Microarreglos no tan exactos

Concerning the Affymetrix™ human genotyping array, we detected 25 differences (5 in different chromosomes), of which 10 (40%) were in different genes. These 25 discrepancies lead to 61,916 SNPs being in a different genomic order, with 89% being less or equal than 2 indexes away (Data S5). By checking manually a subset of those alignment discrepancies, we found that the Affymetrix™ mismappings were due to their hit not being perfect, having one or more extra SNPs on the SNP flanking sequence, or having less flanking sequence aligned. With the Illumina's™ human beadchip, 271 SNPs have different genomic positions (with 22 on different chromosomes), of which 59 (22%) are on different genes. The 271 discrepancies lead to 131,378 SNPs being in a different genomic order, although 98% are less or equal than two indexes away (Data S6). By checking manually a subset of those alignment discrepancies, we found that the Illumina™ mismappings were due to their hit not being perfect, having one or more extra SNPs on the SNP flanking sequence, or having less flanking sequence aligned.


Fuente
Fadista J , Bendixen C , 2012 Genomic Position Mapping Discrepancies of Commercial SNP Chips. PLoS ONE 7(2): e31025. doi:10.1371/journal.pone.0031025