II-74 Zdrav Vestn 2007; 76: SUPPL II
SINGLE NUCLEOTIDE POLYMORPHISM GENOTYPING IN
PHARMACOGENOMICS AND DRUG DISCOVERY USING THE
BECKMAN COULTER GenomeLabTM SNPstream SYSTEM
Suresh Jivan Gadher
Beckman Coulter International S.A., 22, rue Juste Olivier, Casa Postale 1059, CH – 1260 Nyon 1,
Switzerland; sgadher@beckman.com
Abstract Single nucleotide polymorphism (SNP) is the most common type of genetic variation occur-
ring every 300 to 1000 bases in the human genome and many other species. By examining
SNPs, investigators can better understand the genetic variances related to certain disor-
ders and diseases. Hence, SNP identification plays a powerful role in discovering genetic
factors by examining one’s genotype which can ultimately predict one’s risk to developing
certain types of diseases. Clinical genotyping instrumentation and kits play a vital role in
today’s Pharmacogenomic laboratories. To this end, Beckman Coulter developed an auto-
mated, ultra-high throughput system, called the ‘GenomeLabTM SNPstream Genotyping Sys-
tem’. It utilises the single-base primer extension technology together with multiplexed PCR*
in conjunction with tagged-arrays. Today, this System can be seen at the cutting edge of
Pharmacogenomics and Drug Discovery Research throughout the World. Examples of such
system utilisation include projects such as the LRRK2 gene in Parkinson Disease (C. Pai-
san-Ruiz, et al 2005. Neurology 65: 696–700), Measles Vaccine Immunity and SNP in
Cytokine and Cytokine Receptor Genes (Neelam Dhiman, et al. 2007. J. of Infectious Dis-
eases 195: 21–29) and numerous other studies being carried out world wide.
The ‘GenomeLab SNPstream Genotyping 48-plex System delivers between 4,000 to over 3
Million Genotypes per day and is an automated, multiplexed system that can process up to
48 SNPs in each well of an arrayed 384-well plate. SNPstream operates at a consistent cost
regardless of run throughput, allowing users to cost-effectively home in on targets with low-
throughput or high-throughput analyses. This unique opportunity is achieved by lowering
PCR expenses and improving efficiency, thus lowering the cost per genotype and per sam-
ple. The system features a simple protocol with just three steps, compared to more than 15
steps that are often required by other similar systems. Firstly, the SNP primer is hybridized
to the pre-amplified DNA and then the primer is extended by a labeled terminating base at
the target SNP site. Finally, the extended primer is captured on the SNPware Tag Array
plate and detected. With millions of genotypes generated, using single-base primer exten-
sion, the GenomeLab SNPstream Genotyping System has been proven to deliver the accu-
racy (99 %) and reliability of data that today’s researchers demand. Due to the high sensi-
tivity of the system, accurate results can be obtained by using as little as 2 ng of genomic
DNA for either the 12-plex or 48-plex assay. This equates to 0.04 ng DNA required per
genotype. The Multi-well plates are compatible with Biomek® series of liquid handlers, for
fast pre-and post-PCR* set-up. Multiplexing within the system’s 384-well plate enables the
user to run a range of genomic samples on the same plate. The system can be run manually
or integrated with plate-handling robotics for a walk away automation of up to 72 plates.
Data collection, analysis and QC from raw data to genotype are fully automated and a
complete summary report is provided. »The GenomeLab SNPstream systems are validated
on multiple sources and species, including genomic DNA from blood, tissue, cell culture or
buccal swab, and from human, mouse, cow, microbial and plant species.   SNPstream us-
ers have access to Beckman Coulter’s Autoprimer.com, a unique web-based tool that auto-
matically provides primers and tag assignments in a matter of seconds, using proprietary
algorithms. This innovative, on-line resource takes the uncertainty out of assay design by
providing fast, easy-to-use primer design support and tag assignments. Just by uploading
or entering a sequence at www.autoprimer.com and the state-of-the art algorithms instant-
ly design robust, best-fit multiplex PCR and extension primers. By designing panels to work
* The PCR process is covered by patents owned by Roche Molecular Systems, Inc & F. Hoffmann-La Roche Ltd. Key Words: SNP, GenomeLabTM,
SNPstream, Genotyping.
II-75Short invited lectures – abstracts
under a single PCR condition as well as extension conditions, Autoprimer.com software
takes care of the optimisation for the end user.
In summary, Beckman Coulter’s 48-plex GenomeLab SNPstream Genotyping System pro-
vides a scalable solution to meet medium to high-throughput needs where assay automa-
tion, automated data collection, data analysis, and auto QC provides a flexible and fully
automated solution from DNA to genotype calls. Additionally, the GenomeLab CEQTM 8000
Genetic Analysis System also provides automated sequencing for SNP discovery and frag-
ment sizing with size / colour allele identification for single or multiplexed SNP scoring by
utilizing the ‘GenomeLab SNPStart Kit’ and the single base extension technology.
To add to the whole, the recent acquisition of ‘Agencourt Bioscience Corporation’ and its
portfolio of products, should stand the user in good stead to enable identification of new
markers of biological, diagnostic and therapeutic interest.