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6. Smoking interacts with genetic risk factors in the development of rheumatoid arthritis among older Caucasian women

Author

Criswell, L.A., Saag, K.G., Mikuls, T.R., Cerhan, J.R., Merlino, L.A., Lum, R.F., Pfeiffer, K.A., Woehl, B., and Seldin, M.F.

Subjects
Rheumatoid arthritis -- Risk factors, Rheumatoid arthritis -- Genetic aspects, Smoking and women -- Genetic aspects, Smoking and women -- Demographic aspects, Smoking and women -- Research, Histocompatibility antigens -- Analysis, HLA histocompatibility antigens -- Analysis, Glutathione transferase -- Analysis, Health
Published
2006

7. Immune-Array Analysis in Sporadic Inclusion Body Myositis Reveals HLA-DRB1 Amino Acid Heterogeneity Across the Myositis Spectrum

Author

Rothwell, S., Cooper, R.G., Lundberg, I.E., Gregersen, P.K., Hanna, M.G., Machado, P.M., Herbert, M.K., Pruijn, G.J.M., Lilleker, J.B., Roberts, M, Bowes, J., Seldin, M.F., Vencovsky, J., Danko, K., Limaye, V., Selva-O'Callaghan, A., Platt, H., Molberg, O., Benveniste, O., Radstake, T.R., Doria, A., De Bleecker, J., De Paepe, B., Gieger, C., Meitinger, T., Winkelmann, J., Amos, C.I., Ollier, W.E., Padyukov, L., Lee, A.T van der, Lamb, J.A., Chinoy, H., Rothwell, S., Cooper, R.G., Lundberg, I.E., Gregersen, P.K., Hanna, M.G., Machado, P.M., Herbert, M.K., Pruijn, G.J.M., Lilleker, J.B., Roberts, M, Bowes, J., Seldin, M.F., Vencovsky, J., Danko, K., Limaye, V., Selva-O'Callaghan, A., Platt, H., Molberg, O., Benveniste, O., Radstake, T.R., Doria, A., De Bleecker, J., De Paepe, B., Gieger, C., Meitinger, T., Winkelmann, J., Amos, C.I., Ollier, W.E., Padyukov, L., Lee, A.T van der, Lamb, J.A., and Chinoy, H.

Abstract

Contains fulltext : 169069.pdf (publisher's version ) (Open Access)

Published
2017

10. Genetic Susceptibility to Juvenile Rheumatoid Arthritis

Author

Runstadler, J.A., Laiho, K., Tuomilehto, J., and Seldin, M.F.

Subjects
Human genetics -- Research, Human chromosome abnormalities -- Research, Genetic disorders -- Research, Rheumatoid arthritis in children -- Genetic aspects, Biological sciences
Published
2001

11. Novel cellular models of mitochondrial neurological disease

Author

Wong, A., Cavelier, L., Collins, H., Seldin, M.F., Savontaus, M.L., McGrogan, M., and Cortopassi, G.A.

Subjects
Genetic research -- Analysis, Human genetics -- Research, Genetic disorders -- Research, Biological sciences
Published
2000

14. Genome-wide association study identifies novel loci predisposing to cutaneous melanoma

Author

Amos, C.I., Wang, L.E., Lee, J.E., Gershenwald, J.E., Chen, W.V., Fang, S.Y., Kosoy, R., Zhang, M.F., Qureshi, A.A., Vattathil, S., Schacherer, C.W., Gardner, J.M., Wang, Y.L., Bishop, D.T., Barrett, J.H., MacGregor, S., Hayward, N.K., Martin, N.G., Duffy, D.L., Mann, G.J., Cust, A., Hopper, J., Brown, K.M., Grimm, E.A., Xu, Y.J., Han, Y.H., Jing, K.Y., McHugh, C., Laurie, C.C., Doheny, K.F., Pugh, E.W., Seldin, M.F., Han, J.L., Wei, Q.Y., GenoMEL Investigators, Q-Mega Investigators, and AMFS Investigators

Published
2011

16. TYK2 protein-coding variants protect against rheumatoid arthritis and autoimmunity, with no evidence of major pleiotropic effects on non-autoimmune complex traits

Author

Diogo, D., Bastarache, L., Liao, K.P., Graham, R.R., Fulton, R.S., Greenberg, J.D., Eyre, S., Bowes, J., Cui, J., Lee, A., Pappas, D.A., Kremer, H., Barton, A., Coenen, M.J.H., Franke, B., Kiemeney, L.A.L.M., Mariette, X., Richard-Miceli, C., Canhao, H., Fonseca, J.E., Vries, N. de, Tak, P.P., Crusius, J.B.A., Nurmohamed, M.T., Kurreeman, F., Mikuls, T.R., Okada, Y., Stahl, E.A., Larson, D.E., Deluca, T.L., O'Laughlin, M., Fronick, C.C., Fulton, L.L., Kosoy, R., Ransom, M., Bhangale, T.R., Ortmann, W., Cagan, A., Gainer, V., Karlson, E.W., Kohane, I., Murphy, S.N., Martin, J., Zhernakova, A., Klareskog, L., Padyukov, L., Worthington, J., Mardis, E.R., Seldin, M.F., Gregersen, P.K., Behrens, T., Raychaudhuri, S., Denny, J.C., Plenge, R.M., Diogo, D., Bastarache, L., Liao, K.P., Graham, R.R., Fulton, R.S., Greenberg, J.D., Eyre, S., Bowes, J., Cui, J., Lee, A., Pappas, D.A., Kremer, H., Barton, A., Coenen, M.J.H., Franke, B., Kiemeney, L.A.L.M., Mariette, X., Richard-Miceli, C., Canhao, H., Fonseca, J.E., Vries, N. de, Tak, P.P., Crusius, J.B.A., Nurmohamed, M.T., Kurreeman, F., Mikuls, T.R., Okada, Y., Stahl, E.A., Larson, D.E., Deluca, T.L., O'Laughlin, M., Fronick, C.C., Fulton, L.L., Kosoy, R., Ransom, M., Bhangale, T.R., Ortmann, W., Cagan, A., Gainer, V., Karlson, E.W., Kohane, I., Murphy, S.N., Martin, J., Zhernakova, A., Klareskog, L., Padyukov, L., Worthington, J., Mardis, E.R., Seldin, M.F., Gregersen, P.K., Behrens, T., Raychaudhuri, S., Denny, J.C., and Plenge, R.M.

Abstract

Contains fulltext : 154077.pdf (publisher's version ) (Open Access), Despite the success of genome-wide association studies (GWAS) in detecting a large number of loci for complex phenotypes such as rheumatoid arthritis (RA) susceptibility, the lack of information on the causal genes leaves important challenges to interpret GWAS results in the context of the disease biology. Here, we genetically fine-map the RA risk locus at 19p13 to define causal variants, and explore the pleiotropic effects of these same variants in other complex traits. First, we combined Immunochip dense genotyping (n = 23,092 case/control samples), Exomechip genotyping (n = 18,409 case/control samples) and targeted exon-sequencing (n = 2,236 case/controls samples) to demonstrate that three protein-coding variants in TYK2 (tyrosine kinase 2) independently protect against RA: P1104A (rs34536443, OR = 0.66, P = 2.3 x 10(-21)), A928V (rs35018800, OR = 0.53, P = 1.2 x 10(-9)), and I684S (rs12720356, OR = 0.86, P = 4.6 x 10(-7)). Second, we show that the same three TYK2 variants protect against systemic lupus erythematosus (SLE, Pomnibus = 6 x 10(-18)), and provide suggestive evidence that two of the TYK2 variants (P1104A and A928V) may also protect against inflammatory bowel disease (IBD; P(omnibus) = 0.005). Finally, in a phenome-wide association study (PheWAS) assessing >500 phenotypes using electronic medical records (EMR) in >29,000 subjects, we found no convincing evidence for association of P1104A and A928V with complex phenotypes other than autoimmune diseases such as RA, SLE and IBD. Together, our results demonstrate the role of TYK2 in the pathogenesis of RA, SLE and IBD, and provide supporting evidence for TYK2 as a promising drug target for the treatment of autoimmune diseases.

Published
2015

17. Rheumatoid Arthritis Risk Allele PTPRC Is Also Associated With Response to Anti-Tumor Necrosis Factor alpha Therapy

Author

Cui, J., Saevarsdottir, S., Thomson, B., Padyukov, L., Helm-van Mil, A.H.M. van der, Nititham, J., Hughes, L.B., Vries, N. de, Raychaudhuri, S., Alfredsson, L., Askling, J., Wedren, S., Ding, B., Guiducci, C., Wolbink, G.J., Crusius, J.B.A., Horst-Bruinsma, I.E. van der, Herenius, M., Weinblatt, M.E., Shadick, N.A., Worthington, J., Batliwalla, F., Kern, M., Morgan, A.W., Wilson, A.G., Isaacs, J.D., Hyrich, K., Seldin, M.F., Moreland, L.W., Behrens, T.W., Allaart, C.F., Criswell, L.A., Huizinga, T.W.J., Tak, P.P., Bridges, S.L., Toes, R.E.M., Barton, A., Klareskog, L., Gregersen, P.K., Karlson, E.W., Plenge, R.M., and Biol Rheumatoid Arthrit Genet & Ge

Subjects
genome-wide association genetic-variants controlled-trial susceptibility methotrexate locus polymorphism etanercept efficacy phosphatase
Abstract

Objective. Anti-tumor necrosis factor alpha (anti-TNF) therapy is a mainstay of treatment in rheumatoid arthritis (RA). The aim of the present study was to test established RA genetic risk factors to determine whether the same alleles also influence the response to anti-TNF therapy. Methods. A total of 1,283 RA patients receiving etanercept, infliximab, or adalimumab therapy were studied from among an international collaborative consortium of 9 different RA cohorts. The primary end point compared RA patients with a good treatment response according to the European League Against Rheumatism (EULAR) response criteria (n = 505) with RA patients considered to be nonresponders (n = 316). The secondary end point was the change from baseline in the level of disease activity according to the Disease Activity Score in 28 joints (Delta DAS28). Clinical factors such as age, sex, and concomitant medications were tested as possible correlates of treatment response. Thirty-one single-nucleotide polymorphisms (SNPs) associated with the risk of RA were genotyped and tested for any association with treatment response, using univariate and multivariate logistic regression models. Results. Of the 31 RA-associated risk alleles, a SNP at the PTPRC (also known as CD45) gene locus (rs10919563) was associated with the primary end point, a EULAR good response versus no response (odds ratio [OR] 0.55, P = 0.0001 in the multivariate model). Similar results were obtained using the secondary end point, the Delta DAS28 (P = 0.0002). There was suggestive evidence of a stronger association in autoantibody-positive patients with RA (OR 0.55, 95% confidence interval [95% CI] 0.39-0.76) as compared with autoantibody-negative patients (OR 0.90, 95% CI 0.41-1.99). Conclusion. Statistically significant associations were observed between the response to anti-TNF therapy and an RA risk allele at the PTPRC gene locus. Additional studies will be required to replicate this finding in additional patient collections.

Published
2010

18. Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci

Author

Stahl, E.A., Raychaudhuri, S., Remmers, E.F., Xie, G., Eyre, S., Thomson, B.P., Li, Y.H., Kurreeman, F.A.S., Zhernakova, A., Hinks, A., Guiducci, C., Chen, R., Alfredsson, L., Amos, C.I., Ardlie, K.G., Barton, A., Bowes, J., Brouwer, E., Burtt, N.P., Catanese, J.J., Coblyn, J., Coenen, M.J.H., Costenbader, K.H., Criswell, L.A., Crusius, J.B.A., Cui, J., Bakker, P.I.W. de, Jager, P.L. de, Ding, B., Emery, P., Flynn, E., Harrison, P., Hocking, L.J., Huizinga, T.W.J., Kastner, D.L., Ke, X.Y., Lee, A.T., Liu, X.D., Martin, P., Morgan, A.W., Padyukov, L., Posthumus, M.D., Radstake, T.R.D.J., Reid, D.M., Seielstad, M., Seldin, M.F., Shadick, N.A., Steer, S., Tak, P.P., Thomson, W., Helm-van Mil, A.H.M. van der, Horst-Bruinsma, I.E. van der, Schoot, C.E. van der, Riel, P.L.C.M. van, Weinblatt, M.E., Wilson, A.G., Wolbink, G.J., Wordsworth, B.P., Wijmenga, C., Karlson, E.W., Toes, R.E.M., Vries, N. de, Begovich, A.B., Worthington, J., Siminovitch, K.A., Gregersen, P.K., Klareskog, L., Plenge, R.M., BIRAC Consortium, and YEAR Consortium

Subjects
systemic-lupus-erythematosus susceptibility loci celiac-disease variants gene common region polymorphisms confirmation replication
Abstract

To identify new genetic risk factors for rheumatoid arthritis, we conducted a genome-wide association study meta-analysis of 5,539 autoantibody-positive individuals with rheumatoid arthritis (cases) and 20,169 controls of European descent, followed by replication in an independent set of 6,768 rheumatoid arthritis cases and 8,806 controls. Of 34 SNPs selected for replication, 7 new rheumatoid arthritis risk alleles were identified at genome-wide significance (P < 5 x 10(-8)) in an analysis of all 41,282 samples. The associated SNPs are near genes of known immune function, including IL6ST, SPRED2, RBPJ, CCR6, IRF5 and PXK. We also refined associations at two established rheumatoid arthritis risk loci (IL2RA and CCL21) and confirmed the association at AFF3. These new associations bring the total number of confirmed rheumatoid arthritis risk loci to 31 among individuals of European ancestry. An additional 11 SNPs replicated at P < 0.05, many of which are validated autoimmune risk alleles, suggesting that most represent genuine rheumatoid arthritis risk alleles.

Published
2010

21. 1400 DISCOVERY OF A DIRECT ASSOCIATION BETWEEN PRIMARY BILIARY CIRRHOSIS AND LOW BONE MASS: IDENTIFICATION OF TNFSF11/RANKL AS A RISK LOCUS FOR PATIENTS WITH PBC

Author

Hirschfield, G.M., primary, Juran, B.D., additional, Invernizzi, P., additional, Atkinson, E.J., additional, Li, Y., additional, Xie, G., additional, Kosoy, R., additional, Ransom, M., additional, Sun, Y., additional, Bianchi, I., additional, Schlicht, E.M., additional, Lleo, A., additional, Coltescu, C., additional, Bernuzzi, F., additional, Lammert, C., additional, Shigetta, R., additional, Chan, L.L., additional, Balschun, T., additional, Marconi, M., additional, Cusi, D., additional, Mason, A.L., additional, Myers, R.P., additional, Milkiewicz, P., additional, Odin, J.A., additional, Luketic, V.A., additional, Bacon, B., additional, Bodenheimer, H., additional, Liakina, V., additional, Vincent, C., additional, Levy, C., additional, Franke, A., additional, Gregerson, P.K., additional, Annese, V., additional, Gershwin, M.E., additional, de Andrade, M., additional, Amos, C.I., additional, Lazaridis, K.N., additional, Seldin, M.F., additional, and Siminovitch, K.A., additional

Published
2012
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39. Genotype-phenotype correlations in Peutz-Jeghers syndrome.

Author

Amos, C.I., Keitheri-Cheteri, M.B., Sabripour, M., Wei, C., McGarrity, T.J., Seldin, M.F., Nations, L., Lynch, P.M., Fidder, H.H., Friedman, E., and Frazier, M.L.

Subjects
PEUTZ-Jeghers syndrome, PIGMENTATION disorders, SYNDROMES, INTESTINAL polyps, GENETIC disorders, MEDICAL genetics
Abstract

Background and aims: Peutz-Jeghers syndrome (PJS) is a dominantly inherited disorder often caused by mutations in STK11. Time to onset of symptoms was characterised for a large collection of individuals with PJS who had been tested for STK11 mutations and genotype-phenotype correlations were evaluated. Methods: We characterised mutations in 42 independent probands and also used a historical cohort design to study 51 individuals with Peutz-Jeghers syndrome who had completed self-administered questionnaires. Results: Mutations were detected in 22/32 (69%) probands with PJS and 0/10 probands referred to rule out PJS. Real-time PCR analysis to quantitate DNA failed to detect any large deletions in PJS participants without STK11 mutations. The median time to onset for gastrointestinal symptoms or polypectomy was 13 years of age but showed a wide variability. Gastric polyps were frequent in PJS participants, with a median age at onset of 16 years. Individuals with missense mutations had a significantly later time to onset of first polypectomy (p=0.04) and of other symptoms compared with those participants either with truncating mutations or no detectable mutation. Conclusion: STK11 mutation analysis should be restricted to individuals who meet PJS criteria or their close relatives. Direct sequencing of STK11 yields a high rate of point mutations in individuals who meet phenotypic PJS criteria. Individuals with missense mutations of STK11 typically had a later time to onset for PJS symptoms. The common occurrence of gastric polyps may facilitate chemopreventive studies for this disorder. [ABSTRACT FROM AUTHOR]

Published
2004
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40. Association of angiotensin-converting enzyme polymorphisms with systemic lupus erythematosus and nephritis: analysis of 644 SLE families.

Author

Parsa, A., Peden, E., Lum, R.F., Seligman, V.A., Olson, J.L., Li, H., Seldin, M.F., and Criswell, L.A.

Subjects
ANGIOTENSIN II, AUTOIMMUNITY, KIDNEY diseases, GENETIC polymorphisms
Abstract

Angiotensin II is a strong candidate for the perpetuation of autoimmunity, nephritis and visceral damage in systemic lupus erythematosus (SLE). Our goal was to determine whether angiotensin-converting enzyme (ACE) gene polymorphisms are associated with SLE and/or lupus nephritis (LN). We genotyped 644 SLE patients and 1130 family members for three ACE gene polymorphisms: Alu insertion/deletion (I/D), 23949 (CT)[sub 2/3] and 10698 (G)[sub 3/4]. All patients met the American College of Rheumatology (ACR) criteria for SLE, and all LN patients met ACR renal criteria and/or had biopsy evidence of LN. We used the transmission/disequilibrium test (TDT) to examine associations between each polymorphism and SLE, including Caucasian, non-Caucasian, and LN subgroups. We also examined transmission of haplotypes defined by these polymorphisms. The ACE I/D polymorphism was associated with SLE among non-Caucasians (61% transmission, P = 0.026) and the 23949 (CT)[sub 2/3] polymorphism was associated with LN among non-Caucasians (69% transmission, P = 0.014). Several haplotypes defined by these 2 markers demonstrated strikingly increased transmission among nonCaucasians (81% - 66% transmission, P = 0.0046 to 0.010). Due to the choice of study design and analytic method these results are unlikely to be due to population admixture. Our findings suggest that DNA sequence variation in the ACE gene influences the risk of developing SLE and LN. [ABSTRACT FROM AUTHOR]

Published
2002
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42. A 6000 kb segment of chromosome 1 is conserved in human and mouse.

Author

Kingsmore, S.F., Watson, M.L., Howard, T.A., and Seldin, M.F.

Abstract

A murine linkage map generated from analyses of 428 meiotic events in an interspecific cross and pulsed field gel electrophoresis allowed examination of the genomic organization of a 6000 kb segment of mouse and human chromosome 1. Analysis of five genes within this syntenic segment of both species revealed striking conservation of gene order, intergenic distance and, to a lesser extent, CpG dinucleotides. In the mouse, meiotic crossover events were not evenly distributed; a hot spot for meiotic recombination was coincident with a CpG‐island. These studies provide a practical approach to aid physical mapping of the human genome and a model for determining the molecular principles that govern meiotic recombination. In addition, these findings demonstrate profound conservation of genomic organization over mammalian evolution.

Published
1989
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43. Mapping of the bcl-2oncogene on mouse chromosome 1

Author

Mock, B.A., Givol, D., Dhoostelaere, L.A., Huppi, K., Seldin, M.F., Gurfinkel, N., Unger, T., Potter, M., and Mushinski, J.F.

Abstract

Two bcl-2 alleles have been identified in inbred strains of mice by restriction fragment length polymorphism (RFLP). Analysis of a bcl-2 RFLP in a series of bilineal congenic strains (C.D2), developed as a tool for chromosomal mapping studies, revealed linkage of bcl-2 to the Idh-1/Pep-3 region of murine chromosome 1. The co-segregation of bcl-2 alleles with allelic forms of two other chromosome 1 loci, Ren-1,2 and Spna-1 in a set of back-cross progeny, positions bcl-2 7.8 cM centromeric from Ren-1,2.

Published
1988
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