This is the Number One Risk to Your Clinical Sequencing Assay
If youre relying on remnant patient samples to tell you how well your lab's bioinformatics pipeline can call clinically important variants, you might be missing more than you realize.
In our experience, the bioinformatics pipeline can be the weakest link in assay development for many labs. Just because a variant is sequenced correctly doesnt always mean that it will be called. And false-positives are just as bad.
- Sometimes its an issue of allele frequency. For example, weve seen cases where labs could detect certain mutations at 10% allele frequency, but as soon as the frequency dropped to 7%, they stopped detecting it.
- Other cases are caused by the complexity of the variant. For example, even at low allele frequencies, a lab may pick up relatively easy-to-detect single-nucleotide variants (SNVs) but can have problems with insertion/deletion (INDEL) calling errors.
In both examples, the mutations arent missed because of sequencing or library preparation problems. As weve witnessed time and time again, when labs optimize their bioinformatics pipelines, they start picking up the low-frequency and difficult-to-detect variants again.
The catch is, you first have to know youre missing something. In assay development, what you dont know can seriously weaken your test.
