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dc.contributor.authorMn, Weedon
dc.contributor.authorL, Jackson
dc.contributor.authorJw, Harrison
dc.contributor.authorKs, Ruth
dc.contributor.authorJ, Tyrrell
dc.contributor.authorAt, Hattersley
dc.contributor.authorCf, Wright
dc.identifier.citationMn, W. et al. (2021) ‘Use of SNP chips to detect rare pathogenic variants: retrospective, population based diagnostic evaluation.’, BMJ (Clinical research ed.), 372, p. n214. doi: 10.1136/bmj.n214.
dc.description.abstractOBJECTIVE: To determine whether the sensitivity and specificity of SNP chips are adequate for detecting rare pathogenic variants in a clinically unselected population. DESIGN: Retrospective, population based diagnostic evaluation. PARTICIPANTS: 49 908 people recruited to the UK Biobank with SNP chip and next generation sequencing data, and an additional 21 people who purchased consumer genetic tests and shared their data online via the Personal Genome Project. MAIN OUTCOME MEASURES: Genotyping (that is, identification of the correct DNA base at a specific genomic location) using SNP chips versus sequencing, with results split by frequency of that genotype in the population. Rare pathogenic variants in the BRCA1 and BRCA2 genes were selected as an exemplar for detailed analysis of clinically actionable variants in the UK Biobank, and BRCA related cancers (breast, ovarian, prostate, and pancreatic) were assessed in participants through use of cancer registry data. RESULTS: Overall, genotyping using SNP chips performed well compared with sequencing; sensitivity, specificity, positive predictive value, and negative predictive value were all above 99% for 108 574 common variants directly genotyped on the SNP chips and sequenced in the UK Biobank. However, the likelihood of a true positive result decreased dramatically with decreasing variant frequency; for variants that are very rare in the population, with a frequency below 0.001% in UK Biobank, the positive predictive value was very low and only 16% of 4757 heterozygous genotypes from the SNP chips were confirmed with sequencing data. Results were similar for SNP chip data from the Personal Genome Project, and 20/21 individuals analysed had at least one false positive rare pathogenic variant that had been incorrectly genotyped. For pathogenic variants in the BRCA1 and BRCA2 genes, which are individually very rare, the overall performance metrics for the SNP chips versus sequencing in the UK Biobank were: sensitivity 34.6%, specificity 98.3%, positive predictive value 4.2%, and negative predictive value 99.9%. Rates of BRCA related cancers in UK Biobank participants with a positive SNP chip result were similar to those for age matched controls (odds ratio 1.31, 95% confidence interval 0.99 to 1.71) because the vast majority of variants were false positives, whereas sequence positive participants had a significantly increased risk (odds ratio 4.05, 2.72 to 6.03). CONCLUSIONS: SNP chips are extremely unreliable for genotyping very rare pathogenic variants and should not be used to guide health decisions without validation.
dc.rights© Author(s) (or their employer(s)) 2019. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.
dc.subjectMiddle Aged
dc.subjectPredictive Value of Tests
dc.subjectRetrospective Studies
dc.subject*High-Throughput Nucleotide Sequencing
dc.subject*Oligonucleotide Array Sequence Analysis
dc.subjectBreast Neoplasms/*diagnosis/genetics
dc.subjectFalse Negative Reactions
dc.subjectFalse Positive Reactions
dc.subjectGenes, BRCA1
dc.subjectGenes, BRCA2
dc.subjectGenetic Testing/methods
dc.subjectGenotyping Techniques
dc.subjectOvarian Neoplasms/*diagnosis/genetics
dc.subjectPancreatic Neoplasms/*diagnosis/genetics
dc.subjectPolymorphism, Single Nucleotide
dc.subjectProstatic Neoplasms/*diagnosis/genetics
dc.subjectSequence Analysis, DNA
dc.titleUse of SNP chips to detect rare pathogenic variants: retrospective, population based diagnostic evaluation
dc.typeJournal Article
dc.identifier.journalBMJ (Clinical research ed.)
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