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Results of the UK NEQAS for Molecular Genetics reference sample analysis
- Source :
- Journal of Clinical Pathology
- Publication Year :
- 2018
- Publisher :
- BMJ Publishing Group, 2018.
-
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.
- 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
Subjects
Details
- Language :
- English
- ISSN :
- 00219746
- Database :
- OpenAIRE
- Journal :
- Journal of Clinical Pathology
- Accession number :
- edsair.doi.dedup.....a28ecb29d9f6d19085d811a3ba2f49c7