Chip type: GenomeWideSNP_6
Genome-Wide Human SNP Array 6.0
Affymetrix' press release: Affymetrix Sets New Standard in Genotyping With Genome-Wide Human SNP Array 6.0, May 21, 2007.
From the press release: "The Affymetrix SNP Array 6.0 contains more than 900,000 single nucleotide polymorphisms (SNPs) and more than 946,000 non-polymorphic probes for the detection of copy number variation. [...]".
The design of the 6.0 is better than 5.0. For instance, for SNPs the allele A and allele B probes where not necessarily aligned in target sequence on the 5.0 chip, but is (again) on the 6.0 chip.
The Affymetrix SNP 6.0 Array interrogates 934,946 SNPs and 946,371 CNPs totalling 1,878,317 loci.
Enzymes Nsp and Sty are used in parallel in the assay and the amplified targets are mixed together at the very end. For this reason, some of the probes on the array are targeting sequences that may sit on fragments cut by either enzymes or both. According to Jim Veitch (Affymetrix, 2007-10-22): the SNP probes occur in a Nsp, Sty or Nsp+Sty fragment, but the CN probes occur only Nsp and Nsp+Sty fragments (not Sty-alone fragments).
The Broad Institute has a Research News article 'A unique collaboration between Cambridge and Silicon Valley' (Sept 7, 2008), which gives some background on how the GenomeWideSNP_5 and GenomeWideSNP_6 chip types were developed as part of a collaboration between Affymetrix and the Broad Institute.
Early versions of this chip type are GenomeWideEx_6 and GenomeWideEx_6_v2.
This is the CDF file that is recommended and supported by aroma.affymetrix. Note, make sure to rename it such that you replace the dot with a comma.
> cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full") > print(cdf) AffymetrixCdfFile: Path: annotationData/chipTypes/GenomeWideSNP_6 Filename: GenomeWideSNP_6,Full.CDF Filesize: 470.44MB Chip type: GenomeWideSNP_6,Full RAM: 0.00MB File format: v4 (binary; XDA) Dimension: 2572x2680 Number of cells: 6892960 Number of units: 1881415 Cells per unit: 3.66 Number of QC units: 4 > print(getChecksum(cdf))  "3fbe0f6e7c8a346105238a3f3d10d4ec"
- GenomeWideSNP_6,Full,na33,hg19,dbSNP137,HB20140118.ufl.gz (GenomeWideSNP_6,na33,hg19,dbSNP137,HB20140118.ufl.gz)
- Unit Fragment-Length (UFL) annotation file mapping to the units in the GenomeWideSNP_6.Full.CDF (GenomeWideSNP_6.CDF). Human Genome build v37 (hg19). Sources: Affymetrix NetAffx CSV files GenomeWideSNP_6.cn.na33.annot.csv (868MB) and GenomeWideSNP_6.na33.annot.csv (1.38GB). Created by: Henrik Bengtsson, 2014-01-18.
- GenomeWideSNP_6,Full,na33,hg19,dbSNP137,HB20140118.ugp.gz (GenomeWideSNP_6,na33,hg19,dbSNP137,HB20140118.ugp.gz)
- Unit Genome Position (UGP) annotation file mapping to the units in the GenomeWideSNP_6.Full.CDF (GenomeWideSNP_6.CDF). Human Genome build v37 (hg19). Sources: Affymetrix NetAffx CSV files GenomeWideSNP_6.cn.na33.annot.csv (868MB) and GenomeWideSNP_6.na33.annot.csv (1.38GB). Created by: Henrik Bengtsson, 2014-01-18.
- GenomeWideSNP_6,HB20080710.acs.gz - Aroma Cell Sequence (ACS) annotation file mapping cell indices to 25-mer sequences and target strandedness. Sources: Affymetrix probe_tab file. Created by: Henrik Bengtsson, 2008-07-10.
- Product page: http://www.affymetrix.com/support/technical/byproduct.affx?product=genomewidesnp_6
- Support Material: Genome-Wide Human SNP Array 6.0 - Support Materials (SNP annotation files with SNP positions, dbSNP ID, fragment lengths etc. Probe sequences.)