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
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
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
"..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.."
Check out our paper about false positive SNP-chip calls of rare pathogenic variants and the implications for DTC testing. Great team
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!