Round-up March 28th – April 3rd

I will be taking a month off from Round-ups — next install in early May.

In the next step of the CRISPR patent dance, the European Patent Office has announced its intent to grant the UC Berkeley crew a patent that would have broad coverage of CRISPR; though this will almost certainly be challenged.

Analysis of protein truncating variants from the ExAC group to identify which genes have the strongest selection against loss of function finds these have a strong overlap with genes known to be lethal in mouse knockouts.

A large scale joint analysis of Structural Variation and gene expression found that SVs are causal at 3.5–6.8% of expression quantitative trait loci (eQTLs) – a larger estimate than previously thought. Moreover, the effect size of SVs was larger than for SNVs or indels. Most of these SVs effected regulatory elements.

CiVIC is an open data project linking somatic mutations to particulae cancer types. Illumina has just announced that they will contribute over 8,000 associations to CiVIC, tripling the size of the database.

Variation linked to more production of the vitamin folate, and a higher BMI, have been found in Tibetan genomes, potential clues as to how they have evolved to thrive in an environment with 40% less oxygen than sea level.

Stanford researchers introduced Transcribed Genome Array (TGA), for probing transcriptome wide binding affinities using a hardware/software system based on the MiSeq.  “Our work couples transcriptome-wide measurements of binding affinity, sequence, and structural determinants of binding, and phenotypic outcomes to provide a comprehensive portrait of Vts [a developmental regulator] function.”

A win for the intersection of cognitive neuroscience and genetics, with the discovery that the expression of several genes is linked to brain activity during memory processing.

In some parts of the world, infection with the fungal aflatoxin causes 80% of liver cancers. A clear mutational signature of this infection has been reported, holding out promise for early detection and assessing exposure.

A GWAS of over 12,000 cases identified new risk loci of glioma suggest a polygenic susceptibility, and different signatures for glioblastomas and non-glioblastoma tumors.

5% of reading ability is attributable to genetics (compare 1% attributable to gender)

Repositive, a new service for aggregating genomic datasets.