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Multiple common variants for celiac disease influencing immune gene expression.
Dubois PC, Trynka G, Franke L, Hunt KA, Romanos J, Curtotti A, Zhernakova A, Heap GA, Adány R, Aromaa A, Bardella MT, van den Berg LH, Bockett NA, de la Concha EG, Dema B, Fehrmann RS, Fernández-Arquero M, Fiatal S, Grandone E, Green PM, Groen HJ, Gwilliam R, Houwen RH, Hunt SE, Kaukinen K, Kelleher D, Korponay-Szabo I, Kurppa K, MacMathuna P, Mäki M, Mazzilli MC, McCann OT, Mearin ML, Mein CA, Mirza MM, Mistry V, Mora B, Morley KI, Mulder CJ, Murray JA, Núñez C, Oosterom E, Ophoff RA, Polanco I, Peltonen L, Platteel M, Rybak A, Salomaa V, Schweizer JJ, Sperandeo MP, Tack GJ, Turner G, Veldink JH, Verbeek WH, Weersma RK, Wolters VM, Urcelay E, Cukrowska B, Greco L, Neuhausen SL, McManus R, Barisani D, Deloukas P, Barrett JC, Saavalainen P, Wijmenga C, van Heel DA. Dubois PC, et al. Among authors: Saavalainen P. Nat Genet. 2010 Apr;42(4):295-302. doi: 10.1038/ng.543. Epub 2010 Feb 28. Nat Genet. 2010. PMID: 20190752 Free PMC article.
We genotyped 113 selected SNPs with P(GWAS) < 10(-4) and 18 SNPs from 14 known loci in a further 4,918 cases and 5,684 controls. ...In an expression quantitative trait meta-analysis of 1,469 whole blood samples, 20 of 38 (52.6%) tested loci had celiac risk variants correlated (P < 0.0028, FDR 5%) with cis gene expression....

We genotyped 113 selected SNPs with P(GWAS) < 10(-4) and 18 SNPs from 14 known loci in a further 4,918 cases and 5,684 controls. .

Insights into the genetic epidemiology of Crohn's and rare diseases in the Ashkenazi Jewish population.
Rivas MA, Avila BE, Koskela J, Huang H, Stevens C, Pirinen M, Haritunians T, Neale BM, Kurki M, Ganna A, Graham D, Glaser B, Peter I, Atzmon G, Barzilai N, Levine AP, Schiff E, Pontikos N, Weisburd B, Lek M, Karczewski KJ, Bloom J, Minikel EV, Petersen BS, Beaugerie L, Seksik P, Cosnes J, Schreiber S, Bokemeyer B, Bethge J; International IBD Genetics Consortium; NIDDK IBD Genetics Consortium; T2D-GENES Consortium, Heap G, Ahmad T, Plagnol V, Segal AW, Targan S, Turner D, Saavalainen P, Farkkila M, Kontula K, Palotie A, Brant SR, Duerr RH, Silverberg MS, Rioux JD, Weersma RK, Franke A, Jostins L, Anderson CA, Barrett JC, MacArthur DG, Jalas C, Sokol H, Xavier RJ, Pulver A, Cho JH, McGovern DPB, Daly MJ. Rivas MA, et al. Among authors: Saavalainen P. PLoS Genet. 2018 May 24;14(5):e1007329. doi: 10.1371/journal.pgen.1007329. eCollection 2018 May. PLoS Genet. 2018. PMID: 29795570 Free PMC article.
As validation we document 148 AJ enriched protein-altering alleles that overlap with "pathogenic" ClinVar alleles (table available at https://github.com/macarthur-lab/clinvar/blob/master/output/clinvar.tsv), including those that account for 10-100 fold differences in prevalence between AJ and non-AJ populations of some rare diseases, especially recessive conditions, including Gaucher disease (GBA, p.Asn409Ser, 8-fold enrichment); Canavan disease (ASPA, p.Glu285Ala, 12-fold enrichment); and Tay-Sachs disease (HEXA, c.1421+1G>C, 27-fold enrichment; p.Tyr427IlefsTer5, 12-fold enrichment). ...Independently, we find that genomewide common variant risk defined by GWAS shows a strong difference between AJ and non-AJ European control population samples (0.97 s.d. higher, p<10-16). ...
As validation we document 148 AJ enriched protein-altering alleles that overlap with "pathogenic" ClinVar alleles (table available at https: …
A protein-truncating R179X variant in RNF186 confers protection against ulcerative colitis.
Rivas MA, Graham D, Sulem P, Stevens C, Desch AN, Goyette P, Gudbjartsson D, Jonsdottir I, Thorsteinsdottir U, Degenhardt F, Mucha S, Kurki MI, Li D, D'Amato M, Annese V, Vermeire S, Weersma RK, Halfvarson J, Paavola-Sakki P, Lappalainen M, Lek M, Cummings B, Tukiainen T, Haritunians T, Halme L, Koskinen LL, Ananthakrishnan AN, Luo Y, Heap GA, Visschedijk MC; UK IBD Genetics Consortium; NIDDK IBD Genetics Consortium, MacArthur DG, Neale BM, Ahmad T, Anderson CA, Brant SR, Duerr RH, Silverberg MS, Cho JH, Palotie A, Saavalainen P, Kontula K, Färkkilä M, McGovern DP, Franke A, Stefansson K, Rioux JD, Xavier RJ, Daly MJ, Barrett J, de Lane K, Edwards C, Hart A, Hawkey C, Jostins L, Kennedy N, Lamb C, Lee J, Lees C, Mansfield J, Mathew C, Mowatt C, Newman B, Nimmo E, Parkes M, Pollard M, Prescott N, Randall J, Rice D, Satsangi J, Simmons A, Tremelling M, Uhlig H, Wilson D, Abraham C, Achkar JP, Bitton A, Boucher G, Croitoru K, Fleshner P, Glas J, Kugathasan S, Limbergen JV, Milgrom R, Proctor D, Regueiro M, Schumm PL, Sharma Y, Stempak JM, Targan SR, Wang MH. Rivas MA, et al. Among authors: Saavalainen P. Nat Commun. 2016 Aug 9;7:12342. doi: 10.1038/ncomms12342. Nat Commun. 2016. PMID: 27503255 Free PMC article.
Through replication genotyping and imputation we found that a predicted protein-truncating variant (rs36095412, p.R179X, genotyped in 11,148 ulcerative colitis patients and 295,446 controls, MAF=up to 0.78%) in RNF186, a single-exon ring finger E3 ligase with strong colonic expression, protects against ulcerative colitis (overall P=6.89 × 10(-7), odds ratio=0.30). ...
Through replication genotyping and imputation we found that a predicted protein-truncating variant (rs36095412, p.R179X, genotyped in …
Meta-analysis of genome-wide linkage studies in celiac disease.
Forabosco P, Neuhausen SL, Greco L, Naluai AT, Wijmenga C, Saavalainen P, Houlston RS, Ciclitira PJ, Babron MC, Lewis CM. Forabosco P, et al. Among authors: Saavalainen P. Hum Hered. 2009;68(4):223-30. doi: 10.1159/000228920. Epub 2009 Jul 22. Hum Hered. 2009. PMID: 19622889 Free PMC article.
Outside the HLA region, suggestive evidence for linkage was obtained at the telomeric region of chromosome 10 (10q26.12-qter; p = 0.00366), and on chromosome 8 (8q22.2-q24.21; p = 0.00491). ...
Outside the HLA region, suggestive evidence for linkage was obtained at the telomeric region of chromosome 10 (10q26.12-qter; p = 0.0 …
Evolutionary and functional analysis of celiac risk loci reveals SH2B3 as a protective factor against bacterial infection.
Zhernakova A, Elbers CC, Ferwerda B, Romanos J, Trynka G, Dubois PC, de Kovel CG, Franke L, Oosting M, Barisani D, Bardella MT; Finnish Celiac Disease Study Group, Joosten LA, Saavalainen P, van Heel DA, Catassi C, Netea MG, Wijmenga C. Zhernakova A, et al. Among authors: Saavalainen P. Am J Hum Genet. 2010 Jun 11;86(6):970-7. doi: 10.1016/j.ajhg.2010.05.004. Am J Hum Genet. 2010. PMID: 20560212 Free PMC article.
Multiple independent variants in 6q21-22 associated with susceptibility to celiac disease in the Dutch, Finnish and Hungarian populations.
Einarsdottir E, Bevova MR, Zhernakova A, Monsuur A, Koskinen LL, van't Slot R, Mulder C, Mearin ML, Korponay-Szabo IR, Kaukinen K, Kurppa K, Kere J, Mäki M, Wijmenga C, Saavalainen P. Einarsdottir E, et al. Among authors: Saavalainen P. Eur J Hum Genet. 2011 Jun;19(6):682-6. doi: 10.1038/ejhg.2011.2. Epub 2011 Feb 16. Eur J Hum Genet. 2011. PMID: 21326284 Free PMC article. Clinical Trial.
The association to rs9391227 represents the strongest association signal found in the Finnish (P = 0.003, OR 0.66) as well as the combined Dutch, Finnish and Hungarian populations (P = 3.6 × 10(-5), OR 0.76). ...
The association to rs9391227 represents the strongest association signal found in the Finnish (P = 0.003, OR 0.66) as well as the com …
Association study of the IL18RAP locus in three European populations with coeliac disease.
Koskinen LL, Einarsdottir E, Dukes E, Heap GA, Dubois P, Korponay-Szabo IR, Kaukinen K, Kurppa K, Ziberna F, Vatta S, Not T, Ventura A, Sistonen P, Adány R, Pocsai Z, Széles G, Mäki M, Kere J, Wijmenga C, van Heel DA, Saavalainen P. Koskinen LL, et al. Among authors: Saavalainen P. Hum Mol Genet. 2009 Mar 15;18(6):1148-55. doi: 10.1093/hmg/ddn438. Epub 2008 Dec 22. Hum Mol Genet. 2009. PMID: 19103669
The GA haplotype of the markers rs13015714 and rs917997 showed the strongest association (P = 0.0001, odds ratio = 1.475, 95% confidence interval 1.21-1.80). ...
The GA haplotype of the markers rs13015714 and rs917997 showed the strongest association (P = 0.0001, odds ratio = 1.475, 95% confide …
Fine mapping of the CELIAC2 locus on chromosome 5q31-q33 in the Finnish and Hungarian populations.
Koskinen LL, Einarsdottir E, Korponay-Szabo IR, Kurppa K, Kaukinen K, Sistonen P, Pocsai Z, Széles G, Adány R, Mäki M, Kere J, Saavalainen P. Koskinen LL, et al. Among authors: Saavalainen P. Tissue Antigens. 2009 Nov;74(5):408-16. doi: 10.1111/j.1399-0039.2009.01359.x. Tissue Antigens. 2009. PMID: 19845895
Association study of FUT2 (rs601338) with celiac disease and inflammatory bowel disease in the Finnish population.
Parmar AS, Alakulppi N, Paavola-Sakki P, Kurppa K, Halme L, Färkkilä M, Turunen U, Lappalainen M, Kontula K, Kaukinen K, Mäki M, Lindfors K, Partanen J, Sistonen P, Mättö J, Wacklin P, Saavalainen P, Einarsdottir E. Parmar AS, et al. Among authors: Saavalainen P. Tissue Antigens. 2012 Dec;80(6):488-93. doi: 10.1111/tan.12016. Epub 2012 Oct 18. Tissue Antigens. 2012. PMID: 23075394
This was also found in the combined CelD+DH dataset (genotype association: P = 0.0060, OR: 1.28; recessive association: P < 0.011, OR: 1.28). The A allele of rs601338 showed nominal association with dominant protection from UC (P = 0.044, OR: 0.82) and UC+CD (P = 0.035, OR: 0.84). ...
This was also found in the combined CelD+DH dataset (genotype association: P = 0.0060, OR: 1.28; recessive association: P < …
Association of celiac disease genes with inflammatory bowel disease in Finnish and Swedish patients.
Parmar AS, Lappalainen M, Paavola-Sakki P, Halme L, Färkkilä M, Turunen U, Kontula K, Aromaa A, Salomaa V, Peltonen L, Halfvarson J, Törkvist L, D'Amato M, Saavalainen P, Einarsdottir E. Parmar AS, et al. Among authors: Saavalainen P. Genes Immun. 2012 Sep;13(6):474-80. doi: 10.1038/gene.2012.21. Epub 2012 May 17. Genes Immun. 2012. PMID: 22592522
A total of 12 single-nucleotide polymorphisms associated with CD and/or UC (P<0.05). In the subphenotype analysis, rs6974491-ELMO1 (P=0.0002, odds ratio (OR): 2.20) and rs2298428-UBE2L3 (P=5.44 × 10(-5), OR: 2.59) associated with pediatric UC and CD, respectively. In the meta-analysis, rs4819388-ICOSLG (P=0.00042, OR: 0.79) associated with UC. In the subphenotype meta-analysis, rs1738074-TAGAP (P=7.40 × 10(-5), OR: 0.61), rs6974491-ELMO1 (P=0.00052, OR: 1.73) and rs4819388-ICOSLG (P=0.00019, OR: 0.75) associated with familial UC, pediatric UC and sporadic UC, respectively. ...
A total of 12 single-nucleotide polymorphisms associated with CD and/or UC (P<0.05). In the subphenotype analysis, rs6974491-ELMO1 …
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