Dear All.

I am starting up a new project in which we are going to do CGH on a  
large set of paired samples. I have not decided on which platform I  
should use to do this though. The competitors are Agilent 244k, Affy  
SNP 6.0, Illumina 1M.

I have looked in the recent nature and nature genetics papers where  
76 - 27 % of the CNVs detected by a fosmid approach (Mapping and  
sequencing of structural variation from eight human genomes) were  
verified depending on CNV size using affy SNP 6.0 (Integrated  
detection and population-genetic analysis of SNPs and copy number  
variation).

The sensitivity of Illumina 1M was 47% in another paper (Systematic  
assessment of copy number variant detection via genome-wide SNP  
genotyping) compared to again the fosmid approach.

I havent seen any data on the Agilent array for these patients so its  
hard to say anything on this one.

I would greatly appreciate if someone with experience of CGH from  
could comment on which platform that would give the best coverage of  
CNVs and if there are any other reasons to why one should prefer one  
platform over the other.

best regards,

// Johan



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