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On the exploration of Affymetrix ligation-based SNP assays

Carvalho, B (Oncology)
Monday 26 September 2011, 10:20-10:30

Seminar Room 1, Newton Institute


Single Nucleotide Polymorphisms (SNPs) are genetic variants that take place through the alteration of a single nucleotide (A, C, G or T ) on the DNA sequence. At SNP loca- tions, the possible nucleotides are referred to as alleles and are labelled, for simplicity, as A and B. The combination of alleles (AA, AB and BB) are called genotypes and play an important role on genome-wide association studies (GWAS), through which researchers investigate the association between traits of interest (like diseases) and genomic markers. GWASes depend strongly on the availability of accurate genotypes for the samples involved in the study. Several methodologies can be used for genotyping and one of the most common is DNA microarrays. Affymetrix is well-known for manufacturing one- color arrays comprised of 25 nucleotides long probes. However, their latest genotyping platform, called Axiom, uses a multicolor strategy to label the majority of the SNPs on ligation-based assays that use 30nt long probes.

Previous algorithms for both processing and genotype calling relied on the properties of the data generated by the older assays. Therefore, they may require modifications in order to be used with data from this new product. Here, we present a comprehensive investigation on the properties of the data generated using Axiom arrays, including the changes that are to be implemented on our algorithm for preprocessing SNP data and a discussion about the impact of this shift on downstream analyses involving SNP data.


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