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U.S. Genome Variation Estimates


Details of Genotyping Assays

Two laboratories performed the genotyping, each analyzing a subset of polymorphisms on all of the DNA specimens available:

  • The Core Genotyping Facility of the National Cancer Institute
    (NCI) used semiquantitative real-time TaqMan assays (Applied Biosystems, Foster City, California) or MGB Eclipse Probe Systems assays (Nanogen [formerly Epoch Biosciences], Bothell, Washington) for genotyping. Each DNA specimen was also characterized by a microsatellite profile of 15 short tandem repeat markers(AmpFLSTR Identifiler PCR Amplification kit, Applied Biosystems) for identification purposes and as a quality control measure to check against duplication and contamination.
  • CDC’s National Center for Environmental Health (NCEH) laboratory performed MGB Eclipse assays for several polymorphisms. In addition, pyrosequencing technology (Biotage AB, Uppsala, Sweden) was used to determine ADRB2 (rs1042714) and F2 (rs1799963) genotypes, and the ACE insertion-deletion polymorphism (rs4646994) was determined by capillary fragment analysis.

Genotyping details such as primer and probe sequences are available on this Web site. This, and additional details such as assay conditions and software used for sequence detection and genotype calling can be found in the American Journal of Epidemiology article: Prevalence in the United States of Selected Candidate Gene Variants: Third National Health and Nutrition Examination Survey, 1991-1994.

 

 

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  • Additional information for Public Health Genomics is available on our contact page.
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