ArticleScientific reports2016
OpEx - a validated, automated pipeline optimised for clinical exome sequence analysis.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers, 1 of them a synthesis that pooled it.
What it found
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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.
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Who cites it
8 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Challenges targeting cancer neoantigens in 2021: a systematic literature review.Expert review of vaccines · 2021Pooled it
- Insights into BRCA Cancer Predisposition from Integrated Germline and Somatic Analyses in 7632 Cancers.JNCI cancer spectrum · 2019Article
- Identification of new Wilms tumour predisposition genes: an exome sequencing study.The Lancet. Child & adolescent health · 2019Article
- CoverView: a sequence quality evaluation tool for next generation sequencing data.Wellcome open research · 2018Article
- ICR142 Benchmarker: evaluating, optimising and benchmarking variant calling performance using the ICR142 NGS validation series.Wellcome open research · 2018Article
- Biallelic TRIP13 mutations predispose to Wilms tumor and chromosome missegregation.Nature genetics · 2017Article
- Mutations in Epigenetic Regulation Genes Are a Major Cause of Overgrowth with Intellectual Disability.American journal of human genetics · 2017Article
- Accurate clinical detection of exon copy number variants in a targeted NGS panel using DECoN.Wellcome open research · 2016Article
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
We present an easy-to-use, open-source Optimised Exome analysis tool, OpEx (http://icr.ac.uk/opex) that accurately detects small-scale variation, including indels, to clinical standards. We evaluated OpEx performance with an experimentally validated dataset (the ICR142 NGS validation series), a large 1000 exome dataset (the ICR1000 UK exome series), and a clinical proband-parent trio dataset. The performance of OpEx for high-quality base substitutions and short indels in both small and large datasets is excellent, with overall sensitivity of 95%, specificity of 97% and low false detection rate (FDR) of 3%. Depending on the individual performance requirements the OpEx output allows one to optimise the inevitable trade-offs between sensitivity and specificity. For example, in the clinical setting one could permit a higher FDR and lower specificity to maximise sensitivity. In contexts where experimental validation is not possible, minimising the FDR and improving specificity may be a preferable trade-off for slightly lower sensitivity. OpEx is simple to install and use; the whole pipeline is run from a single command. OpEx is therefore well suited to the increasing research and clinical laboratories undertaking exome sequencing, particularly those without in-house dedicated bioinformatics expertise.
Identifiers
What OpenQuestion holds
Registered trials
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.