METHODS FOR PRECISE SIZING, AUTOMATED BINNING OF ALLELES, AND REDUCTION OF ERROR RATES IN LARGE-SCALE GENOTYPING USING FLUORESCENTLY LABELED DINUCLEOTIDE MARKERS

Large-scale genotyping is required to generate dense identity-by-desce nt maps to map genes for human complex disease. In some studies the nu mber of genotypes needed can approach or even exceed million. Generall y, linkage and linkage disequilibrium analyses depend on clear allele identification and subsequent allele frequency estimation. Accurate gr ouping or categorization of each allele in the sample [allele calling or binning) is therefore an absolute requirement. Hence,a genotyping s ystem that can reliably achieve this is necessary. In the case of affe cted sib-pair analysis without parents, the need for accurate allele c alling is even more critical. We describe methods that permit precise sizing of alleles across multiple gels using the fluorescence-based, A pplied Biosystems (ABI] genotyping technology and discuss ways to redu ce genotyping error rates. Using database utilities, we show how to mi nimize intergrel allele size variation, to combine data effectively fr om different models of ABI sequencing machines, and automatically bin alleles. The final data can then be converted into a format ready for analysis by statistical genetic packages such as MENDEL.