"GenotypeColour": colour visualisation of SNPs and CNVs

Background: The volume of data available on genetic variations has increased considerably with
the recent development of high-density, single-nucleotide polymorphism (SNP) arrays. Several
software programs have been developed to assist researchers in the analysis of this huge amount
of data, but few can rely upon a whole genome variability visualisation system that could help data
interpretation.
Results: We have developed GenotypeColour™ as a rapid user-friendly tool able to upload, visualise
and compare the huge amounts of data produced by Affymetrix Human Mapping GeneChips
without losing the overall view of the data.
Some features of GenotypeColour™ include visualising the entire genome variability in a single
screenshot for one or more samples, the simultaneous display of the genotype and Copy Number
state for thousands of SNPs, and the comparison of large amounts of samples by producing
"consensus" images displaying regions of complete or partial identity. The software is also useful
for genotype analysis of trios and to show regions of potential uniparental disomy (UPD). All
information can then be exported in a tabular format for analysis with dedicated software. At
present, the software can handle data from 10 K, 100 K, 250 K, 5.0 and 6.0 Affymetrix chips.
Conclusion: We have created a software that offers a new way of displaying and comparing SNP
and CNV genomic data. The software is available free at http://www.med.unibs.it/~barlati/
GenotypeColour and is especially useful for the analysis of multiple samples.