Turbotodd

Ruminations on tech, the digital media, and some golf thrown in for good measure.

Posts Tagged ‘genetics

Out Of Africa: IBM And National Geographic Map The Human Genography

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My father’s name is James Watson.  But alas, he’s no relation to the co-discoverer of DNA.

Click to expand. Using new analytical capabilities, IBM and the Genographic Project have found new evidence to support a southern route of human migration from Africa before any movement heading north, suggesting a special role for south Asia in the "out of Africa" expansion of modern humans.

Just as I’m no relation to the founder of IBM, T.J. Watson.  You’d be surprised how many people ask if I am related to the IBM Watsons.  I politely explain that if I were, I’d probably be on a yacht in the Caribbean somewhere.  And I still aspire to discover a long lost genetic connection.

But who I AM related to is part of the study that will be related today at the National Geographic Society in partnership with IBM’s Genographic Project.

Flash back a few million years.

Evolutionary history has demonstrated human populations likely originated in Africa.  The Genographic Project, which is the most extensive survey of human population genetic data to date, suggests where they went next.

No, not to McDonalds.  That came much later.

Rather, a study by the project finds that modern humans migrated out of Africa via a southern route through Arabia, rather than a northern route by way of Egypt.

It’s those findings that will be highlighted today at the National Geographic Society conference.

Mapping The Human Geno-ography

National Geographic and IBM’s Genographic Project scientific consortium have developed a new analytical method that traces the relationship between genetic sequences from patterns of recombination — the process by which molecules of DNA are broken up and recombine to form new pairs.

Ninety-nine percent of the human genome goes through this shuffling process as DNA is being transmitted from one generation to the next. These genomic regions have been largely unexplored to understand the history of human migration.

By looking at similarities in patterns of DNA recombination that have been passed on and in disparate populations, genographic scientists confirm that African populations are the most diverse on Earth, and that the diversity of lineages outside of Africa is a subset of that found on the continent.

The divergence of a common genetic history between populations showed that Eurasian groups were more similar to populations from southern India, than they were to those in Africa.

This supports a southern route of migration from Africa via the Bab-el-Mandeb Strait in Arabia before any movement heading north, and suggests a special role for south Asia in the “out of Africa” expansion of modern humans.

The new analytical method looks at recombinations of DNA chromosomes over time, which is one determinant of how new gene sequences are created in subsequent generations.

Imagine a recombining chromosome as a deck of cards. When a pair of chromosomes is shuffled together, it creates combinations of DNA. This recombination process occurs through the generations.

Recombination contributes to genome diversity in 99% of the human genome. However, many believed it was impossible to map the recombinational history of DNA due to the complex, overlapping patterns created in every generation.

Now, by applying detailed computational methods and powerful algorithms, scientists can provide new evidence on the size and history of ancient populations.

Ajay Royyuru, senior manager at IBM’s Computational Biology Center, had this to say about the effort: “Over the past six years, we’ve had the opportunity to gather and analyze genetic data around the world at a scale and level of detail that has never been done before.

“When we started, our goal was to bring science expeditions into the modern era to further a deeper understanding of human roots and diversity. With evidence that the genetic diversity in southern India is closer to Africa than that of Europe, this suggests that other fields of research such as archaeology and anthropology should look for additional evidence on the migration route of early humans to further explore this theory.”

Filling In The Genographic Gaps

The Genographic Project continues to fill in the gaps of our knowledge of the history of humankind and unlock information from our genetic roots that not only impacts our personal stories, but can reveal new dimensions of civilizations, cultures and societies over the past tens of thousands of years.

“The application of new analytical methods, such as this study of recombinational diversity, highlights the strength of the Genographic Project’s approach.  Having assembled a tremendous resource in the form of our global sample collection and standardized database, we can begin to apply new methods of genetic analysis to provide greater insights into the migratory history of our species,” said Genographic Project Director Spencer Wells.

The recombination study highlights the initial six-year effort by the Genographic Project to create the most comprehensive survey of human genetic variation using DNA contributed by indigenous peoples and members of the general public, in order to map how the Earth was populated.

Nearly 500,000 individuals have participated in the Project with field research conducted by 11 regional centers to advance the science and understanding of migratory genealogy. This database is one of the largest collections of human population genetic information ever assembled and serves as an unprecedented resource for geneticists, historians and anthropologists.

At the core of the project is a global consortium of 11 regional scientific teams following an ethical and scientific framework and who are responsible for sample collection and analysis in their respective regions.

The Project is open to members of the public to participate through purchasing a public participation kit from the Genographic Web site (www.nationalgeographic.com/genographic), where they can also choose to donate their genetic results to the expanding database. Sales of the kits help fund research and support a Legacy Fund for indigenous and traditional peoples’ community-led language revitalization and cultural projects.

Banking On Genetics

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It’s Friday.

What’s going on in the world?

The question this Friday is, what’s not??

We’re still anxiously awaiting whether the U.S. government is going to come an agreement and raise the debt ceiling.

“Carmageddon” is going to shut down the 405 freeway in Los Angeles for 53 hours this weekend.

News Corporation continues to announce a doozy a day, with today’s big one being the resignation of  News Intl. Corp. executive Rebekah Brooks.

Casey Anthony is expected to be released from prison this weekend in Florida.

And the U.S. Women’s soccer team takes on Japan Sunday in Germany for this year’s FIFA Women’s World Cup title.

Oh, and the British Open is this weekend.

My DVR hard drive is gonna be burning it up!

But today, the big news from IBM is how its technology is being used to help advance the research of human genetic disease.

IBM announced today that Coriell Institute for Medical Research, the largest biobank of living human cells, is using IBM technology to help the institute more efficiently maintain its massive collection of biological resources. As a vital player in modern biomedical research, Coriell manages cryogenic freezers that can house up to 48,000 samples and which may experience a mechanical failure while in use.

In the past, response teams had only been alerted in the event of a total failure of the unit requiring the staff to quickly move the biological samples to a standby unit.

Coriell can now better protect millions of genetic samples while also increasing its capacity to manage the volume of data generated by analyzing the genomes of large and diverse populations needed to examine the causes of critical diseases such as diabetes, cancer, and heart disease.

With the implementation of IBM monitoring software, Coriell researchers are now also instantly alerted in advance to quickly respond before any mechanical failure occurs and in turn, protect the integrity of the sample.

Big Science, Big Data

Scientists from major research centers around the world draw upon Coriell’s diverse collections of biomaterials, which contain cell lines, DNA, and other samples, representing more than half of  approximately 4,000 known genetic diseases.

In addition, Coriell is exploring advancement in personalized medicine using one’s genetic information to tailor individual patient medical care while ensuring an individual’s privacy.

“The healthcare industry is placing greater emphasis on the use of genetic information in making medical decisions,” said Scott Megill, Coriell’s Chief Information Officer.  “As a leader in genomics, Coriell is exploring the clinical utility of this personalized approach to medicine.  The breadth of data output created by our research introduced new challenges to analyze and store this information,” Megill added. “IBM is enabling Coriell to more effectively gather and analyze this data for our research.”

Coriell needed to address the challenge of supporting data collections generated from more than two million ampules of cells, one million vials of DNA, and hundreds of thousands of other biomaterials.

In addition, the Coriell Personalized Medicine Collaborative Research Study – which captures an individual’s genetic differences to better understand causes for diseases – created an additional data challenge to the Institute.  Each participant in the study is genotyped using an array-based technology producing more than two million points of data, equaling approximately 1.5 GB of information per person.

With a target goal of 100,000 participants for the study, Coriell faced a massive information storage demand that was simply too cost prohibitive using legacy storage platforms.

Coriell turned to IBM and IBM Business Partner Mainline to help drive the organization’s technology transformation to help manage the millions of biological samples and associated data.  The use of  IBM storage system at Coriell scales more cost effectively than traditional disk storage and, as a result of using  IBM’s low-cost storage technology, Coriell has reduced its information storage costs by 30 percent.

Banking On Genetics

In order to meet the challenges of a biobanking center that supports national and international scientific research, Coriell also looked to IBM to provide a process tracking system to quickly and easily adapt to the nuances of such a diverse biological collection.

Layered with Coriell’s inventory management system, IBM software allows Coriell to electronically track each sample as it moves through various laboratory processes. These samples vary greatly in type, disease state, age, and other characteristics, and the ability to quickly pinpoint the location and specific processing stage of a particular sample provides a key advantage to Coriell.

“Globalization has created an enormous opportunity for small to midsize firms such as Coriell to collaborate with research centers around the world.  As advanced technologies have become affordable and available, Coriell is able to keep costs down and increase efficiency while also driving innovation in the area of personalized medicine,” said Andy Monshaw, general manager of IBM’s Global Midmarket Business. “Aligning the right technology infrastructure to meet its Big Data challenges, Coriell is well positioned to promote tomorrow’s medicines and treatments to help usher in a new era of medicine.”

The complete Coriell solution is powered by IBM technology that includes IBM XIV Storage System, IBM Tivoli Maximo, IBM Tivoli Netcool and IBM WebSphere Lombardi Edition.

Written by turbotodd

July 15, 2011 at 3:00 pm

Live From SXSW Interactive: J. Craig Venter On Writing The Genetic Code

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Have you had your genes sequenced lately?

How about synthetic biology? Create any synthetic widgets in your spare time?

J. Craig Venter, one of the first humans to crack, and have cracked, the human genetic code is at it again, and boy did he deliver this morning at SXSW.

His appearance alone was an interesting mashup, introducing the first biological scientist to speak at this digital festouche.

So what was Venter’s message?

Well, first, it was to answer some big questions: What is life? Can we digitize it? How extensive is it? Can we pare it down to its most basic components?

As Venter and company have started filling up their computer databases with more and more digitized biological information, they’re starting to answer those questions.

This presents the world with some unique opportunities, science that could help with everything from synthetic fuels to enhanced crop production to helping create vaccines using synthetic biology (a flu vaccine was created using this methodology in less than 24 hours, a process that typically takes months).

Yes, of course, there are far-reaching ethical and moral questions about such scientific investigations, which Venter readily admitted. And the Obama White House even issued a report on the ethics of synthetic biology just last year.

But perhaps conspicuously masked behind the opportunity was a reveal that Venter himself may not have been conscious of in his talk.

Science fiction writer Bruce Sterling approached the microphone during the Q&A to ask the follow question: “How do you see what you’re doing?,” a reference to the nanotechnological scale at which most synthetic biological science is occurring.

Venter’s response: “You can’t see what you’re doing at scale…you have to take it on faith.”

I think I almost heard Sterling snickering as he shuffled away from the microphone.

Written by turbotodd

March 14, 2011 at 3:32 pm

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