KUGR Facility Genotyping Assays

Genotyping assays measure allelic differences, especially differences in Single Nucleotide Polymorphisms (SNPs), which are the differences in the DNA between individuals. The KUGR facility can measure allelic differences in up to 100 SNPs using TaqMan real-time PCR assays. Alternatively, Affymetrix whole genome SNP arrays can be used to follow nearly 2 million SNPs across the whole genome. The latter assays are intended for mapping phenotypes to particular regions of the genome, experiments known as whole genome association studies.

The ultimate method of mapping allelic differences is whole genome sequencing, which will be available in the KUGR facility beginning in summer, 2009. Visit our Genome Sequencing page for more information, or contact the Facility Director: Scott A. Ness, Ph.D.

TaqMan Real-Time Genotyping Assays

Quantitative Real-Time PCR, or QPCR, measures increases in the production of PCR products during the PCR reaction, using a fluorescent assay. TaqMan genotyping assays use quantitative PCR to measure the relative levels of two possible alleles at a particular genomic position, e.g. A vs. T. The TaqMan assays cost about $1 per sample, so are generally too expensive to screen large sample sets (e.g. more than 100 patients).

More information about TaqMan assays is available on our Real Time PCR page.

Affymetrix Whole Genome Genotyping Assays

Affymetrix Genome-Wide Human SNP 6.0 Arrays feature 1.8 million genetic markers, including more than 900,000 single nucleotide polymorphisms (SNPs) and more than 946,000 probes for the detection of copy number variation. The Affymetrix GeneChips have the SNPs arrayed more or less evenly across the genome, so they can be used to follow whether particular genetic markers (e.g. SNPs) correlate with a biological phenotype (e.g. diabetes).

More information about the SNP microarrays is available on our Affymetrix Genotyping page.

Please contact the KUGR Facility staff for more information.

Faculty Director:
Scott A. Ness, Ph.D.
Professor, Molecular Genetics and Microbiology
Office: CRF 121; Tel: (505) 272-9883

Technical Director:
Gavin Pickett, Ph.D.
CRF 118
Tel: (505) 272-5564

Senior Technical Staff:
Jamie Padilla
CRF 118
Tel: (505) 272-5564