Due to a communication breakdown, no-one wrote a Friday Links post yesterday, so today we have a Saturday Links to make up for it.
Steve Hsu has a very appropriately named post, News from the future, about the Beijing Genomics Institute. The BGI is the largest genome sequencing center in China, and one of the largest in the world, and is growing faster than any other, and loading up on a shedload of high-tech HiSeq machines.
Steve reports that the BGI are claiming that their sequencing rate will soon be at 1000 genomes per day, with a cost of about $5k (£3.2k) each. To put a slight downer on these amazing numbers, he clarifies that this might be referring to 10X genomes, which would realistically mean ~300 high quality genomes a day, at $15k (£9.6). Either way, if you want to keep an eye on how fast whole-genome sequencing is progressing, perhaps with an eye to when you’re ready to shell out to get your own done.
A question for the comments: how cheap would a whole-genome sequence have to get before you’d order one?
On the subject of whole-genome sequencing, Dan Kobolt has written about annotating a mutation as functional. This is a pretty common problem with whole-genome sequencing; you identify a variant that is present in a tumour sample, or in a few patients with a Mendelian disease, or perhaps in a personal genome. However, we are packed full of mutations, most of which have no little or effect on our biology. So, how can we find out if this mutation is functional, if it is contributing to the disease, or any other phenotype? Most of the techniques are computational, and thus can be rolled into your variant calling stage, though good experimental validation is also very valuable.
Finally, an interesting little video profile of Jill Steinberg, who had a double mastectomy after discovering that she was carried a BRCA mutation that put her at high risk of developing breast cancer. This is common, and women with a family history of breast cancer will often get BRCA tested, and many have (pretty drastic) preventative surgery. However, the notable thing about Jill’s case was that she had no family history of cancer, and learned of the mutation via a DTC genetic test.