title: Arrayed primer extension in the "array of arrays" format: a rational approach for microarray-based SNP genotyping.
abstract: 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.
authors.affiliation: Department of Biochemistry, Pharmacology and Genetics, Human MicrroArray Centre, Odense University Hospital, Odense, DK-5000 Odense C, Denmark. niels.klitoe@mail.dk
authors.forename: Niels G F
authors.initials: NG
authors.lastname: Klitø
authors.forename: Qihua
authors.initials: Q
authors.lastname: Tan
authors.forename: Mette
authors.initials: M
authors.lastname: Nyegaard
authors.forename: Klaus
authors.initials: K
authors.lastname: Brusgaard
authors.forename: Mads
authors.initials: M
authors.lastname: Thomassen
authors.forename: Charlotte
authors.initials: C
authors.lastname: Skouboe
authors.forename: Jesper
authors.initials: J
authors.lastname: Dahlgaard
authors.forename: Torben A
authors.initials: TA
authors.lastname: Kruse
mesh_terms: D002874:Chromosome Mapping; D002893:Chromosomes, Human, Pair 3; D017931:DNA Primers; D005838:Genotype; D006801:Humans; D015810:Linkage Disequilibrium; D020411:Oligonucleotide Array Sequence Analysis; D011110:Polymorphism, Genetic; D020641:Polymorphism, Single Nucleotide
chemical_list: D017931:DNA Primers