Chip type: ax13339

There exists little information on this chip type, but it "appears" (see reference below) to be the Early Access version of the 10K SNP chip. I would appreciate any further comments/references about this chip type from anyone who knows. /Henrik 2008-07-04

In Zhao X et al. (2004), the ax13339 chip type is referred to as "XbaI mapping array 130" (p 3061), which further indicates that this is an early version of the Mapping10K_Xba131 and the successor Mapping10K_Xba142.

ax13339

> cdf <- AffymetrixCdfFile$byChipType("ax13339")
> cdf
AffymetrixCdfFile:
Path: annotationData/chipTypes/ax13339
Filename: ax13339.CDF
Filesize: 8.22MB
Chip type: ax13339
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 712x712
Number of cells: 506944
Number of units: 10043
Cells per unit: 50.48
Number of QC units: 9

Comparing to the Mapping10K_Xba131 chip type, we note that they have the same dimensions but different number of units. This could mean that the two chip types ax13339 and Mapping10K_Xba131 are identical, but that the annotation has been updated.

All units are listed as 'CustomSeq' (unit type 1) units, whereas for the 10K SNP chips we should see 'Genotyping' (unit type 2) units:

> unitTypes <- getUnitTypes(cdf)
> print(table(unitTypes))
unitTypes
   1
10043

Resources

By dChip.org:

CDF, dChip genome information file: http://www.hsph.harvard.edu/cli/complab/dchip/snp.htm

By Harvard:

CDF, dChip genome information file & other genomic annotation files: http://research.dfci.harvard.edu/meyersonlab/snp/snp.htm (under 'Data download')

References

[Affymetrix 2007] Affymetrix, Improved gridding algorithms in AGCC produce equivalent biological results, White paper, 2007(?). URL: http://www.affymetrix.com/support/technical/whitepapers/agcc_gridding_whitepaper.pdf

[GEO-GPL3400] GEO, Platform GPL3400: Affymetrix GeneChip Mapping Pre-Release 10K Array (ax13339), August 29, 2006. URL: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL3400

[LiC_2008] Cheng Li, dChip: SNP array data processing, July 2008. URL: http://www.hsph.harvard.edu/cli/complab/dchip/

[Lindblad-Toh et al. 2000] Lindblad-Toh K et al., Loss-of-heterozygosity analysis of small-cell lung carcinomas using single-nucleotide polymorphism arrays, Nature Biotechnology 18, 1001-1005, 2000. [DOI:10.1038/79269]

[McCann et al. 2007] McCann et al., ChIP on SNP-chip for genome-wide analysis of human histone H4 hyperacetylation. BMC Genomics, 2007, 8, 322. [PMID: 17868463]

[Zhao X et al. 2004] Zhao X et al., An Integrated View of Copy Number and Allelic Alterations in the Cancer Genome Using Single Nucleotide Polymorphism Arrays, Cancer Research, 64, 3060-3071, May 2004.