Round-up Feb 26th – March 2nd

More details of the Precision Medicine Initiative (PMI) announced by White House, Google’s involvement — Vanderbildt and Verily (subsidiary of Alphabet) to oversee a pilot program “evaluating the best ways to engage, enroll, and retain participants in the PMI cohort.”

We tend to interpret loss of function mutations as bad. Each individual carries about 200 loss-of-function variants. Some of these are advantageous, for example those with truncated versions of CASP12 are more resistant to infection and severe sepsis, and those with truncated versions of ACTN3 have increased endurance in athletic performance. Several stop-gain variants have evolved recently in humans, particularly in genes involved in taste and smell, but many others. There are more such variants in Asians than Europeans, and more in Europeans than Africans:

Structural Variation does not appear randomly in the genome, but is sensitive to genome architecture “the local organization of repeat and other sequences, including their relative orientation, size, density and distribution”. One data point: approximately 50% of the human genome consists of repeat sequences, and much structural variation is association with repeat regions of different types. Review:

And while on the subject of genome architecture, some regions are just hard to sequence, align, and call, and moreover many of these areas are clinically important. This serves as the hook for the Genome in a Bottle folks, who continue to make the case for gold standard reference material:

DNA is considered a fairly boring, inert molecule in terms of functional form, but it can fold into a structure that then acts as an enzyme — this structure has been solved for the first time:

A review giving a snapshot of use of sequencing for breast cancer, shows patchy uptake, diverse rationale and patient attitudes:

The gene IRF4 involved in going grey:



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