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Department of Environmental Health

Center for Environmental Genetics


Genotyping Facility

The Genotyping Core Facility provides cost-effective and efficient genotyping services using state-of-the-art technologies available to investigators at the UC College of Medicine and Cincinnati Children’s Hospital Medical Center. Genotyping services include selection of markers, design of assays and protocols. In addition to proving technical support for genotyping, the scientific laboratory staff offers expert consultations in developing study design, data analysis and interpretation. Assistance is also provided in preparation of budget and grant proposals.

The core laboratory is equipped with the latest versions of genotyping equipment including ABI3100 and ABI3130 DNA Analyzers, HT7900 machine, Affymetrix GCS3000 platform and robotic liquid handling stations. It is located in the second floor of the Kettering Laboratories (Department of Environmental Health). The space consists of eight adjacently located working laboratories with overall space of approximately 4500sq-ft. Separate rooms are used for handling of blood samples, DNA extraction, pre- and post-PCR processing.

The genotyping facility provides high-throughput microsatellite and single nucleotide polymorphism (SNP) genotyping spanning the whole genome or targeted regions and sequencing. SNP genotyping is performed using three platforms: TaqMan, OpenArray and Affymetrix.

TaqMan SNP Assay: For small to medium sized studies requiring less than ~30 SNPs, TaqMan is an ideal platform for genotyping thousands of samples.

TaqMan OpenArray Genotyping Assay: For medium size studies requiring targeted genotyping of several hundred SNPs, OpenArray system (Applied Biosystems/Life Technologies) is an ideal platform. This is a high-throughput multiplex genotyping platform providing PCR-based SNP analysis of hundreds to thousands of samples and candidate SNPs. Multiplex assays of 16, 32, 48, 64 — up to 256 SNPs can be designed in a single array.

Affymetrix GCS3000 Platform: GFCGI is equipped with the latest version of the Affymetrix genotyping platform providing researchers the capability of genotyping hundreds of thousands of SNPs in a single assay. This platform is based on the state-of-the-art technology enabling large scale genome-wide linkage and association studies.


  • Ranjan Deka, Ph.D.  Molecular Epidemiology
  • Guangyun Sun, Ph.D TaqMan, OpenArray and Affymetrix
  • Subba Rao Indugula, Ph.D.  Affymetrix platforms, microsatellite genotyping, DNA extraction.