Arrayed primer extension in the "array of arrays" format: a rational approach for microarray-based SNP genotyping

Niels G F Klitø, Qihua Tan, Mette Nyegaard, Klaus Brusgaard, Mads Thomassen, Charlotte Skouboe, Jesper Dahlgaard, Torben A Kruse

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

Resumé

 
Udgivelsesdato: 2007 Summer
OriginalsprogEngelsk
TidsskriftGenetic Testing
Vol/bind11
Udgave nummer2
Sider (fra-til)160-6
Antal sider6
ISSN1090-6576
DOI
StatusUdgivet - 1. jan. 2007

Fingeraftryk

Linkage Disequilibrium
HapMap Project
Chromosome Mapping
Databases
Population

Citer dette

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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.",
keywords = "Chromosome Mapping, Chromosomes, Human, Pair 3, DNA Primers, Genotype, Humans, Linkage Disequilibrium, Oligonucleotide Array Sequence Analysis, Polymorphism, Genetic, Polymorphism, Single Nucleotide",
author = "Klit{\o}, {Niels G F} and Qihua Tan and Mette Nyegaard and Klaus Brusgaard and Mads Thomassen and Charlotte Skouboe and Jesper Dahlgaard and Kruse, {Torben A}",
year = "2007",
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journal = "Genetic Testing and Molecular Biomarkers",
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Arrayed primer extension in the "array of arrays" format: a rational approach for microarray-based SNP genotyping. / Klitø, Niels G F; Tan, Qihua; Nyegaard, Mette; Brusgaard, Klaus; Thomassen, Mads; Skouboe, Charlotte; Dahlgaard, Jesper; Kruse, Torben A.

I: Genetic Testing, Bind 11, Nr. 2, 01.01.2007, s. 160-6.

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

TY - JOUR

T1 - Arrayed primer extension in the "array of arrays" format: a rational approach for microarray-based SNP genotyping

AU - Klitø, Niels G F

AU - Tan, Qihua

AU - Nyegaard, Mette

AU - Brusgaard, Klaus

AU - Thomassen, Mads

AU - Skouboe, Charlotte

AU - Dahlgaard, Jesper

AU - Kruse, Torben A

PY - 2007/1/1

Y1 - 2007/1/1

N2 - 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.

AB - 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.

KW - Chromosome Mapping

KW - Chromosomes, Human, Pair 3

KW - DNA Primers

KW - Genotype

KW - Humans

KW - Linkage Disequilibrium

KW - Oligonucleotide Array Sequence Analysis

KW - Polymorphism, Genetic

KW - Polymorphism, Single Nucleotide

U2 - 10.1089/gte.2007.9998

DO - 10.1089/gte.2007.9998

M3 - Journal article

C2 - 17627387

VL - 11

SP - 160

EP - 166

JO - Genetic Testing and Molecular Biomarkers

JF - Genetic Testing and Molecular Biomarkers

SN - 1945-0265

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ER -