GMT Tutorial Exercise 29

Search SNPDB - Find samples whose AR values fall outside the defined thresholds

SNPscorer compares the reporter dye intensity detected for a pair of SNP probes to determine an "allele ratio" (AR) value. AR values are then translated into genotypes by applying thresholds beyond which samples are considered as either homozygous or heterozygous.
By default, the "SNPscorer" macro scores samples with allele ratios below "0.25" and above "0.75" as homozygous, samples with AR values between "0.45" and "0.55" as heterozygous.
Use SNPDB»SEARCH to find samples whose allele ratios fall outside these AR value thresholds:

1. Select SNPDB and then SEARCH.
2. Select Project: "your name_demo" (as created in Exercise 4, and where demo genotype data was imported in Exercise 27. Please ensure both exercises have been completed beforehand.).
3. Enter AR Range: '0.25' to '0.45'.
4. Click Search. Take note of the search history number (e.g. "3")
5. Repeat the search, but this time, enter '0.55' to '0.75' for AR Range. Take note of the search history number (e.g. "4")
6. The number of hits for these two searches in the Search History table is equivalent to the number of samples with an allele ratio value outside the thresholds applied by "SNPscorer" to assign a genotype as either "homozygous" or "heterozygous".
7. Display the combined results from both searches by entering their search history numbers, separated with "OR" (e.g. "3 OR 4") in the "Combine Searches" textbox. Click on View Results.

Identifying samples with allele ratio values outside the homozygous / heterozygous threshold values with SNPDB»SEARCH.