Automated Affymetrix Human Mapping 500K Target Preparation on Biomek® FX Laboratory Automation Workstation

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Poster: Handy Yowanto, Noel Ruppert, Debbie Benitex, David J. Duggan, William Biggs and Cynthia French: The single nucleotide polymorphism (SNP) is becoming an invaluable tool to investigate the genetic causes of complex human diseases. Because of collaborative SNP discovery initiatives, sequence polymorphism data became readily available and millions of human SNPs have been catalogued. Assays have evolved from a locus-specific amplification with an allele discrimination step capable of analyzing 1000 SNPs or less, to a robust high-throughput non locus-specific amplification assay that genotypes more than 200K SNPs on a single microarray.	Click here to enlarge image Figure 1. ArrayPlex SNPrep Application on Biomek FX Laboratory Automation Workstation from Beckman Coulter

DNA target preparation has been the rate-limiting step in genotyping analysis; and manual target preparation of DNA is tedious, time-consuming and has a high degree of variability. To better address the variability, consistency and throughput issues associated with manual target preparation, the ArrayPlex SNPrep automated application was developed specifically for the Affymetrix 500K SNP GeneChips.

The ArrayPlex SNPrep application on Beckman Coulter’s Biomek® FX offers a turnkey solution with focus on the quality, quantity and integrity of the DNA prepared for SNP microarray analysis. The system is capable of processing up to 96 samples in multiples of eight samples and automates all of the five Affymetrix Mapping assay steps starting with restriction enzyme digestion, ligation of adaptor, amplification plate preparation, fragmentation and labeling.

In this study, genomic DNA was extracted from 30 clinical samples (five males and five females) using the Agencourt Genfind blood isolation chemistry on Biomek NX Span-8. The genomic DNA targets were then processed using the ArrayPlex SNPrep application on the Biomek FX workstation. Restriction enzyme NspI was used to digest all genomic DNA targets during the study.

Click here for this poster (PDF)

Additional Information:

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* All trademarks are the property of their respective owners. Where applicable, the PCR process is covered by patents owned by Roche Molecular Systems, Inc., and F. Hoffmann-LaRoche, Ltd.

For Research Use Only; not for use in diagnostic procedures.

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