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

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.

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.

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.

Learn More

Learn more about the Affymetrix Genome-Wide Human SNP Array 5.0

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Data Sheets

Genome-Wide Human SNP Array 5.0 (pdf, 589 KB)

White Papers

BRLMM-P: a Genotype Calling Method for the SNP 5.0 Array (pdf, 163 KB)

FAQs

Genome-Wide Human SNP Array 5.0

Manuals

Genome-Wide Human SNP Nsp/Sty Assay 5.0 (pdf, 2.46 MB)

Probe Set Data in MAGE-ML Format

Sample Data

Genome-Wide Human SNP Array 5.0 Sample Data Set

Material Safety Data Sheets

Genome-Wide Human SNP 5.0/6.0 Assay Kits, with Reference DNA (zip, 333 KB)

Genome-Wide SNP 5.0/6.0 Assay Kits, without Reference DNA (zip, 292 KB)

Product Updates

GeneChip® Operating Software (GCOS) Service Pack 2 Software Update

Library Files

Alternative CDF Files, Genome-Wide Human SNP Array 5.0 (zip, 70 MB)

Genome-Wide Human SNP Array 5.0 (zip, 90 MB)

Package Inserts

Genome-Wide Human SNP Array 5.0 (pdf, 138 KB)

Genome-Wide Human SNP Nsp/Sty Assay Kit 5.0/6.0 (pdf, 76 KB)

Alignment, Annotation, and Sequence Files

Information about using Alignment, Annotation, and Sequence files

NetAffx Alignment Files

GenomeWideSNP_5 SNP Genomic Positions in BED Format (6.1 MB, 2/9/07)

Current NetAffx Annotation Files

GenomeWideSNP_5 Annotations, CSV format (132 MB, 11/25/08)

GenomeWideSNP_5 CN Annotations, CSV format (22 MB, 11/25/08)

Note: NetAffx annotation files are intended for use in automated analysis. Some are not compatible with all spreadsheet applications. Please use the NetAffx Analysis Center to limit download data to your probe sets of interest. Annotation CSV files for the exon arrays are split into a probe set-level annotation file and a transcript cluster-level annotation file; exon array CSV files are compatible with ExACT.

Sequence Files

GenomeWideSNP_5 CN Probe Sequences, tabular format (13 MB, 6/7/07)

GenomeWideSNP_5 Flanking Sequences, FASTA format (5.9 MB, 3/19/07)

GenomeWideSNP_5 Probe Sequences, tabular format (30 MB, 3/16/07)

Archived NetAffx Annotation Files

GenomeWideSNP_5 Annotations, CSV format (132 MB, 3/9/07)

GenomeWideSNP_5 Annotations, CSV format (137 MB, 7/12/07)

GenomeWideSNP_5 Annotations, CSV format (122 MB, 11/28/07)

GenomeWideSNP_5 Annotations, CSV format (144 MB, 4/7/08)

GenomeWideSNP_5 Annotations, CSV format (22 MB, 10/1/08)

GenomeWideSNP_5 Annotations, CSV format (144 MB, 10/1/08)

GenomeWideSNP_5 Annotations, CSV format (146 MB, 7/9/08)

GenomeWideSNP_5 CN Annotations, CSV format (10 MB, 6/15/07)

GenomeWideSNP_5 CN Annotations, CSV format (20 MB, 8/23/07)

GenomeWideSNP_5 CN Annotations, CSV format (21 MB, 4/7/08)

GenomeWideSNP_5 CN Annotations, CSV format (21 MB, 7/9/08)

Additional Support

Fluidics Scripts

Genome-Wide SNP 5.0 Array Reference DNA Concordance (zip, 15 MB)

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Part #	Description	Details
901167	Genome-Wide Human SNP Array 5.0	Contains 50 arrays
901071	Genome-Wide Human SNP Array 5.0	Contains 100 arrays
901152	Genome-Wide Human SNP Nsp/Sty Assay Kit 5.0/6.0	Sufficient for 50 reactions
901015	Genome-Wide Human SNP Nsp/Sty Assay Kit 5.0/6.0	Sufficient for 100 reactions

Required Products

Part #	Description	Details
	GeneChip® Operating Software	Available Via Download
	Genotyping Console™ Software	Available Via Download
00-0079	GeneChip® Fluidics Station 450
00-0331	GeneChip® Hybridization Oven 645
00-0211	GeneChip® Scanner 3000 7G

Related Products

Part #	Description	Details
000592	Genome-Wide Human SNP Array 5.0 Genotyping Services	For more information on pricing, minimum number of samples or a list of third-party service providers, please consult the Affymetrix Services Home Page.
901153	Genome-Wide Human SNP Array 6.0