Sneak Peak: ABRF and Software Systems for Clinical Research

The Association for Biomedical Research Facilities conference begins this weekend (2/19) with workshops on Saturday and sessions Sunday through Tuesday.  This year's theme is: Technologies to Enable Personalized Medicine, and appropriately a team from Geospiza will be there at our booth and participating in scientific sessions. 

I will be presenting a poster entitled, "Clinical Systems for Cancer Research" (abstract below). In addition to great science and technology ABRF has a large number of tweeting participants including @finchtalk. You can follow along using the #ABRF and (or) #ABRF2011.  

Abstract

By the end of 2011 we will likely know the DNA sequences for 30,000 human genomes. However, to truly understand how the variation between these genomes affect phenotype at a molecular level, future research projects need to analyze these genomes in conjunction with data from multiple ultra-high throughput assays obtained from large sample populations. In cancer research, for example, studies that examine 1000s of specific tumors in 1000s of patients are needed to fully characterize the more than 10,000 types and subtypes of cancer and develop diagnostic biomarkers. These studies will use high throughput DNA sequencing to characterize tumor genomes and their transcriptomes. Sequencing results will be validated with non-sequencing technologies and putative biomarkers will be examined in large populations using rapid targeted assay approaches.

Geospiza is transforming the above scenario from vision into reality in several ways. The Company’s GeneSifter platform utilizes scalable data management technologies based on open-source HDF5 and BioHDF technologies to capture, integrate, and mine raw data and analysis results from DNA, RNA, and other high-throughput assays. Analysis results are integrated and linked to multiple repositories of information that include variation, expression, pathway, and ontology databases to enable discovery process and support verification assays. Using this platform and RNA-Sequencing and Genomic DNA sequencing from matched tumor/normal samples, we were able to characterize differential gene expression, differential splicing, allele specific expression, RNA editing, somatic mutations and genomic rearrangements as well as validate these observations in a set of patients with oral and other cancers.

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.

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.

Abstract

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.