ArticleCell genomics2022
PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions.
Abstract read
In one paragraph
Article in Cell genomics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 138 papers.
0numbers the graph read from it
0cells of the map it votes in
138citing papers in PubMed
–field-weighted citation impact
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.
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.
Who cites it
138 citing papers in PubMed.
- Nanopore Sequencing for Chikungunya Virus: Principles and Application.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Telomere-to-telomere CHM13 reference reveals missing truth variants and improves deep learning-based variant calling in long-read sequencing data.Quantitative biology (Beijing, China) · 2026Article
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- Benchmarking long-read variant sensitivity across ONT and PacBio platforms using known clinically reported variants in a cohort of critically ill newborns.medRxiv : the preprint server for health sciences · 2026Article
- Computational strategies for copy number variation detection, disease association, and beyond.Genome biology · 2026Review
- Draft genome sequence ofMicrobiology resource announcements · 2026Article
- VCboost: reducing false positives in long-read variant calling for single-nucleotide polymorphism and indel detection in challenging genomic regions.Briefings in bioinformatics · 2026Article
- Article
- Article
- Aardvark: sifting through differences in a mound of variants.Genome biology · 2026Article
- Article
- Genome-wide associations of structural variants with human traits through imputation from long-read assemblies.Nature genetics · 2026Article
- Distinct repair outcomes from single and convergent replication fork collapse.Nature structural & molecular biology · 2026Article
- A sibling study of variation in parental mutation rates.bioRxiv : the preprint server for biology · 2026Article
- Duplex-Indel: a Snakemake pipeline for somatic Indel calling in Tn5 transposase-based duplex sequencing data.Bioinformatics (Oxford, England) · 2026Article
- Article
- Draft genome sequence ofMicrobiology resource announcements · 2026Article
- Benchmarking of sequencing technologies defines optimal strategies for genetic variants detection in a human genome.Genome biology · 2026Article
- Convergence of machine learning and genomics for precision oncology.Nature reviews. Cancer · 2026Review
- A universal indel filtering workflow for both long-read and short-read NGS data.BMC research notes · 2026Article
78 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
73 authors.
Nathan D OlsonMaterial Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Dr, MS8312, Gaithersburg, MD 20899, USA.
Justin WagnerMaterial Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Dr, MS8312, Gaithersburg, MD 20899, USA.
Jennifer McDanielMaterial Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Dr, MS8312, Gaithersburg, MD 20899, USA.
Sarah H StephensBooz Allen Hamilton, 8283 Greensboro Drive, Mclean, VA 22102, USA.
Samuel T WestreichDNAnexus, Inc., 1975 W El Camino Real #204, Mountain View, CA 94040, USA.
Anish G PrasannaBooz Allen Hamilton, 8283 Greensboro Drive, Mclean, VA 22102, USA.
Elaine JohansonOffice of Health Informatics, Office of the Chief Scientist, Office of the Commissioner, US Food and Drug Administration, Silver Spring, MD, USA.
Emily BojaOffice of Health Informatics, Office of the Chief Scientist, Office of the Commissioner, US Food and Drug Administration, Silver Spring, MD, USA.
Ezekiel J MaierBooz Allen Hamilton, 8283 Greensboro Drive, Mclean, VA 22102, USA.
Omar SerangDNAnexus, Inc., 1975 W El Camino Real #204, Mountain View, CA 94040, USA.
David JáspezGenomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain.
José M Lorenzo-SalazarGenomics 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.
Luis A Rubio-RodríguezGenomics 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.
Konstantinos KyriakidisSchool of Pharmacy, Aristotle University of Thessaloniki (AUTH), 541 24 Thessaloniki, Greece.
Andigoni MalousiGenomics and Epigenomics Translational Research (GENeTres), Center for Interdisciplinary Research and Innovation, 570 01 Thessaloniki, Greece.
Kishwar ShafinUC Santa Cruz Genomics Institute, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, USA.
Trevor PesoutUC Santa Cruz Genomics Institute, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, USA.
Miten JainUC Santa Cruz Genomics Institute, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, USA.
Benedict PatenUC Santa Cruz Genomics Institute, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, USA.
Pi-Chuan ChangGoogle Inc, 1600 Amphitheater Pkwy, Mountain View, CA 94040, USA.
Alexey KolesnikovGoogle Inc, 1600 Amphitheater Pkwy, Mountain View, CA 94040, USA.
Maria NattestadGoogle Inc, 1600 Amphitheater Pkwy, Mountain View, CA 94040, USA.
Gunjan BaidGoogle Inc, 1600 Amphitheater Pkwy, Mountain View, CA 94040, USA.
Sidharth GoelGoogle Inc, 1600 Amphitheater Pkwy, Mountain View, CA 94040, USA.
Howard YangGoogle Inc, 1600 Amphitheater Pkwy, Mountain View, CA 94040, USA.
Andrew CarrollGoogle Inc, 1600 Amphitheater Pkwy, Mountain View, CA 94040, USA.
Robert EveleighThe Canadian Center for Computational Genomics (C3G), Montréal, QC, Canada.
Mathieu BourgeyThe Canadian Center for Computational Genomics (C3G), Montréal, QC, Canada.
Guillaume BourqueThe Canadian Center for Computational Genomics (C3G), Montréal, QC, Canada.
Gen LiHuXinDao, QingZhuHu TaiYangShan Road, KaiFu, ChangSha, HuNan, China.
ChouXian MaHuXinDao, QingZhuHu TaiYangShan Road, KaiFu, ChangSha, HuNan, China.
LinQi TangHuXinDao, QingZhuHu TaiYangShan Road, KaiFu, ChangSha, HuNan, China.
YuanPing DuHuXinDao, QingZhuHu TaiYangShan Road, KaiFu, ChangSha, HuNan, China.
ShaoWei ZhangHuXinDao, QingZhuHu TaiYangShan Road, KaiFu, ChangSha, HuNan, China.
Jordi MorataCNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain.
Raúl TondaCNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain.
Genís ParraCNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain.
Jean-Rémi TrottaCNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain.
Christian BruefferDivision of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden.
Sinem Demirkaya-BudakSeven Bridges Genomics, Inc, Charlestown, MA, USA.
Duygu Kabakci-ZorluSeven Bridges Genomics, Inc, Charlestown, MA, USA.
Deniz TurgutSeven Bridges Genomics, Inc, Charlestown, MA, USA.
Özem KalaySeven Bridges Genomics, Inc, Charlestown, MA, USA.
Gungor BudakSeven Bridges Genomics, Inc, Charlestown, MA, USA.
Kübra NarcıSeven Bridges Genomics, Inc, Charlestown, MA, USA.
Elif ArslanSeven Bridges Genomics, Inc, Charlestown, MA, USA.
Richard BrownSeven Bridges Genomics, Inc, Charlestown, MA, USA.
Ivan J JohnsonSeven Bridges Genomics, Inc, Charlestown, MA, USA.
Alexey DolgoborodovSeven Bridges Genomics, Inc, Charlestown, MA, USA.
Vladimir SemenyukSeven Bridges Genomics, Inc, Charlestown, MA, USA.
Amit JainSeven Bridges Genomics, Inc, Charlestown, MA, USA.
H Serhat TetikolSeven Bridges Genomics, Inc, Charlestown, MA, USA.
Varun JainIllumina, Inc., San Diego, CA, USA.
Mike RuehleIllumina, Inc., San Diego, CA, USA.
Bryan LajoieIllumina, Inc., San Diego, CA, USA.
Cooper RoddeyIllumina, Inc., San Diego, CA, USA.
Severine CatreuxIllumina, Inc., San Diego, CA, USA.
Rami MehioIllumina, Inc., San Diego, CA, USA.
Mian Umair AhsanRaymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
Qian LiuRaymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
Kai WangRaymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
Sayed Mohammad Ebrahim SahraeianRoche Sequencing Solutions, Santa Clara, CA 95050, USA.
Li Tai FangRoche Sequencing Solutions, Santa Clara, CA 95050, USA.
Marghoob MohiyuddinRoche Sequencing Solutions, Santa Clara, CA 95050, USA.
Calvin HungWASAI Technology, Taipei, Taiwan.
Chirag JainNational Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
Hanying FengSentieon Inc., San Jose, CA, USA.
Zhipan LiSentieon Inc., San Jose, CA, USA.
Luoqi ChenSentieon Inc., San Jose, CA, USA.
Fritz J SedlazeckHuman Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
Justin M ZookMaterial Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Dr, MS8312, Gaithersburg, MD 20899, USA.
Funding
Genomic Architecture of Common Disease in Diverse Populations: WGS of Ongoing Hemorrhagic Stroke Study SupplementUM1HG008898 · NHGRI · BAYLOR COLLEGE OF MEDICINE · PI GIBBS, RICHARD A · 2016 to 2020
$77.0MDetection and annotation of structural variants from long-read sequencingR01GM132713 · NIGMS · CHILDREN'S HOSP OF PHILADELPHIA · PI WANG, KAI · 2019 to 2022
$1.9MNHGRI NIH HHS UM1 HG008898NIGMS NIH HHS R01 GM132713
Abstract
The precisionFDA Truth Challenge V2 aimed to assess the state of the art of variant calling in challenging genomic regions. Starting with FASTQs, 20 challenge participants applied their variant-calling pipelines and submitted 64 variant call sets for one or more sequencing technologies (Illumina, PacBio HiFi, and Oxford Nanopore Technologies). Submissions were evaluated following best practices for benchmarking small variants with updated Genome in a Bottle benchmark sets and genome stratifications. Challenge submissions included numerous innovative methods, with graph-based and machine learning methods scoring best for short-read and long-read datasets, respectively. With machine learning approaches, combining multiple sequencing technologies performed particularly well. Recent developments in sequencing and variant calling have enabled benchmarking variants in challenging genomic regions, paving the way for the identification of previously unknown clinically relevant variants.
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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 Socratic graph.