omation mbers - Society for Laboratory Automation and Screening

12:00 pm Wednesday, February 4 Genomics – SNPs Room A1
Tom Willis
ParAllele BioScience, Inc.
384 Oyster Point Boulevard Suite 8
South San Francisco, California 94080
tom@p-gene.com
101
Co-Author(s)
Malek Faham, Paul Hardenbol,
Maneesh Jain, Eugeni Namsaraev,
George Karlin-Neumann, Hosssein Fakhrai Rad,
Mostafa Ronaghi, Ronald W. Davis
Comprehensive Genetic Analysis Using Highly Multiplexed SNP Discovery and Genotyping
The elucidation of complex genetic traits increasingly necessitates comprehensive genetic analysis.
Comprehensive coverage of the human genome is required in order to unlock the potential of association studies.
At the same time allelic heterogeneity will necessitate comprehensive discovery of alleles within genes in order to
capture the contribution of collections of rare alleles to the phenotype (e.g., BRCA mutations for breast cancer).
New technologies are needed to address these fundamental challenges to human genetics. ParAllele BioScience
has developed a set of technologies that enable such comprehensive coverage by providing a flexible platform
that enables tens of thousands of interrogations to occur within a single tube reaction. The authors have used
the concept of Molecular Inversion Probes (MIP) to build a SNP scoring technology that allows allele specific
amplification of oligo probes through a process of self inversion. These molecular inversion probes can be
multiplexed to the level of over 10,000 SNP calls per assay. Whole genome analysis is being enabled by this
technology. In order to capture the important information from rare alleles and private mutation, a high throughput
variation scanning technology has also been developed. This technology exploits the exquisite sensitivity of
bacterial DNA repair to produce a multiplexed assay that allows thousands of DNA fragments to be sorted into
those that contain mutations and those that do not. This technique, called Mismatch Repair Detection (MRD),
allows comprehensive SNP discovery in patient populations. We have built a comprehensive genome analysis
platform around these concepts by incorporating a molecular tagging strategy to allow robust detection of
thousands of allele specific amplicons using a robust, generic chip platform. We believe that this technology will
bring comprehensive association studies within reach by greatly reducing the cost and sample requirements of
SNP discovery and genotyping. Multiplexed genotyping and SNP discovery results are discussed and performance
metrics presented.
3:30 pm Wednesday, February 4 Genomics – Informatics Room A1
Terrence Smallmon
LabVantage Solutions
2355 Menard Street
St. Louis, Missouri 63104
tsmallmon@labvantage.com
The Benefits of a Laboratory Information Management System (LIMS) in Genomics
A genomic LIMS must streamline the data flow beyond the four walls of the laboratory. By centralizing all
information about a sample, and relating it to other scientific information, scientists can improve productivity as
well as the quality of information. The key benefits of a Genomics LIMS are:
• Provides complete traceability of every sample.
• Can acquire, integrate and manage multiple sources of dynamic and static data across the enterprise.
• Reduces the amount of clerical work done by highly trained professionals – allows scientists to do more science.
• Provides seamless integration with public/private databases.
• Integrates with the solutions of your choice for scientific data interpretation and analysis.
• Supports 21 CFR Part 11 Compliance.
• Increases communication throughout the organization.
• Reduces the number of times data is transcribed, increasing the integrity of the data.
• Eliminates the need for human interaction with automatic features to generate routine reports.
We now know as scientists expand the world’s understanding of complex biological systems, the volume of
analytical data will continue to rise. This talk will discuss how the Genomics LIMS allows the researcher to manage
this data and optimize their discovery process.
PODIUM ABSTRACTS