Category Archives: Genome

In 2005, next-generation sequencing began to change the field of genetics research. Obtaining a persons entire genome became fast and relatively cheap. Databases of genetic information were growing by the terabyte, and doctors and researchers were in desperate need of a way to efficiently sift through the information for the cause of a particular disorder or for clues to how patients might respond to treatment.

Companies have sprung up over the past five years that are vying to produce the first DNA search engine. All of them have different tacticssome even have their own proprietary databases of genetic informationbut most are working to link enough genetic databases so that users can quickly identify a huge variety of mutations. Most companies also craft search algorithms to supplement the genetic information with relevant biomedical literature. But as in the days of the early Web, before Google reigned supreme, a single company has yet to emerge as the clear winner.

Making a functional search engine is a classic big-data problem, says Michael Gonzalez, the vice president of bioinformatics at one such company, ViaGenetics, which was expected to relaunch its platform in March. Before doctors or researchers can use the data, genomic data must be organized so that humans can read and search it. The first step toward that is to put it in a standard form called the variant call format, or VCF. As raw data, a persons complete sequenced genome would take up about 100 gigabytes, so a database that adds the genomes of even 10 patients per day would quickly get out of hand. But VCF files are more compact, requiring only a few hundred megabytes per genome, which helps researchers find the specific variants they want to search in a fraction of the time. Unlike a fully sequenced genome, VCF files point only to where a persons genetic data deviates from the standardthe genome originally compiled by the Human Genome Project in 2001.

With VCF, sifting the genomes themselves for pinpoint mutations isnt the challenge for search engine companies. Most of these companies are allocating their resources toward efforts to seamlessly compile supplementary information about a specific mutation from other databases across the Web, such as the biomedical research archive PubMed or various troves of electronic medical records. Many of these tools have finely tuned algorithms that prioritize the results by credibility or relevance. You want to be able to pull together the information known about a mutation in that position [of the genome] and quickly make an assessment, says David Mittelman, the chief scientific officer for Tute Genomics, based in Provo, Utah, another company designing a genetic-search engine.

In an effort to expand the information that can be attached to a genome under examination, ViaGenetics, based in Miami Beach, Fla., is making its newly updated platform useful for researchers who want to collaborate across institutions. With ViaGenetics tools, researchers can make their data available to other users, so other people can come across these projects, request access, and form a collaboration, Gonzalez says. It helps people connect the dots between different researchers and institutions. This is especially helpful for smaller labs that may not have very extensive genome databases or for researchers from different universities working to decode the same mutation.

Although the genomic-search industry is now focused on serving scientists, that might not always be the case. Mittelman envisions that Tute Genomics could eventually serve consumers directly. People are already demanding information about their genomes just to understand themselves better, Mittelman says, but most companies dont yet consider the average person to be their primary customer. In order to make that shift, the tool will have to be even more intuitive and user-friendly. Fire-hosing someone with data thats not easy to interpret, or using terminology thats not standardized, has the potential to confuse people, he says. Privacy is also a major concern for the average user; the information that Tute users upload isnt stored permanently, Mittelman says, but users will need extra reassurance if the platform becomes available to the lay public.

And a further evolution of the industry is in the offing. Both ViaGenetics and Tute are hoping to be able to run the entire process in-housefrom the initial DNA sequencing to the presentation of final searchable results to users. The market for analyzing and interpreting genomic data is very fragmented, like the computer industry in the 1990s, where you had to go to separate providers to buy a video card or a motherboard and then try to put it together, Mittelman says. Soon this field will consolidate, as the computer industry did.

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The race to build search engine for your DNA

By Nick Kennedy

Better treatments for hookworm are on the horizon after the genome of Ancylostoma ceylanicum, the less common of the two hookworm species that affect humans, was sequenced in the United States.

The genome data offers more targets for drug and vaccine research. Hookworm infects around 440 million people in low- and middle-income countries. It is a leading cause of iron-deficiency, which can cause disability and even death, says Peter Hotez, a professor of tropical pediatrics at Baylor College of Medicine in the US.

The research, published in Nature Genetics this month (2 March), found an extensive set of genes that control the hookworm's ability to survive by suppressing the host's immune system.

The paper identifies some essential hookworm enzymes as likely vaccine targets. Without these enzymes, called proteases, hookworms cannot digest human proteins such as haemoglobin, the research found.

Because hookworm infection stunts physical and mental development, it can have a crippling cost on the economy and choke economic growth, says Erich Schwarz, a researcher at US-based Cornell University, who led the study.

More than three-quarters of hookworm infections in humans are caused by Necator americanus, the genome of which was sequenced last year.

Schwarz estimates that A. ceylanicum infects about 40 million people, largely in South-East Asia and particularly in Vietnam. Now that Schwarz and his colleagues have sequenced this hookworm's genome, they plan to start testing vaccine candidates for A. ceylanicum in hamsters this year.

Even though N. americanus infects more people, A. ceylanicum is used more in laboratories, because it infects both humans and other mammals, meaning treatments can be tested more easily.

A. ceylanicum already has a treatment, a single-dose drug called albendazole. However, albendazole doesn't protect people living in hookworm-endemic areas from becoming reinfected. "An inexpensive, safe vaccine administered once to small children would abolish their risk of contracting this disease," says Schwarz.

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Africa: Second Hookworm Genome Hoped to Lead to Vaccines

PNAS : Histone titration against the genome sets the DNA-to-cytoplasm threshold for the Xenopus...
Histone titration against the genome sets the DNA-to-cytoplasm threshold for the Xenopus midblastula transition. Amanda A. Amodeo et al (2015), Proceedings of the National Academy of Sciences...

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PNAS : Histone titration against the genome sets the DNA-to-cytoplasm threshold for the Xenopus... - Video

CRISPR-Cas genome surveillance: From basic biology to transformative technology
CRISPR-Cas genome surveillance: From basic biology to transformative technology Air date: Wednesday, March 11, 2015, 3:00:00 PM Category: WALS - Wednesday Afternoon Lectures Runtime: ...

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CRISPR-Cas genome surveillance: From basic biology to transformative technology - Video

Introduction to Ensembl Genome Browser/Biomart : answer 9
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Introduction to Ensembl Genome Browser/Biomart : answer 9 - Video

Introduction to Ensembl Genome Browser/Biomart - bioMart : answer 4
Practical session of a training on Ensemble Genome Brower/Biomart : Answer to question 4 (Biomart) (http://ngs.igbmc.fr/~royl/wiki/doku.php?id=training:introduction2ensembl)

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Introduction to Ensembl Genome Browser/Biomart - bioMart : answer 4 - Video

Scientists Seek Ban On Method of Editing the Human Genome
http://www.undergroundworldnews.com A group of leading biologists on Thursday called for a worldwide moratorium on use of a new genome-editing technique that would alter human DNA in a way...

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Scientists Seek Ban On Method of Editing the Human Genome - Video

Introduction to Ensembl Genome Browser/Biomart - bioMart : answer 3
Practical session of a training on Ensemble Genome Brower/Biomart : Answer to question 3 (Biomart) (http://ngs.igbmc.fr/~royl/wiki/doku.php?id=training:introduction2ensembl)

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Introduction to Ensembl Genome Browser/Biomart - bioMart : answer 3 - Video

Scientists Seek Ban On Method of Editing the Human Genome YouTube
A group of leading biologists on Thursday called for a worldwide moratorium on use of a new genome-editing technique that would alter human DNA in a way that can be inherited. The biologists...

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Scientists Seek Ban On Method of Editing the Human Genome YouTube - Video

Recommendations related to genome function from NHGRI #39;s Planning Workshop on ... - Mark Gerstein
March 10-11, 2015 - From Genome Function to Biomedical Insight: ENCODE and Beyond More: http://www.genome.gov/27560819.

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Recommendations related to genome function from NHGRI's Planning Workshop on ... - Mark Gerstein - Video