McMaster University

Centre for
Functional Genomics

Scope of Search

Genome-wide SNP and Mapping Arrays

Overview

Single nucleotide polymorphism (SNP) arrays combine copy number, LOH and SNP genotyping analysis into a single assay thus enabling the detection of copy number neutral LOH events. The new Affymetrix® Genome-Wide Human SNP Array 6.0 features more than 1.8 million markers for genetic variation, including more than 906,600 single nucleotide polymorphisms (SNPs) and more than 946,000 probes for the detection of copy number variation including:

  • Genome-wide SNP and Mapping Arrays202,000 probes targeting 5,677 known CNV regions from the Toronto Database of Genomic Variants
  • Regions resolve into 3,182 distinct, non-overlapping segments; on average 61 probes per region
  • 744,000 probes, evenly spaced along the genome

SNP Arrays enable scientists to conduct large-scale linkage analysis, association, and copy number studies pertaining to common diseases such as diabetes, heart disease and cancer.

Academic Price List

Price reflects current total processing cost per DNA sample including a chip and labeling reagents.

Affymetrix GeneChip Price CAD$
Human SNP 6.0 700
Human SNP 5.0 600
Mapping 250K Nsp 400
Mapping 250K Sty 400
Mapping 50K Hind 550
Mapping 50KXba 550
Mapping 10K 2.0 300

Sample Preparation Instructions

The SNP protocol uses 500 ng total genomic DNA with concentration of 50 ng/uL from various sources including blood, freshly-isolated or formalin-fixed, paraffin-embedded tissues suspended in reduced EDTA (10 mM Tris, 0.1 mM EDTA) buffer. Starting genomic DNA should be double-stranded and free from PCR inhibitors

Data Transfer

Results from a microarray experiment including *.dat, *cel, *chip and *exp files are sent to the customer via CD/DVD or FTP. For data analysis options please see the Bioinformatics page.