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dc.contributor.authorMahamdallie, Sen_US
dc.contributor.authorRuark, Een_US
dc.contributor.authorYost, Sen_US
dc.contributor.authorMünz, Men_US
dc.contributor.authorRenwick, Aen_US
dc.contributor.authorPoyastro-Pearson, Een_US
dc.contributor.authorStrydom, Aen_US
dc.contributor.authorSeal, Sen_US
dc.contributor.authorRahman, Nen_US
dc.coverage.spatialEnglanden_US
dc.date.accessioned2019-03-04T14:42:50Z
dc.date.issued2018en_US
dc.identifierhttps://www.ncbi.nlm.nih.gov/pubmed/29992192en_US
dc.identifier.citationWellcome Open Res, 2018, 3 pp. 37 - ?en_US
dc.identifier.issn2398-502Xen_US
dc.identifier.urihttps://repository.icr.ac.uk/handle/internal/3116
dc.identifier.doi10.12688/wellcomeopenres.14307.1en_US
dc.description.abstractNext generation sequencing (NGS) is routinely used in clinical genetic testing. Quality management of NGS testing is essential to ensure performance is consistently and rigorously evaluated. Three primary metrics are used in NGS quality evaluation: depth of coverage, base quality and mapping quality. To provide consistency and transparency in the utilisation of these metrics we present the Quality Sequencing Minimum (QSM). The QSM defines the minimum quality requirement a laboratory has selected for depth of coverage (C), base quality (B) and mapping quality (M) and can be applied per base, exon, gene or other genomic region, as appropriate. The QSM format is CX_BY(P Y)_MZ(P Z). X is the parameter threshold for C, Y the parameter threshold for B, P Y the percentage of reads that must reach Y, Z the parameter threshold for M, P Z the percentage of reads that must reach Z. The data underlying the QSM is in the BAM file, so a QSM can be easily and automatically calculated in any NGS pipeline. We used the QSM to optimise cancer predisposition gene testing using the TruSight Cancer Panel (TSCP). We set the QSM as C50_B10(85)_M20(95). Test regions falling below the QSM were automatically flagged for review, with 100/1471 test regions QSM-flagged in multiple individuals. Supplementing these regions with 132 additional probes improved performance in 85/100. We also used the QSM to optimise testing of genes with pseudogenes such as PTEN and PMS2. In TSCP data from 960 individuals the median number of regions that passed QSM per sample was 1429 (97%).  Importantly, the QSM can be used at an individual report level to provide succinct, comprehensive quality assurance information about individual test performance. We believe many laboratories would find the QSM useful. Furthermore, widespread adoption of the QSM would facilitate consistent, transparent reporting of genetic test performance by different laboratories.en_US
dc.format.extent37 - ?en_US
dc.languageengen_US
dc.language.isoengen_US
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en_US
dc.subjectNGSen_US
dc.subjectQuality Sequencing Minimumen_US
dc.subjectbase qualityen_US
dc.subjectdepth of coverageen_US
dc.subjectgenetic testingen_US
dc.subjectmapping qualityen_US
dc.subjectquality assuranceen_US
dc.subjectquality controlen_US
dc.titleThe Quality Sequencing Minimum (QSM): providing comprehensive, consistent, transparent next generation sequencing  data quality assurance.en_US
dc.typeJournal Article
dcterms.dateAccepted2018-03-27en_US
rioxxterms.versionofrecord10.12688/wellcomeopenres.14307.1en_US
rioxxterms.licenseref.startdate2018en_US
rioxxterms.typeJournal Article/Reviewen_US
dc.relation.isPartOfWellcome Open Resen_US
pubs.notesNot knownen_US
pubs.organisational-group/ICR
pubs.organisational-group/ICR/Primary Group
pubs.organisational-group/ICR/Primary Group/ICR Divisions
pubs.organisational-group/ICR/Primary Group/ICR Divisions/Breast Cancer Research
pubs.organisational-group/ICR/Primary Group/ICR Divisions/Breast Cancer Research/Genetic Susceptibility
pubs.organisational-group/ICR/Primary Group/ICR Divisions/Genetics and Epidemiology
pubs.organisational-group/ICR/Primary Group/ICR Divisions/Genetics and Epidemiology/Genetic Susceptibility
pubs.publication-statusPublished onlineen_US
pubs.volume3en_US
pubs.embargo.termsNot knownen_US
icr.researchteamGenetic Susceptibilityen_US
dc.contributor.icrauthorRahman, Saberaen_US


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