Open AccessArrayed Primer Extension in the “Array of Arrays” Format: A Rational Approach for Microarray-Based SNP Genotyping
Author(s) -
Niels G.F. Klitø,
Qihua Tan,
Mette Nyegaard,
Klaus Brusgaard,
Mads Thomassen,
Charlotte Skouboe,
Jesper Dahlgaard,
Torben A. Kruse
Publication year - 2007
Publication title -
genetic testing
Language(s) - English
Resource type - Journals
eISSN - 1557-7473
pISSN - 1090-6576
DOI - 10.1089/gte.2007.9998
Subject(s) - international hapmap project , genotyping , single nucleotide polymorphism , snp genotyping , genetics , biology , snp , snp array , computational biology , linkage disequilibrium , genotype , gene
This study provides a new version of the arrayed primer extension (APEX) protocol adapted to the 'array of arrays' platform using an instrumental setup for microarray processing not previously described. The primary aim of the study is to implement a system for rational cost-efficient genotyping where multiple singlenucleotide polymorphisms (SNPs) and individuals are genotyped on each microarray slide. Genotyping results are collected across 185 healthy Danish subjects and 76 SNPs on chromosome 3q13.31, because linkage to atopic disease phenotypes have been suggested in the Danish population. Linkage disequilibrium (LD) results from the experimental data are used in a novel comparison to baseline data defined by the international HapMap SNP database. Comparison on the LD results reveals a strong linear correlation irrespective of LD measure considered: R2 (D') = 0.73 and R2(r2) = 0.54. In conclusion, our results show that this setup is strong enough to support high-throughput genotyping, and these observations support that the HapMap genotype resource is important for defining SNP panels aimed at gene mapping in local subpopulations from Europe.