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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.

The Scan

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.