Monthly Archives: October 2013

Surprises discovered in decoded kiwifruit genome
Surprises discovered in decoded kiwifruit genome.

By: Gaurav Acharya

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There may be a new record for the largest family tree ever assembled. The thing dates back to the 15th century. It is comprised of 13 million individuals. And it is only one part of an even larger collection of genomic information: a collection compiled by thecomputational biologist Yaniv Erlichand stored not in albums or on walls, but in machines. Presented at the annual meetingAmerican Society of Human Genetics in Boston, and discussed in the journal Nature, the mega-repositorycould offer a new way for researchers to analyze the relationships between human genotypes and phenotypesbetween, essentially, nature and nurture.

In the past, such expansively branched informational trees would have been painstaking to cultivate. We have documentation, sure, of family relationships and the traits associated with themchurch records, hospital logs, that kind of thingbut gathering those documents for analysis took time. Assembling genealogical data for even just a few thousand individuals, Erlich noted during his ASHG presentation, couldtake years.

So here's where the hacking comes in.Erlich and his team, rather than gathering those data themselves, went to a more streamlined source: geni.com. Which is a genealogy website with43 million public profiles. Those profiles offered a wealth of information, typically including not just individuals' birth and death dates, but also the locations of their births and deaths. Occasionally, they'd even contain photos uploaded by the site's users.

What resulted, in turn, was an extensive collection of trait-and-gene information, ripe for analysis. And it was from that collection that Erlich and his colleagues were able to compile what Nature calls "asingle uber-pedigree" involving some 13 million individuals. "We Are Family," as performed by a huge swath of humanity.(But performed anonymously: In making that and similar pedigreesavailable to other researchers, Erlich and his team stripped names from the data to protect individuals' privacy.)

So what does a database like thatthe family tree, digitizedget us? For one thing, it allows for a kind of longitudinal analysis of given traits, helping researchers to gain insights into the nature-vs.-nurture aspects of those traits as they played out over time.It can also offer insights into how traits are, ultimately, controlled. Given a trait like fertility, say, are there a few genes that exert broad influence ... or is fertility influenced by many genes that have smaller effects? It might also help us to understand inherited diseases. (See, for example, theIceland-based genetics firm deCODE, which is taking advantage of the country's famously rich genealogical data to help determine genetic signatures that can influence diseasesand their treatment.)

For all that, Nature notes, it's unclear how, exactly, researchers will use the database for their own purposes. ("Some scientists at the meeting expressed enthusiasm for the project," Heidi Ledford puts it, "but were hard-pressed to come up with a specific experiment using the data.")Put another way, though, the biggest uses for the results of Erlich's genome-hacking may simply be to come. And those uses would rely on developments that are cultural as much as scientific: on medical records being stored and analyzed in digital, and potentially public, forms. Imagine Erlich's database being linked to individual medical information. Imagine it being linked to DNA sequence data. AsNancy Cox, a human geneticist at the University of Chicago,tells Ledford: "Weve really only begun to scratch the surface of what these kinds of pedigrees can tell us."

Via Nature

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This 'Genome Hacker' Is Building Family Trees With Millions of Branches

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Using data pulled from online genealogy sites, a renowned genome hacker has constructed what is likely the biggest family trees ever assembled. The researcher and his team now plan to use the data including a single uber-pedigree comprising 13 million individuals, which stretches back to the 15th century to analyse the inheritance of complex genetic traits, such as longevity and facial features.

In addition to providing the invitation list to what would be the worlds largest family reunion, the work presented by computational biologist Yaniv Erlich at the American Society of Human Genetics annual meeting in Boston could provide a new tool for understanding the extent to which genes contribute to certain traits. The pedigrees have been made available to other researchers, but Erlich and his team at the Whitehead Institute in Cambridge, Massachusetts, have stripped the names from the data to protect privacy.

The structures of the trees themselves could provide interesting information about human demographics and population expansions, says Nancy Cox, a human geneticist at the University of Chicago, Illinois, who was not involved in the study. But more interesting, she says, is the possibility that such data may one day be linked to medical information or to DNA sequence data as more people have their genomes sequenced and deposit that information in public databases.

Weve really only begun to scratch the surface of what these kinds of pedigrees can tell us, she says.

Pedigrees provide clues about genetic inheritance. For instance, by comparing an individual to their more distant relatives on the family tree, the change in frequency of a given trait, such as fertility, can indicate to what extent the trait has its roots in genetics. It can also provide clues as to whether the trait is controlled by a few genes that have large effects, or by many genes that each make smaller contributions.

But it takes years to assemble genealogical data for even just a few thousand individuals, said Erlich during a presentation at the meeting on 24 October. In the past, researchers have painstakingly gathered such data from church records and individual volunteers. Erlich and his team decided to streamline the process by collecting data from more than 43 million public profiles on the genealogy website geni.com. The profiles typically included birth and death dates, as well as locations and, occasionally, photos uploaded by the users.

The team assembled the data into family trees that ranged from a few thousand individuals up to 13 million people in size. Erlich says that pedigrees previously available for genetic studies contained hundreds of thousands of family members at best.

Lisa Cannon-Albright, a geneticist at the University of Utah in Salt Lake City, urges caution when using self-reported genealogical data. She has worked extensively with a large Utah genealogy database that is linked to some medical information. Everyone wants to trace their family back to royalty, she says. For these giant pedigrees, we just dont believe them beyond a certain date. Cannon-Albright says that she cuts off her data at the year 1500.

Ultimately, the value of a pedigree is in the information you can link it to, she adds. At the same meeting in Boston, Cannon-Albright presented data from the Utah database suggesting that the Y chromosome, which only passes from father to son, can carry risk factors for prostate cancer. She has also recently launched a new programme to link genealogical data to medical records from the federal Veterans Health Administration.

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Genome hacker uncovers largest-ever family tree

52462425 story Posted by Soulskill on Tuesday October 29, 2013 @08:00PM from the turns-out-several-million-people-married-their-cousins dept. ananyo writes "Using data pulled from online genealogy sites, a renowned 'genome hacker' has constructed what is likely the biggest family tree ever assembled. The researcher and his team now plan to use the data including a single uber-pedigree comprising 13 million individuals, which stretches back to the 15th century to analyze the inheritance of complex genetic traits, such as longevity and facial features. In addition to providing the invitation list to what would be the world's largest family reunion, the work presented by computational biologist Yaniv Erlich at the American Society of Human Genetics annual meeting in Boston could provide a new tool for understanding the extent to which genes contribute to certain traits. The pedigrees have been made available to other researchers, but Erlich and his team at the Whitehead Institute in Cambridge, Massachusetts, have stripped the names from the data to protect privacy." You may like to read: Post

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Genome Hacker Uncovers 13-Million-Member Family Tree