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Massive-scale research finds genetic testing expertise falsely detects very uncommon variants


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A expertise that’s broadly utilized by industrial genetic testing firms is “extremely unreliable” in detecting very uncommon variants, which means outcomes suggesting people carry uncommon disease-causing genetic variants are often flawed, in response to new analysis printed within the BMJ.

After listening to of circumstances the place girls had surgical procedure scheduled after wrongly being instructed they’d very uncommon genetic variations within the gene BRCA1 that might considerably improve danger of breast most cancers, a crew on the College of Exeter performed a large-scale evaluation of the expertise utilizing knowledge from practically 50,000 folks. They discovered that the expertise wrongly recognized the presence of very uncommon genetic variants within the majority of circumstances.

The crew analyzed SNP chips, which take a look at genetic variation at hundreds-of-thousands of particular areas throughout the genome. Whereas glorious at detecting widespread genetic variation that may improve the chance of illnesses resembling sort 2 diabetes, geneticists have lengthy identified they’re much less dependable at detecting rarer variation. Nonetheless, this downside is much less well-known outdoors the genetic analysis group, and SNP chips are broadly utilized by industrial firms that supply genetic testing direct to customers.

Caroline Wright, Professor in Genomic Medication on the College of Exeter Medical College, senior creator on the paper, stated: “SNP chips are fantastic at detecting common genetic variants, yet we have to recognize that tests that perform well in one scenario are not necessarily applicable to others. We’ve confirmed that SNP chips are extremely poor at detecting very rare disease-causing genetic variants, often giving false positive results that can have profound clinical impact. These false results had been used to schedule invasive medical procedures that were both unnecessary and unwarranted.”

The crew in contrast knowledge from SNP chips with knowledge from the extra dependable software of subsequent era sequencing in 49,908 members of UK Biobank, and an extra 21 individuals who shared outcomes of their shopper genetic assessments through the Private Genome Challenge.

The research concluded that SNP chips carried out extraordinarily effectively in detecting widespread genetic variants. Nonetheless, the rarer the variation was, the much less dependable the outcomes grew to become. In very uncommon variants, current in fewer than 1 in 100,000 people, typical of these inflicting uncommon genetic illness, 84 per cent had been false positives in UK Biobank. Within the knowledge from industrial prospects, 20 of 21 people analyzed had at the very least one false optimistic uncommon disease-causing variant that had been incorrectly genotyped.

Dr. Leigh Jackson, Lecturer in Genomic Medication on the College of Exeter and co-author of the paper, stated: “The number of false positives on rare genetic variants produced by SNP chips was shockingly high. To be clear: a very rare, disease-causing variant detected using a SNP chip is more likely to be wrong than right. Although some consumer genomics companies perform sequencing to validate important results before releasing them to consumers, most consumers also download their “uncooked” SNP chip data for secondary analysis, and this raw data still contain these incorrect results. The implications of our findings are very simple: SNP chips perform poorly for detecting very rare genetic variants and the results should never be used to guide a patient’s medical care, unless they have been validated.”

The paper printed in the present day within the BMJ is entitled “Using SNP chips to detect very rare pathogenic variants: retrospective population-based diagnostic evaluation.”


Utilizing DNA sequencing knowledge with digital well being data to search out uncommon variants behind inherited illnesses


Extra info:
BMJ (2021). www.bmj.com/content/372/bmj.n214

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College of Exeter

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Massive-scale research finds genetic testing expertise falsely detects very uncommon variants (2021, February 15)
retrieved 15 February 2021
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