Using SNP-chips to call very rare variants? Watch out! They can perform really really badly (>85% false positives!). See our new preprint from the team using the amazing resource
84% of very rare pathogenic genetic variants detected by genotyping-chips are false positives in this study - sequencing remains gold standard for clinical use of these variants #cautionwarranted
Can we please talk about this problematic manuscript? "Very rare pathogenic genetic variants detected by SNP-chips are usually false positives: implications for direct-to-consumer genetic testing"
THREAD: In response to comments on our preprint (), we’ve looked at some DTC data from the fantastic site thanks to a really helpful comment from . In short, we are seeing similar performance on Illumina and Affy chips. (1/5)
Rough set of results for DTC genetic testing companies: and co. show SNP-chips have >85% false positive genotype calls for very rare variants (AF < 0.001%) using 50k exome and genotype data
Very rare pathogenic genetic variants detected by SNP-chips are usually false positives: implications for direct-to-consumer genetic testing | bioRxiv
If you get a direct-to-consumer genetic test, and it thinks you have a rare disease ... you probably don't. Important paper from details at
Check out our paper about false positive SNP-chip calls of rare pathogenic variants and the implications for DTC testing. Great team
"..for variants with a frequency <0.001% in UK Biobank the PPV is very low, and only 16% of 4,711 heterozygote genotypes from the SNP-chip confirm with sequencing data.."
Genotyping chips used by DTC companies have ~85% false positive rate for rare variants (like breast cancer risk variants) This paper is a must-read if you are interested in population-scale medical genetics or DTC testing Well done team!
Needs peer review, but potentially extremely important preprint: Very rare pathogenic genetic variants detected by SNP-chips are usually false positives: implications for direct-to-consumer genetic testing | bioRxiv #BRCA1 #BRCA2
Can't use SNP chips for rare variants screening. This has implications for embryo selection, which must rely on deep sequencing, not SNP chips, for these health screening uses.
Very rare pathogenic genetic variants detected by SNP-chips are usually false positives: implications for direct-to-consumer genetic testing There is some thoughtful discussion in the comments section, as well.