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Elisa Alonso-Perez Marian Suarez-Gestal Manuel Calaza Josep Ordi-Ros Eva Balada Marc Bijl Chryssa Papasteriades Patricia Carreira Fotini N. Skopouli Torsten Witte Em?ke Endreffy Maurizio Marchini Sergio Migliaresi Gian Domenico Sebastiani Maria Jose Santos Ana Suarez Francisco J. Blanco Nadia Barizzone Rudolf Pullmann Sarka Ruzickova Bernard R. Lauwerys Juan J. Gomez-Reino Antonio Gonzalez European Consortium of SLE DNA Collections 《PloS one》2012,7(9)
Introduction
Systemic Lupus Erythematosus (SLE) shows a spectrum of clinical manifestations that complicate its diagnosis, treatment and research. This variability is likely related with environmental exposures and genetic factors among which known SLE susceptibility loci are prime candidates. The first published analyses seem to indicate that this is the case for some of them, but results are still inconclusive and we aimed to further explore this question.Methods
European SLE patients, 1444, recruited at 17 centres from 10 countries were analyzed. Genotypes for 26 SLE associated SNPs were compared between patients with and without each of 11 clinical features: ten of the American College of Rheumatology (ACR) classification criteria (except ANAs) and age of disease onset. These analyses were adjusted for centre of recruitment, top ancestry informative markers, gender and time of follow-up. Overlap of samples with previous studies was excluded for assessing replication.Results
There were three new associations: the SNPs in XKR6 and in FAM167A-BLK were associated with lupus nephritis (OR = 0.76 and 1.30, Pcorr = 0.007 and 0.03, respectively) and the SNP of MECP2, which is in chromosome X, with earlier age of disease onset in men. The previously reported association of STAT4 with early age of disease onset was replicated. Some other results were suggestive of the presence of additional associations. Together, the association signals provided support to some previous findings and to the characterization of lupus nephritis, autoantibodies and age of disease onset as the clinical features more associated with SLE loci.Conclusion
Some of the SLE loci shape the disease phenotype in addition to increase susceptibility to SLE. This influence is more prominent for some clinical features than for others. However, results are only partially consistent between studies and subphenotype specific GWAS are needed to unravel their genetic component. 相似文献92.
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Zalloua PA Xue Y Khalife J Makhoul N Debiane L Platt DE Royyuru AK Herrera RJ Hernanz DF Blue-Smith J Wells RS Comas D Bertranpetit J Tyler-Smith C;Genographic Consortium 《American journal of human genetics》2008,82(4):873-882
Lebanon is an eastern Mediterranean country inhabited by approximately four million people with a wide variety of ethnicities and religions, including Muslim, Christian, and Druze. In the present study, 926 Lebanese men were typed with Y-chromosomal SNP and STR markers, and unusually, male genetic variation within Lebanon was found to be more strongly structured by religious affiliation than by geography. We therefore tested the hypothesis that migrations within historical times could have contributed to this situation. Y-haplogroup J*(xJ2) was more frequent in the putative Muslim source region (the Arabian Peninsula) than in Lebanon, and it was also more frequent in Lebanese Muslims than in Lebanese non-Muslims. Conversely, haplogroup R1b was more frequent in the putative Christian source region (western Europe) than in Lebanon and was also more frequent in Lebanese Christians than in Lebanese non-Christians. The most common R1b STR-haplotype in Lebanese Christians was otherwise highly specific for western Europe and was unlikely to have reached its current frequency in Lebanese Christians without admixture. We therefore suggest that the Islamic expansion from the Arabian Peninsula beginning in the seventh century CE introduced lineages typical of this area into those who subsequently became Lebanese Muslims, whereas the Crusader activity in the 11(th)-13(th) centuries CE introduced western European lineages into Lebanese Christians. 相似文献
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DAVID L. BRAFF TIFFANY A. GREENWOOD NEAL R. SWERDLOW GREGORY A. LIGHT NICHOLAS J. SCHORK The Investigators of the Consortium on the Genetics of Schizophrenia 《World psychiatry》2008,7(1):11-18
The search for the genetic architecture of schizophrenia has employed multiple, often converging strategies. One such strategy entails the use of tracing the heritability and neurobiology of endophenotypes. Endophenotypes are quantifiable traits not visible to the eye, which are thought to reflect an intermediate place on the path from genes to disorder. Endophenotype abnormalities in domains such as neurophysiology or neurocognition occur in schizophrenia patients as well as their clinically “unaffected” relatives, and reflect polymorphisms in the DNA of schizophrenia spectrum subjects which create vulnerability to developing schizophrenia. By identifying the single nucleotide polymorphisms (SNPs) associated with endophenotypes in schizophrenia, psychiatric neuroscientists can select new strong inference based molecular targets for the treatment of schizophrenia. 相似文献
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Mohammed Mamdani Vernell Williamson Gowon O. McMichael Tana Blevins Fazil Aliev Amy Adkins Laura Hack Tim Bigdeli Andrew D. van der Vaart Bradley Todd Web Silviu-Alin Bacanu Gursharan Kalsi COGA Consortium Kenneth S. Kendler Michael F. Miles Danielle Dick Brien P. Riley Catherine Dumur Vladimir I. Vladimirov 《PloS one》2015,10(9)
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Pier?Francesco Palamara Laurent?C. Francioli Peter?R. Wilton Giulio Genovese Alexander Gusev Hilary?K. Finucane Sriram Sankararaman Genome of the Netherlands Consortium Shamil?R. Sunyaev Paul?I.W. de?Bakker John Wakeley Itsik Pe’er Alkes?L. Price 《American journal of human genetics》2015,97(6):775-789
The rate at which human genomes mutate is a central biological parameter that has many implications for our ability to understand demographic and evolutionary phenomena. We present a method for inferring mutation and gene-conversion rates by using the number of sequence differences observed in identical-by-descent (IBD) segments together with a reconstructed model of recent population-size history. This approach is robust to, and can quantify, the presence of substantial genotyping error, as validated in coalescent simulations. We applied the method to 498 trio-phased sequenced Dutch individuals and inferred a point mutation rate of 1.66 × 10−8 per base per generation and a rate of 1.26 × 10−9 for <20 bp indels. By quantifying how estimates varied as a function of allele frequency, we inferred the probability that a site is involved in non-crossover gene conversion as 5.99 × 10−6. We found that recombination does not have observable mutagenic effects after gene conversion is accounted for and that local gene-conversion rates reflect recombination rates. We detected a strong enrichment of recent deleterious variation among mismatching variants found within IBD regions and observed summary statistics of local sharing of IBD segments to closely match previously proposed metrics of background selection; however, we found no significant effects of selection on our mutation-rate estimates. We detected no evidence of strong variation of mutation rates in a number of genomic annotations obtained from several recent studies. Our analysis suggests that a mutation-rate estimate higher than that reported by recent pedigree-based studies should be adopted in the context of DNA-based demographic reconstruction. 相似文献