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Improvements in methods of DNA separation by capillary electrophoresis and advancements in cost effective automated platforms for genome wide studies are a driving force behind the development of newer, more sophisticated software packages for handling the data analysis needs of a dedicated genotyping laboratory. GeneMapper v4.1 software is designed to provide high performance fragment analysis for low to high throughput labs by combining the functions of the older Genescan and Genotyper software packages into one. Using any one of the available sizing standards, a researcher can distinguish fragments between 12bp and 1200bp in size. From simple fragment sizing to more complicated calculations and reporting, GeneMapper v4.1 was designed to analyze genotype applications data from techniques including amplified fragment length polymorphism (AFLP®), Microsatellite and Loss of Heterozygosity (LOH), deletion and duplication analysis (ex: aneuploidy), conformation analysis (ex: SSCP) and analysis of single nucleotide polymorphisms (SNPs) assays. The customizable report features allow individual labs to design, calculate and report the important data for ongoing research. The purpose of this poster is to compare and demonstrate the advances in genotype analysis available through the GeneMapper® software v4.1 with sample files originally analyzed with Genescan® and Genotyper® software.