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      A large-scale genome-wide association and meta-analysis identified four novel susceptibility loci for leprosy

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      Nature Communications
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          Abstract

          Leprosy, a chronic infectious disease, results from the uncultivable pathogen Mycobacterium leprae ( M. leprae), and usually progresses to peripheral neuropathy and permanent progressive deformity if not treated. Previously published genetic studies have identified 18 gene/loci significantly associated with leprosy at the genome-wide significant level. However as a complex disease, only a small proportion of leprosy risk could be explained by those gene/loci. To further identify more susceptibility gene/loci, we hereby performed a three-stage GWAS comprising 8,156 leprosy patients and 15,610 controls of Chinese ancestry. Four novel loci were identified including rs6807915 on 3p25.2 ( P=1.94 × 10 −8, OR=0.89), rs4720118 on 7p14.3 ( P=3.85 × 10 −10, OR=1.16), rs55894533 on 8p23.1 ( P=5.07 × 10 −11, OR=1.15) and rs10100465 on 8q24.11 ( P=2.85 × 10 −11, OR=0.85). Altogether, these findings have provided new insight and significantly expanded our understanding of the genetic basis of leprosy.

          Abstract

          Previous studies have shown genetic associations between leprosy and 18 different genes/loci. Here, Wang and colleagues perform genome-wide association study in Han Chinese leprosy patients and describe four novel loci to be associated to the disease.

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          Most cited references23

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          Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis.

          By combining genome-wide association data from 8,130 individuals with type 2 diabetes (T2D) and 38,987 controls of European descent and following up previously unidentified meta-analysis signals in a further 34,412 cases and 59,925 controls, we identified 12 new T2D association signals with combined P<5x10(-8). These include a second independent signal at the KCNQ1 locus; the first report, to our knowledge, of an X-chromosomal association (near DUSP9); and a further instance of overlap between loci implicated in monogenic and multifactorial forms of diabetes (at HNF1A). The identified loci affect both beta-cell function and insulin action, and, overall, T2D association signals show evidence of enrichment for genes involved in cell cycle regulation. We also show that a high proportion of T2D susceptibility loci harbor independent association signals influencing apparently unrelated complex traits.
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            Genomewide association study of leprosy.

            The narrow host range of Mycobacterium leprae and the fact that it is refractory to growth in culture has limited research on and the biologic understanding of leprosy. Host genetic factors are thought to influence susceptibility to infection as well as disease progression. We performed a two-stage genomewide association study by genotyping 706 patients and 1225 controls using the Human610-Quad BeadChip (Illumina). We then tested three independent replication sets for an association between the presence of leprosy and 93 single-nucleotide polymorphisms (SNPs) that were most strongly associated with the disease in the genomewide association study. Together, these replication sets comprised 3254 patients and 5955 controls. We also carried out tests of heterogeneity of the associations (or lack thereof) between these 93 SNPs and disease, stratified according to clinical subtype (multibacillary vs. paucibacillary). We observed a significant association (P<1.00x10(-10)) between SNPs in the genes CCDC122, C13orf31, NOD2, TNFSF15, HLA-DR, and RIPK2 and a trend toward an association (P=5.10x10(-5)) with a SNP in LRRK2. The associations between the SNPs in C13orf31, LRRK2, NOD2, and RIPK2 and multibacillary leprosy were stronger than the associations between these SNPs and paucibacillary leprosy. Variants of genes in the NOD2-mediated signaling pathway (which regulates the innate immune response) are associated with susceptibility to infection with M. leprae. 2009 Massachusetts Medical Society
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              Susceptibility to leprosy is associated with PARK2 and PACRG.

              Leprosy is caused by Mycobacterium leprae and affects about 700,000 individuals each year. It has long been thought that leprosy has a strong genetic component, and recently we mapped a leprosy susceptibility locus to chromosome 6 region q25-q26 (ref. 3). Here we investigate this region further by using a systematic association scan of the chromosomal interval most likely to harbour this leprosy susceptibility locus. In 197 Vietnamese families we found a significant association between leprosy and 17 markers located in a block of approx. 80 kilobases overlapping the 5' regulatory region shared by the Parkinson's disease gene PARK2 and the co-regulated gene PACRG. Possession of as few as two of the 17 risk alleles was highly predictive of leprosy. This was confirmed in a sample of 975 unrelated leprosy cases and controls from Brazil in whom the same alleles were strongly associated with leprosy. Variants in the regulatory region shared by PARK2 and PACRG therefore act as common risk factors for leprosy.
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                Author and article information

                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group
                2041-1723
                15 December 2016
                2016
                : 7
                : 13760
                Affiliations
                [1 ]Shandong Provincial Institute of Dermatology and Venereology, Shandong Academy of Medical Sciences , Jinan, Shandong 250000, China
                [2 ]Shandong Provincial Key Laboratory for Dermatovenereology , Jinan, Shandong 250000, China
                [3 ]School of Medicine, Shandong University , Jinan, Shandong 250000, China
                [4 ]School of Medicine and Life Science, University of Jinan-Shandong Academy of Medical Sciences , Jinan, Shandong 250022, China
                [5 ]Shandong Provincial Hospital for Skin Diseases, Shandong University , Jinan, Shandong 250000, China
                [6 ]Human Genetics, Genome Institute of Singapore , Singapore 138672, Singapore
                [7 ]National Clinical Key Project of Dermatology and Venereology , Jinan, Shandong 250000, China
                Author notes
                [*]

                These authors contributed equally to this work

                Article
                ncomms13760
                10.1038/ncomms13760
                5172377
                27976721
                b592ad08-b88a-4813-bbfe-57febc8c2e27
                Copyright © 2016, The Author(s)

                This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/

                History
                : 01 April 2016
                : 31 October 2016
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