Daily Archives: November 8, 2014

Prof. Kristiina Aittomki: Why researching human genome matters
Better understanding of rare diseases better cure for common diseases - that is why researching human genome matters. See this talk by Prof. Kristiina Aitt...

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Prof. Kristiina Aittomki: Why researching human genome matters - Video

Another week, another ancient human genome. We just recently covered the oldest modern human genome yet described. Now, another paper takes a look at the DNA from a different modern human genome and comes to similar conclusions: interbreeding with Neanderthals was already deep in the past as of37,000 years ago. But researchers were able to find stretches of the Neanderthal genome that are no longer present in any modern human populations that we've sampled.

The skeleton in this case comes from the European area of Russia; it was found at a site called Kostenki-Borshchevo north of the Black Sea. The team behind the new paper (which does not include Svante Pbo, who has pioneered ancient genomics) was only able to get a rough draft of the individual's genome, on average sequencing every base 2.4 times. Thus, the sequence is likely to include a large number of errors and gaps. These make the conclusions a bit more tenuous than previous work but shouldn't bias them in any particular direction.

One thing the results make clear is that humanity's migration out of Africa was complicated. K-14, as the skeleton is called, shares very few of the DNA differences that are associated with East Asian populations, as has been the case withthe Siberian modern human skeletons we've looked at. All of which suggests that East Asians and Eurasians split off early and may even have engaged in separate migrations out of Africa or the Middle East. K-14 also lacks common variants found in Native Americans, leaving a single Siberian skeleton as the only one that has an affinity to them.

Despite its location, K-14 also lacks a strong genetic connection to modern Europeans, instead having a general affinity for other early Eurasian populations. In fact, the authors conclude, it may not even make sense to look for specific affinities. "Instead of inferring a few discrete migration events from Asia into Europe," the authors write, "we now see evidence that humans in Western Eurasia formed a large meta-population with gene flow in multiple directions occurring repeatedly and perhaps continuously."

In other words, don't expect to find a couple of populations that were the European ancestors; instead, there was a large pool of Eurasian populations that regularly intermingled.

Speaking of intermingling, we have the Neanderthals. Just as with the recent Siberian results, the absolute percentage of Neanderthal DNA was similar in K-14 and current human populations. But the length of the average stretch of Neanderthal DNA was longer, suggesting that there had been less time for recombination to scramble these sequences. The authors used this to estimate the time when interbreeding took place, and they come up 54,000 years agovery similar to the 60,000-year figure estimated using the ancient Siberian DNA.

The authors performed one other test involving Neanderthal DNA: identifying the areas where current human populations lack Neanderthal DNA and seeing if any samples from ancient skeletons have it there. Most individuals have nothing; about one percent of K-14's Neanderthal DNA comes from these regions,suggesting that, in the intervening 37,000 years, these stretches of Neanderthal DNA have either been selected against or simply lost by random chance.

The sequencing of ancient genomes is now clearly a competitive field. In fact, last week's paper on the Siberian skeleton came out while this paper was still in review, suggesting Science rushed to get it into print while it was still considered relevant. It's a reasonable fear; as similar results pile up, it's likely that each further advance won't be considered as newsworthy.

But the cumulative weight of these and other results may ultimately be more important than most of the earlier finds. Some aspects, like the ancestry of current Europeans, aren't becomingany clearerwith more samples, suggesting that the ancestry itself is confused. Others, like the Native American affinities found in the Altaiskeleton's genome, might suggestthere was a large overlap between Eurasians and Native Americans. Now, with more genomes, it now looks like this skeleton is a rare exception.

So in a few decades, when textbooks are written about humanity's journey out of Africa, the story will probably be built from the results that appeared long after the papers that made headlines.

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37,000-year-old Russian skeleton has Neanderthal DNA thats gone missing

A Google platform will allow hospitals and universities to upload human genomes to the cloud. Image by Wikimedia user Webridge

It turns out that a human genome the complete set of genetic material encoded as DNA sequences is 100 gigabytes.

Thats the amount of storage space the average human genome would occupy when the decoded and raw DNA data is moved onto the cloud. Google, through its product Google Genomics, is offering hospitals and universities the ability to store the genomes they have on file. The hope is to start a network helping researchers around the world to compare genetics and multiply the rate at which discoveries are made.

We saw biologists moving from studying one genome at a time to studying millions, David Glazer, Google Genomics software engineer, told MIT Technology Review. The opportunity is how to apply breakthroughs in data technology to help with this transition.

The cost of the storing the complete raw data of the genome is set at $25 per year, per genome. However, after being cleaned up, the genome data can be pared down to under one gigabyte and stored for only 25 cents per year. Further computations on the genome data would cost extra.

It is unknown how many genomes are currently stored, but the project is already off to a healthy start. A collaboration with the Institute for Systems Biology, funded through a $6.5 million grant from the National Cancer Institute, will see the Cancer Genome Atlas uploaded to Genomics platform, making data related to the molecular basis for cancer available to anybody around the world.

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Google launches service to store and share human DNA in the cloud