow, 115522, Russia.
Yana StepanchukInstitute of Cytology and Genetics, 10, Prospekt Akademika Lavrent'yeva, Novosibirsk, 630090, Russia.
Anna KhabarovaInstitute of Cytology and Genetics, 10, Prospekt Akademika Lavrent'yeva, Novosibirsk, 630090, Russia.
Alexandra YanInstitute of Cytology and Genetics, 10, Prospekt Akademika Lavrent'yeva, Novosibirsk, 630090, Russia.
Emil ValeevInstitute of Cytology and Genetics, 10, Prospekt Akademika Lavrent'yeva, Novosibirsk, 630090, Russia.
Galina KoksharovaInstitute of Cytology and Genetics, 10, Prospekt Akademika Lavrent'yeva, Novosibirsk, 630090, Russia.
Elena V Grigor'evaInstitute of Cytology and Genetics, 10, Prospekt Akademika Lavrent'yeva, Novosibirsk, 630090, Russia.
Natalia KokhInstitute of Cytology and Genetics, 10, Prospekt Akademika Lavrent'yeva, Novosibirsk, 630090, Russia.
Tatiana LukjanovaCenter for Family Care and Reproduction, 1 Kiyevskaya Str, Novosibirsk, 6300136, Russia.
Yulia MaximovaCenter for Family Care and Reproduction, 1 Kiyevskaya Str, Novosibirsk, 6300136, Russia.
Elizaveta MusatovaGenetics and Reproductive Medicine Center, "GENETICO" PJSC, Moscow, 119333, Russia.
Elena ShabanovaNorth-Western State Medical University named after I.I. Mechnikov, Saint-Petersburg, 191015, Russia.
Andrey KechinNovosibirsk State University, 1, Pirogova Str, Novosibirsk, 630090, Russia.
Evgeniy KhrapovInstitute of Chemical Biology and Fundamental Medicine, Novosibirsk, 630090, Russia.
Uliana BoyarskihInstitute of Chemical Biology and Fundamental Medicine, Novosibirsk, 630090, Russia.
Oxana RyzhkovaResearch Centre for Medical Genetics, Moscow, 115522, Russia.
Maria SuntsovaSechenov First Moscow State Medical University, Moscow, 119435, Russia.
Alina MatrosovaSechenov First Moscow State Medical University, Moscow, 119435, Russia.
Mikhail KaroliSirius University of Science and Technology, Sirius Federal Territory, Sochi, 354340, Russia.
Andrey ManakhovSirius University of Science and Technology, Sirius Federal Territory, Sochi, 354340, Russia.
Maxim FilipenkoInstitute of Chemical Biology and Fundamental Medicine, Novosibirsk, 630090, Russia.
Evgeny RogaevSirius University of Science and Technology, Sirius Federal Territory, Sochi, 354340, Russia.
Nadezhda V ShilovaResearch Centre for Medical Genetics, Moscow, 115522, Russia.
Igor N LebedevResearch Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, 10, Nab. Ushaiki, Tomsk, 634050, Russia.
Veniamin FishmanInstitute of Cytology and Genetics, 10, Prospekt Akademika Lavrent'yeva, Novosibirsk, 630090, Russia. minja-f@yandex.com.

Funding

Russian Science Foundation 21-65-00017
6 · The paper itself

Abstract

backgroundEffective 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).

methodsWe 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.

resultsApplied 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.

conclusionsThrough 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.

Indexed as

Exome SequencingGenomic Structural VariationPolymorphism, Single NucleotideDNA Copy Number VariationsGenome, HumanHumans

Identifiers

PMID40336115
PMCPMC12060427

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