Evidence map›Paper›PMID 41963325›Full record

ArticleNPJ genomic medicine2026

Clinical validation of a high-performance somatic exome sequencing assay: from target-enrichment strategy to variant calling.

Junko Tsuji, Micah Rickles-Young, Justin Abreu, Alyssa Friedman, Caroline Petersen, J Bryan, Konrad Scheffler, Taylor O'Connell, Theo Heyns, Edyta Malolepsza and 16 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in NPJ genomic medicine, 2026. 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

26 authors.

Junko Tsuji *Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Micah Rickles-Young *Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Justin AbreuBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Alyssa FriedmanBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Caroline PetersenBroad Institute of MIT and Harvard, Cambridge, MA, USA.
J BryanMolecular Diagnostics Laboratory, Division of Pathology and Laboratory Medicine, the University of Texas, MD Anderson Cancer Center, Houston, TX, USA.
Konrad SchefflerIllumina, Inc, San Diego, CA, USA.
Taylor O'ConnellIllumina, Inc, San Diego, CA, USA.
Theo HeynsIllumina, Inc, San Diego, CA, USA.
Edyta MalolepszaBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Mark FlehartyBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Katie LarkinBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Kenneth J LivakDepartment of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA.
Shuqiang LiDepartment of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA.
David A ReardonDepartment of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA.
Catherine J WuBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Patrick A OttBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Fanny DaoBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Heidi RehmBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Max JanBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Chip StewartBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Gad GetzBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Varun JainIllumina, Inc, San Diego, CA, USA.
Severine CatreuxIllumina, Inc, San Diego, CA, USA.
Carrie CibulskisBroad Institute of MIT and Harvard, Cambridge, MA, USA. carrie@broadinstitute.org.
Niall LennonBroad Institute of MIT and Harvard, Cambridge, MA, USA. nlennon@broadinstitute.org.

Funding

Single cell investigation of co-evolution in cancer cells and host cell immune microenvironmentR50CA251956 · NCI · DANA-FARBER CANCER INST · PI Shuqiang Li · 2020 to 2026
$1.4M
NCI NIH HHS R50 CA251956NCI NIH HHS R50CA251956
6 · The paper itself

Abstract

Clinical whole-exome sequencing (WES) has revolutionized clinical diagnostics by enabling scalable, cost-effective molecular profiling to detect somatic variants and identify novel therapeutic targets. In particular, the clinical evaluation of somatic variants relies on both high-quality sequencing data and robust variant detection with rapid turnaround times. We developed an updated WES workflow utilizing a co-developed Twist Bioscience targeting panel and the DRAGEN (Dynamic Read Analysis for GENomics) platform, benchmarked with cell line mixtures containing >40,000 simulated variants and a clinical cohort of FFPE tumor specimens. Our assay, the Broad Clinical Somatic Whole Exome Assay V6.0, demonstrated high sensitivity (96.9% for SNVs with variant allele fraction [VAF] >10% at ≥125X; 93.5% for InDels with VAF > 20% at ≥125X) and low false positive rates (0.04 and 0.01 per Mb, respectively). The assay meets clinical requirements and enables large-scale, accurate variant profiling of cancers, expanding opportunities for molecular diagnostics across diverse clinical settings.

Identifiers

PMID41963325
PMCPMC13230904

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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.