Evidence map›Paper›PMID 38589653›Full record

ArticleScientific reports2024

Towards accurate indel calling for oncopanel sequencing through an international pipeline competition at precisionFDA.

Binsheng Gong, Samir Lababidi, Rebecca Kusko, Khaled Bouri, Sarah Prezek, Vishal Thovarai, Anish Prasanna, Ezekiel J Maier, Mahdi Golkaram, Xingqiang Sun and 8 more

Abstract 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 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. Article
  2. Article
  3. 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

18 authors.

Binsheng GongDivision of Bioinformatics and Biostatistics, Office of Research, National Center for Toxicological Research, Office of the Chief Scientist, Office of the Commissioner, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA.
Samir LababidiHealth Informatics Staff, Office of Data, Analytics, and Research, Office of Digital Transformation, Office of the Commissioner, U.S. Food and Drug Administration, Silver Spring, MD, 20993, USA.
Rebecca KuskoCellino Biotech, 750 Main Street, Cambridge, MA, 02143, USA.
Khaled BouriOffice of Regulatory Science and Innovation, Office of the Chief Scientist, Office of the Commissioner, U.S. Food and Drug Administration, Silver Spring, MD, 20993, USA.
Sarah PrezekBooz Allen Hamilton, McLean, VA, 22102, USA.
Vishal ThovaraiBooz Allen Hamilton, McLean, VA, 22102, USA.
Anish PrasannaBooz Allen Hamilton, McLean, VA, 22102, USA.
Ezekiel J MaierBooz Allen Hamilton, McLean, VA, 22102, USA.
Mahdi GolkaramIllumina, Inc., San Diego, CA, 92122, USA.
Xingqiang SunGenetalks, Changsha, Hunan, China.
Konstantinos KyriakidisUC Santa Cruz Genomics Institute, Santa Cruz, CA, 95060, USA.
João Paulo KitajimaMendelics, Av. Braz Leme, 1631-Santana, São Paulo, SP, 02511-000, Brazil.
Sayed Mohammad Ebrahim SahraeianRoche Sequencing Solutions, Santa Clara, CA, 95050, USA.
Yunfei GuoRoche Sequencing Solutions, Santa Clara, CA, 95050, USA.
Elaine JohansonHealth Informatics Staff, Office of Data, Analytics, and Research, Office of Digital Transformation, Office of the Commissioner, U.S. Food and Drug Administration, Silver Spring, MD, 20993, USA.
Wendell JonesQ squared Solutions Genomics, 2400 Elis Road, Durham, NC, 27703, USA.
Weida TongDivision of Bioinformatics and Biostatistics, Office of Research, National Center for Toxicological Research, Office of the Chief Scientist, Office of the Commissioner, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA.
Joshua XuDivision of Bioinformatics and Biostatistics, Office of Research, National Center for Toxicological Research, Office of the Chief Scientist, Office of the Commissioner, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA. Joshua.Xu@fda.hhs.gov.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Accurately calling indels with next-generation sequencing (NGS) data is critical for clinical application. The precisionFDA team collaborated with the U.S. Food and Drug Administration's (FDA's) National Center for Toxicological Research (NCTR) and successfully completed the NCTR Indel Calling from Oncopanel Sequencing Data Challenge, to evaluate the performance of indel calling pipelines. Top performers were selected based on precision, recall, and F1-score. The performance of many other pipelines was close to the top performers, which produced a top cluster of performers. The performance was significantly higher in high confidence regions and coding regions, and significantly lower in low complexity regions. Oncopanel capture and other issues may have occurred that affected the recall rate. Indels with higher variant allele frequency (VAF) may generally be called with higher confidence. Many of the indel calling pipelines had good performance. Some of them performed generally well across all three oncopanels, while others were better for a specific oncopanel. The performance of indel calling can further be improved by restricting the calls within high confidence intervals (HCIs) and coding regions, and by excluding low complexity regions (LCR) regions. Certain VAF cut-offs could be applied according to the applications.

Indexed as

High-Throughput Nucleotide SequencingINDEL MutationPolymorphism, Single NucleotideIndel calling pipelineNext-generation sequencingPersonalized medicineprecisionFDA challengePrecision medicine

Identifiers

PMID38589653
PMCPMC11001604

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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.