Hi Everybody,
I am validating a BRCA 1 2 Panel from Thermo Fisher.
The Hot Spot variants are ok (good coverage with 80-100 reads), but I am worried about No Call variants. In my first chip (8 samples) we observed that all individuals had at least 5 similar variants (No Call) with low coverage and low Phred score (
We mainly work with RNA-seq so my answer may not be appropriate for your question, but I will first check with Sanger sequencing to match up with the Ion NGS data before going any further as you are intent to do. Have you already checked about heterozygosity of BRCA1 and 2?
Yes, I checked the heterozygosity. I will try Sanger to confirm these No Calls.
Thank you!
I have read "benign" and "non-pathogenic" to classify the variants regarding a genetic cancer investigation. Do you know if these two terms have the same meaning? I know that ACMG don't recommend classify a variant as non-pathogenic, they suggest VUS, likely benign, benign, like pathogenic or pathogenic.
Best regards,
Low-coveage and low-phred Score probably means sequencing artifact. Ion Torrent data is known for making insertion/deletion artifacts around homopolymers. Is there a nearby stretch of the same nucleotide (e.g.: AAAAA), I know there are some in the BRCA genes. Moreover, I thought as a classical tumor suppressor BRCA genes actually should not have hotspot mutations (unlike oncogenes).
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