SNP Chart: an integrated platform for visualization and interpretation of microarray genotyping data

  • Authors:

  • Scott J. Tebbutt;Igor V. Opushnyev;Ben W. Tripp;Ayaz M. Kassamali;Wendy L. Alexander;Marilyn I. Andersen

  • Affiliations:

  • James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research, St Paul's Hospital, University of British Columbia Vancouver, Canada V6Z 1Y6;James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research, St Paul's Hospital, University of British Columbia Vancouver, Canada V6Z 1Y6;James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research, St Paul's Hospital, University of British Columbia Vancouver, Canada V6Z 1Y6;James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research, St Paul's Hospital, University of British Columbia Vancouver, Canada V6Z 1Y6;James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research, St Paul's Hospital, University of British Columbia Vancouver, Canada V6Z 1Y6;James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research, St Paul's Hospital, University of British Columbia Vancouver, Canada V6Z 1Y6

  • Venue:
  • Bioinformatics
  • Year:
  • 2005

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Abstract

Summary: SNP Chart is a Java application for the visualization and interpretation of microarray genotyping data primarily derived from arrayed primer extension-based chemistries. Spot intensity output files from microarray analysis tools are imported into SNP Chart, together with a multi-channel TIFF image of the original array experiment and a list of the actual single nucleotide polymorphisms (SNPs) being tested. Data from different and/or replicate probes that interrogate the same SNP, but that are scattered across the array grid, can be reassembled into a single chart format, specific for the SNP. This allows a quick and very effective 'visualization'/'quality control' of the data from multiple probes for the same SNP that can be easily interpreted and manually scored as a genotype. Availability: http://www.snpchart.ca Contact: stebbutt@mrl.ubc.ca Supplementary information: A comprehensive manual describing SNP Chart is available at the above website, together with sample data files.