Friday, March 19, 2010

RNA Deep Sequencing - Beyond Proof of Concept

ABRF 2010 begins this weekend.  In addition to my LIMS presentation on Sunday, I will present our poster featuring data analysis of sequences from "Sex-specific and lineage-specific alternative splicing in primates" (Blekhman et. al) in GeneSifter Analysis Edition.

The poster number is RP-3. Stop by and see how we learned that not all samples are what they seem to be ...


Next Generation DNA Sequencing (NGS) technologies are powerful tools for rapidly sequencing genomes and studying functional genomics. Presently, the value of NGS technology has been largely demonstrated on individual sample analyses (1-3). The full potential of NGS will be realized when it can be used in multisample experiments that involve different measurements and include replicates, and controls to make valid statistical comparisons. Arguably, improvements in current technology, and soon to be available “third” generation systems, will make it possible to simultaneously measure 100’s to1000’s of individual samples in single experiments to study transcription, alternative splicing, and how sequences vary between individuals and within expressed genes. However, several bioinformatics systems challenges must be overcome to effectively manage both the volumes of data being produced and the complexity of processing the numerous datasets that will be generated.

In this poster we present a system that is used it to verify and further characterize previously published data from a gene expression study that includes both replicates and experimental values comparing sex and lineage specific alternative splicing in primates (4). This system, developed on a high performance computing architecture, stores and organizes the data, aligns millions of reads to different reference sequences, identifies and removes artifacts, executes comparative and statistical analyses, and finally links results to pathway and ontological information for making discoveries and confirming hypotheses. The supporting infrastructure includes intuitive user interfaces for organizing data, executing analytical operations, viewing summarized reports, navigating through details in the results and can be easily operated by biologists.

1. Marioni JC, et. al. (2008) Genome Res.

2. Ramsk├Âld D, et. al. (2009) PLoS Comput Biol.

3. Pleasance ED, et. al.(2010) Nature.

4. Blekhman R, et. al. (2009) Genome Res.

Sunday, March 14, 2010

Keeping Your DNA Sequencing, Genotyping, and Microarray Laboratory Competitive in a New Era of Genomics

ABRF 2010 is next week. The conference will be in sunny Sacramento CA. About 1000 technology geeks will convene to learn about the latest advances in DNA sequencing, genotyping, and proteomics instrumentation, lab protocols, and core lab services. We will be there with our booth and participate with LIMS and NGS data analysis presentations.

The first presentation, entitled "Keeping Your DNA Sequencing, Genotyping, and Microarray Laboratory Competitive in a New Era of Genomics," will be on Sunday Mar. 20 in the second concurrent workshop (w2) at 1:00 pm.


Laboratory directors are facing enormous challenges with respect to keeping their laboratories competitive and retaining customers in the face of shrinking budgets and rapidly changing technology. A well-designed Laboratory Information Management System (LIMS) can help meet these challenges and manage costs as the scale and complexity of data collection and related services increase. LIMS can also offer competitive advantages through increased automation and improved customer experiences.

Implementing a LIMS strategy that will reduce data collection costs while improving competitiveness is a daunting proposition. LIMS are computerized data and information tracking systems that are highly variable with respect to their purpose, customization capabilities, and overall acquisition (initial purchase) and ownership (maintenance) costs. A simple LIMS can be built from a small number of spread sheets and track a few specific processes. Sophisticated LIMS rely on databases to manage multiple laboratory processes, capture and analyze different kinds of data, and provide decision support capabilities.

In this presentation, I will share 20 years of academic and industrial LIMS experiences and perspectives that have been informed through 100’s of interactions with core, research, and manufacturing laboratories engaged in DNA sequencing, genotyping, and microarrays. We’ll explore the issues that need to be addressed with respect to either building a LIMS, or acquiring a LIMS product. A new model that allows laboratories to offer competitive services, utilizing cost-effective laboratory automation strategies and new technologies like next generation sequencing, will be presented. We’ll also compare different IT infrastructures and discuss their advantages and how investments can be made to protect against unexpected costs as new instruments, like the HiSeq 2000(TM) or SOLiD 4 (TM), third generation sequencing, or other genetic analysis platforms are introduced.

Sunday, March 7, 2010

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 (

Anthony Fejes' conference notes. Great read, lots of detail. (

Genetic Inference summarizes instruments, talks, and speculates on single molecule sequencing (

Genetic Future's coverage of the new sequencing instruments (

MassGenomics' coverage of the cancer genomics session (

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.