Next Generation Sequencing

Via GenomeWeb, I had quite a laugh at Keith Robinson’s recent blog post on Metagenomic Analysis with Galaxy: Windshield Genomics and Beyond - a dataset he came across while browsing the NCBI Short Read Archive, with the following abstract:

When I drive through Pennsylvania in June my windshield gets quite dirty with all these bugs. Yet do I know what they are? How many beetles versus butterflies? Is there a difference between day and night? Is there a difference between Pennsylvania and Connecticut? So we scraped the windshield, isolated genomic DNA, and subjected it to 454 FLX sequencing. We then uploaded the data into Galaxy and attempted answering these questions. In the end Pennsylvania turned out to be different from Connecticut.

It’s certainly an alternative use of high-throughput sequencing capacity at this point, but a fun one!

On a related note I might add that I would like to read a physics article on windshield dynamics, as I - through ongoing empirical observations - experience a dramatical increase in the number of bugs squashed on my windshield if my average commuting speed is raised by around 10%…

Research by a group of Montreal scientists calls into question one of the most basic assumptions of human genetics: that when it comes to DNA, every cell in the body is essentially identical to every other cell.

This discovery sprang from an investigation into the underlying genetic causes of abdominal aortic aneurysms (AAA) led by Dr. Morris Schweitzer, Dr. Bruce Gottlieb, Dr. Lorraine Chalifour and colleagues at McGill University and the affiliated Lady Davis Institute for Medical Research at Montreal’s Jewish General Hospital. The researchers focused on BAK, a gene that controls cell death.

What they found surprised them.

AAA is one of the rare vascular diseases where tissue samples are removed as part of patient therapy. When they compared them, the researchers discovered major differences between BAK genes in blood cells and tissue cells coming from the same individuals, with the suspected disease “trigger” residing only in the tissue. Moreover, the same differences were later evident in samples derived from healthy individuals.

Click here to read more at sciencedaily.com, including statements from Dr. Bruce Gottlieb from McGill University in Montreal, Canada.

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Journal reference:
Gottlieb et al. BAK1 gene variation and abdominal aortic aneurysms. Human Mutation, 2009; 30 (7): 1043 DOI: 10.1002/humu.21046

Today, Bio-IT World’s Editor-in-Chief, Kevin Davies, wrote about our next big move: Launching CLC Genomics Machine at ISMB in Stockholm, one week from now.

CEO at CLC bio, Thomas Knudsen, states

We have gone in a different direction than all other teams developing and refining algorithms for analyzing the massive amounts of data coming from the NGS instruments. Instead of constantly scaling up your hardware to the point where you need very big clusters or a cloud computing setup in order to do de novo assembly of large genomes, our scientific developers started from scratch and thought out some quite clever ways of handling those large amounts of data — to the point where a single CLC Genomics Machine can handle these tasks without breaking a sweat.

Click here to read the entire piece at bio-itworld.com

You can read the official press release here

CLC bio’s enterprise platform for Next Generation Sequencing data analysis, CLC Genomics Server, has just been awarded the “Best of Show” prize at the Bio-IT World Conference & Expo 2009 - an award judged by a team of Bio-IT World magazine editors and leading industry experts.

Bio-IT World Editor-in-Chief Kevin Davies, PhD., comments

Each year we go through a process where our judging panel debates the technical merits and likely business impact of the different technologies presented at the Best of Show awards. CLC bio’s success this year clearly reflects the importance of the incredibly exciting Next Generation Sequencing space, with a solution that is obviously gaining traction with it’s capabilities to handle the immense data management and analytical challenges required in this area.

M. Michael Barmada, Ph.D. - member of the “Best of Show” judging panel and Director of the Center for Computational Genetics at the Graduate School of Public Health, University of Pittsburgh says

Judging on several criteria, such as the importance of the problem being addressed and the elegance of the solution provided, it was clear to the judging panel that CLC Genomics Server, and the flexible plug-in structure it provides, delivers an ideal platform for researchers working with Next Generation Sequencing data. It’s nice to see complex computational algorithms and routines presented with an elegant interface in a user-friendly way, which lowers the technical barriers for all researchers working with high-throughput sequence data analysis.

CLC Genomics Server is CLC bio’s advanced and powerful bioinformatics solution which is built upon a powerful and modern three-tier server architecture, that yields flexible options of executing centralized services, easy integration with other applications and services, powerful database communication and data integration, and secure access control framework and central action logging. Customers already using this enterprise platform, includes J. Craig Venter Institute, Albert Einstein College of Medicine, Veridex, and University of California - Berkeley. Read more about this solution.

This news just came through in my inbox - more details later…!

You can read more about the price at Bio IT Worlds homepage.