Evidence map›Paper›PMID 38528062›Full record

ArticleScientific reports2024

Extend the benchmarking indel set by manual review using the individual cell line sequencing data from the Sequencing Quality Control 2 (SEQC2) project.

Binsheng Gong, Dan Li, Yifan Zhang, Rebecca Kusko, Samir Lababidi, Zehui Cao, Mingyang Chen, Ning Chen, Qiaochu Chen, Qingwang Chen and 50 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Scientific reports, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed
1.4field-weighted citation impact, top 19% of its field
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

5 citing papers in PubMed, 5 citations in OpenAlex.

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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

60 authors at 17 institutions in 2 countries.

Binsheng GongDivision of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA.
Dan LiDivision of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA.
Yifan ZhangDivision of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA.
Rebecca KuskoCellino Bio, 750 Main Street, Cambridge, MA, 02143, USA.
Samir LababidiOffice of Data Analytics and Research, Office of Digital Transformation, Office of the Commissioner, U.S. Food and Drug Administration, Silver Spring, MD, 20993, USA.
Zehui CaoState Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200438, China.
Mingyang ChenHuman Phenome Institute, Fudan University, Shanghai, 201203, China.
Ning CheniGeneTech Bioscience Co., Ltd., 8 Shengmingyuan Rd., Changping, Beijing, China.
Qiaochu ChenState Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200438, China.
Qingwang ChenState Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200438, China.
Jiacheng DaiHuman Phenome Institute, Fudan University, Shanghai, 201203, China.
Qiang GanClinical Diagnostics Division, Thermo Fisher Scientific, 46500 Kato Rd., Fremont, CA, 94538, USA.
Yuechen GaoState Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200438, China.
Mingkun GuoCollege of Chemistry, Sichuan University, Chengdu, 610064, Sichuan, China.
Gunjan HarianiQ squared Solutions Genomics, 2400 Ellis Road, Durham, NC, 27703, USA.
Yujie HeCollege of Chemistry, Sichuan University, Chengdu, 610064, Sichuan, China.
Wanwan HouState Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200438, China.
He JiangState Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200438, China.
Garima KushwahaGuardant Health, Inc., 505 Penobscot Drive, Redwood City, CA, 94063, USA.
Jian-Liang LiIntegrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA.
Jianying LiIntegrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA.
Yulan LiCollege of Life Sciences, Shanghai Normal University, Shanghai, 200234, China.
Liang-Chun LiuClinical Diagnostics Division, Thermo Fisher Scientific, 46500 Kato Rd., Fremont, CA, 94538, USA.
Ruimei LiuState Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200438, China.
Shiming LiuCenter for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China.
Edwin MeriauxCMINDS Research Center, University of Massachusetts, Lowell, MA, 01854, USA.
Mengqing MoDepartment of Epidemiology, School of Public Health, Fudan University, Shanghai, 200032, China.
Mathew MooreResearchDx, Irvine, CA, 92618, USA.
Tyler J MossEurofins Viracor, LLC, 18000 W 99th St., Lenexa, KS, 66219, USA.
Quanne NiuState Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200438, China.
Ananddeep PatelEurofins Viracor Biopharma Services, Inc., 18000 W 99th St., Lenexa, KS, 66219, USA.
Luyao RenState Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200438, China.
Nedda F SaremiAgilent Technologies, Inc., 11011 N Torrey Pines Rd., La Jolla, CA, 92037, USA.
Erfei ShangState Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200438, China.
Jun ShangState Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200438, China.
Ping SongCancer Genomics Laboratory, Department of Genomic Medicine, MD Anderson Cancer Center, Houston, TX, 77030, USA.
Siqi SunResearchDx, Irvine, CA, 92618, USA.
Brent J UrbanEurofins Viracor Biopharma Services, Inc., 18000 W 99th St., Lenexa, KS, 66219, USA.
Danke WangHuman Phenome Institute, Fudan University, Shanghai, 201203, China.
Shangzi WangState Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200438, China.
Zhining WenCollege of Chemistry, Sichuan University, Chengdu, 610064, Sichuan, China.
Xiangyi XiongCollege of Life Sciences, Shanghai Normal University, Shanghai, 200234, China.
Jingcheng YangState Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200438, China.
Lihui YinPathGroup, Nashville, TN, 37217, USA.
Chao ZhangState Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200438, China.
Ruolan ZhangState Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200438, China.
Ambica BhandariResearchDx, Irvine, CA, 92618, USA.
Wanshi CaiiGeneTech Bioscience Co., Ltd., 8 Shengmingyuan Rd., Changping, Beijing, China.
Agda Karina EterovicEurofins Viracor Biopharma Services, Inc., 18000 W 99th St., Lenexa, KS, 66219, USA.
Dalila B MegherbiCMINDS Research Center, University of Massachusetts, Lowell, MA, 01854, USA.
Tieliu ShiCenter for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China.
Chen SuoDepartment of Epidemiology, School of Public Health, Fudan University, Shanghai, 200032, China.
Ying YuState Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200438, China.
Yuanting ZhengState Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200438, China.
Natalia NovoradovskayaAgilent Technologies, Inc., 11011 N Torrey Pines Rd., La Jolla, CA, 92037, USA.
Renee L SearsVelsera, 6 Cityplace Dr Suite 550, Creve Coeur, MO, 63141, USA.
Leming ShiState Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200438, China.
Wendell JonesQ squared Solutions Genomics, 2400 Ellis Road, Durham, NC, 27703, USA.
Weida TongDivision of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA.
Joshua XuDivision of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA. Joshua.Xu@fda.hhs.gov.
Fudan University · CNState Key Laboratory of Genetic EngineeringUnited States Food and Drug Administration · USSichuan University · CNAgilent Technologies (United States) · USEast China Normal University · CNNational Center for Toxicological Research · USShanghai Normal University · CNThermo Fisher Scientific (United States) · USUniversity of Massachusetts Lowell · USBioscience (China) · CNEurofins (United States) · USGuardant (United States) · USNational Institute of Environmental Health Sciences · USNational Institutes of Health · USNovogene Bioinformatics Institute · CNThe University of Texas MD Anderson Cancer Center · US

Funding

Integrative BioinformaticsZICES103371 · NIEHS · NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES · PI LI, JIAN-LIANG · 2022 to 2025
$11.5M
Intramural NIH HHS ZIC ES103371
6 · The paper itself

Abstract

Accurate indel calling plays an important role in precision medicine. A benchmarking indel set is essential for thoroughly evaluating the indel calling performance of bioinformatics pipelines. A reference sample with a set of known-positive variants was developed in the FDA-led Sequencing Quality Control Phase 2 (SEQC2) project, but the known indels in the known-positive set were limited. This project sought to provide an enriched set of known indels that would be more translationally relevant by focusing on additional cancer related regions. A thorough manual review process completed by 42 reviewers, two advisors, and a judging panel of three researchers significantly enriched the known indel set by an additional 516 indels. The extended benchmarking indel set has a large range of variant allele frequencies (VAFs), with 87% of them having a VAF below 20% in reference Sample A. The reference Sample A and the indel set can be used for comprehensive benchmarking of indel calling across a wider range of VAF values in the lower range. Indel length was also variable, but the majority were under 10 base pairs (bps). Most of the indels were within coding regions, with the remainder in the gene regulatory regions. Although high confidence can be derived from the robust study design and meticulous human review, this extensive indel set has not undergone orthogonal validation. The extended benchmarking indel set, along with the indels in the previously published known-positive set, was the truth set used to benchmark indel calling pipelines in a community challenge hosted on the precisionFDA platform. This benchmarking indel set and reference samples can be utilized for a comprehensive evaluation of indel calling pipelines. Additionally, the insights and solutions obtained during the manual review process can aid in improving the performance of these pipelines.

Indexed as

BenchmarkingHigh-Throughput Nucleotide SequencingComputational BiologyHumansINDEL MutationPolymorphism, Single NucleotideQuality ControlBenchmarkingBioinformaticsIndelPrecision medicineQuality control

Identifiers

PMID38528062
PMCPMC10963753
OpenAlexW4393147863

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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.