High throughput genotyping of SNPs promises to revolutionize our understanding of genetic variation and the ability to relate genetic variation to phenotypic variation, including disease for 3 reasons: (1) the number of SNPs which are potentially available -more than 300,000 across the human genome; (2)SNPs represent the majority of sequence variants which alter the structure and expression of gene products; (3) these variants are amenable to analysis by automated methods. We have implemented high throughput genotyping of SNPs using TaqMan type primer/probe methodology in which each allele in a biallelic polymorphism generates a different fluorescent signal which can be quantitated immediately following PCR [on an end-point multiwell fluorescent detector - the Cytofluor 4000] or even during PCR [using the PE 7700 which permits quantitation during each PCR cycle]. A critical issue is the ability to develop algorithms for automated allele calling. Using a set of readily genotyped and more problematically genotyped SNPs, we have made an advance over the available technology for automated genotype calling. We have used a K- means clustering algorithm that evaluates the ratio of the two fluuorescent allele signals to make accurate genotype calls on data that would have needed manual evaluation. - automated genotyping, single nucleotide polymorphisms

Agency
National Institute of Health (NIH)
Institute
National Institute on Alcohol Abuse and Alcoholism (NIAAA)
Type
Intramural Research (Z01)
Project #
1Z01AA000301-02
Application #
6431389
Study Section
(LNG)
Project Start
Project End
Budget Start
Budget End
Support Year
2
Fiscal Year
2000
Total Cost
Indirect Cost
Name
Alcohol Abuse and Alcoholism
Department
Type
DUNS #
City
State
Country
United States
Zip Code
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