PolITiGenomics

We made Parade

dd — Mon, 29 Dec 2008 04:25:15 +0000

Our sequencing of the first cancer genome made Parade Magazine’s Breakthroughs Of The Year. I guess we have really made it.

CC bioinformatics

dd — Wed, 24 Dec 2008 16:02:45 +0000

Thanks to the beauty of Creative Commons, the folks over at CLC bio have posted a version of my next-generation sequencing informatics table that adds a new metric, Yield per hour: NGS Platform Overview. Their updated table is also available under a CC-BY-SA license.

Elaine Mardis on Cancer in Technology Review

dd — Wed, 24 Dec 2008 14:40:50 +0000

Elaine Mardis, Co-Director of The Genome Center has a brief article in the January/February 2009 issue of Technology Review discussing the application of next-generation sequencing technologies to cancer research entitled Cancer Genomics: DNA sequencing will transform our understanding of cancer. In the same issue, there is an article that discusses the oncoming age of genomics, including its affect on personalized medicine, “third-generation” sequencing technology player Pacific Biosciences, and the Personal Genome Project.

1000 Genome SNPs released

dd — Wed, 24 Dec 2008 13:49:14 +0000

The 1000 Genomes Project has announced its initial release of SNP data from four of the individuals sequenced to high depth-of-coverage as part of the second pilot project (trios). Here is the announcement from Paul Flicek of EBI and the 1000 Genomes Data Coordination Center (and formerly of Washington University).

Dear All,

I’m pleased to provide everyone a stocking stuffer in the form of the first release of data from the 1000 Genomes project.

The preliminary list of SNPs for 4 of the high coverage individuals are now available on the EBI and NCBI 1000 Genomes FTP sites. Instructions on how to access the data can be found at http://www.1000genomes.org.

In addition, we have created a project specific genome browser to allow the data to be visualised in the context of genome annotations and data from other projects including the Venter and Watson genomes. The browser is based on the Ensembl platform and is available at http://browser.1000genomes.org. We will be making updates to the browser throughout January to ensure the 1000 Genomes data is visible by default and is easy to find (SNP tracks can now be found on the “Features” menu). I welcome any comments, questions or suggestions that that you have about the workings of the browser.

A long list of people worked very hard to get this done and any attempt to mention people will certainly miss some. However, I would like to specifically acknowledge Tom Blackwell, Goncalo Abecasis, Fiona Hyland, Zam Iqbal, Laura Clarke, Eugene Kulesha, Yuan Chen, Stephen Keenan, Fiona Cunningham, Justin Paschall, Martin Shumway,
Hoda Kouri and Steve Sherry.

All the very best for the holiday season.

Paul Flicek

Obviously, the three 1000 Genomes pilot projects have been a massive undertaking that has strained not only the production centers, but the IT and informatics infrastructures of the production and analysis centers. To date, over 3.8 terabases (3.8×10¹² or 3.8 trillion bases which is equivalent to about 1270 haploid human genomes) have been submitted as part of these pilot projects. The average SRF file submitted to the NCBI SRA stored 50 bytes of information per base; so the amount of data submitted so far is nearly 200 TB! At current broadband rates in the United States, it would take nearly 10 years to download all of this data (those still using 1600 baud modems may want to request they ship you the data on hard drives). Did I mention these are just the pilot projects?

Letting kids be kids

dd — Wed, 17 Dec 2008 15:15:52 +0000

There is a good article in the St. Louis Post-Dispatch about the St. Louis Crisis Nursery entitled St. Louis Crisis Nursery helps kids, parents. This holiday season, the Crisis Nursery has lots of opportunities to help those who are less fortunate. Check out their web site and volunteer your time or make a contribution.

AML at ASH

dd — Wed, 10 Dec 2008 16:03:17 +0000

It seems the publication of the first whole cancer genome sequence is getting a good reception in hematology circles. This past Saturday at the 50^th Annual Meeting of the American Society of Hematology, Dr. Tim Ley presented our AML sequencing work to a packed room of over 2000 people. In fact, there was such demand to see the talk that they scheduled a second time for Dr. Ley to give the talk so that all those that were turned away the first time could get a chance to see it. There is a lot of excitement in these oncology circles because the initiating events for many of these tumors are not known and an unbiased, whole-genome sequencing approach is currently the best chance to discover them.

Using the next-generation sequencing statistics table

dd — Wed, 10 Dec 2008 15:49:09 +0000

Since posting the next-generation sequencing informatics statistics table I have received several requests asking if they could reproduce the table in one format or another. The answer is yes, as long as you adhere to the license it is published under: the Creative Commons Attribution-Share Alike 3.0 License. Basically, if you allow other people to do to the table you present what you are asking me to do for you (reproduce the table with proper credit and, possibly, alteration), you are free to republish the content. If you have any questions, feel free to post a comment and ask. Enjoy.

Ensembl on Amazon

dd — Fri, 05 Dec 2008 15:46:08 +0000

The Amazon Web Services (AWS) blog has an entry on using Amazon’s Elastic Compute Cloud (EC2) to host and access public data sets, including Ensembl release 51. The data are stored as Amazon Elastic Block Store (Amazon EBS) snapshots. Anyone using EC2 can then create their own EBS using the public data EBS as a starting point. The data are then available to the user to modify, update, and perform calculations using the cloud. You can find more information on how to use the available public data sets and even upload your own data sets at Public Data Sets on AWS.

Next-Generation Sequencing Informatics

dd — Thu, 04 Dec 2008 22:15:59 +0000

I have put together a table with a bunch of important metrics for the major next-generation sequencing platforms: Next-Generation Sequencing Informatics (there is also a link on the left-hand side of the page). It includes number of reads, read length, data sizes, computational time, etc. I will try to keep it as up to date as I can and add new platforms and revisions as they become available. Consider it an early Christmas present.

The Bully YouTube

dd — Wed, 03 Dec 2008 17:22:05 +0000

In recent years, the term “bully pulpit” has erroneously become conflated with the modern meaning of the word bully, someone who harasses or intimidates. As such, people see the term as pejorative, an indication that someone is abusing power. This is more than wrong, it is unfortunate, as a look at history and the true meaning of bully pulpit will show. The term bully pulpit was coined by Theodore Roosevelt. As anyone who has seen Arsenic and Old Lace can attest, President Theodore Roosevelt was fond of the word bully, not the modern day noun, but the turn of the century interjection meaning “Well done!” or “Excellent!”. When he coined the phrase, he was describing the excellent opportunity the American Presidency offered to advance a political agenda. Not to intimidate people into submission, but to advocate a good cause that otherwise might not rise to public attention. The bully pulpit provided an opportunity to do good. The association of the term bully pulpit with the noun bully diminishes the the ability of the President to use this power; as often such uses are cast in term of left/right politics or political opportunism. It’s time to take the term back and ensure the connotation of the term is positive rather than negative.

The concurrent ascendancy of Web 2.0 technologies and President-elect Obama provide an opportunity to update the term while returning it to its true meaning. Through the Change.gov web site, the transition team is posting its press conferences, weekly “radio” addresses, and other transition information on YouTube. In other words, the bully pulpit has become the bully YouTube. While many of the topics presented on Change.gov are front and center in the minds of most Americans, one of interest to me has not been: Creative Commons. While YouTube does not support Creative Commons licensing at present and until recently the content on Change.gov was not under a CC license, it appears the Obama-Biden transition team has done the right thing and put the content of Change.gov under a CC Attribution license. Bully!