Genotyping Becomes More Affordable


A new machine called OpenArray(TM) from BioTrove, Inc. now allows genomic research to conduct genotyping (SNP) analysis across much larger patient groups.

As described on Traditional Medicine:

Unlike other technologies, which can genotype hundreds of thousands of SNPs in a few patient samples, OpenArray allows researchers to analyze SNPs across tens of thousands of patient samples – dramatically expanding study size and data significance. OpenArray SNP genotyping is also more efficient than previous technology because of its flexible design. A single OpenArray plate holds as few as 16 or as many as 3072 separate assays, which can be run against 48-144 samples per plate. Since the OpenArray NT Imager can process three OpenArray plates at once, it can generate more than 9000 data points in less than 10 minutes, ultimately generating over 100,000 data points per day with a single employee.

This is a huge step forward in genetics research, but we are still awaiting the $1 genomic sequence. Right now we are bordering on the $1000 dollar genome, which was talked about by Michael J. Heller, Ph.D., Departments of Bioengineering/Electrical and Computer Engineering, University of California, San Diego – yesterday at the Cambridge Healthtech Institute’s “Next Generation Sequencing Applications and Cast Studies” conference in San Diego, CA.

If you’re wondering just how competitive this space is, there is a $10 million X-Prize for Genomics that was issued by Craig Venter, for the first team to successfully sequence 100 human genomes in 10 days. Details of the prize are as follows:

The $10 million X PRIZE for Genomics prize purse will be awarded to the first
Team that can build a device and use it to sequence 100 human genomes within 10
days or less, with an accuracy of no more than one error in every 100,000 bases
sequenced, with sequences accurately covering at least 98% of the genome, and at
a recurring cost of no more than $10,000 per genome.

As it seems, the race is on!

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Genetic Goldmine Found by Global Ocean Sampling Expedition


Craig J. Venter has accomplished yet another feat in his conquest to sequence everything under the sun. Venter is best known for leading Celera in their challenge to beat the National Institute of Health (NIH) in a race to sequence the human genome. Since then he has lead numerous sequencing projects including the genetic analysis of New York City’s air [or the Nature publication], searching to discover the minimum genome at his company Synthetic Genomics, and most recently the Sorcerer II Global Ocean Sampling Expedition.

Results from the oceanic voyage that traveled from Halifax, Nova Scotia to the Eastern Tropical Pacific during the two year circumnavigation by the Sorcerer II Expedition have finally been released. The announcement from the J. Craig Venter Institute (JCVI) detailed several publications that were made in PLoS Biology. Highlights of the publication include:

Rusch et al. describe the results of metagenomic analysis of 37 samples taken aboard Sorcerer II during its voyage between Halifax, Nova Scotia and French Polynesia in 2003 to 2004, combined with seven samples collected during the pilot study in the Sargasso Sea. To capture the DNA, scientists onboard the Sorcerer II collected water every 200 nautical miles and then filtered it through progressively smaller filters to collect bacteria and then viruses. The DNA extracted for these publications were from the filter that collects mostly bacteria.

The group analyzed a massive dataset consisting of 7.7 million DNA sequences totaling 6.3 billion base pairs. Following from the Sargasso Sea pilot study, they continued to find a great degree of diversity both within and across the sampling sites. Researchers identified 60 highly abundant ribotypes (roughly equivalent to species) however, the inter-species variation and the variation of organisms within the same environment suggests that while the microbes might be similar at an rRNA level they can differ greatly at a biochemical and genomic level.

Yooseph et al. report on the 6.12 million new proteins uncovered from 7.7 million GOS sequences by using a novel sequence clustering approach. This nearly doubles the number of known proteins. The researchers found that the GOS dataset covered almost all of the known prokaryote (bacterial and archaeal) protein families and that there were 1,700 totally unique large protein families in the GOS dataset, not matching any known families. A surprising number of the new protein families discovered are in viruses. Researchers were also able to match 6,000 previously unmatched sequences in current protein databases to proteins found in the GOS dataset.

Previously, it was thought that different families of kinases were responsible for these types of cell regulation in prokaryotes (bacteria) versus eukaryotes (animals and other non-bacteria). Eukaryote protein kinases (ePK) were most common in eukaryotes, histidine kinases in bacteria. However, in their PloS Biology publication Kennan et al. show that with the scope and diversity of the GOS data that ePK-like kinases (ELKs) are indeed very prevalent in bacteria, in fact, more so than histidine kinases. This finding is even shedding some light on human kinases.

The research team has shown that the ePK is just one family in a diverse superfamily of enzymes that all share a common protein kinase-like (PKL) fold (shape). Using sensitive profile methods, the researchers discovered more than 45,000 kinase sequences from the GOS and other public data sources and grouped these into 20 diverse families, of which ePKs were just one. The GOS data doubles the size of most PKL families and triples the number of known ePK-like kinases (ELK). Many of these families exhibited eukaryote-like structure and function of their proteins and thus the researchers conclude that several of these protein families existed before the divergence of the three domains of life.

For more information, please see the press release at the J. Craig Venter Institute.

The data recovered from this mission is likely to yield a number of findings, and will be the focus of much scientific research from years to come. Kudos to you and your team Dr. Venter, and it was nice seeing you in Toronto last fall!