Friday, June 10, 2011

Sneak Peak: NGS Resequencing Applications: Part I – Detecting DNA Variants

Join us next Wed. June 15 for a webinar on resequencing applications.

This webinar will focus on DNA variant detection using Next Generation Sequencing for the applications of targeted and exome resequencing as well as, whole transcriptome sequencing. The presentation will include an overview of each application and its specific data analysis needs and challenges. Topics covered will include Secondary Analysis (alignments, reference choices, variant detection) with a particular emphasis on DNA variant detection as well as multi-sample comparisons. For in depth comparisons of variant detection methods, Geospiza’s cloud-based GeneSifter Analysis Edition software will be used to assess sample data from NCBI’s GEO and SRA. The webinar will also include a short presentation on how these tools can be deployed for both individual researchers as well as through Geospiza’s Partner Program for NGS sequencing service providers.

Date and time: Wednesday, June 15, 2011 10:00 am
Pacific Daylight Time (San Francisco, GMT-07:00)
Wednesday, June 15, 2011 1:00 pm 
Eastern Daylight Time (New York, GMT-04:00)
Wednesday, June 15, 2011 6:00 pm
GMT Summer Time (London, GMT+01:00)
Duration: 1 hour

Tuesday, June 7, 2011

DOE's 2011 Sequencing, Finishing, Analysis in the Future Meeting

Cactus at Bandelier
National Monument 
Last week, June 1-3, the Department of Energy held their annual Sequencing, Finishing, Analysis in the Future (SFAF) meeting in Santa Fe, New Mexico.  SFAF, also sponsored b the Joint Genome Institute, and Los Alamos National Laboratory and was attended by individuals from the major genome centers, commercial organizations, and smaller labs.

In addition to standard presentations and panel discussions from the genome centers and sequencing vendors (Life Technologies, Illumina, Roche 454, and Pacific Biosciences), and commercial tech talks, this year's meeting included a workshop on hybrid sequence assembly (mixing Illumina and 454 data, or Illumina and PacBio data). I also presented recent work on how 1000 Genomes and Complete Genomics data are changing our thinking about genetics (abstract below).

John McPherson from the Ontario Cancer Research Institute (OICR, a Geospiza client) gave the kickoff keynote. His talk focused on challenges in cancer sequencing. One of those being that DNA sequencing costs are now predominated by instrument maintenance, sample acquisition, preparation, and informatics, which are never included in the $1000 genome conversation. OICR is now producing 17 trillion bases per month and as they, and others, learn about cancer's complexity, the idea of finding single biochemical targets for magic bullet treatments is becoming less likely.

McPherson also discussed how OICR is getting involved clinical cancer sequencing. Because cancer is a genetic disease, measuring somatic mutations and copy number variations will be best for developing prognostic biomarkers. However, measuring such biomarkers in patients in order to calibrate treatments requires a fast turnaround time between tissue biopsy, sequence data collection, and analysis. Hence, McPherson sees IonTorrent and PacBio as the best platforms for future assays. McPherson closed his presentation stating that data integration is the grand challenge.  We're on it!

The remaining talks explored several aspects of DNA sequencing ranging from high throughput single cell sample preparation, to sequence alignment and de novo sequence assembly, to education and interesting biology. I especially liked Dan Distal's (New England Biolabs) presentation on the wood eating microbiome of shipworms. I learned that shipworms are actually little clams that use their shells as drills to harvest the wood. Understanding how the bacteria eat wood is important because we may be able to harness this ability for future energy production.

Finally, there was my presentation for which I've included the abstract.

What's a referenceable reference?

The goal behind investing time and money into finishing genomes to high levels of completeness and accuracy is that they will serve as a reference sequences for future research. Reference data are used as a standard to measure sequence variation, genomic structure, and study gene expression in microarray and DNA sequencing assays. The depth and quality of information that can be gained from such analyses is a direct function of the quality of the reference sequence and level of annotation. However, finishing genomes is expensive, arduous work. Moreover, in the light of what we are learning about genome and species complexity, it is worthwhile asking the question whether a single reference sequence is the best standard of comparison in genomics studies.

The human genome reference, for example, is well characterized, annotated, and represents a considerable investment. Despite these efforts, it is well understood that many gaps exist in even the most recent versions (hg19, build 37) [1], and many groups still use the previous version (hg18, build 36). Additionally, data emerging from the 1000 Genomes Project, Complete Genomics, and others have demonstrated that the variation between individual genomes is far greater than previously thought. This extreme variability has implications for genotyping microarrays, deep sequencing analysis, and other methods that rely on a single reference genome. Hence, we have analyzed several commonly used genomics tools that are based on the concept of a standard reference sequence, and have found that their underlying assumptions are incorrect. In light of these results, the time has come to question the utility and universality of single genome reference sequences and evaluate how to best understand and interpret genomics data in ways that take a high level of variability into account.

Todd Smith(1), Jeffrey Rosenfeld(2), Christopher Mason(3). (1) Geospiza Inc. Seattle, WA 98119, USA (2) Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA (3) Weill Cornell Medical College, New York, NY 10021, USA

Kidd JM, Sampas N, Antonacci F, Graves T, Fulton R, Hayden HS, Alkan C, Malig M, Ventura M, Giannuzzi G, Kallicki J, Anderson P, Tsalenko A, Yamada NA, Tsang P, Kaul R, Wilson RK, Bruhn L, & Eichler EE (2010). Characterization of missing human genome sequences and copy-number polymorphic insertions. Nature methods, 7 (5), 365-71 PMID: 20440878

You can obtain abstracts for all of the presentations at the SFAF website.