Evidence map›Paper›PMID 41421359›Full record

ArticleCell genomics2026

Characterization of subclonal variants in HG002 Genome in a Bottle reference material as a resource for benchmarking variant callers.

Camille A Daniels, Adetola A Abdulkadir, Megan H Cleveland, Jennifer H McDaniel, David Jáspez, Luis Alberto Rubio-Rodríguez, Adrián Muñoz-Barrera, José Miguel Lorenzo-Salazar, Carlos Flores, Byunggil Yoo and 28 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell genomics, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. Article
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

38 authors.

Camille A DanielsMedical Device Innovation Consortium (MDIC), 1655 N Ft. Myer Drive, Suite 250, Arlington, VA 22209, USA.
Adetola A AbdulkadirMedical Device Innovation Consortium (MDIC), 1655 N Ft. Myer Drive, Suite 250, Arlington, VA 22209, USA.
Megan H ClevelandMaterial Measurement Laboratory, National Institute of Standards and Technology (NIST), 100 Bureau Dr, MS8312, Gaithersburg, MD 20899, USA.
Jennifer H McDanielMaterial Measurement Laboratory, National Institute of Standards and Technology (NIST), 100 Bureau Dr, MS8312, Gaithersburg, MD 20899, USA.
David JáspezGenomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain.
Luis Alberto Rubio-RodríguezGenomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain.
Adrián Muñoz-BarreraGenomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain.
José Miguel Lorenzo-SalazarGenomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain.
Carlos FloresGenomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain; Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Instituto de Investigación Sanitaria de Canarias, Santa Cruz de Tenerife, Spain; CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain; Facultad de Ciencias de la Salud, Universidad Fernando de Pessoa Canarias, Las Palmas de Gran Canaria, Spain.
Byunggil YooGenomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA.
Sayed Mohammad Ebrahim SahraeianRoche Sequencing Solutions, Santa Clara, CA 95050, USA.
Yina WangIllumina, Inc., San Diego, CA, USA.
Massimiliano RossiIllumina, Inc., San Diego, CA, USA.
Arun VisvanathIllumina, Inc., San Diego, CA, USA.
Lisa MurrayIllumina, Inc., San Diego, CA, USA.
Wei-Ting ChenIllumina, Inc., San Diego, CA, USA.
Severine CatreuxIllumina, Inc., San Diego, CA, USA.
James HanIllumina, Inc., San Diego, CA, USA.
Rami MehioIllumina, Inc., San Diego, CA, USA.
Gavin ParnabyIllumina, Inc., San Diego, CA, USA.
Andrew CarrollGoogle, Inc., Mountain View, CA, USA.
Pi-Chuan ChangGoogle, Inc., Mountain View, CA, USA.
Kishwar ShafinGoogle, Inc., Mountain View, CA, USA.
Daniel CookGoogle, Inc., Mountain View, CA, USA.
Alexey KolesnikovGoogle, Inc., Mountain View, CA, USA.
Lucas BrambrinkGoogle, Inc., Mountain View, CA, USA.
Mohammed Faizal Eeman MootorDepartment of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA.
Yash PatelDepartment of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA.
Takafumi N YamaguchiDepartment of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA.
Paul C BoutrosDepartment of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA.
Karolina SienkiewiczDepartment of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.
Jonathan FooxDepartment of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
Christopher E MasonDepartment of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA; The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA.
Bryan R LajoieElement Biosciences, San Diego, CA, USA.
Carlos A Ruiz-PerezElement Biosciences, San Diego, CA, USA.
Semyon KruglyakElement Biosciences, San Diego, CA, USA.
Justin M ZookMaterial Measurement Laboratory, National Institute of Standards and Technology (NIST), 100 Bureau Dr, MS8312, Gaithersburg, MD 20899, USA. Electronic address: justin.zook@nist.gov.
Nathan D OlsonMaterial Measurement Laboratory, National Institute of Standards and Technology (NIST), 100 Bureau Dr, MS8312, Gaithersburg, MD 20899, USA. Electronic address: nolson@nist.gov.

Funding

Women's CancersP30CA016042 · NCI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI Robert Damoiseaux · 1985 to 2026
$134.5M
VAST Center: Viromes Across Space(s) and TimeU54AG089334 · NIA · STANFORD UNIVERSITY · PI Christopher Edward Mason · 2025 to 2026
$13.3M
Advancing method benchmarking and data sharing through crowd-sourced competitions in cancer researchU24CA248265 · NCI · SAGE BIONETWORKS · PI BOUTROS, PAUL CHRISTOPHER, VARMA, SUSHEEL · 2020 to 2024
$4.1M
The Epitranscriptome as a Novel Mechanism of Arsenic-Induced Diabetes.R01ES032638 · NIEHS · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI KUPSCO, ALLISON, MASON, CHRISTOPHER EDWARD · 2021 to 2025
$3.9M
Virginia-UCLA-Toronto Biomarker Characterization CenterU2CCA271894 · NCI · OLD DOMINION UNIVERSITY · PI OLIVER John SEMMES · 2022 to 2026
$3.2M
NCI NIH HHS P30 CA016042NCI NIH HHS U24 CA248265NCI NIH HHS U2C CA271894NIA NIH HHS U54 AG089334NIEHS NIH HHS R01 ES032638
6 · The paper itself

Abstract

We developed a benchmark set of subclonal variants in the Genome in a Bottle (GIAB) Consortium HG002 reference material (RM) DNA for evaluating lower-frequency variant callsets. We used a somatic variant caller with high-coverage (300×) whole-genome sequencing data from the GIAB Ashkenazi Jewish trio to identify potential subclonal variants in the HG002 RM DNA. Using orthogonal sequencing data and manual curation, we defined a benchmark set with 85 high-confidence subclonal single-nucleotide variants (SNVs) (allele frequency [AF] > 5%) and a benchmark region covering 2.45 Gbp of the autosomes. External validation supported that it can be used to reliably identify both false negatives and false positives for a variety of sequencing technologies and variant callers. By adding our characterization of mosaic SNVs in this widely used cell line, we have expanded the scope of bioinformatic and sequencing applications for which the HG002 GIAB RM can be used to include benchmarking subclonal SNVs.

Indexed as

Genome, HumanPolymorphism, Single NucleotideBenchmarkingComputational BiologyGene FrequencyHigh-Throughput Nucleotide SequencingHumansReference StandardsSequence Analysis, DNAWhole Genome SequencingGenome In A Bottlegenome sequencingmosaic variantreference materialSNVsomatic mosaicismsomatic variantvariant benchmarkingvariant calling

Identifiers

PMID41421359
PMCPMC13069850

What OpenQuestion holds

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LicenceCC BY
Read underepoch 390

Registered trials

None linked

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.