TRANSCRIPTOME 2002: From Functional Genomics to Systems Biology
March 10-13, 2002
Seattle, Washington, USA


High Throughput Detection of Single Nucleotide Polymorphisms (SNPs) by OCP Microarrays

Zailin Yu, Allan Peng, Amy Cernetich and Qianjin Hu, Mergen LTD., San Leandro, CA

Mergen's patented method (OCP: On-Chip PCR) enables us to quickly screen thousands of SNPs by combining the advantages of the high throughput and detection from DNA microarray with the sensitivity and specificity from in situ PCR.The key advantages of the method are high throughput, specificity and low price  The targeted end user price is  $0.35 per SNP  score and the technique has a high success rate. Mergen's technique allows up to 40,000 SNPs (for example, all four alleles and both strands scored among 10,000 loci) to be detected per microarray pair. In a "proof of principle", experiment Mergen screened a hundred human SNPs that were randomly chosen from a public accessible SNP database - The SNP Consortium Ltd. (Cold Spring Harbor Laboratory, Up to 85% of SNPs tested were detected  and the results matched the data generated from a standard sequence method. (These failures are caused by poor SNP and PCR primers design and, if needed, the rate of failures could be reduced by subsequent redesign of the oligos.) In another experiment, a mutation at 273C/T on a human tumor suppressor gene (p53) was identified from normal and tumor DNA samples.

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