Seven Bridges Genomics - a commercial curated DB for genetic information?

Spotted on Google ads .. 

You HAVE to love the titles for some of the staff/founders

Igor Bogicevic

Founder/CTO

Ultimate Gandalf. The Architect.

 ... they are in beta now .. I think a lot of people are racing to be in the same bandwagon .. notably you do not see a clinician / psychologist/ counsellor  amidst them ... perhaps they are aiming for a different angle ...

See you at the end of the race! 

Meet Our Team

The mission of Seven Bridges Genomics is to enable people to make sense of the world's biological information, in order to improve lives and to share in the joy of discovery.
https://igor.sbgenomics.com/about/sbg/

Improving Detection of Genome Structural Variation

Improving Detection of Genome Structural Variation

from MassGenomics by Dan Koboldt

Large-scale structural variation (SV) is pervasive in the human genome, both in healthy individuals and in tumor cells. Numerous methods have been developed to detect such variants, most of which rely on the information provided by molecularly paired reads. Even the most sophisticated methods, however, still generate numerous false positives. A new study in Nature Genetics describes an innovative, population-based method to improve the accuracy of SV calling. In their introduction, Handsaker et al offer four main causes underlying false positives in SV calls:

1. Sequencing errors, which occur more frequently in next-generation sequencing data and exhibit both random and platform-specific bias distributions.
2. Chimeric molecules, in which read pairs linking two non-continguous segments of DNA masquerade as SVs. Sequencing libraries can contain millions of such fragments, which represent ~1% of sequence reads.
3. Read depth variation, which fluctuates across the genome for both biological and technical reasons.
4. Genome repeats, which confound most short-read aligners even when read pairing information is available.

These issues are exacerbated in population-scale sequencing, which often yields lower coverage across large numbers of samples. As more genomes are sequenced, false positives accumulate faster than real variants do. However, the authors hypothesized that population-scale sequencing might enable new analytical approaches. Here, they describe three strategies to do just that: allele sharing, population heterogeneity, and allelic substitution.

References
Handsaker RE, Korn JM, Nemesh J, & McCarroll SA (2011). Discovery and genotyping of genome structural polymorphism by sequencing on a population scale. Nature genetics, 43 (3), 269-76 PMID: 21317889

Complete Genomics on the $10,000 Human genome

Read the complete article here

By Kevin Davies 
February 7, 2011 | MARCO ISLAND, FL – It is a testament to the remarkable progress in next-generation sequencing and analysis that when neurobiologist Tim Yu described the complete sequencing of 40 human genomes in a successful search for gene mutations that cause autism, it barely registered a ripple from the large audience. 

“We’re still the only company that’s published a 10^-5 error-rate [human] genome,” Reid says (average 1 error/100,000 bases). He asserts that Illumina’s current system consumes $5,000 in reagents, and that cost swells to $20-25,000 when the full cost of informatics and labor is included.  
After claiming last year that CGI had cracked the $1,000 genome threshold for reagent costs, Reid now says that CGI’s all-in cost for a complete human genome is under $10,000. “With all of it added in, we’re below $10,000 now. We’ve got a 2-3X cost advantage [over Illumina], and a 10X quality advantage.”   
CGI currently charges $9,500 per genome for a minimum order of eight genomes. “You can’t pay $20,000 [per genome] any more, even if you try. We just send the money back!”   

How a programmer views the human genome

Grabbed this fantastic description on the ultimate question in the galaxy.

The genome is the source of a program to build and run a human

But: the author is not available for comment

It’s 3GB in size

In a single line

Due to constant forking, there are about 7 billion different versions

It’s full of copy-and-paste and cruft

And it’s completely undocumented

Q: How do you debug it?

 

Brilliant

I agree!

I forgot there are 7 billion versions when actually only 1000 are publicly avail for download! Lol

Author is 

Jim Stalker, the Senior Scientific Manager in charge of vertebrate resequencing informatics at the Sanger center. Grabbed off Todd Smith's post

 

178 Microbial Reference Genomes Associated with the Human Body

Venter Institute Scientists, Along with Consortium Members of the NIH's Human Microbiome Project, Sequence 178 Microbial Reference Genomes Associated with the Human Body

Researchers from the J. Craig Venter Institute, a not-for-profit genomic research organization, have published (along with other members of the National Institutes of Health (NIH) Human Microbiome Jumpstart Reference Strains Consortium), a catalog of 178 microbial reference genomes isolated from the human body.  Other members of the Consortium are: Baylor College of Medicine Human Genome Sequencing Center, the Broad Institute, and the Genome Center at Washington University. The paper is being published in the May 21 issue of the journal Science. 
The human body is teeming with a variety of microbial species. This collective community is called the human microbiome. The role these microbes play in human health and disease is still relatively unknown but likely very important. The NIH Human Microbiome Project was launched in 2007, as part of the National Institutes of Health’s (NIH) Common Fund’s Roadmap for Medical Research. It is a $157 million, five-year effort that will implement a series of increasingly complicated studies that reveal the interactive role of the microbiome in human health. 

Venter Institute Press Release 20th May

Knome invites researchers to apply for free sequencing and analysis of human exomes

I think there's nothing like the word 'free' that gets researchers to stand up and listen ;p

The 2010 KnomeDISCOVERY Research Awards
Knome invites researchers to apply for free sequencing and analysis of human exomes

Knome announces the launch of the KnomeDISCOVERY Research Awards, designed to spur novel discoveries by researchers working at the nexus of genomics and human health. Given annually, the KnomeDISCOVERY Research Awards will fund innovative projects that help reveal the genetic underpinnings of disease.

This year, Knome will award comprehensive sequencing and discovery-supportive analysis of a total of six (6) human exomes. These services will be distributed among three winning biomedical research groups, each of whom will use the award to study a pair of human exomes of their choice in order to answer a compelling biological question.