Category Archives: Genome

Genome providesexperts with a more accurate window into exactly when modern humans mated with their Neanderthal cousins Itoccurredwhen they moved from Africa into Europe, between 50,000 and 60,000years ago - a more accurate date than previously known DNA was collected from a bone found near Ust-Ishim in western Siberia

By Sarah Griffiths for MailOnline

Published: 12:00 EST, 22 October 2014 | Updated: 02:16 EST, 23 October 2014

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Scientists have sequenced the oldest complete human genome.

The DNA comes from an anatomically modern man who roamed Western Siberia 45,000 years ago.

It provides experts with a more accurate timeline of when modern humans mated with their Neanderthal cousins as they moved from Africa into Europe, between 50,000 and 60,000 years ago.

Scientists have sequenced the oldest complete human genome. The DNA comes from an anatomically modern man who roamed Western Siberia 45,000 years ago. His remains were fund near thesettlement of Ust-Ishim in western Siberia in 2008. A view of the river Irtysh and the village is pictured

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Oldest complete human genome sequenced: DNA of 45,000-year-old man who roamed Siberia unravelled - and it sheds light ...

The femur from which the DNA samples originated.

Bence Viola, MPI EVA

Svante Pbo's lab at the Max Planck Institute for Evolutionary Anthropology in Germany has mastered the process of obtaining DNA from ancient bones. With the techniques in hand, the research group has set about obtaining samples from just about any bones they can find that come from the ancestors and relatives of modern humans. In their latest feat, they've obtained a genome from a human femur found in Siberia that dates from roughly the time of our species' earliest arrival there. The genome indicates that the individual it came from lived at a time where our interbreeding with Neanderthals was relatively recent, and Europeans and Asians hadn't yet split into distinct populations.

The femur comes from near the town of Ust-Ishim in western Siberia. It eroded out of a riverbank that contains a mixture of bones, some from the time where the sediments were deposited (roughly 30 to 50,000 years ago), and some likely older that had been washed into the sediments from other sites. The femur shows features that are a mixture of those of paleolithic and modern humans and lacks features that are typical of Neanderthal skeletons.

Two separate samples gave identical carbon radioisotope dates; after calibration to the 14C record, this places the bone at 45,000 years old, give or take a thousand years. That's roughly when modern humans first arrived in the region. That also turned out to be consistent with dates estimated by looking at the DNA sequence, which placed it at 49,000 years old (the 95 percent confidence interval was 30 to 65,000 years).

Even though the majority of the DNA obtained from similar bones is typically bacterial, Pbo's group managed to obtain collections of short DNA molecules that were between two and 10 percent human. Contamination with current human sequences, which was often a problem in earlier work, appears to be less than half a percent of the total sequences.

The short DNA fragments that persist in these ancient samples limit the areas of the human genome that you can match the fragments tolots of the human genome is repetitive, and you can't tell which repeat a fragment comes from. Of the 1.9 billion bases that can be matched uniquely, the genome the researchers obtained covered the typical base over 40 times (in the lingo of the field, it provided 42-fold coverage). That's more than enough to do some comparisons with other humans, current and past.

Because the human population is genetically diverse, the two copies of each chromosome we possess differ at known rates. In Africans, the oldest and thus most genetically diverse populations, there are about 10 differences for every 10,000 DNA bases. Non-Africans, by contrast, typically only have six or seven differences in the same amount of DNA. The Ust-Ishim genome clearly groups with non-Africans, at 7.7 differences every 10,000 bases. This is consistent with the idea that the migration out of Africa created a bottleneck, with only a fraction of our genetic diversity getting exported to populations that left the continent.

So, who was this individual related to? Based on Y chromosome and mitochondrial genome, the Ust-Ishim DNA appears to reside at the base of a broad group of populations that exist in current Eurasia. The rest of the genome indicates that it lacks many of the individual DNA changes that have appeared in current populations. All of which suggests that the population it belongs to is ancestral to Europeans and Asians.

But if you look at overall relatedness, the genome is slightly closer to current Asian populations than it is to Europeans. The authors note that other data has led researchers to hypothesize that Europeans have had an influx of DNA from a population that did not participate in the initial migration out of Africaperhaps a second wave out of Africa.

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45,000-year-old modern human bone yields a genome

LEIPZIG, Germany, Oct. 23 (UPI) -- Scientists have reconstructed the oldest known human genome after finding the bones of a 45,000-year-old man in Siberia.

The findings allowed scientists to further confirm that early humans and Neanderthals mixed and had children, said the researchers of the study published in Nature.

"What's exciting about this paper is that it's looking at a very ancient modern human who would have lived around the same time as Neanderthals," said Sarah Tishkoff, a geneticist at the University of Pennsylvania, who was not on the research team.

The bone and genetic sequence showed the man had both human and Neanderthal genes.

The one mystery that remains is what happened after the two interbred. Humans survived and Neanderthals died out but scientists still don't understand why.

The study also alludes to humans leaving Africa 60,000 years ago, much later than previously thought.

"We have caught evolution red handed!" said Svante Pbo, a director at the Max Planck Institute for Evolutionary Anthropology and lead on the study.

2014 United Press International, Inc. All Rights Reserved. Any reproduction, republication, redistribution and/or modification of any UPI content is expressly prohibited without UPI's prior written consent.

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45,000-year-old man reveals earliest human genome

Genome Engineering with CompoZr Custom Zinc Finger Nucleases (ZFNs)

By: Sigma-Aldrich

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Genome Engineering with CompoZr Custom Zinc Finger Nucleases (ZFNs) - Video

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21-Oct-2014

Contact: Mick Kulikowski mick_kulikowski@ncsu.edu 919-515-8387 North Carolina State University @NCStateNews

Customized genome editing the ability to edit desired DNA sequences to add, delete, activate or suppress specific genes has major potential for application in medicine, biotechnology, food and agriculture.

Now, in a paper published in Molecular Cell, North Carolina State University researchers and colleagues examine six key molecular elements that help drive this genome editing system, which is known as CRISPR-Cas.

NC State's Dr. Rodolphe Barrangou, an associate professor of food, bioprocessing and nutrition sciences, and Dr. Chase Beisel, an assistant professor of chemical and biomolecular engineering, use CRISPR-Cas to take aim at certain DNA sequences in bacteria and in human cells. CRISPR stands for "clustered regularly interspaced short palindromic repeats," and Cas is a family of genes and corresponding proteins associated with the CRISPR system that specifically target and cut DNA in a sequence-dependent manner.

Essentially, the authors say, bacteria use the system as a defense mechanism and immune system against unwanted invaders such as viruses. Now that same system is being harnessed by researchers to quickly and more precisely target certain genes for editing.

"This paper sheds light on how CRISPR-Cas works," Barrangou said. "If we liken this system to a puzzle, this paper shows what some of the system's pieces are and how they interlock with one another. More importantly, we find which pieces are important structurally or functionally and which ones are not."

The CRISPR-Cas system is spreading like wildfire among researchers across the globe who are searching for new ways to manipulate genes. Barrangou says that the paper's findings will allow researchers to increase the specificity and efficiency in targeting DNA, setting the stage for more precise genetic modifications.

The work by Barrangou and Beisel holds promise in manipulating relevant bacteria for use in food think of safer and more effective probiotics for your yogurt, for example and in model organisms used in agriculture, including gene editing in crops to make them less susceptible to disease.

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NC State researchers advance genome editing technique

Privacy Preserving Personal Genome Analysis / Studies (Joint Studies Application) - PRACTICE Project
Privacy Preserving Personal Genome Analysis and Studies (Joint Studies Application) - PRACTICE Project Donors can submit their genome data and enter their phenotype data to receive feedback...

By: technikon3a

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Privacy Preserving Personal Genome Analysis / Studies (Joint Studies Application) - PRACTICE Project - Video

Genome by Dr Anatholy

By: Huruy Sahle

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Genome by Dr Anatholy - Video

16 hours ago The process of selecting the right genome assembler for the job is being automated at the DOE JGI, and bioinformaticist Michael Barton welcomes other assembler submissions to the nucleotid.es repository. Credit: Michael Barton

A repository of genome assemblers is being developed to automate the process of selecting the best assembler for the task at hand.

There are many different genome assemblers being introduced and touted. On the nucleotid.es site (nucleotid.es/), the test results for various genome assemblers provide reproducible findings that genomics researchers can use to select the appropriate assembler for their needs.

After an organism's genetic code has been sequenced, researchers have to assemble the DNA fragments into a single sequence to be able to parse the information. However, selecting an assembler while considering factors such as the large number of short sequence reads generated, repeated sequences, and lack of a reference genome sequence against which to compare the draft assembly can be challenging.

At the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science user facility, bioinformatics systems analyst Michael Barton has been developing a repository of genome assemblers called nucleotid.es to help the DOE JGI team address these questions for sequencing projects in process. Right now, he said, the process of selecting a genome assembler is manual so an automated pipeline would be very helpful. The repository at http://nucleotid.es/ is publicly available so that other bioinformaticists can benefit from the findings being generated.

"A lot of assemblers are being produced in the bioinformatics community, and instead of reading subjective papers with assemblers, you can test the assemblers for yourself," Barton said, "with the added benefit of having reproducible research so that anyone can produce the results."

Barton started with genome assemblers that are being used by the DOE JGI, and he tested them against an internal dataset of several microbial genomes. The findings are categorized by benchmarks such as NG50 (a statistic which tracks the average length of a set of DNA sequences) on the website so that bioinformaticists can see how each assembler fared at the criteria of interest to them.

Each of the assemblers on the nucleotid.es site is enclosed in virtual boxes called docker containers. The docker containers make it easy to share and use the software. If a bioinformaticist finds a particular assembler useful, they can easily download it from the nucleotid.es site. Conversely, if other bioinformaticists want to see another assembler on the site, Barton said, they can send him the docker container for posting.

So far, he said, the genome assemblers on nucleotid.es are testing microbial genomes that have come off Illumina sequencers. He plans to add assemblers such as meraculous, an assembler for plant genomes developed at the DOE JGI, and jigsaw and allpaths. Barton said eventually he also hopes to have assemblers for other types of genome projects on nucleotides.

Explore further: A decade of improvements on the reference green alga genome

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Automating the selection process for a genome assembler

Harvard Medical School professor George M. Church discussed the possibilities and potential dangers of genetic engineering on Wednesday. The lecture event, presented by the Harvard Museum of Natural History, covered a range of topics, including potential gains for genetic information and technologies and considerations of ethics and efficacy.

Church began the evening by highlighting the importance of genome testing, stressing that whether or not you have family history, whether or not you [are of] a particular ethnicity, all of us are at risk for rare diseases.

Genome testing has made advances in recent years, with the cost of sequencing an individuals genome having decreased in the past decade.But further advances in genome testing, Church said, could allow us to essentially see whats currently invisible, to essentially see the genomes around us.

Advances in the portability and affordability of genome testing, for instance, could lead to a sort of handheld DNA sequencing device that could dramatically impact diagnostics and field studies.

Moreover, Church said, if you have an inexpensive way of [sequencing genomes] you can really start testing a lot of ideas about cause and effect, with the potential to identify rare protective gene variants that could alleviate or eliminate some diseases.

Your genetics is not your destiny, Church said.

Church also discussed the possibility of de-extinction, bringing back species like the woolly mammoth. He predicted that the de-extinction process would largely depend on both ecological and economic considerations, in which species are judged both on their viability in modern ecosystems and their utility. He highlighted the woolly mammoth as an example of such a keystone species that could dramatically and positively impact the global ecosystem, citing his 2013 Scientific American article which outlined how mammoths could contribute to the reversal of global warming by keeping the tundra frozen.

Letting the tundra melt, Church said, is the equivalent to burning all of the forests in all of the world and their roots two and a half times over. Bringing back the woolly mammoth could be one important step toward preventing this catastrophic release of carbon, according to Church.

Church also briefly touched on human genetic enhancements, noting that changes in the modern environment and human behavior have framed the topic of altering ones genome in terms of necessity.

Our ancestors didnt need any genetic enhancements to be able to sit for twelve hours a day and eat fatty, sugary foods, but we need enhancements that handle that altered environment, he said. If we go into space, we need enhancements that handle radiation and osteoporosis...or else were dead. So what seems like an enhancement in one generation becomes life and death in another generation.

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Professor Outlines Risks, Benefits of Genome Editing

When Meg DeBoe decided to tap her Christmas fund to order a $99 consumer DNA test from 23andMe last year, she was disappointed: it arrived with no information on what her genes said about her chance of developing Alzheimers and heart disease. The report only delved into her genetic genealogy, possible relatives, and ethnic roots.

Thats because just a month earlier, in November 2013, the Food and Drug Administration had cracked down on 23andMe. The direct-to-consumer gene testing companys popular DNA health reports and slick TV ads were illegal, it said, since theyd never been cleared by the agency.

But DeBoe, a mommy blogger and author of childrens books, found a way to get the health information she wanted anyway. Using a low-budget Web service called Promethease, she paid $5 to upload her raw 23andMe data. Within a few minutes she was looking into a report with entries dividing her genes into Bad news and Good news.

As tens of thousands of others seek similar information about their genetic disposition, they are loading their DNA data into several little-known websites like Promethease that have become, by default, the largest purveyors of consumer genetic health services in the United Statesand the next possible targets for nervous regulators.

After the FDA crackdown, consumers are trading information on where to learn about their genes. Dont let the man stop you, said one.

Promethease was created by a tiny, two-man company run as a side project by Greg Lennon, a geneticist based in Maryland, and Mike Cariaso, a computer programmer. It works by comparing a persons DNA data with entries in SNPedia, a sprawling public wiki on human genetics that the pair created eight years ago and run with the help of a few dozen volunteer editors. Lennon says Promethease is being used to build as many as 500 gene reports a day.

Many people are arriving from directly from 23andMe. After its health reports were blocked, consumers complained angrily about the FDA on the companys Facebook page, where they also uploaded links to the Promethease website, calling it a workaround, a way to get exhaustive medical info in reports that are similar, but not as pretty. The mood was one of civil disobedience. Dont let the man stop you from getting genotyped, wrote one.

The FDA is being cautious with personal genomics because although DNA data is easy to gather, its medical meaning is less certain.

Consumer DNA tests determine which common versions of the 23,000 human genes make up your individual genotype. As science links these variants to disease risk, the idea has been that genotypes could predict your chance of getting cancer or heart disease, or losing your eyesight. But predicting risk is tricky. Most genes dont say anything decisive about you. And if they do, you might well wish for a doctor at your side when you find out. I dont believe that this kind of risk assessment is mature enough to be a consumer product yet, says David Mittelman, chief scientific officer of Gene by Gene, a genetic laboratory that performs tests.

In barring 23andMes health reports, the FDA also cited the danger that erroneous interpretations of gene data could lead someone to seek out unnecessary surgery or take a drug overdose. Critics of the decision said it had more to do with questions about whether consumers should have the right to get genetic facts without going through a doctor. Its an almost philosophical issue about how medicine is going to be delivered, says Stuart Kim, a professor at Stanford University who helped developed a DNA interpretation site called Interpretome as part of a class he teaches on genetics. Is it going to be concentrated by medical associations, or out there on the Internet so people can interact?

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How a Wiki Is Keeping Direct-to-Consumer Genetics Alive