News and Events

12/9/2008

Affymetrix Technology Powers Cincinnati Children's Hospital's Innovative Test for Jaundice

12/8/2008

Affymetrix Completes Acquisition of Panomics

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Plant and Animal Genome XVII Conference

1/10/2009-1/14/2009

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Achieving ROI in Personalized Medicine: Barriers, Incentives, and Pathways to Commercialization

1/27/2009-1/28/2009

Scientific Publications

Search our database of 16170 publications.

GeneChip^® Human Mapping 500K Array Set

Figure 1

The GeneChip® Human Mapping 500K Array Set provides consistently high coverage across different populations. It is comprised of two arrays, each capable of genotyping on average 250,000 SNPs (approximately 262,000 for Nsp arrays and 238,000 for Sty arrays). The Mapping 500K Array Set uses the same proven assay as the GeneChip® Mapping 10K Array and Mapping 100K Set that has been validated in over 120 published studies in less than three years.

May 2006 — A series of updates to the Mapping 500K system is launched, including:

BRLMM, a new genotype calling algorithm. New and existing Mapping 500K Array Set data can now be re-analyzed to increase both call rates and accuracy.
96-well plate protocol, enabling faster and more consistent ramp-up to high throughput sample processing.

Benefits of the Mapping 500K Array Set

Consistently high coverage across different populations
View Genome coverage of 500K SNPs (Figure 1)
Reference standard for whole-genome association
Community creating database of >10,000 control samples
Gain consortium to release Mapping 500K Array Set data to the public domain
Proven approach for discovery
See list of nearly 250 publications (pdf, 159 KB) on mapping assay
Download updated Assay Manual (pdf, 3.4 MB) which includes protocol for 96-well plate processing
Broad compatibility with DNA sample collections
250 ng of raw genomic DNA
Compatible with whole-genome amplified DNA
Highest throughput on the market
100 samples/week/instrument
Learn more about GeneChip® Scanner 3000, with AutoLoader
Innovative solutions available for data analysis and management
Learn about BRLMM, a genotype calling algorithm
Learn about GeneChip-compatible™ third-party software for downstream analysis

Find out more about Clontech's Titanium™ DNA Amplification Kit for use with the Whole Genome Sampling Assay.

Data Sheets

GeneChip® Human Mapping 500K Array Set (pdf, 192 KB)

Application Notes

Microarrays in Cancer Research (pdf, 423 KB)

White Papers

BRLMM Algorithm for Affymetrix Mapping Arrays (pdf, 278 KB)

GeneChip^® Human Mapping 500K Array Set

Part #	Description	Details
900767	GeneChip® Human Mapping 250K Nsp Array	Contains 5 Mapping 250K Nsp Arrays
900768	GeneChip® Human Mapping 250K Nsp Array	Contains 30 Mapping 250K Nsp Arrays
901189	GeneChip® Human Mapping 250K Nsp Array	Contains 100 Mapping 250K Nsp Arrays
900769	GeneChip® Human Mapping 250K Sty Array	Contains 5 Mapping 250K Sty Arrays
900770	GeneChip® Human Mapping 250K Sty Array	Contains 30 Mapping 250K Sty Arrays
901188	GeneChip® Human Mapping 250K Sty Array	Contains 100 Mapping 250K Sty Arrays

GeneChip^® Human Mapping 500K Assay Kits

Part #	Description	Details
900766	GeneChip® Human Mapping 250K Nsp Assay Kit	Sufficient for 30 reactions
900753	GeneChip® Human Mapping 250K Nsp Assay Kit	Sufficient for 100 reactions
900765	GeneChip® Human Mapping 250K Sty Assay Kit	Sufficient for 30 reactions
900754	GeneChip® Human Mapping 250K Sty Assay Kit	Sufficient for 100 reactions

Required Products

Part #	Description	Details
	Affymetrix® GeneChip® Command Console® Software	See product page for more information
	Affymetrix® Genotyping Console™ Software	See product page for more information
00-0079	GeneChip® Fluidics Station 450
00-0331	GeneChip® Hybridization Oven
00-0213	GeneChip® Scanner 3000 High-Resolution Scanning Patch

Related Products

Part #	Description	Details
901153	Genome-Wide Human SNP Array 6.0	See product page for more information
901167	Genome-Wide Human SNP Array 5.0	See product page for more information

FAQs

Human Mapping 500K Array Set

Manuals

Mapping 500K Assay Manual (pdf, 3.4 MB)

Probe Set Data in MAGE-ML Format

Quick Reference Cards

GeneChip® Mapping 500K Array Set (zip, .99 MB)

Sample Data

Mapping 500K HapMap Genotype Data Set

Mapping 500K Sample Data Set

Material Safety Data Sheets

Mapping 500K Array Set, Nsp Array (zip, 303 KB)

Mapping 500K Array Set, Sty Array (zip, 345 KB)

Library Files

Mapping 250K Nsp Array (zip, 43 MB)

Mapping 250K Sty Array (zip, 42 MB)

Package Inserts

Mapping 500K Array Set (pdf, 97 KB)

Mapping 500K Assay Kit (pdf, 83 KB)

Alignment, Annotation, and Sequence Files

Information about using Alignment, Annotation, and Sequence files

NetAffx Alignment Files

Mapping250K_Nsp BED File (3.9 MB, 11/28/07)

Mapping250K_Sty BED File (3.6 MB, 11/28/07)

Current NetAffx Annotation Files

Mapping250K_Nsp Annotations, CSV format (79 MB, 11/25/08)

Mapping250K_Sty Annotations, CSV format (73 MB, 11/25/08)

Mapping250K_Nsp Annotations, GTYPE Format (50 MB, 1/2/07)

Mapping250K_Sty Annotations, GTYPE Format (46 MB, 1/2/07)

Mapping250K_Nsp GC Content Data, NCBI Build 36, TSV Format (3.8 MB, 1/2/07)

Mapping250K_Sty GC Content Data, NCBI Build 36, TSV Format (3.5 MB, 1/2/07)

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 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.