Evidence map›Paper›PMID 41415395›Full record

ArticlebioRxiv : the preprint server for biology2025

Widespread Epistasis between Cancer Driver Mutations and Allele-Specific Copy Number Variations.

Serge Merzliakov, Guanlan Dong, Andrea Castro, Mahad Bihie, Yve Nichols-Evans, Hannah Carter, Kuan-Lin Huang

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

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

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

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

7 authors.

Serge MerzliakovBioinformatics Research Network, Atlanta, GA, USA.
Guanlan DongDivision of Genetics and Genomics, Boston Children's Hospital, Department of Pediatrics, Harvard Medical School, Bioinformatics and Integrative Genomics PhD Program, Harvard Medical School, Boston, MA, USA.
Andrea CastroDepartment of Medicine, Division of Genomics and Precision Medicine, University of California San Diego, La Jolla, CA, 92093, USA.
Mahad BihieMcMaster University, Hamilton, Canada.
Yve Nichols-EvansBioinformatics Research Network, Atlanta, GA, USA.
Hannah CarterDepartment of Medicine, Division of Genomics and Precision Medicine, University of California San Diego, La Jolla, CA, 92093, USA.
Kuan-Lin HuangDepartment of Genetics and Genomic Sciences, Department of Artificial Intelligence and Human Health, Center for Transformative Disease Modeling, Tisch Cancer Institute, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.

Funding

Conduits: Mount Sinai Health System Translational Science HubUL1TR004419 · NCATS · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI Rosalind J Wright · 2022 to 2026
$46.4M
Integrative Approaches for Identifying Causal Gene-Cell Type Pairs of Complex DiseaseR35GM138113 · NIGMS · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI Kuan-lin Huang · 2020 to 2026
$3.0M
COVID and Translational Science supercomputer (CATS)S10OD030463 · OD · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI KOVATCH, PATRICIA · 2021 to 2021
$2.0M
Big Omics Data Engine 2 SupercomputerS10OD026880 · OD · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI KOVATCH, PATRICIA · 2019 to 2019
$2.0M
HSRD VA IVI 22-115NCATS NIH HHS UL1 TR004419NIGMS NIH HHS R35 GM138113NIH HHS S10 OD026880NIH HHS S10 OD030463
6 · The paper itself

Abstract

Cancer driver mutations alone are often insufficient to fully explain tumorigenesis. We demonstrate that these mutations cooperate with somatic copy number variations (CNVs) in a tissue-specific pattern of genomic epistasis. Analyzing 93,462 tumors, we identified 54 gene-cancer type pairs with significant co-occurrence of somatic mutations and CNVs. Our new Binoculars algorithm, which resolved phased DNA/RNA reads, revealed frequent preferential amplification in oncogenic mutation alleles, including AKT1 p.E17K, BRAF p.V600E, KRAS p.G12C/D/V, NRAS p.Q61K, and a fraction of gain-of-function TP53 p.R175H. Conversely, deletions selectively targeted the reference alleles, leading to loss of heterozygosity of IDH1 p.R132H and tumor suppressor mutations, including

Identifiers

PMID41415395
PMCPMC12710650

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.