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Genome-Wide Human SNP Array 5.0, Made to Order

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The Affymetrix Genome-Wide Human SNP Array 5.0 reduces genotyping costs per sample, which allows you to include more samples, run higher-powered studies and detect more true associations.

Part # Description Unit Size
Genome-Wide Human SNP Array 5.0, MTO
contains 64 arrays (1 wafer)   

The SNP Array 5.0 and the reagent kit are now made to order (MTO) products. As a result, please allow up to 10 weeks for your reagents and up to six weeks for the array.


The Affymetrix Genome-Wide Human SNP Array 5.0 reduces genotyping costs per sample, which allows you to include more samples, run higher-powered studies and detect more true associations.

The SNP Array 5.0 is a single microarray featuring all single nucleotide polymorphisms (SNPs) from the original two-chip Mapping 500K Array Set, as well as 420,000 additional non-polymorphic probes that can measure other genetic differences, such as copy number variation. The SNP Array 5.0 gives researchers a significant increase in information compared to the original 500K Array Set, while reducing the array processing time.

SNPs on the array are present on 200 to 1,100 base pair (bp) Nsp I or Sty I digested fragments in the human genome, and are amplified using the fifth generation of the Whole-genome Sampling Assay (WGSA). This assay now combines the Nsp and Sty fractions previously assayed on two separate arrays. Using the current version of the Affymetrix® Genotyping Console™ Software, a set of 440,794 SNPs on the array exhibit the performance capabilities.

Profiled Research

Patrick Gaffney

New Study Looks at Families to Find the Genetic Basis of Lupus

The University of Minnesota's Kathy Moser and Patrick Gaffney discuss their new microarray investigation into the genetic causes of lupus.

Researchers at the University of Minnesota have launched a comprehensive search for genes involved in systemic lupus erythematosus (SLE), a project that may provide new information about how this chronic inflammatory autoimmune disease develops and critical clues on how to treat it.

Dietrich Stephan

Researchers Uncover Key Pathways Behind ALS

Scientists at the Translational Genomics Research Institute (TGen) have discovered 50 genes associated with Amyotrophic Lateral Sclerosis (ALS, or Lou Gehrig's disease) in a project that took just nine months to complete. Half of the genetic associations belong to a cell-cell adhesion pathway that gives researchers one of the first explanations into this deadly disease.

Stephen Scherer

Researchers Report Copy Number Variation in the Human Genome More Common than Previously Thought

The Toronto Hospital for Sick Children's Stephen Scherer and Affymetrix' Keith Jones discuss the first study to use whole-genome SNP arrays to detect copy number variation in the general population

The International Genome Structural Variation Consortium has developed a genome-wide map of thousands of large-scale structural changes in DNA, called copy number variations, that differ from person to person.


Product Specs
Number of SNPs accessible using Genotyping Console
Number of SNPs accessible using BAT 2.0
Number of Arrays
DNA Required
500 ng
Expected minimum BRLMM-P Call Rate (0.05)
≥97 percent
Average Minor Allele Frequency (MAF)
Average Heterozygosity
PCR Primers
1 per sample
GeneChip® Scanner 3000 7G with AutoLoader
>21 million genotypes per day per scanner with three Gene Chip® Fluidics Station 450s

Performance Data

To test the performance of the SNP Array 5.0, Affymetrix and the Broad Institute jointly ran the 270 samples from the International HapMap Project. In addition, two external sites and one internal validation group ran a plate of 44 HapMap DNAs, which includes 30 unique samples, 10 trios and five samples with multiple replicates.

The arrays that passed the QC call rate threshold were analyzed using the BRLMM-P algorithm at the default setting of 0.05. The average call rate for each set was greater than 99 percent, and the concordance with HapMap genotypes was observed to be greater than or equal to 99.5 percent. For the 10 trios, the Mendelian inheritance consistency was found to be greater than 99.9 percent. Reproducibility was measured at 99.9 percent.

270 HapMap
Site 1
Site 2
Call Rate
HapMap Concordance
Mendelian Consistency

Refer to the Affymetrix® Genome-Wide Human SNP Nsp/Sty 5.0 Assay Manual for details on the QC call rate thresholds, as well as procedures on DNA target preparation, target hybridization, fluidics setup, array scanning and data analysis.

Non-Polymorphic Probes

Learn more about the non-polymorphic probes on the Genome-Wide SNP Array 5.0

Coverage of SNPs and non-polymorphic probes on the Genome-Wide SNP Array 5.0
Figure 1
Coverage of SNPs and non-polymorphic probes on the Genome-Wide SNP Array 5.0

The SNP Array 5.0 contains 420,000 non-polymorphic probes for researchers to examine germline copy number variation (CNV) in association studies. One hundred thousand non-polymorphic probes cover 2,000 known CNVs identified in the UCSC Genome Browser database (50 probes per CNV). Another 320,000 probes were chosen to give even spacing across the genome, concentrating on areas not represented by SNPs. Current Affymetrix software does not support analysis of the non-polymorphic probes.

Learn More

The Affymetrix Genome-Wide Human SNP Nsp/Sty Assay Kit 5.0/6.0

The Affymetrix Genome-Wide Human SNP Array 5.0


For research use only. Not for use in diagnostic procedures.

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