Sneak Peek: Poster Presentations at AGBT

The annual Advances in Genome Biology and Technology (AGBT) begins tomorrow and would not be complete without a couple of contributions by @finchtalk.

Follow the tweets at #AGBT and if you are at the conference visit posters 334 and 335 (abstracts below). Also, visit Lanai 189 to see the latest advances in genome technology and software from the Caliper and Geospiza organizations within PerkinElmer. 

Poster Abstracts

Poster 335: Why is the $1000 Genome so Expensive? 

Rapid advances in sequencing technology are enabling leading institutions to establish programs for genomics-based medicine. Some estimate that 5000 genomes were sequenced during 2011, and an additional 30,000 will be sequenced by the end of 2012. Despite this terrific progress, the infrastructure required to make genomics-based medicine a norm, rather than a specialized application, are lacking. Although DNA sequencing costs are decreasing, sample preparation bottlenecks and data handling costs are increasing. In many instances, the resources (e.g. time, capital investment, experience) required to effectively conduct medical-based sequencing is prohibitive.

We describe a model system that uses a variety of PerkinElmer products to address three problems that continue to impact the widescale adoption of genomics-based medicine: organizing and tracking sample information, sample preparation, and whole genome data analysis. Specifically, PerkinElmer’s GeneSifter® LIMS and analysis software, Caliper instrumentation, and DNA sequencing services can provide independent or integrated solutions for generating and processing data from whole-genome sequencing.

Poster 334: Limitations of the Human Reference Genome Sequence

The human genome reference sequence is well characterized, highly annotated, and its development represents a considerable investment of time and money. This sequence is the foundation for genotyping microarrays and DNA sequencing analysis. Yet, in several critical aspects the reference sequence remains incomplete as are the many research tools that are based on it. We have found that, when new variation data from 1000 Genome Project (1Kg) and Complete Genomics (CG) are used to measure the effectiveness of existing tools and concepts, approximately 50% of probes on commonly used genotyping arrays contain confounding variation, impacting the results of 37% of GWAS studies to date. The sources of confounding variation include unknown variants in close proximity to the probed variant and alleles previously assumed to be di-allelic that are poly-allelic. When mean linkage disequillibrium (LD) lengths from HapMap are compared to 1Kg data, LD decreases from 16.4 Kb to 7.0 Kb within common samples and further decreases to 5.4 Kb when random samples are compared.

While many of the observations have been anecdotally understood, quantitative assessments of resources based on the reference sequence have been lacking. These findings have implications for the study of human variation and medical genetics, and ameliorating these discrepancies will be essential for ushering in the era of personalized medicine.

AGBT 2011

More.

That's how I describe this year's conference.

• More attendees
• More data
• More genomes
• More instruments
• More tweeters
• More tweeting controversy
• More software
• More ...

Feel free to add more comments.

Sneak Peak: AGBT and the Next Gen Software Challenge

The Advances in Genome Biology and Technology meeting begins Thursday (2/3) morning with pre-conference workshops on Wed.  I will be there representing Geospiza and presenting a poster entitled, "The Next Gen Software Challenge: Integrating Diverse Assay-Seq and Validation Systems" (abstract below)

In addition to great science and technology AGBT has a large number of tweeting participants including @finchtalk. You can follow along using the #AGBT and (or) #AGBT2011.  

Abstract

By the end of 2011 we will know the DNA sequences for 30,000 human genomes. Understanding how the variation between these genomes affects phenotype at a molecular level, requires that future research projects integrate genome sequences with data from multiple ultra-high throughput assays obtained from large sample populations. Further insights are gained when these data are combined with additional information from external databases and data resources.

Geospiza is meeting the above challenges with its GeneSifter® platform and underlying open-source HDF5 and BioHDF technologies. Our approach centralizes and structures data in a scalable way so that features can be queried across many samples and between different assays to quickly add context to genome sequences as they are collected. Unlike approaches that rely on collections of flat files, specialized software tool kits, isolated genome-browsers, and independent statistical tool environments, GeneSifter integrates common components into a system that provides researchers with a rich, easy to use, environment to explore their data and develop clinical insights.

By: Todd Smith (1), N. Eric Olson (1), Rebecca Laborde (3), Christopher E Mason (2), David Smith (3):  (1) Geospiza, Inc., Seattle WA. (2) Weil Cornell Medical College, NY NY.(3) Mayo Clinic, Rochester MN.

AGBT Round Up

This year's AGBT conference created a lot of excitement in the sequencing community.  It's a been a week since the show, so everyone has had a chance to write up their blogs and news.

AGBT - Advances in Genome Biology and Technology

As the name implies, the AGBT conference focuses on genomics technologies and how they are applied to study biology.  Conference sessions cover the a gamut of new genomics-based discoveries, new technologies, and informatics.  The predominant technology used in genomics research is DNA sequencing, hence a large portion of the conference is devoted to learning how next generation sequencing (NGS) instruments are improving and how new instruments will change the NGS landscape.  Because informatics is so important in NGS, the conference is attended by a lot of bioinformatics specialists who like to blog and communicate what they are learning in real time through twitter.  Links to their posts are listed below.

Blogs other summarized coverage

BioTechniques summary of single molecule sequencing (http://bit.ly/cjzth1).

Anthony Fejes' conference notes. Great read, lots of detail. (http://is.gd/9vmJX).

Genetic Inference summarizes instruments, talks, and speculates on single molecule sequencing (http://bit.ly/cWJyo7).

Genetic Future's coverage of the new sequencing instruments (http://bit.ly/d1UxZg).

MassGenomics' coverage of the cancer genomics session (http://bit.ly/cImXxZ).

The above sites also have other posts sharing the author's perspectives on instruments and companies working in the NGS space.

Raw Data

For those interested in the blow by blow tweets as they occurred in real time, visit twitter and search on #AGBT.