john hawks weblog

paleoanthropology, genetics and evolution

Complete genomes

Thu, 2009-11-05 22:02 -- John Hawks

John Timmer gives a great summary of the new paper in Science covering the Complete Genomics sequencing method.

A surprising (to me, at least) fact:

But, because each of these nanoballs was so small, it's possible to do massive amounts of sequencing in parallel, simply by washing different solutions across the surface they were stuck to. The authors were able to get anywhere from 45- to 87-fold coverage of the genome—meaning that, on average, each base in the genome had been sequenced 45 or 87 times, respectively. That's just an average, of course, as chance will ensure that some sequences are under- or overrepresented. Still, given an algorithm designed to work with these specific results and the reference human genome sequence, Complete Genomics was able to get excellent coverage of the genome.

Oh, yeah -- the lede from the paper:

Validation of one genome data set demonstrates a sequence accuracy of about 1 false variant per 100 kilobases. The high-accuracy, affordable cost of $4,400 for sequencing consumables and scalability of this platform enable complete human genome sequencing for the detection of rare variants in large-scale genetic studies.

Neandertals

For years, I've worked on their bones. Now I'm working on their genes. Read more about the science studying these ancient people.

Denisova

From a finger bone of an ancient human came the record of a completely unexpected population. My lab is working on the science of the Denisova genome.

Acceleration

The advent of agriculture caused natural selection to speed up greatly in humans. We're uncovering some of the ways that populations have rapidly changed during the last 10,000 years.

Malapa

Just outside Johannesburg, the Malapa site is producing some of the most exciting finds in human evolution. This site is the headquarters of the Malapa Soft Tissue Project.