Genotyping and GWAS

Genotyping assays measure allelic differences, especially differences in Single Nucleotide Polymorphisms (SNPs), which are the differences in the DNA between individuals. The ATG 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.

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).

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).

Please contact the KUGR Facility staff for more information.


Technical Director:
Gavin Pickett, Ph.D.
CRF G-21
Tel: (505) 272-0680

Bioinformatics:
Jason Byars
CRF G-21
Tel: (505) 272-0675

Senior Technical Staff:
Jamie Padilla, M.S.
CRF 118
Tel: (505) 272-5564

Jennifer Woods
CRF 121
Tel: (505) 272-3464

Faculty Director:
Scott A. Ness, Ph.D.
Professor, Internal Medicine
Office: CRF 121; Tel: (505) 272-9883