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Chip type: Cytogenetics_Array

Cytogenetics_Array (Whole-Genome 2.7M Array; CYTO2)

From the Affymetrix press release 'New Cytogenetics Products Offer Best Overall Approach for Detection of Chromosome Aberrations' (March 25, 2009): "The [two] Affymetrix Cytogenetics (i) Whole-Genome 2.7M Array and (ii) Cytogenetics Focused Array include copy number (CN) and single nucleotide polymorphism (SNP) content to identify loss of heterozygosity (LOH), uniparental disomy (UPD), and regions identical-by-descent. [...] The (i) Whole-Genome 2.7M Array [...] provides 2.7 million markers, including 400,000 SNPs, to offer superior resolution and enable detection of even the smallest structural changes and regions of autozygosity. The (ii) Focused Array includes more than 330,000 markers to enable efficient detection of aberrations within focused regions of known cytogenetic importance. At the same time, it maintains a backbone of markers at 16 kb spacing to provide whole-genome coverage."

Cytogenetics_Array

> cdf <- AffymetrixCdfFile$byChipType("Cytogenetics_Array")
> print(cdf)
AffymetrixCdfFile:
Path: annotationData/chipTypes/Cytogenetics_Array
Filename: Cytogenetics_Array.CDF
Filesize: 538.32MB
Chip type: Cytogenetics_Array
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 2015x2015
Number of cells: 4060225
Number of units: 2795708
Cells per unit: 1.45
Number of QC units: 4

There are 400,103 SNPs and 2,394,920 CN units in this CDF. 267,197 SNPs have only one probe pair, 104,264 SNPs have two probe pairs and 10,786 have three. There are also a small number of SNPs with more probe pairs. 2,377,527 of the CN units are single CN probes (as in GWS5 and GWS6). In addition to this, there are 1,775 CN units with two probes, 5,618 with 3 probes, 1,496 with 7 probes, and 8,504 with 8 probes.

Resources

By aroma-project.org:

  • Cytogenetics_Array,na28,HB20090519.ugp.gz Unit Genome Position (UGP) annotation file. Human Genome build v36. Sources: Affymetrix NetAffx CSV files Cytogenetics_Array.na28.annot.csv (141Mb) and Cytogenetics_Array.cn.na28.annot.csv (852Mb). Created by: Henrik Bengtsson, 2009-05-19.
  • To the best of my understanding, the assay does not use restriction enzymes. Hence, no fragment-length annotation files.
  • This chip types has probe sequences of variable lengths in the range of 38 to 50-mers. The aroma.affymetrix package does not support variable length probe sequences at this stage.

Affymetrix: