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Genome-Wide Human SNP Array 6.0 - Support Materials

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Application Notes

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

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

Data Sheets

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

Genome-Wide Human SNP Array 6.0 (pdf, 846 KB)

Frequently Asked Questions

Genome-Wide Human SNP Array 6.0

Library Files

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

Note: Affymetrix is providing alternative CDF files, for the Affymetrix genotyping array- Genome-Wide Human SNP Array 5.0. These CDF files provide uniform access to the Copy Number probe content by presenting "one probe per probeset" in both the full and default updated CDF files. This uniform access applies to both Affymetrix genotyping arrays with Copy Number content- Genome-Wide Human SNP Array 5.0 and Genome-Wide Human SNP Array 6.0.

Manuals

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

Cytogenetics Copy Number Assay User Guide (pdf, 2.6 MB)

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

Probe Set Data in MAGE-ML Format

Material Safety Data Sheets

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

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

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)

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

Technical Notes

Associating Copy Number and SNP Variation with Human Disease (pdf, 593 KB)

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

Use of Saliva gDNA for SNP Genotyping (pdf, 556 KB)

White Papers

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

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

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, Release 30 (283 MB, 11/15/09)

GenomeWideSNP_6 Annotations, SQLite Format, Release 30 (471 MB, 11/15/09)

GenomeWideSNP_6 CN Annotations, CSV format, Release 30 (63 MB, 11/15/09)

GenomeWideSNP_6 Copy Number Analysis HapMap Reference, Release 30 (164 MB, 11/19/09)

GenomeWideSNP_6 Meta Probeset File (805 KB, 5/25/07)

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 probesets of interest. Annotation CSV files for the exon arrays are split into a probeset 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, Release 22 (292 MB, 5/25/07)

GenomeWideSNP_6 Annotations, CSV format, Release 23 (291 MB, 7/18/07)

GenomeWideSNP_6 Annotations, CSV format, Release 24 (260 MB, 11/28/07)

GenomeWideSNP_6 Annotations, CSV format, Release 25 (301 MB, 4/29/08)

GenomeWideSNP_6 Annotations, CSV format, Release 26 (301 MB, 10/3/08)

GenomeWideSNP_6 Annotations, CSV format, Release 26 (306 MB, 7/9/08)

GenomeWideSNP_6 Annotations, CSV format, Release 27 (280 MB, 3/25/09)