Genomic profiling technology has greatly advanced our understanding of the genetic basis of various diseases ranging from Alzheimer’s disease to cancer. Central to this technology are DNA microarrays, which have become indispensible in identifying cohort-specific genes or genetic variations, deciphering the role of such genes or variations in the disease mechanisms, and assessing the efficacy of therapeutic regimens. Various DNA microarrays exist, depending on the objective of the study; for example, single nucleotide polymorphisms (SNP) arrays from Affymetrix, one of the major manufacturers of DNA microarrays, boasts 1.8 million genetic markers, with over 900,000 SNPs. While such DNA microarrays generate a huge amount of information and are very powerful, their analysis may be complex and intensive.
Researchers at the University of Michigan have developed a software program PLUT, which allows importation of data files generated through Affymetrix gene console software to enter the Loss of Heterozygosity (LOH) tool. The LOH tool enables display of loss of heterozygosity between genotype calls for paired DNA samples (tumor/ normal) using data from latest generation SNP array (6.0) from Affymetrix. Both programs are unique in the current marketplace.
Applications and Advantages
- Display of Affymetrix 6.0 SNP array data
- Allows import of data files through Affymetrix gene console software
- Display of loss of heterozygosity between genotype calls for paired DNA samples