Evidence map›Paper›PMID 40523952›Full record

ArticleCommunications medicine2025

Clinical and analytical validation of a combined RNA and DNA exome assay across a large tumor cohort.

Anastasiya Yudina, Cagdas Tazearslan, Artur Baisangurov, Ekaterina Nuzhdina, Kelley Lauziere, Vitaly Segodin, Svetlana Podsvirova, Sergey Starikov, Madison Chasse, Kirill Shaposhnikov and 22 more

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Article in Communications medicine, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing 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

3 citing papers in PubMed.

  1. Review
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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

32 authors.

Anastasiya YudinaBostonGene Corporation, Waltham, MA, USA.
Cagdas TazearslanBostonGene Corporation, Waltham, MA, USA.
Artur BaisangurovBostonGene Corporation, Waltham, MA, USA.
Ekaterina NuzhdinaBostonGene Corporation, Waltham, MA, USA.
Kelley LauziereBostonGene Corporation, Waltham, MA, USA.
Vitaly SegodinBostonGene Corporation, Waltham, MA, USA.
Svetlana PodsvirovaBostonGene Corporation, Waltham, MA, USA.
Sergey StarikovBostonGene Corporation, Waltham, MA, USA.
Madison ChasseBostonGene Corporation, Waltham, MA, USA.
Kirill ShaposhnikovBostonGene Corporation, Waltham, MA, USA.ORCID http://orcid.org/0009-0006-2153-8565
Leznath KaneunyenyeBostonGene Corporation, Waltham, MA, USA.
Olesia KlimchukBostonGene Corporation, Waltham, MA, USA.
Natalia KuzkinaBostonGene Corporation, Waltham, MA, USA.
Noel EnglishBostonGene Corporation, Waltham, MA, USA.
Gleb KhegaiBostonGene Corporation, Waltham, MA, USA.ORCID http://orcid.org/0009-0003-2505-3846
Danielle SookiasianBostonGene Corporation, Waltham, MA, USA.
Daria ShafranskayaBostonGene Corporation, Waltham, MA, USA.
Dawn FernandezBostonGene Corporation, Waltham, MA, USA.
Yaroslav LozinskyBostonGene Corporation, Waltham, MA, USA.
Andrew SobolevBostonGene Corporation, Waltham, MA, USA.
Mary AbdouBostonGene Corporation, Waltham, MA, USA.
Polina TurovaBostonGene Corporation, Waltham, MA, USA.
Konstantin ChernyshovBostonGene Corporation, Waltham, MA, USA.
Alexey EfremovBostonGene Corporation, Waltham, MA, USA.
Samuel AndrewesBostonGene Corporation, Waltham, MA, USA.
Aviva FeinbergBostonGene Corporation, Waltham, MA, USA.
Brianna McKennaBostonGene Corporation, Waltham, MA, USA.
Jessica H BrownBostonGene Corporation, Waltham, MA, USA.
Anna LoveBostonGene Corporation, Waltham, MA, USA.ORCID http://orcid.org/0000-0003-4627-3138
John CurranBostonGene Corporation, Waltham, MA, USA.
Jochen LennerzBostonGene Corporation, Waltham, MA, USA.ORCID http://orcid.org/0000-0003-2434-4978
Alexander BagaevBostonGene Corporation, Waltham, MA, USA. aleksander.bagaev@bostongene.com.ORCID http://orcid.org/0000-0002-8680-854X

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundCombining RNA sequencing (RNA-seq) with whole exome sequencing (WES) from a single tumor sample can substantially improve the detection of clinically relevant alterations in cancer. However, routine clinical adoption of this integrated approach remains limited, especially for RNA-seq, due to the absence of standardized validation frameworks.

methodsWe developed and validated an assay that integrates RNA-seq and WES for evaluating gene expression, gene fusions, tumor microenvironment signatures, somatic single nucleotide variants (SNVs), insertions/deletions (INDELs), and copy number variations (CNVs). Exome-wide somatic reference standards were generated to support analytical validation using multiple sequencing runs of cell lines at varying purities.

resultsAssay validation involves 3 steps: (1) analytical validation using custom reference samples containing 3042 SNVs and 47,466 CNVs; (2) orthogonal testing in patient samples; and (3) assessment of clinical utility in real-world cases. Applied to 2230 clinical tumor samples, the integrated assay enables direct correlation of somatic alterations with gene expression, recovery of variants missed by DNA-only testing, and improves detection of gene fusions. In addition to uncovering clinically actionable alterations in 98% of cases, the assay also reveals complex genomic rearrangements that would likely have remained undetected without RNA data.

conclusionsThis study provides practical validation guidelines for integrated RNA and DNA sequencing in clinical oncology. The combined assay enhances the detection of actionable alterations, thereby facilitating personalized treatment strategies for cancer patients.

Identifiers

PMID40523952
PMCPMC12170858

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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.