Monthly Archives: October 2014

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...

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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.

Continue reading here:
Professor Outlines Risks, Benefits of Genome Editing