Tag Archives: Genetic sequencing

DNA strands.

Blood DNA sequencing reveals there’s a lot more microbes living inside you — and we’ve never seen over 99% of them before

A new paper looking at the DNA fragments floating around in human blood reports that there are way more microbes living inside us than we thought — and we’ve never seen most of them before.

DNA strands.

Image credits Colin Behrens.

The idea behind this paper started taking shape as a team led by Stephen Quake, a professor of bioengineering and applied physics, a member of Stanford Bio-X and the paper’s senior author, were looking for a new non-invasive method to determine the risk of rejection in transplant patients. This is traditionally done using a biopsy, which involves a very large needle and quite a bit of ‘ow’.

Needless to say, nobody was very big on the procedure. So Quake’s lab wanted to see if they can work around the issue by looking at the bits of DNA floating around in patients’ blood — what’s known as cell-free DNA. The team expected to find the patient’s DNA, the donor’s DNA, and genetic material from all the bacteria, viruses, and all the other critters that make up our personal microbiome. A spike of donor DNA would, in theory, be one of the first signs of organ rejection.

But what the team didn’t expect to find was the sheer quantity and diversity of microbiome-derived DNA in the blood samples they used.

Bugs galore

“We found the gamut,” says professor Quake. “We found things that are related to things people have seen before, we found things that are divergent, and we found things that are completely novel.”

 

Throughout their project (which spanned several studies), the team gathered samples from 156 heart, lung, and bone marrow transplant recipients, and 32 from pregnant woman — pregnancy also has a huge effect on the immune system, similar to immunosuppressants, although we don’t really know how.

Of all the non-human DNA bits found in these samples, a whopping 99% couldn’t be matched to anything in existing genetic databases. In other words, they came from strains we didn’t even know existed. So the team went to work on characterizing all that genetic material. According to them, the “vast majority” falls into the phylum proteobacteria. The largest single group of viruses identified in this study belong to the torque teno family (TTVs). In fact, Quake says their work has “doubled the number of known viruses in that family” in one fell swoop.

Known torque teno viruses infect either animals or humans, but many of the TTVs the team identified don’t fit in either group.

 

“We’ve now found a whole new class of human-infecting ones that are closer to the animal class than to the previously known human ones, so quite divergent on the evolutionary scale,” Quake adds.

The team believes that we’ve missed all these microbes up to now because narrow studies, by their very nature, miss the bigger picture. Researchers often focus their attention on a few interesting microbes and glance over everything else. Blood samples, by contrast, allowed them to look at everything swimming around inside of us, instead of looking at a few individual pieces. It was this net-cast-wide approach — which the team humorously refer to as a “massive shotgun sequencing” of cell-free DNA — that allowed the team to discover how hugely diverse human microbiomes are.

In the future, the team plans to take a similar look at other animals to see what species their microbiomes harbor.

“There’s all kinds of viruses that jump from other species into humans, a sort of spillover effect, and one of the dreams here is to discover new viruses that might ultimately become human pandemics,” Quake says.

“What this does is it arms infectious disease doctors with a whole set of new bugs to track and see if they’re associated with diseases. That’s going to be a whole other chapter of work for people to do.”

The paper “Numerous uncharacterized and highly divergent microbes which colonize humans are revealed by circulating cell-free DNA” has been published in the journal Proceedings of the National Academy of Sciences.

Blood test can find cancer even before any symptoms emerge

The accuracy can still be improved, but early results are very promising.

Genetic sequencing could pave the way for a new age of cancer detection. Image via Wikipedia.

Nowadays, with adequate treatment, many cancers are highly treatable if detected early. The problem is that symptoms are rarely clear, and cancer can get time to develop before being spotted. This is why a screening test that could detect cancer before any symptoms can make a huge difference — especially for breast, colon, lung and ovarian cancers. The new method isn’t a slam dunk yet, but it successfully managed to identify cancer in more than half of patients.

There were also no false positives, lead author Victor Velculescu of Johns Hopkins in Baltimore said.

“Almost all of the studies have involved patients with late-stage cancer or used information from tumor specimens to go back and look in the blood of those patients,” he told MedPage Today. “This is one of the first studies to use an unbiased approach — you don’t know where the mutations are going to be — and to look at the blood of early-stage cancer patients to see whether we could detect alterations.”

He and his colleagues used what is called a liquid biopsy — the sampling and analysis of blood — to test the patients. They developed an approach called targeted error correction sequencing (TEC-Seq for short) to look for tumor DNA. They looked at 58 cancer-related genes, sequencing the DNA over 30,000 times looking for any traces of tumors floating around.

Basically, when tumors emerge and decay, they can leave pieces of DNA floating in the blood and these pieces can be detected, at least in some cases.

“The surprising result is that we can find a high fraction of early-stage patients having alterations in their blood,” said Velculescu, who led the study team.

From a total of 194 patients, including 138 patients with stage I or II disease, they successfully detected 45 percent of the lung cancer patients with stage I disease, 67 percent of ovarian cancer patients with stage I disease and 67 percent of breast cancer patients with stage I disease. They also tested 44 healthy patients, with the test giving no false positives.

Again, that’s not stellar, but it’s an encouraging result. Keep in mind that this was a completely blind test, they had no idea what they were looking for.

“It’s actually very hard to find these mutations in the blood, especially when you don’t know what the mutations are upfront,” he added. “There are a number of confounding errors that can come up. Besides sequencing and technical errors, you can get alterations that come from the germline and can also get mutations that come from blood cells. We developed a way in which you could distinguish tumor driver mutations from these other alterations that might be in the blood.”

Velculescu also says that studies need to be replicated on a larger sample size to better assess the accuracy and safety of the test.

Several liquid biopsies already exist on the market, but there’s nothing to assess a person who hasn’t already been diagnosed. It’s easy to find mutations if you know what you’re looking for, but if you’re just poking in the dark, things get much more difficult. Still, even with an imperfect detection rate, the test could make a big difference. Detecting cancers sooner rather than later can save over 1 million lives every year — and even if it just works half of the time, it could still save many lives. The price of genetic sequence is also an obstacle, but it has steadily gone down year after year. It may not be tomorrow or next year, but at some point in the not-so-distant future, such tests could become routine.

Journal Reference: Jillian Phallen et al — Direct detection of early-stage cancers using circulating tumor DNA. DOI: 10.1126/scitranslmed.aan2415

 

The first Americans came from Russia’s frozen expanse, Siberia, some 23,000 years ago

A new study comes to dismiss the popular idea that Native Americans draw their genetic heritage from Polynesians or European peoples.

The first humans to reach the Americas came from Siberia in a single group some 23,000 years ago, at the height of the last Ice Age, says the new study. On their way to Alaska, they hanged around in the northern regions for a few thousands of years before moving deeper into North and South America.

Presumably for that delicious, cave-made maple syrup.

Presumably for that delicious, cave-made maple syrup.

They lived in low-land, shrubby areas for an estimated 10.000 years, but archaeological evidence is hard to come by to help reach a definite number.

This map shows the outlines of modern Siberia (left) and Alaska (right) with dashed lines. The broader area in darker green (now covered by ocean) represents the Bering land bridge near the end of the last glacial maximum, a period that lasted from 28,000 to 18,000 years ago when sea levels were low and ice sheets extended south into what is now the northern part of the lower 48 states. University of Utah anthropologist Dennis O’Rourke argues in the Feb. 28 issue of the journal Science that the ancestors of Native Americans migrated from Asia onto the Bering land bridge or “Beringia” some 25,000 years ago and spent 10,000 years there until they began moving into the Americas 15,000 years ago as the ice sheets melted.
Credit: Wlliam Manley, Institute of Arctic and Alpine Research, University of Colorado.

They settled on a land bridge that connected Eurasia to the Americas, named Beringia. The ice sheets extended south into the Pacific Northwest, Wyoming, Wisconsin and Ohio. Large expanses of Siberia and Beringia were cold but lacked glaciers. As the planet warmed up however, ice melted, sea levels rose the area got slowly flooded, creating what we today know as the Bering Strait. These early settlers were forced to relocate and some of them found their way to America, but their settlements, and any traces of their daily lives were lost under the waters.

The lack of archaeological evidence makes precisely dating these events very tricky, but scientists are confident that genetic sequencing can help us with that:

“There is some uncertainty in the dates of the migration and the divergence between the northern and southern Amerindian populations. But as we get more ancient genomes sequenced, we will be able to put more precise dates on the times of migration,” said one of the study authors Yun Song, associate professor at University of California, Berkeley.

The analysis, using the most comprehensive genetic data set from Native Americans to date, was conducted using three different statistical models. The data consisted of the sequenced genomes of 31 living Native Americans, Siberians and people from around the Pacific Ocean, and the genomes of 23 ancient individuals from North and South America, spanning a time between 200 and 6,000 years ago.

The international team concluded that the northern and southern Native American populations diverged between 11,500 and 14,500 years ago.

The southern branch peopled Central and South America as well as part of northern North America. The findings will be presented in the forthcoming issue of the journal Science.

“The diversification of modern Native Americans appears to have started around 13,000 years ago when the first unique Native American culture appears in the archaeological record: the Clovis culture,” said Rasmus Nielsen, a professor at the California university. “We can date this split so precisely in part because we previously have analysed the 12,600-year-old remains of a boy associated with the Clovis culture,” Nielsen added.