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2009 Vienna - European Society of Human Genetics

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Complex traits and polygenic disorders<br />

ment <strong>of</strong> Biomedical <strong>Genetics</strong>, University Medical Centre Utrecht, Utrecht, The<br />

Netherlands, 4 Department <strong>of</strong> Paediatric Gastroenterology, University Medical<br />

Centre Utrecht, Utrecht, The Netherlands, 5 Institute <strong>of</strong> Cell and Molecular Science,<br />

Barts and The London School <strong>of</strong> Medicine and Dentistry, London, United<br />

Kingdom, 6 Department <strong>of</strong> Gastroenterology, VU Medical Centre, Amsterdam,<br />

The Netherlands, 7 Wellcome Trust Sanger Institute, Hinxton, Cambridge, United<br />

Kingdom, 8 Department <strong>of</strong> Medical <strong>Genetics</strong>, and Research Program <strong>of</strong> Molecular<br />

Medicine, University <strong>of</strong> Helsinki, Helsinki, Finland, 9 Department <strong>of</strong> Experimental<br />

Medicine, University <strong>of</strong> Milano Bicocca, Monza, Italy, 10 Fondazione<br />

IRCCS Ospedale Maggiore Policlinico, Mangiagalli e Regina Elena, Milan, Italy,<br />

11 Institute <strong>of</strong> Molecular Medicine, Trinity College Dublin, Dublin, Ireland.<br />

Coeliac disease (CD) is a common, complex trait with high heritability<br />

and strong association to the HLA locus. In the first genome-wide<br />

association study (GWAS) we found 10 new loci and pointed to the<br />

altered innate and adaptive immunity pathways in CD. There is a remarkable<br />

overlap between these loci and those known to be involved<br />

in other inflammatory disorders.<br />

We aimed to expand the number <strong>of</strong> samples and single nucleotide<br />

polymorphisms (SNPs) tested in this GWAS. We expanded our cohort<br />

to 4,200 cases and 10,500 controls, originating from four <strong>European</strong><br />

populations and genotyped for the Illumina 550K tag SNP set.<br />

We are currently integrating the data and performing a meta-analysis.<br />

Validation <strong>of</strong> the most significant SNPs will be carried out in CD and<br />

in samples from patients with inflammatory bowel disease, multiple<br />

sclerosis and rheumatoid arthritis. We also extend the analysis <strong>of</strong> genetic<br />

variation from SNPs to common copy number variants (CNVs).<br />

We used custom, high-density Illumina <strong>Human</strong>-670 Quad Genotyping<br />

BeadChips, enriched for a novel set <strong>of</strong> 120,000 CNV probes capturing<br />

5,000 common heritable CNVs. We are now applying different CNV<br />

algorithms, including TriTyper and PennCNV.<br />

GWA studies in other autoimmune diseases (e.g. type 1 diabetes,<br />

Crohn’s disease) have shown that enlarging the sample size enabled<br />

many more risk variants to be identified. We expect to double the number<br />

<strong>of</strong> genetic variants and gain novel biological insights into the pathogenesis<br />

<strong>of</strong> CD by discovering further SNP risk variants and, for the first<br />

time, performing CNV analysis in coeliac disease.<br />

P09.033<br />

several genes on chromosome 4q27 are involved in coeliac<br />

Disease susceptibility<br />

H. Perdry 1,2 , M. P. Sperandeo 3 , G. Turner 4 , M. C. Babron 2,1 , A. W. Ryan 4 , R.<br />

McManus 4 , F. Clerget-Darpoux 2,1 , L. Greco 3 ;<br />

1 Univ. Paris-Sud, Villejuif, France, 2 INSERM UMR 535, Villejuif, France, 3 University<br />

<strong>of</strong> Naples Federico II, Naples, Italy, 4 Trinity College Dublin, Dublin,<br />

Ireland.<br />

Association between Coeliac Disease (CD) and SNPs in the 4q27 region,<br />

containing the KIAA1109, TENR, IL2 and IL21 genes was detected<br />

in British coeliac cases and controls and confirmed in Dutch and<br />

Irish collections [van Heel et al. 2007].<br />

To better understand how this region is involved in susceptibility to<br />

CD, five SNPs were studied in Italian 407 CD cases and 406 controls.<br />

The Combination Test [Jannot et al, 2003] was applied to select the<br />

subset <strong>of</strong> SNPs showing the most significant difference in the genotypic<br />

distribution between patients and controls. The best discrimination<br />

is obtained though the joint information <strong>of</strong> 3 SNPs, one located in<br />

KIAA1109, the other two on each side <strong>of</strong> IL21. The range <strong>of</strong> the relative<br />

risks <strong>of</strong> the 3-SNP genotypes is very impressive, one genotype conferring<br />

9 times more risk than the least at-risk. Our result strongly suggests<br />

that several genes in 4q27 are involved in CD susceptibility. The<br />

probable role <strong>of</strong> KIAA1109 and IL21 is also supported by expression<br />

studies showing a difference <strong>of</strong> mRNA levels between CD cases and<br />

controls for these two genes.<br />

The importance <strong>of</strong> the 4q27 region in auto-immunity is well established.<br />

The difficulty <strong>of</strong> identifying causal genotypic variations is illustrated<br />

by the problems encountered in disentangling the HLA component<br />

<strong>of</strong> most auto-immune diseases. The modelling <strong>of</strong> the 4q27 region<br />

is likely to also be a long quest, not to mention the added complexity <strong>of</strong><br />

uncovering its interaction with other genes involved in the pathological<br />

pathway(s).<br />

P09.034<br />

sp1-binding site polymorphism <strong>of</strong> cOL1A1 gene, juvenile<br />

idiopathic arthritis course and bone metabolism<br />

M. V. Moskalenko 1 , M. M. Kostik 2 , G. S. Demin 1 , M. N. Ostroumova 3 , M. M.<br />

Mnuskina 3 , L. A. Scheplyagina 4 , V. I. Larionova 2 ;<br />

1 Gene, Ltd., Saint-Petersburg, Russian Federation, 2 Saint-Petersburg State<br />

Pediatric Medical Academy, Saint-Petersburg, Russian Federation, 3 City’s Diagnostic<br />

Center for Adults N1, Saint-Petersburg, Russian Federation, 4 Scientific<br />

and Research Center <strong>of</strong> Pediatric Hematology, Oncology and Immunology,<br />

Moscow, Russian Federation.<br />

Objectives: To detect an association between the alpha 1 chain <strong>of</strong> collagen<br />

type 1 (COL1A1) gene Sp1-binding site polymorphism and juvenile<br />

idiopathic arthritis (JIA) course and bone mineralization in JIA patients.<br />

Study Population: 192 children with JIA (81 boys and 111 girls). The<br />

average age was 11.22±4.43 years.<br />

Methods: In all children we checked more than 20 clinical and laboratorial<br />

arthritis activity parameters, such as the time <strong>of</strong> visual activity score<br />

(VAS), Ritchie arthicular index (RAI), DAS, DAS28, Shteinbroker index,<br />

platelets and leucocytes count, erythrocyte sedimentation rate (ESR).<br />

Bone mineralization <strong>of</strong> lumbar spine (L1-L4) was assessed by dualenergy<br />

X-ray absorbtiometry with pediatric referral database. About 10<br />

bone metabolic markers, such as total Ca, Ca/P and Ca++/P ratios,<br />

total alkaline phosphatase, osteocalcine, C-terminal telopeptides and<br />

parathyroid hormone also were determined. Molecular testing <strong>of</strong> Sp1<br />

COL1A1 polymorphism (rs1800012, +2046G>T) was carried out by<br />

polymerase chain reaction followed by Bse1I enzymatic restriction.<br />

Results: We did not reveal any differences in polymorphic Sp1 alleles<br />

and genotypes distribution between children with normal and low<br />

BMD. Girls with GG genotype <strong>of</strong> Sp1 COL1A1 polymorphism had lower<br />

ESR (p=0.01), platelets (p=0.03), higher Hb (pT) was carried out by polymerase<br />

chain reaction followed by PsyI enzymatic restriction.<br />

Results: We did not reveal any differences in polymorphic PCOL2 alleles<br />

and genotypes distribution between children with normal and low<br />

BMD. Girls with GG genotype <strong>of</strong> the PCOL2 COL1A1 polymorphism<br />

had lower Ca/P (p

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