Instability index determination using a relative peak height threshold. To quantify the levels of instability from GeneMapper traces peak height was used to determine a relative threshold of 20%. Peaks falling below his threshold were excluded from analysis. Peak heights normalized to the total of all peak heights were multiplied by the change in CAG length of each peak relative to the highest peak in tail (main allele). These values were summed to generate an instability index. Striatum analysis is shown as an example (HdhQ 111/+, 5 months, 100 ng genomic DNA). Open, blue, black, and red peaks represent background, contracted alleles, main allele from tail analysis of same mouse, and expanded alleles, respectively.