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Position specific effect of SNP on signal ratio from long oligonucleotide CGH microarrays; most single probe aberrations represent genuine genomic variants

Noyes, Harry; Rennie, Catriona; Hulme, Helen; Kemp, Stephen; Hoyle, DC and Brass, Andy (2009) Position specific effect of SNP on signal ratio from long oligonucleotide CGH microarrays; most single probe aberrations represent genuine genomic variants. In: Mouse Genetics Conference, 05-09 September 2007, Wellcome Trust Conference Centre, Hinxton Hall, Hinxton, UK. (Unpublished)

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Abstract

Detection of copy number variations (CNV) on microarrays can be hampered by the presence of Single Nucleotide Polymorphisms (SNP). In order to be confident of calling genuine CNV rather than SNP, multiple contiguous probes are required to have non-zero log2 signal ratios. Consequently, only large CNV > ~5kb can be detected on typical CNV long-oligo arrays with probe densities 1 per 2kb. However the majority of CNV are probably <5kb (Nat Genet 2006, 38:82-85). SNP data from the Perlegen 8 million SNP set and log2 signal ratios from ~300,000 long oligos were integrated in order to characterise the effect of SNP on log2 signal ratio and the effect of the position of the SNP within the probe. The maximum length of perfect match between probe and target appeared to be the dominant factor that affected hybridisation. The reduction in effective length of probe meant that single base changes could have a large effect on signal ratio and therefore be detectable on the long oligo arrays. Sequence differences were only expected to give high log2 signal ratios in our study design; therefore probes with low log2 signal ratios were potentially caused by CNV. Approximately 1000 probes with low log signal ratios were identified which were candidates for small CNV that would not have been identified by existing analysis approaches. Most single probe aberrations appeared to be caused by genuine biological variants and were not due to experimental noise. Long-oligo CGH arrays can therefore provide more information than previously thought. The position specific effect of SNP will be useful for microarray design.

Item Type:Conference or Workshop Item (Other)
Uncontrolled Keywords:microarray; Mouse; genetics; Wellcome Trust; Number; polymorphism; SEQUENCE; Difference; Design; analysis
Subjects:Q Science > QH Natural history > QH426 Genetics
Q Science > QH Natural history > QH301 Biology
Q Science > QA Mathematics > QA76 Computer software
Departments, Research Centres and Related Units:Academic Faculties, Institutes and Research Centres > Faculty of Science > Department of Biological Sciences
Refereed:No
Status:Unpublished
ID Code:323
Deposited On:20 Apr 2010 14:41
Last Modified:20 May 2011 17:16

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