Filters and False Positives

Over at MassGenomics, Dan Koboldt discusses a talk given by Jay Shendure on applications of next-gen sequencing. One part of the talk was on “saturation mutagenesis” which Shendure’s lab is using to find “single nucleotide changes in the core promoter that alter gene transcription,” Koboldt explains, before describing the three steps of the process. Then Shendure talked about generating localized assemblies of kilobase-length fragments before discussing his recent exome sequencing work. That work used a sequence capture method, followed by filtering, to find a causal gene for a monogenic disease. Koboldt adds that better filters of common variants are needed. “What’s more, with the advent of next-generation sequencing, I hate to tell you, but people are going to be reporting a lot of false positives. I guarantee it. So when you filter all of the variants, you might actually remove the ones you’re looking for,” Koboldt writes.