dc.contributor.author |
Steer, S |
en |
dc.contributor.author |
Abkevich, V |
en |
dc.contributor.author |
Gutin, A |
en |
dc.contributor.author |
Cordell, HJ |
en |
dc.contributor.author |
Gendall, KL |
en |
dc.contributor.author |
Merriman, ME |
en |
dc.contributor.author |
Rodger, RA |
en |
dc.contributor.author |
Rowley, KA |
en |
dc.contributor.author |
Chapman, P |
en |
dc.contributor.author |
Gow, P |
en |
dc.contributor.author |
Harrison, AA |
en |
dc.contributor.author |
Highton, J |
en |
dc.contributor.author |
Jones, Peter |
en |
dc.contributor.author |
O'Donnell, J |
en |
dc.contributor.author |
Stamp, L |
en |
dc.contributor.author |
Fitzgerald, Lesley |
en |
dc.contributor.author |
Iliev, D |
en |
dc.contributor.author |
Kouzmine, A |
en |
dc.contributor.author |
Tran, T |
en |
dc.contributor.author |
Skolnick, MH |
en |
dc.contributor.author |
Timms, KM |
en |
dc.contributor.author |
Lanchbury, JS |
en |
dc.contributor.author |
Merriman, TR |
en |
dc.date.accessioned |
2012-05-27T20:08:48Z |
en |
dc.date.issued |
2007 |
en |
dc.identifier.citation |
GENES AND IMMUNITY 8(1):57-68 01 Jan 2007 |
en |
dc.identifier.issn |
1466-4879 |
en |
dc.identifier.uri |
http://hdl.handle.net/2292/18594 |
en |
dc.description.abstract |
A pragmatic approach that balances the benefit of a whole-genome association (WGA) experiment against the cost of individual genotyping is to use pooled genomic DNA samples. We aimed to determine the feasibility of this approach in a WGA scan in rheumatoid arthritis (RA) using the validated human leucocyte antigen (HLA) and PTPN22 associations as test loci. A total of 203 269 single-nucleotide polymorphisms (SNPs) on the Affymetrix 100K GeneChip and Illumina Infinium microarrays were examined. A new approach to the estimation of allele frequencies from Affymetrix hybridization intensities was developed involving weighting for quality signals from the probe quartets. SNPs were ranked by z-scores, combined from United Kingdom and New Zealand case-control cohorts. Within a 1.7 Mb HLA region, 33 of the 257 SNPs and at PTPN22, 21 of the 45 SNPs, were ranked within the top 100 associated SNPs genome wide. Within PTPN22, individual genotyping of SNP rs1343125 within MAGI3 confirmed association and provided some evidence for association independent of the PTPN22 620W variant (P=0.03). Our results emphasize the feasibility of using genomic DNA pooling for the detection of association with complex disease susceptibility alleles. The results also underscore the importance of the HLA and PTPN22 loci in RA aetiology. |
en |
dc.publisher |
Nature Publishing Group |
en |
dc.relation.ispartofseries |
Genes and Immunity |
en |
dc.rights |
Items in ResearchSpace are protected by copyright, with all rights reserved, unless otherwise indicated. Previously published items are made available in accordance with the copyright policy of the publisher. Details obtained from http://www.sherpa.ac.uk/romeo/issn/1466-4879/ |
en |
dc.rights.uri |
https://researchspace.auckland.ac.nz/docs/uoa-docs/rights.htm |
en |
dc.subject |
*Arthritis, Rheumatoid/ge [Genetics] Case-Control Studies Cohort Studies DNA/ge [Genetics] Female *Genetic Predisposition to Disease *Genome, Human *Genomics/mt [Methods] HLA Antigens/ge [Genetics] Humans Male Oligonucleotide Array Sequence Analysis Polymorphism, Single Nucleotide Protein Tyrosine Phosphatase, Non-Receptor Type 22 Protein Tyrosine Phosphatases/ge [Genetics] 0 (HLA Antigens) 9007-49-2 (dna) EC 3-1-3-48 (PTPN22 protein, human) EC 3-1-3-48 (Protein Tyrosine Phosphatase, Non-Receptor Type 22) EC 3-1-3-48 (Protein Tyrosine Phosphatases) |
en |
dc.title |
Genomic DNA pooling for whole-genome association scans in complex disease: empirical demonstration of efficacy in rheumatoid arthritis |
en |
dc.type |
Journal Article |
en |
dc.identifier.doi |
10.1038/sj.gene.6364359 |
en |
pubs.issue |
1 |
en |
pubs.begin-page |
57 |
en |
pubs.volume |
8 |
en |
dc.rights.holder |
Copyright: Nature Publishing Group |
en |
dc.identifier.pmid |
17159887 |
en |
pubs.end-page |
68 |
en |
dc.rights.accessrights |
http://purl.org/eprint/accessRights/RestrictedAccess |
en |
pubs.subtype |
Article |
en |
pubs.elements-id |
102534 |
en |
pubs.record-created-at-source-date |
2010-09-01 |
en |
pubs.dimensions-id |
17159887 |
en |