1. Results of the UK NEQAS for Molecular Genetics reference sample analysis
- Author
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Nakul Nataraj, Jennifer A. Fairley, Mrudul Bhide, Kara L. Norman, Zandra C. Deans, Jacqueline A Hall, Susan D. Richman, and Aron Lau
- Subjects
Genetic Markers ,Quality Control ,0301 basic medicine ,Neuroblastoma RAS viral oncogene homolog ,Laboratory Proficiency Testing ,medicine.medical_specialty ,Routine testing ,EQA ,colorectal cancer ,Cell Line ,Pathology and Forensic Medicine ,03 medical and health sciences ,0302 clinical medicine ,Gene Frequency ,Predictive Value of Tests ,Molecular genetics ,External quality assessment ,melanoma ,Biomarkers, Tumor ,medicine ,Humans ,Medical physics ,Molecular Biology ,Quality Indicators, Health Care ,Observer Variation ,Molecular pathology ,business.industry ,Genetic Variation ,High-Throughput Nucleotide Sequencing ,Reproducibility of Results ,General Medicine ,Reference Standards ,lung cancer ,030104 developmental biology ,Reference sample ,030220 oncology & carcinogenesis ,Original Article ,business - Abstract
AimsIn addition to providing external quality assessment (EQA) schemes, United Kingdom National External Quality Assessment service (UK NEQAS) for Molecular Genetics also supports the education of laboratories. As an enhancement to the Molecular Pathology EQA scheme, a human cell-line reference sample, manufactured by Thermo Fisher Scientific (AcroMetrix), was provided for analysis. This contained many variants, present at frequencies between 1% and 17.9%.MethodsOne hundred and one laboratories submitted results, with a total of 2889 test results on 53 genes being reported. Known polymorphisms, 46/2889 (1.59%) results, were excluded. Variants detected in the seven most commonly reported (and clinically relevant) genes, KRAS, NRAS, BRAF, EGFR, PIK3CA, KIT and PDGFRA, are reported here, as these genes fall within the scope of UK NEQAS EQA schemes.ResultsNext generation sequencing (NGS) was the most commonly performed testing platform. There were between 5 and 27 validated variants in the seven genes reported here. Eight laboratories correctly reported all five NRAS variants, and two correctly reported all eight BRAF variants. The validated mean variant frequency was lower than that determined by participating laboratories, with single-gene testing methodologies showing less variation in estimated frequencies than NGS platforms. Laboratories were more likely to correctly identify clinically relevant variants.ConclusionsOver 100 laboratories took the opportunity to test the ‘educational reference sample’, showing a willingness to further validate their testing platforms. While it was encouraging to see that the most widely reported variants were those which should be included in routine testing panels, reporting of variants was potentially open to interpretation, thus clarity is still required on whether laboratories selectively reported variants, by either clinical relevance or variant frequency.
- Published
- 2018