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Leigh Jackson, PhD, Lecturer in Genomic Medicine at University of Exeter and co-author of the BMJ study, said in the news release, “The number of false positives on rare genetic variants produced by SNP chips was shockingly high. The conclusion reached by the Exeter researchers, the BMJ study states, is that “SNP chips are extremely unreliable for genotyping very rare pathogenic variants and should not be used to guide health decisions without validation.” The objective of the Exeter study published in British Medical Journal ( BMJ), titled, “ Use of SNP Chips to Detect Rare Pathogenic Variants: Retrospective, Population Based Diagnostic Evaluation,” was “To determine whether the sensitivity and specificity of SNP chips are adequate for detecting rare pathogenic variants in a clinically unselected population.” UK Researchers Find ‘Shockingly High False Positives’
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Why is this a significant finding for clinical laboratories? Because medical laboratories performing genetic tests that use SNP chips should be aware that rare genetic variants-which are clinically relevant to a patient’s case-may not be detected and/or reported by the tests they are running.
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According to research conducted at the University of Exeter in Devon, UK, Single-nucleotide polymorphism (SNP) chips (aka, SNP microarrays)-technology commonly used in commercial genetic testing-is inadequate at detecting rare gene variants that can increase breast cancer risk.Ī news release announcing the results of the large-scale study states, “A technology that is widely used by commercial genetic testing companies is ‘extremely unreliable’ in detecting very rare variants, meaning results suggesting individuals carry rare disease-causing genetic variants are usually wrong.” Here is another example of a long-established clinical laboratory test that-upon new evidence-turns out to be not as accurate as once thought. Results of the UK study confirm for clinical laboratory professionals the importance of fully understanding the design and function of SNP chips they may be using in their labs