Metagenomics – Emerging Field


Metagenomics is defined as the study of genomes recovered from environmental samples as opposed to from clonal cultures (wikipedia). The National Research Council says that these new capabilities in genomics will revolutionize understanding of the microbial world.

The Research Council report was requested by several federal agencies interested in the potential of metagenomics and how best to encourage its success. In particular, the committee was asked to recommend promising directions for future studies. It concluded that the most efficient way to boost the field of metagenomics overall would be to establish a Global Metagenomics Initiative that includes a few large-scale, internationally coordinated projects and numerous medium- and small-size studies.

Metagenomics studies begin by extracting DNA from all the microbes living in a particular environmental sample; there could be thousands or even millions of organisms in one sample.

Please see the article at Science Daily for more information.

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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Music Genome Project: Pandora


Last night I was talking to a friend (credit: Ilan Jacobson) about music and he mentioned a really innovative online service called Pandora. So … what is this ‘Pandora’? It is modelled after the Human Genome Project, but for music, and coined the “Music Genome Project“. Who would have thought that a ‘whole genome shotgun’ approach to music could work just as well as it did with DNA! I wonder if they sent Craig Venter a thank you note? Do you think they only did 3x coverage, or did they go all out with a 5x (gotta love a lame genetics joke…) ?

So, how does their algorithm work? Well, they set out to “capture the essence of music at the most fundamental level” and pick out musical “genes”, which distinguish different musical attributes such as melody, harmony and rhythm among other characteristics. The service also asks you to identify certain songs or bands that you like to determine a starting point within their system. I have been using it for only a few hours now, and I can already see its potential. With every piece of feedback I provide, the system becomes more accurate at determining the best songs to suit my taste. Cool idea!

They even let you RSS your personal radio stations, check out my streams. Enjoy!