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Genome-wide Human SNP 6.0 Array

The Genome-Wide Human SNP 6.0 Array can be used for single nucleotide polymorphism (SNP) genotyping, copy number variation (CNV) association studies, de novo CNV and loss of heterozygosity (LOH) detection for association studies and cytogenetics research.

Platform Affymetrix
Deliverables
  • Analytical report
  • Raw .CEL files
  • QC measurements
Research Objectives SNP genotyping, CNV association studies, de novo CNV and LOH detection for association studies and cytogenetics research.
Related Services
  • Cytogenetic analysis
  • DNA-Seq

Overview

The Genome-Wide Human SNP 6.0 Array contains more than 1.8 million markers of genetic variation, including more than 906,600 SNPs and more than 946,000 probes for CNV detection. This array can be used for SNP genotyping, CNV association studies, de novo CNV and LOH detection for association studies and cytogenetics research. The SNP Array 6.0 contains more genetic variation on a single array than any other product, so as to provide maximum panel power and the highest overall coverage of the human genome.

Service Details

For each sample to be analysed, a total of 500 ng of DNA is required for the parallel NspI and StyI assays. Following restriction digests with StyI and NspI, DNA is ligated to adaptors recognising the cohesive four base pair (bp) overhangs. PCR is carried out using generic primers to amplify the adaptor-ligated DNA – this assay has been optimised to preferentially amplify fragments in the 200 – 1,100 bp size range. The StyI and NspI PCR products are combined, purified and subsequently fragmented. The fragmented products are then labelled and hybridised to the SNP 6.0 Array. Following hybridization, the arrays are washed and stained using the GeneChip Fluidics Station 450 and scanned using the GeneChip® Scanner 3000 7G. Positive and negative controls are included to monitor assay performance. Affymetrix Genotyping Console Software is utilised to determine the quality of the generated data. Bioinformatics support is available if required.

Service Deliverables

An Analytical Report is provided containing an in-depth analysis of the project results. The report includes QC results for critical stages of the assay. Raw data files are also sent to the client along with the data QC report.

Starting Material

  • DNA Quantity:  1µg
  • DNA Concentration: 100 ng/µl