Fixed Targeted Genotyping

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The GeneChip® Scanner 3000 Targeted Genotyping System enables you to perform hypothesis-driven association studies using a targeted approach. This next-generation tool can genotype specific sets of targeted SNPs and enables you to uncover the basis of complex human and animal genetics.

Combined with the GeneChip Scanner 3000 Targeted Genotyping System, the targeted genotyping assay addresses these challenges by offering:

• Flexible multiplexing from 3,000 to 20,000 SNPs per individual assay
• Industry-leading conversion rates from database SNPs to functioning assays
• Targeted and specific high-value SNP content

The GeneChip Scanner 3000 Targeted Genotyping System uses a single workflow to enable a broad range of multiplexing, irrespective of the multiplex level chosen.

Features and Benefits

Figure 1

• Molecular Inversion Probe (MIP) Technology that enables a broad range of multiplexing. Get higher throughput with low capital investment.
• A single workflow for all multiplex panels ranging from 3,000 to 20,000 SNPs.
• Detection on proven Affymetrix GeneChip® technology that is in widespread use in a variety of application areas. Easy path to upgrade your current system to include targeted genotyping.
• Highest conversion rates available for custom genotyping (typically greater than 90 percent for conversion of SNPs retained in the Human HapMap database). Get more of the SNPs you need in your assay panel.
• Comprehensive targeted genotyping software package that allows for easy management of sample and project information and the integration of genotype calls.
• Catalog products available for more focused studies in human disease and agricultural research.

The GeneChip® Scanner 3000 Targeted Genotyping System (incorporating MIP technology) provides multiplexed assays designed for your custom SNPs, publicly available SNPs or the opportunity to choose from a menu of standard catalog products directed at hypothesis-driven human disease and agriculture research applications. Additionally, you have the flexibility to run mapping, resequencing, gene expression and targeted genotyping applications using one platform. This high-performance system will provide you with a means of generating quality data, giving you the information you need to solve complex research problems.

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Targeted Genotyping Panels

Researchers interested in hypothesis-driven studies may use standard catalog targeted genotyping panels (predefined human content-specific or animal content-specific panels) or custom targeted genotyping panels (sizes 3K, 5K, 10K or 20K panels). Targeted genotyping panels are available as standard and/or custom products and/or services to suit your particular research needs. Current application-specific fixed assays include:

• GeneChip® Bovine Mapping 10K SNP Kit & Bovine Mapping 25K SNP Kit
• GeneChip® Custom SNP Kits
• GeneChip® Human Immune and Inflammation 9K SNP Kit
• GeneChip® Human MALD 3K SNP Kit
• GeneChip® Human (Panels 1 and 2) 20K cSNP Kit
• GeneChip® Mouse Mapping 5K SNP Kit
• GeneChip® Rat Mapping 10K SNP Kit

GeneChip® Targeted Genotyping Analysis Software (GTGS)

Affymetrix GeneChip® Targeted Genotyping Analysis Software (GTGS) is part of the GeneChip® Targeted Genotyping System. GTGS is specifically designed to give highly accurate, automated SNP allele calls for the Targeted Genotyping MIP assay, available for application-specific fixed assays and custom SNP assays.

Affymetrix GeneChip® Targeted Genotyping Publications

Dumaual C., et al. Comprehensive assessment of metabolic enzyme and transporter genes using the Affymetrix Targeted Genotyping System. Pharmacogenomics 8(3):293-305 (2007).

Hardenbol P., et al. Highly multiplexed molecular inversion probe genotyping: over 10,000 targeted SNPs genotyped in a single tube assay. Genome Research 15:269-75 (2005).

Khatkar M. S., et al. A Primary Assembly of a Bovine Haplotype Block Map Based on a 15,036-Single-Nucleotide Polymorphism Panel Genotyped in Holstein-Friesian Cattle. Genetics 176:763-772 (2007).

Laurie C. C., et al. Linkage Disequilibrium in Wild Mice. PLoS Genetics 3(8):e144 (2007).

Moorhead M., et al. Optimal genotype determination in highly multiplexed SNP data. European Journal of Human Genetics 14:207-15 (2006).

Smith E. M., et al. Comparison of linkage disequilibrium patterns between the HapMap CEPH samples and a family-based cohort of Northern European descent. Genomics 88:407-414 (2006).

Smyth D. J., et al. A genome-wide association study of nonsynonymous SNPs identifies a type 1 diabetes locus in the interferon-induced helicase (IFIH1) region. Nature Genetics 38(6):617-619 (2006).

Zanke B. W., et al. Genome-wide association scan identifies a colorectal cancer susceptibility locus on chromosome 8q24. Nature Genetics 39:989-994 (2007).

Zheng S. L., et al. A comprehensive Association Study for Gene in Inflammation Pathway Provides Support for Their Roles in Prostate Cancer Risk in the CAPS Study. The Prostate 66:1556-1564 (2006).