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SNP Microarray

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CD Genomics offers SNP Microarray service to interrogate up to five million SNPs in a single assay, allowing genome-wide SNP genotyping needs, and providing you with the reliable, high quality data you need to study genetic variations that contribute to disease, drug and vaccine response, environmental factor response, and other phenotypic characteristics.

SNP Microarray

We offer both Affymetrix and Illumina arrays for SNP genotyping service, which are the most widely used platforms. Our clients can find out about the full catalog of arrays that are available from both Affymetrix and Illumina at their websites ( and (

Although both are named as ‘array’ with convergence of DNA hybridization, fluorescence microscopy, and solid surface DNA capture and have similar throughput, these two platforms differ substantially in many aspects. First of all, they use different methods for discriminating the two alleles of a SNP. The Affymetrix SNP array uses 25-mers for SNP calling via differential hybridization, while the Illumina BeadArray uses 50-mers for target capture and primer extension via hybridization. Another important difference between the two platforms is the selection of SNPs. The Illumina system places more emphasis on tagging SNPs than the Affymetrix system.


We offer the entire range of Affymetrix GeneChip and GeneTitan DNA analysis solutions, covering up to millions of markers in human and many other species.

Differential hybridization relies on different melting temperatures for matched and mismatched probes binding to the target DNA sequences. The Affymetrix SNP microarray employs this principle by applying a combination of photolithography and combinatorial chemistry to directly synthesize oligonucleotides on a glass surface. Affymetrix arrays can achieve very high density to accommodate millions of probes on a single chip.


We offer genome-wide high throughput SNP Genotyping using the Illumina iScan platform and any available Illumina Infinium or GoldenGate genotyping arrays. Illumina’s unique BeadArray technology is based on 3 micron silica beads that self-assemble in micro-wells on planar silica slides. Each bead is covered with hundreds of thousands of copies of a specific oligonucleotide, which acts as the capture sequence.

The Infinium genotyping arrays can be used to genotype between 300,000 and 5 million SNPs based on chip format and used to interrogate from a few dozen to thousands of samples, which offer researcher the flexibility to profile samples in various multiplex formats, and deliver dense genome-wide coverage with carefully selected tag SNPs. Accuracy and reliability for the assays are usually above 99.5%. CD Genomics will perform the array processing, array scanning, and data export from Illumina’s GenomeStudio software.

SNP Microarray

Sample Requirements

We require at least 2 µl of DNA sample at 50 ng/µl for most of our arrays. Samples should be high quality genomic DNA with minimal fragmentation for best results. A 260/280 OD ratio range from 1.8 to 2.0 is recommended.

Key Features and Advantages

  • An authorized service provider for Affymetrix and Illumina provider
  • Highest quality standards
  • Highly experienced staff who have proceed with over 10,000 samples
  • Complete data confidentiality
  • Professional assistance for both planning experiments as well as further data analysis and interpretation
  • Other genetic differences, such as copy number variations, can be measured in addition to SNPs
  • The low amount of genomic DNA needed
  • High call rates >99%, and high accuracy

For genotyping studies, microarrays are still widely adopted as they are substantially less expensive than NGS and much more conducive to processing thousands of samples required for typical genome-wide associations studies (GWAS) with much less prone to design bias.

Our Full Service covers the complete process, from quality control of genomic DNA, to determination of genotypes. Besides, CD Genomics can also help create your own custom microarray which can be tailored to meet specific project requirements. We are ready to help you with your custom array needs, whether it’s a standard design or something more creative.

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45-1 Ramsey Road, Shirley, NY 11967, USA
Tel: 1-631-275-3058
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