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DNA Array Core Facility

Genotyping Data Analysis

LightTyper:

The LightTyper Instrument analyzes the melting temperatures of the probes hybridized to single stranded complementary DNA. The instrument displays the melting information for each sample as both a melting curve and melting peak (the negative first derivative of the melting curve). This information can be used to identify genotypes because perfectly matched and mismatched probes have different melting curves and melting peaks.

To make genotype calls, the software analyzes the shapes of the melting curves and groups together curves with similar profiles. Each group is defined as a genotype. If the software is allowed to determine standards, each genotype is represented by the median curve of the group. The software then compares the melting curves of individual samples to the median genotype curves for that group.

You can also import an analysis file that contains melting curves of known genotypes. In this case, the software compares the melting curves of the individual samples to the imported standard curves.

Affymetrix Mapping Arrays:

Mapping Arrays provide an efficient method for genotyping 10,000 SNPs in a single experiment. Each SNP that can be detected with the array has a group of probe cells, known as a probe set, on the array.

The mapping algorithm makes the allele call for a SNP by comparing the intensity data from the SNP's probe cells with a model of the intensity values for different allele calls of the SNP. This model is created by analyzing the cell intensity data from many different samples.

The analysis results are displayed in the Mapping window of the GeneChip DNA Analysis Software (GDAS). You can perform comparisons between samples for loss of heterozygosity and export the analysis results in formats that other software applications can use.

-from the GeneChip DNA Analysis Software (GDAS) User Guide