Category Archives: Genome

A genome taken from a 36,000-year-old skeleton has helped scientists shed new light on interbreeding between humans and Neanderthals.

The ground-breaking study of DNA recovered from a fossil of one of the earliest known Europeans - a man who lived in western Russia - shows that the genetics of the earliest inhabitants of the continent survived the last ice age, helping form the basis of the modern-day population.

Known as the Kostenki genome, the DNA also contained evidence the man shared, as with all people of Eurasia today, a small percentage of Neanderthal genes, confirming previous findings which show a period when Neanderthals and the first humans to leave Africa for Europe briefly interbred.

This means that, even today, anyone with a Eurasian ancestry - from Chinese to Scandinavian and North American - has a small element of Neanderthal DNA.

But despite Western Eurasians going on to share the European landmass with Neanderthals for another 10,000 years, no further periods of interbreeding occurred, the study said.

Robert Foley, a University of Cambridge professor, said: "Were Neanderthal populations dwindling very fast?

"Did modern humans still encounter them?

"We were originally surprised to discover there had been interbreeding.

"Now the question is, why so little?

"It's an extraordinary finding that we don't understand yet."

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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...

By: SitraFund

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

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

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

Breast Cancer Genome Guided Therapy (BEAUTY) Study - Matthew Goetz, M.D., Judy Boughey, M.D.
Dr. Goetz is a consultant in the Division of Medical Oncology at Mayo Clinic in Rochester, Minn., and a professor of oncology and associate professor of pharmacology at Mayo Clinic College...

By: Mayo Clinic

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Breast Cancer Genome Guided Therapy (BEAUTY) Study - Matthew Goetz, M.D., & Judy Boughey, M.D. - Video

Genome Editing with CRISPR-Cas9
This animation depicts the CRISPR-Cas9 method for genome editing a powerful new technology with many applications in biomedical research, including the potential to treat human genetic...

By: McGovern Institute for Brain Research at MIT

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Genome Editing with CRISPR-Cas9 - Video

A team of international scientists has analysed the DNA of 36,000-year-old Russian man. Photo: Supplied

A genome taken from a 36,000-year-old skeleton has helped scientists shed new light on interbreeding between humans and Neanderthals.

The ground-breaking study of DNA recovered from a fossil of one of the earliest known Europeans - a man who lived in western Russia - shows that the genetics of the earliest inhabitants of the continent survived the last ice age, helping form the basis of the modern-day population.

Known as the Kostenki genome, the DNA also contained evidence the man shared, as with all people of Eurasia today, a small percentage of Neanderthal genes, confirming previous findings which show a period when Neanderthals and the first humans to leave Africa for Europe briefly interbred.

This means that, even today, anyone with a Eurasian ancestry - from Chinese to Scandinavian and North American - has a small element of Neanderthal DNA.

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But despite Western Eurasians going on to share the European landmass with Neanderthals for another 10,000 years, no further periods of interbreeding occurred, the study said.

Robert Foley, a University of Cambridge professor, questioned whether Neanderthal populations were quickly dwindling and whether modern humans still encountered them.

"We were originally surprised to discover there had been interbreeding," Foley said.

"Now the question is, why so little?

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DNA from 36,000-year-old skeleton sheds light on interbreeding between humans and Neanderthals

For $25 a year, Google will keep a copy of any genome in the cloud.

Google is approaching hospitals and universities with a new pitch. Have genomes? Store them with us.

The search giants first product for the DNA age is Google Genomics, a cloud computing service that it launched last March but went mostly unnoticed amid a barrage of high profile R&D announcements from Google, like one late last month about a far-fetched plan to battle cancer with nanoparticles (see Can Google Use Nanoparticles to Search for Cancer?).

Google Genomics could prove more significant than any of these moonshots. Connecting and comparing genomes by the thousands, and soon by the millions, is whats going to propel medical discoveries for the next decade. The question of who will store the data is already a point of growing competition between Amazon, Google, IBM, and Microsoft.

Google began work on Google Genomics 18 months ago, meeting with scientists and building an interface, or API, that lets them move DNA data into its server farms and do experiments there using the same database technology that indexes the Web and tracks billions of Internet users.

We saw biologists moving from studying one genome at a time to studying millions, says David Glazer, the software engineer who led the effort and was previously head of platform engineering for Google+, the social network. The opportunity is how to apply breakthroughs in data technology to help with this transition.

Some scientists scoff that genome data remains too complex for Google to help with. But others see a big shift coming. When Atul Butte, a bioinformatics expert at Stanford heard Google present its plans this year, he remarked that he now understood how travel agents felt when they saw Expedia.

The explosion of data is happening as labs adopt new, even faster equipment for decoding DNA. For instance, the Broad Institute in Cambridge, Massachusetts, said that during the month of October it decoded the equivalent of one human genome every 32 minutes. That translated to about 200 terabytes of raw data.

This flow of data is smaller than what is routinely handled by large Internet companies (over two months, Broad will produce the equivalent of what gets uploaded to YouTube in one day) but it exceeds anything biologists have dealt with. Thats now prompting a wide effort to store and access data at central locations, often commercial ones. The National Cancer Institute said last month that it would pay $19 million to move copies of the 2.6 petabyte Cancer Genome Atlas into the cloud. Copies of the data, from several thousand cancer patients, will reside both at Google Genomics and in Amazons data centers.

The idea is to create cancer genome clouds where scientists can share information and quickly run virtual experiments as easily as a Web search, says Sheila Reynolds, a research scientist at the Institute for Systems Biology in Seattle. Not everyone has the ability to download a petabyte of data, or has the computing power to work on it, she says.

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Google Wants to Store Your Genome

The 37,000-year-old body of a man found in 1954 in south-west Russia has delivered the oldest European DNA. The analysis of his genome, published this week, shows that much of Europe's diverse genetic makeup stretches back over 30,000 years and survived the last ice age.

The study is the latest in a slew of attempts to tease apart the origins of modern Europeans. We know that modern humans left Africa around 60,000 years ago at least, and that an early group migrated east, possibly along the coast, to south-east Asia and Oceania. We also know that Europeans and Asians parted ways more recently.

Today, Europeans are a hybrid breed that show traces of DNA from several distinct early populations. How Europeans came to acquire their diverse genetic heritage is something that several groups studying ancient human DNA are currently trying to decipher.

A leading proposal is that Europeans hail from three separate populations that migrated into Europe and mated with each other at different times in history.

To add to our understanding, a group of scientists led by the Centre for GeoGenetics at the University of Copenhagen in Denmark delved into the DNA of Kostenki-14, a man whose 37,000-year-old body was found on the banks of the Don river in southern Russia, several hundred kilometres from the border with Ukraine.

They compared markers in his DNA to other ancient humans found in Eurasia and to modern humans. They found that Kostenki-14's DNA was closely related to early European hunter-gatherers, contemporary Europeans and some contemporary Siberians. What they did not find was any relation to East Asians, suggesting that by the time Kostenki-14 was born the European and Asian lineages had already split from each other.

By contrast, another ancient genome published just a few weeks ago, belonging to a 45,000-year-old west-Siberian known as Ust'-Ishim, was related to both Europeans and Asians. That suggests the two groups parted ways between 45,000 and 37,000 years ago and makes Kostenki-14 the oldest European to have his genome sequenced.

What's more, Kostenki-14's Y-chromosome shares features with a 7000-year-old hunter-gatherer from Spain. "This shows some level of continuity in European populations across almost 30,000 years," says Iosif Lazaridis at Harvard University.

During that time, European populations ebbed and flowed as ice sheets grew and shrank, at times covering large swathes of the continent. Although new cultures emerged, the study shows that the population remained broadly of the same original stock.

Because European genomes seem to have remained relatively similar over such a long period of time, Eske Willerslev at the Centre for GeoGenetics believes their results undermine the idea proposed by Lazaridis and colleagues earlier this year that the modern European genome arose from three populations intermingling and swapping genes. Instead, he believes that a mega-population stretched from Europe all the way to Central Asia 36,000 years ago, and that sub-groups within this mated to produce the modern European mix.

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Oldest European genome illuminates diverse ancestry

Eight percent of your genome derives from retroviruses that inserted themselves into human sex cells millions of years ago. Right now the koala retrovirus (KoRV) is invading koala genomes, a process that can help us understand our own viral lineage and make decisions about managing this vulnerable species.

In a recent study, published in Molecular Biology and Evolution, scientists from the University of Illinois discovered that 39 different KoRVs in a koala's genome were all endogenous, which means passed down to the koala from one parent or the other; one of the KoRVs was found in both parents.

Koalas are the only known organisms where a retrovirus is transitioning from exogenous to endogenous. An exogenous retrovirus infects a host, inserts its genetic information into the cell's DNA, and uses the host cell's machinery to manufacture more viruses. When an exogenous retrovirus infects an egg or sperm cell and the viral genetic information is then passed down to the host's offspring, the virus becomes an endogenous retrovirus (ERV).

Becoming part of the koala genome

Like humans, koalas have evolutionary defenses against endogenization.

"During the early stages of endogenization, there are huge numbers of retroviruses. KoRVs are present all across koalas' genomes, with many thousands or tens of thousands of KoRVs in the population," said Alfred Roca, a Professor of Animal Sciences and member of the Institute for Genomic Biology at the University of Illinois at Urbana-Champaign. "Over time most of them will disappear because these copies of the virus may be present in as few as one individual chromosome. If that one individual happens to not reproduce, or if it reproduces and the other chromosome is passed down, then that ERV will disappear."

In order to end up with 100 ERVs in an organism, the species may have to start with 10,000 ERVs in its ancestors, Roca said. It takes retroviruses, like KoRV, many thousands of years to become a fixed part of the koala genome, like the eight percent of retroviral DNA that all humans share.

The ERVs that are successfully passed down are protected by the koala's DNA repair mechanisms so that their rate of mutation is extremely low. Based on the dearth of mutations in the endogenous koala retroviruses, Roca's team was able to estimate that the KoRVs integrated into the host germ line less than 50,000 years ago. "This is quite recent compared with other ERVs that are millions of years old and have accumulated mutations," said first author Yasuko Ishida, a research specialist in Roca's lab.

Overcoming retroviral fitness effects

In koalas, KoRV has been linked to leukemia, lymphoma, and immune suppression, which can lead to increased susceptibility to chlamydia.

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Koala study reveals clues about origins of the human genome