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This Week in Genome Research: Jun 22, 2016

Researchers from the UK and the US introduce a tool called TransRate, for assessing the quality of de novo transcriptome assemblies based on the assembly itself and sequenced reads with no reference. The approach assigns a diagnostic quality score for each contig before bringing these together to consider the entire score, the team explains, noting that the approach can detect common artifacts such as base errors, chimeras, structural errors, or incomplete assemblies. For example, the group used the approach to look at how factors such as read length, quality, and assembly method affected the quality of more than 150 published de novo transcriptome assemblies.

A Baylor College of Medicine-led team combines whole-genome sequencing with saturation chemical mutagenesis screens to characterize genes in the soil amoeba Dictyostelium discoideum. The researchers demonstrated the utility of the approach by performing three D. discoideum screens, focusing on phenotypes such as light-induced cell death resistance, loss of aggregation on bacterial lawns, and adhesion protein mismatch suppression. The study's authors say the approach "should be applicable to many microbial systems, and it is expected to revolutionize the field of functional genomics in Dictyostelium by greatly expanding the mutation spectrum relative to other common mutagenesis methods."

Stanford University and University of California at San Francisco researchers report on results from a chromatin immunoprecipitation and sequencing study of TBR1, a transcription factor involved in cortical development regulation that has been implicated in autism spectrum disorder risk through past studies on de novo loss-of-function variants in ASD. In a mouse model of cortical neurogenesis, the team found that TBR1 frequently turned up near other genes linked to ASD development and at sites in the genome with low loss-of-function mutation rates in available human sequences. Likewise, the absence of the TBR1 gene in knockout mice led to altered expression of ASD-related genes.