3 ms·
For this task, the low throughput harms performance. There are genotyping methods which will measure tens of thousands of common variants for a couple of bucks.
by AlexCoventry 9y ago
For this task, the low throughput harms performance. There are genotyping methods which will measure tens of thousands of common variants for a couple of bucks. And the more genotypes you have, the surer you can be of a match, even given a slightly higher genotyping error rate.
- dekhn 9y agoI think you may be misunderstanding my point (it's not clear if you are an expert in this area; I have more than a passing knowledge of DNA). In every area I have worked in, Sanger sequencing is considered gold standard and is used whenver the results are being used for medical purposes. That includes genotyping as well as verifying the results of WGS> It's considered a critical QC step. Throughput doesn't matter if you have false-positive or false negative errors that cause erroneous medical decisions.
- AlexCoventry 9y agoI'm very familiar with Sanger sequencing. Base for base it's one of the most accurate methods. It is by no means worthy of being considered a gold standard, it's just somewhat better. And the drawback is that dollar for dollar, it's pretty inefficient. You can genotype all the common variants using an Affymetrix gene chip,and base your inference on vastly more data. For forensic analysis, where the goal is to discriminate genomes, that would be much more accurate. Maybe go back and verify the most discriminatory/confirmatory loci with Sanger sequencing after that.