Pure Power and Performance

The new Affymetrix Genome-Wide Human SNP Array 6.0 features 1.8 million genetic markers, including more than 906,600 single nucleotide polymorphisms (SNPs) and more than 946,000 probes for the detection of copy number variation. The SNP Array 6.0 is the only platform with analysis tools to truly bridge copy number and association, including a new, high-resolution reference map and a copy number polymorphism (CNP) calling algorithm developed by the Broad Institute. The SNP Array 6.0 demonstrates industry-leading performance and represents more genetic variation on a single array than any other product, providing maximum panel power and the highest physical coverage of the genome.

The high price-performance value of the SNP Array 6.0 enables researchers to design association studies with larger sample sizes in the initial scan and replication phases, thereby significantly increasing the overall genetic power of their studies.

New! Copy Number and LOH analysis tools in Genotyping Console

New! Affymetrix Cytogenetics Solution

New! Automation Solution

More than 906,600 SNPs:

• Unbiased selection of 482,000 SNPs; historical SNPs from the SNP Array 5.0
• Selection of additional 424,000 SNPs
  • Tag SNPs
  • SNPs from chromosomes X and Y
  • Mitochondrial SNPs
  • New SNPs added to the dbSNP database
  • SNPs in recombination hotspots

More than 946,000 copy number probes:

• 202,000 probes targeting 5,677 CNV regions from the Toronto Database of Genomic Variants
• 744,000 probes, evenly spaced along the genome
• Detected 10 times more copy number changes than other SNP/CN platforms
• Three times more coverage of CNPs; only platform with non-polymorphic probes
• GTC 3.0 leverages new, high-resolution reference map and CNP calling algorithm developed by the Broad Institute

More Information:

New Software Tools for Copy Number and LOH Analysis

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Data Sheets

Automated Genotyping Using the SNP Array 6.0 (pdf, 259 KB)

Genome-Wide Human SNP Array 6.0 (pdf, 473 KB)

Technical Notes

Associating Copy Number and SNP Variation with Human Disease (pdf, 1.63 MB)

Linking Whole-genome Amplification to SNP Genotyping (pdf, 346 KB)

Application Notes

A New Paradigm for Two-stage Association Studies (pdf, 144 KB)

Copy-neutral Loss of Heterozygosity in Cancer (pdf, 1.07 MB)

White Papers

Genotyping Console™ Quality Control Assessment (pdf, 1.07 MB)

FAQs

Genome-Wide Human SNP Array 6.0

Manuals

Affymetrix® Human SNP Assay 6.0 User Guide for Automated Target Preparation (pdf, 2.62 MB)

Genome-Wide Human SNP Nsp/Sty 6.0 User Guide (pdf, 2.97 MB)

Probe Set Data in MAGE-ML Format

Quick Reference Cards

Affymetrix® Human SNP Assay 6.0 Automated Target Preparation (pdf, 496 KB)

SNP 6.0 Protocol for 48 Samples (pdf, 458 KB)

SNP 6.0 Protocol for 96 Samples (pdf, 512 KB)

Sample Data

Genome-Wide Human SNP Array 6.0 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)

Library Files

Genome-Wide Human SNP Array 6.0 (zip, 246 MB)

Package Inserts

Genome-Wide Human SNP Array 6.0 (pdf, 102 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_6 BED File (25 MB, 11/28/07)

Current NetAffx Annotation Files

GenomeWideSNP_6 Annotations, CSV format (57 MB, 10/3/08)

GenomeWideSNP_6 Annotations, CSV format (301 MB, 10/3/08)

GenomeWideSNP_6 Copy Number Analysis HapMap Reference (149 MB, 10/13/08)

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_6 CN Probe Sequences, tabular format (31 MB, 5/25/07)

GenomeWideSNP_6 Flanking Sequences, FASTA format (12 MB, 5/25/07)

GenomeWideSNP_6 Probe Sequences, tabular format (48 MB, 5/25/07)

Archived NetAffx Annotation Files

GenomeWideSNP_6 Annotations, CSV format (292 MB, 5/25/07)

GenomeWideSNP_6 Annotations, CSV format (291 MB, 7/18/07)

GenomeWideSNP_6 Annotations, CSV format (260 MB, 11/28/07)

GenomeWideSNP_6 Annotations, CSV format (301 MB, 4/29/08)

GenomeWideSNP_6 Annotations, CSV format (306 MB, 7/9/08)

GenomeWideSNP_6 CN Annotations, CSV format (24 MB, 5/25/07)

GenomeWideSNP_6 CN Annotations, CSV format (48 MB, 7/18/07)

GenomeWideSNP_6 CN Annotations, CSV format (49 MB, 11/28/07)

GenomeWideSNP_6 CN Annotations, CSV format (53 MB, 4/29/08)

GenomeWideSNP_6 CN Annotations, CSV format (53 MB, 7/9/08)

GenomeWideSNP_6 Copy Number Analysis HapMap Reference (149 MB, 6/2/08)

GenomeWideSNP_6 Copy Number Analysis HapMap Reference (149 MB, 7/14/08)

Additional Support

Fluidics Scripts

Literature and Resource Guide for the Genome-Wide SNP Array 6.0 (pdf, 71 KB)

ReadMe, Genome-Wide Human SNP Array 6.0 Sample Data Set

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Part #	Description	Details
901182	Genome-Wide Human SNP Array 6.0	Contains 5 arrays
901153	Genome-Wide Human SNP Array 6.0	Contains 50 arrays
901150	Genome-Wide Human SNP Array 6.0	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® Command Console® Software	Available Via Download
	Genotyping Console™ Software	Available Via Download
00-0079	GeneChip® Fluidics Station 450
00-0331	GeneChip® Hybridization Oven 645	Can be configured for 110 or 220V operation; includes eight probe array carriers
00-0218	GeneChip® Scanner 3000 7G System w/Workstation and Autoloader	Worldwide
00-0362	GeneChip® Scanner 3000 7G Whole Genome Association System	Worldwide

Related Products

Part #	Description	Details
000593	Genome-Wide Human SNP Array 6.0 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.
901167	Genome-Wide Human SNP Array 5.0