Dataset Information

WTCCC2 Ankylosing spondylitis cases - individual

ABSTRACT: WTCCC1 project Ankylosing Spondylitis (AS) samples

PROVIDER: EGAD00000000010 | EGA |

REPOSITORIES: EGA

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Publications

Association scan of 14,500 nonsynonymous SNPs in four diseases identifies autoimmunity variants.

Burton Paul R PR Clayton David G DG Cardon Lon R LR Craddock Nick N Deloukas Panos P Duncanson Audrey A Kwiatkowski Dominic P DP McCarthy Mark I MI Ouwehand Willem H WH Samani Nilesh J NJ Todd John A JA Donnelly Peter P Barrett Jeffrey C JC Davison Dan D Easton Doug D Evans David M DM Evans David M DM Leung Hin-Tak HT Marchini Jonathan L JL Morris Andrew P AP Spencer Chris C A CC Tobin Martin D MD Attwood Antony P AP Boorman James P JP Cant Barbara B Everson Ursula U Hussey Judith M JM Jolley Jennifer D JD Knight Alexandra S AS Koch Kerstin K Meech Elizabeth E Nutland Sarah S Prowse Christopher V CV Stevens Helen E HE Taylor Niall C NC Walters Graham R GR Walker Neil M NM Watkins Nicholas A NA Winzer Thilo T Jones Richard W RW McArdle Wendy L WL Ring Susan M SM Strachan David P DP Pembrey Marcus M Breen Gerome G St Clair David D Caesar Sian S Gordon-Smith Katharine K Jones Lisa L Fraser Christine C Green Elaine K EK Grozeva Detelina D Hamshere Marian L ML Holmans Peter A PA Jones Ian R IR Kirov George G Moskivina Valentina V Nikolov Ivan I O'Donovan Michael C MC Owen Michael J MJ Collier David A DA Elkin Amanda A Farmer Anne A Williamson Richard R McGuffin Peter P Young Allan H AH Ferrier I Nicol IN Ball Stephen G SG Balmforth Anthony J AJ Barrett Jennifer H JH Bishop Timothy D TD Iles Mark M MM Maqbool Azhar A Yuldasheva Nadira N Hall Alistair S AS Braund Peter S PS Dixon Richard J RJ Mangino Massimo M Stevens Suzanne S Thompson John R JR Bredin Francesca F Tremelling Mark M Parkes Miles M Drummond Hazel H Lees Charles W CW Nimmo Elaine R ER Satsangi Jack J Fisher Sheila A SA Forbes Alastair A Lewis Cathryn M CM Onnie Clive M CM Prescott Natalie J NJ Sanderson Jeremy J Matthew Christopher G CG Barbour Jamie J Mohiuddin M Khalid MK Todhunter Catherine E CE Mansfield John C JC Ahmad Tariq T Cummings Fraser R FR Jewell Derek P DP Webster John J Brown Morris J MJ Lathrop Mark G MG Connell John J Dominiczak Anna A Marcano Carolina A Braga CA Burke Beverley B Dobson Richard R Gungadoo Johannie J Lee Kate L KL Munroe Patricia B PB Newhouse Stephen J SJ Onipinla Abiodun A Wallace Chris C Xue Mingzhan M Caulfield Mark M Farrall Martin M Barton Anne A Bruce Ian N IN Donovan Hannah H Eyre Steve S Gilbert Paul D PD Hilder Samantha L SL Hinks Anne M AM John Sally L SL Potter Catherine C Silman Alan J AJ Symmons Deborah P M DP Thomson Wendy W Worthington Jane J Dunger David B DB Widmer Barry B Frayling Timothy M TM Freathy Rachel M RM Lango Hana H Perry John R B JR Shields Beverley M BM Weedon Michael N MN Hattersley Andrew T AT Hitman Graham A GA Walker Mark M Elliott Kate S KS Groves Christopher J CJ Lindgren Cecilia M CM Rayner Nigel W NW Timpson Nicolas J NJ Zeggini Eleftheria E Newport Melanie M Sirugo Giorgio G Lyons Emily E Vannberg Fredrik F Hill Adrian V S AV Bradbury Linda A LA Farrar Claire C Pointon Jennifer J JJ Wordsworth Paul P Brown Matthew A MA Franklyn Jayne A JA Heward Joanne M JM Simmonds Matthew J MJ Gough Stephen C L SC Seal Sheila S Stratton Michael R MR Rahman Nazneen N Ban Maria M Goris An A Sawcer Stephen J SJ Compston Alastair A Conway David D Jallow Muminatou M Newport Melanie M Sirugo Giorgio G Rockett Kirk A KA Bumpstead Suzannah J SJ Chaney Amy A Downes Kate K Ghori Mohammed J R MJ Gwilliam Rhian R Hunt Sarah E SE Inouye Michael M Keniry Andrew A King Emma E McGinnis Ralph R Potter Simon S Ravindrarajah Rathi R Whittaker Pamela P Widden Claire C Withers David D Cardin Niall J NJ Davison Dan D Ferreira Teresa T Pereira-Gale Joanne J Hallgrimsdo'ttir Ingeleif B IB Howie Bryan N BN Su Zhan Z Teo Yik Ying YY Vukcevic Damjan D Bentley David D Brown Matthew A MA Compston Alastair A Farrall Martin M Hall Alistair S AS Hattersley Andrew T AT Hill Adrian V S AV Parkes Miles M Pembrey Marcus M Stratton Michael R MR Mitchell Sarah L SL Newby Paul R PR Brand Oliver J OJ Carr-Smith Jackie J Pearce Simon H S SH McGinnis R R Keniry A A Deloukas P P Reveille John D JD Zhou Xiaodong X Sims Anne-Marie AM Dowling Alison A Taylor Jacqueline J Doan Tracy T Davis John C JC Savage Laurie L Ward Michael M MM Learch Thomas L TL Weisman Michael H MH Brown Mathew M

Nature genetics 20071021 11

We have genotyped 14,436 nonsynonymous SNPs (nsSNPs) and 897 major histocompatibility complex (MHC) tag SNPs from 1,000 independent cases of ankylosing spondylitis (AS), autoimmune thyroid disease (AITD), multiple sclerosis (MS) and breast cancer (BC). Comparing these data against a common control dataset derived from 1,500 randomly selected healthy British individuals, we report initial association and independent replication in a North American sample of two new loci related to ankylosing spon ...[more]

PMID: 17952073

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Project description:We have compared synovial biopsies from ankylosing spondylitis and undifferentiated spondylitis patients with healthy controls and osteoarthritis patients Objective: In spondylarthropies, whole-genome gene expression profiling studies have been limited to peripheral blood to date. By undertaking a study in knee synovial biopsies from spondylarthropy (SpA) and ankylosing spondylitis (AS) patients we aimed to identified joint-specific candidate genes and pathways. These pathways may mediate systemic inflammation driven joint damaging processes and more specifically, the osteoproliferation that is characteristic of these conditions. Methods: RNA was extracted from six seronegative SpA, two AS, three osteoarthritis (OA) and four normal control knee synovial biopsies. Whole genome expression profiling was undertaken using the Illumina DASL system, which assays 24000 cDNA probes. Differentially expressed candidate genes were then validated using quantitative PCR and immunohistochemistry. Results: 416 differentially expressed genes were identified that clearly delineated between AS/SpA and control groups. Pathway analysis showed altered gene-expression in oxidoreductase activity, osteoblast activity, B-cell associated, matrix catabolic, and metabolic pathways. The inflammatory mediator, MMP3, was strongly upregulated in AS/SpA samples and the Wnt pathway inhibitors DKK3 and Kremen1 were downregulated. Conclusion: Pathways mediating both systemic inflammation as well as local tissue changes were identified. This suggests initial systemic inflammation in spondylarthropies transfers to and persists in the local joint environment, subsequently mediating changes in genes directly involved in the destructive tissue remodelling. Fifteen knee synovial biopsy tissue samples consisting of six seronegative spondyloarthropy (SpA), two ankylosing spondylitis (AS), three osteoarthritis (OA) and four normal control biopsies were obtained from the Synovial Tissue Bank at the Repatriation General Hospital in Adelaide, South Australia with the appropriate ethical approval (Supplementary Table 1). All patients provided informed written consent.

Project description:Genotyping was performed using a custom-designed Illumina 384-SNP VeraCode microarray (Illumina) to determine possible associations of genes encoding PADI1, PADI2, PADI3, PADI4, PADI6, PRKD3, Gc, GLRX,CDSN, PSORS1C1, TXNDC5, CA1, bub3, SORBS1, VDR,SERPNA1, PCSK6, DNAH9 to rheumatoid arthrities (RA) and ankylosing spondylitis (AS). We previously found that encoding genes of PADI1, PADI2, PADI3, PADI4, PADI6, PRKD3, Gc, GLRX,CDSN, PSORS1C1, TXNDC5, CA1, bub3, SORBS1, VDR, SERPNA1, PCSK6 and DNAH9 could be associated with rheumatoid arthritis (RA) and ankylosing spondylitis (AS). We used illumina customer designed microarray to verify the above finding with an increased numbers of samples. Genotyping was performed using a custom-designed Illumina 384-SNP VeraCode microarray (Illumina) to determine possible associations of genes encoding PADI1, PADI2, PADI3, PADI4, PADI6, PRKD3, Gc, GLRX,CDSN, PSORS1C1, TXNDC5, CA1, bub3, SORBS1, VDR, SERPNA1, PCSK6, DNAH9 to RA and AS. A case-control study was performed with 51 AS patients, 266 rheumatoid arthritis (RA) and 163 health controls. Tag single nucleotide polymorphisms (tag SNPs) across the above genes were determined by searching the HapMap database. The tag SNPs were selected on the basis of linkage disequilibrium patterns observed in the Han Chinese in Beijing (CHB) samples that were genotyped as a part of the International HapMap Project. Only SNPs with a minor allele frequency of greater than 5% with a pair-wise r2 ≥ 0.8 in the HapMap were considered. SNPs that were in exons and untranslated regions (UTR), as well as promoters and introns within 500 bp of exons were also selected. Candidate SNPs were submitted to Illumina for a design score. The Illumina Assay Design Tool filtered out SNPs that were not suitable for the Illumina platform. Finally, 382 SNPs with a design score of “1” were selected. 382 SNPs within PADI1, PADI2, PADI3, PADI4, PADI6, PRKD3, Gc, GLRX,CDSN, PSORS1C1, TXNDC5, CA1, bub3, SORBS1, VDR,SERPNA1, PCSK6, DNAH9 encoding genes were selected. Genotyping was performed using Illumina VeraCode microarray in a case-control study including 51 AS patients, 266 rheumatoid arthritis (RA) and 163 health controls We performed genotyping using a custom-designed Illumina 384-SNP VeraCode microarray (Illumina). Peripheral blood samples were collected from patients with RA (n=266, 183 female) and AS (n=51, 10 female). RA patients had a mean age of 51.7 years, while AS patients had a mean age of 35.9 years. A total of 163 (60 female) healthy individuals with a mean age of 48.0 years were blood donors. Blood samples were put into Monovette tubes containing 3.8% sodium citrate. The genotyping was conducted with the BeadXpress Reader using the Illumina VeraCode GoldenGate Assay kit. 500 ng of sample DNA were used per assay. Genotype clustering and calling were performed using BeadStudio software (Genomestudio V2010.2 Genotyping module V1.6) (Illumina). This work was completed at the Beijing Institute of Genomics.

Dataset Information

WTCCC2 Ankylosing spondylitis cases - individual

Publications

Association scan of 14,500 nonsynonymous SNPs in four diseases identifies autoimmunity variants.

Similar Datasets

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