Perlegen Sciences proposes to use its high throughput genotyping platform to successfully genotype at least 2.25 million SNPs in 270 HapMap samples within one year, to supplement the HapMap Consortium's genotyping efforts. Our unique high-density oligonucleotide array-based genotyping platform is well suited to this large-scale project, being cost-effective, accurate, and rapid. For example, in the first six months of this year we performed over 1.3 billion genotyping assays, and in the last quarter alone we performed over 770 million genotyping assays, at a rate of more than 250 million per month. With constant improvements to genotyping efficiency, we continue to reduce the cost of our assays, with recent studies costing less than one cent per genotype. We have extensive experience performing very large scale studies, while maintaining high genotyping quality: in a recent internal project we performed over 115 million genotyping assays, with genotyping quality scores of 98.3% completeness and 99.5% accuracy. Perlegen Sciences was a participant in the ENCODE HapMap project, in which the genotyping quality of the HapMap Consortium Centers was evaluated. We genotyped all known SNPs (both those discovered by Perlegen Sciences and those derived solely from dbSNP), without prior selection, from ten diverse genomic regions chosen by the HapMap Consortium in 90 samples. We submitted the data to the HapMap Consortium without prior knowledge of the results from the HapMap Centers. We achieved excellent genotyping quality, with a call-rate of 98.3%, and, based on the publicly available data from the HapMap Centers, a concordance of between 97.63% and 99.87%, depending on the platform with which our results were compared. Our unique genotyping technology is highly flexible: we have previously developed successful genotyping assays for ~1.6 million SNPs, distributed across the entire genome, and including both SNPs discovered by Perlegen Sciences and those derived from dbSNP. In addition, because our platform is highly scalable, we are flexible in terms of how we design and genotype SNPs. For example, for the proposed HapMap project, we can either design genotyping assays for all 2.25 million SNPs up-front, or design smaller numbers of genotyping assays for batches of SNPs as they are chosen throughout the year. With our current throughput of over 250 million genotypes per month, completing the genotyping of at least 648 million SNPs (i.e. 2.25 million SNPs in 270 samples, plus 15 duplicates and 3 blanks) within one year, at the cost and quality specified by the HapMap Project, is well within our capacity. ? ?
