Affymetrix - Genome-Wide Human SNP Array 6.0 Sample Data Set



		Genome-Wide Human SNP Array 6.0 Sample Data Set

The Genome-Wide Human SNP Array 6.0 Sample Data Set is a useful tool for software and workflow demonstrations, the development of probe-level analysis methods for making genotype calls from probe intensity data and a variety of other applications.

Additional information about the Affymetrix® Genome-Wide SNP Array 6.0 can be found on the Genome-Wide Human SNP Array 6.0 support page.

HapMap Data Set
This data set contains the 270 samples from the International HapMap Project run on the Affymetrix Genome-Wide Human SNP Array 6.0. The 270 samples are comprised of 30 CEPH trios, 30 Yoruban trios, 45 unrelated Han Chinese samples and 45 unrelated Japanese samples.

The Genome-Wide Human SNP Array 6.0 consists of 906,600 SNPs (or 931,946 SNPs in the full version of the CDF file). As of HapMap release 21a, a total of about 828,000 SNPs have reference genotypes available for at least 180 of the 270 HapMap samples shared here. These numbers are steadily increasing with each HapMap update.

Chromosome X Titration Data Set
An additional collection of samples provided here are of particular use for exploring copy number variation. The copy number variation data set consists of five replicates each of five samples. Three of the samples have abnormal copies of the X chromosome, having three, four and five copies, respectively. The remaining two are a normal male and a normal female, but are of special interest as the female is the sample studied by fosmid paired-end sequencing in Tuzun et al. (2005), and much work has been done on this sample (Redon et al., 2006) relative to the included male HapMap sample NA10851.

Data Set Distribution Information
The data consists of Affymetrix GeneChip® Command Console™ Software (AGCC) ARR, CEL and/or CHP files. AGCC will be the replacement for GCOS. The README file contains additional information about these samples.

Ordering Data Sets
The data sets are made available in three DVDs from Globalware Solutions.

Library files for analyzing the CEL files can be accessed here.
Annotation files can be accessed here.