Round-up Feb 19 – March 12

Two truly ginormous releases of data

  • The Biobank, ~500,000 individuals with extensive phenotypes, has released the first ~50,000 whole exome sequences (complementing the Chip data that has been around for longer).
  • The National Heart, Lung, and Blood Institute’s Trans-Omics for Precision Medicine (TOPMed) program has a data set of ~50,000 whole genomes (of a planned 145,000). An exciting fact about this data set is that ~30% are from individuals with African ancestry. The individuals are extensively phenotyped. Much of the genetic data (I’m unclear how much) is available on dbGap.

The size of NGS data has truly exploded. Here’s hoping that this sort of size dataset will allow us to peel back the curtain on the clinical relevance of rare variation.

Controversy — mostly China



  • 23andMe have launched a Type 2 Diabetes score. Using a freshly developed polygenic score based on their 2.5 million customers, it adjusts the score based on ethnicity and age to give not just a relative odds, but a percentage chance of developing the condition in the next x years. I was unable to confirm this as it doesn’t work on my report — perhaps because it only works for the latest chip.
  • The PeopleSeq consortium has partnered with the major projects that offer genome sequencing to healthy individuals (“predispositional screening”). They send out surveys to participants before and after screening. In their first published results covering several hundred people, they found that while most individuals discussed the results with their doctor, only 13.5% made an appointment specifically for that purpose. About 40% reported that they learnt something new about their health, but fewer than 10% made any changes. More than half were disappointed that they did not receive more actionable information. One message the authors want us to take home: patients felt empowered rather than distressed by their results.
  • A group of 8 institutions wants to see whole genome sequencing in the clinic, and have formed the Medical Genome Initiative to help establish best practices etc to make this happen.


And in other interesting things, here is a nice write-up of the extent to which humans are innately violent — tracing the debates, and pointing to the question, do we need an answer to this question? Also, whether our views on this question affect our beliefs about peace-keeping efforts.