SNP and CNV Microarray Analysis

We have recently implemented an additional service employing microarrays for mapping genome integrity. The Affymetrix CytoScan HD Array includes 750,000 SNPs and 2.6 million copy number markers to enable detection of accurate breakpoint assignment and high-resolution (~25kb resolution) detection of copy number variation (CNV), loss of heterozygosity (LOH), uniparental disomy (important for imprinting syndrome studies) and low-level mosaicism in cell lines.


  • To identify chromosome abnormalities at less than 5MB resolution
  • To confirm G-band and FISH findings
  • To define specific breakpoints and/or gene insertions
  • When LOH and/or CNV analyses are needed
  • To identify amplifications or deletions for genes of interest
  • When whole genome genotyping is needed
  • To derive genomic information on subtelomeric and pericentromeric regions

Genomic microarray analysis and G-banded karyotyping are complementary and provide a comprehensive panel of genome integrity assessment.


High quality genomic DNA is submitted to the Core at 50 ng/ml in TE buffer, as verified by Nanodrop and a quality assessment via electrophoresis. DNA is then fragmented and amplified using Affymetrix adaptors. Following quantification, DNA is further fragmented and labeled, hybridized to the Affymetrix CytoScan HD array, and scanned for data acquisition. Using the ChAS Software, data will be obtained to suit the user’s needs, including:

  • Summarizing chromosomal aberrations genome-wide
  • User-defined size and number of markers
  • Focused analysis on selected regions of interest
  • Analysis of allele-specific copy number and SNP genotypes
  • Independent confirmation of copy number changes with SNP allelic information
  • Differentiation of aneuoploidy, sample heterogeneity, and sample contamination, low-level mosaicism and uniparental disomyNote that balanced rearrangements cannot be detected with this technique and require G-banded karyotyping.

Affymetrix Cytoscan HD Sample Submission Instructions