Category Archives: Transhuman News

Let #39;s Play FF9 part 57: Genome #39;s Purpose
So Zidane meets Garland the Creator of the Genome. We now learn about Zidane #39;s purpose, and some one else as well.

By: Aceofspadesth

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Let's Play FF9 part 57: Genome's Purpose - Video

A recently published global genome study that used the data-intensive Gordon supercomputer at the San Diego Supercomputer at the University of California, San Diego, has researchers rethinking how avian lineages diverged after the extinction of the dinosaurs.

The four-year project, called the Avian Genome Consortium and published in the journal Science, resulted in a new family "tree" for nearly all of the 10,000 species of birds alive today by comparing the entire DNA codes (genomes) of 48 species as varied as parrot, penguin, downy woodpecker, and Anna's hummingbird. The massive undertaking, started in 2011, involved more than 200 researchers at 80 institutions in 20 countries, with related studies involving scientists at more than 140 institutions worldwide.

The genome-scale phylogenetic analysis of the 48 bird species considered approximately 14,000 genes. This presented computational challenges not previously encountered by researchers in smaller-scale phylogenomic studies based on analyses of only a few dozen genes. The inclusion of hundreds of times more genetic data per species allowed the researchers to realize the existence of new inter-avian relationships.

"Characterization of genomic biodiversity through comprehensive species sampling has the potential to change our understanding of evolution," wrote Erich Jarvis, associate professor of neurobiology at the Howard Hughes Medical Institute at Duke University and the study's principal investigator, in an introduction to a special issue of the journal Science containing eight papers from the study. An additional 20 papers generated by the study were simultaneously published in other journals.

"For 50 species, more than 10 to the power of 76 possible trees of life exist. Of these, the right one has to be found," said Andre J. Aberer, with the Heidelberg Institute for Theoretical Studies (HITS), in a news release at the time of the study's publication in Science. "For comparison: About 10 to the power of 78 atoms exist in the universe."

Many of the computations were done on SDSC's Gordon supercomputer by Aberer with the assistance of SDSC Distinguished Scientist Wayne Pfeiffer. They ran a new code called ExaML (Exascale Maximum Likelihood) to infer phylogenetic trees using Gordon soon after it debuted in 2012 as one of the 50 most powerful supercomputers in the world.

Developed by Alexandros Stamatakis, head of the Scientific Computing Group at HITS, ExaML couples the popular RAxML search algorithm for inference of phylogenetic trees using maximum likelihood with an innovative MPI parallelization approach. This yields improved parallel efficiency, especially on partitioned multi-gene or whole-genome data sets.

"I had previously collaborated with Alexis on improving the performance of RAxML," said Pfeiffer. "He described the goals of the Avian Genome Consortium, and we agreed that Gordon, with its just-released fast processors, could provide much of the computer time needed for this ambitious project. In the end, more than 400,000 core hours of computer time were consumed on Gordon."

"After doing initial analyses on our institutional cluster, we rapidly realized that comprehensive analysis of the more challenging data sets being considered would require supercomputer resources," said Aberer. "Access to Gordon was thus invaluable for achieving results in a timely manner."

In all, high-performance computing (HPC) resources at nine supercomputer centers were used to analyze the complete genomes because of the scope of the undertaking. In addition to Gordon, several other U.S.-based supercomputers that are or have been part of the National Science Foundation's eXtreme Science Engineering and Discovery Environment (XSEDE) were used: Ranger, Lonestar, and Stampede at the Texas Advanced Computing Center (TACC) at the University of Texas at Austin; and Nautilus at the National Institute of Computational Sciences (NICS) at the University of Tennessee.

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Researchers rethink how our feathered friends evolved

Maybe it was the Jolie effect. Or you want to find out if youre carrying a silent genetic mutation that could be passed on to a child. Or perhaps youre just really hoping you can blame your DNA for how awful cilantro tastes. Whatever the reason, youre interested in finding out something about your genome. Now what?

Though consumer genetic testing and personal genome sequencing are still nascent fields, every indication suggests that the public will have a virtually insatiable appetite for genetic data. And as scientists get better at establishing links between DNA and diseases or specific traits, that demand will only increase.

But are we ready for this data? Sure, massive-scale scientific instruments can churn out DNA information at breakneck pace, but is the rest of the scientific, medical, and social infrastructure in place to analyze, interpret, and protect it? At the moment, the short answer is no. But this is a major focus for the biomedical community right now, and improved solutions are being developed almost daily.

(Image via Shutterstock)

At the moment, there are several ways to get your hands on your own genetic data. Services like 23andMe and Ancestry.com offer direct access to basic genealogical information that can be gleaned from your genome. By going through a physician or genetic counselor, you can get targeted clinical resultssuch as your carrier status for a certain disease or whether you have a genetic variant that makes you more susceptible to canceror even your whole genome sequence. (As we reported earlier this year, genetic counselors may be more likely to order a DNA test on your behalf than a physician. Heres a list of companies offering personal genomic tests.)

For the most part, providers of this information will attempt to offer a useful interpretation of your data. A hereditary cancer test or carrier screening test will come back indicating positive (increased risk) or negative (normal risk). Ancestry testing will show on a map where your ancestors came from, likely with percentages for how much different regions contributed to your DNA. Even if you get your whole genome sequenced, part of the service will include talking with a genetic counselor to go over any major findings. Given how early we are in the genomic era, there are relatively few major findings; most people who get their genome sequenced today wont learn anything truly life-changing.

Its worth noting that the interpretation you get may not be complete. For example, if youre clinically tested for a mutation linked to heart disease, the result you get backan interpretation of whether your genetic code places you at increased risk for heart diseasemay not mention it if one of the genes analyzed also happens to reveal your risk for developing Alzheimers disease.

Most people who get genetic results today, especially if they go through a medical professional, stop the journey when they learn the answer to their specific question. But some people dig deeper, which is possible with low-cost services such as Promethease. You upload your genetic data, and these services churn through it to deliver more information. In our earlier heart disease example, these kinds of services might alert you to your Alzheimers risk even though the clinical lab didnt. This kind of offering has great value, but comes with a significant caveat emptor: you may learn something you didnt want to know.

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How To Get And Protect Your Genetic Data