What Does The "Complex" Snp Type Mean In The Illumina Gene Annotation File?

Question

[dolores]

Hi everybody,

I'm working in the analysis of a gwas illumina 610 quad array and the illumina gene annotation file classifies SNPs in 5 categories: coding, intergenic, intron, UTR and complex.

Does anyone know what "complex" means in this context?

Thank you very much!

[Phil S.]

AFAIK: they are also known as 'polymorphism multisite variation'. One definition is: "... it appears that the SNPs in databases mapped in the segmental duplications are, in fact, variants in paralogous sequences (Estivill et al. 2002). Fredman et al. (2004) defined a new type of polymorphism—multisite variation (MSV)—representing the sum of the signals from many individual duplicon copies that vary in sequence content because of duplication, deletion, or gene conversion, and attributed 28% of the SNPs in duplicons to MSVs." from Hallast et al. . Maybe you want to read further: Gidskehaug et al. and Fredman et al..

Hope that helps...

[dolores]

Thanks for your help and for the links. I'll take a look.