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Article ; Online: Reply to Zhang et al.: The differential role of LRRK2 variants in nested leprosy phenotypes.

Fava, Vinicius M / Cobat, Aurélie / Gzara, Chaïma / Alcaïs, Alexandre / Abel, Laurent / Schurr, Erwin

Proceedings of the National Academy of Sciences of the United States of America

2020 Volume 117, Issue 19, Page(s) 10124–10125

MeSH term(s)	Humans ; Leprosy ; Leucine-Rich Repeat Serine-Threonine Protein Kinase-2/genetics ; Parkinson Disease ; Phenotype ; Ubiquitin-Protein Ligases
Chemical Substances	Ubiquitin-Protein Ligases (EC 2.3.2.27) ; LRRK2 protein, human (EC 2.7.11.1) ; Leucine-Rich Repeat Serine-Threonine Protein Kinase-2 (EC 2.7.11.1)
Language	English
Publishing date	2020-04-28
Publishing country	United States
Document type	Letter ; Comment
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2002654117
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Article ; Online: Taking population stratification into account by local permutations in rare-variant association studies on small samples.

Mullaert, Jimmy / Bouaziz, Matthieu / Seeleuthner, Yoann / Bigio, Benedetta / Casanova, Jean-Laurent / Alcaïs, Alexandre / Abel, Laurent / Cobat, Aurélie

Genetic epidemiology

2021 Volume 45, Issue 8, Page(s) 821–829

Abstract: Many methods for rare variant association studies require permutations to assess the significance of tests. Standard permutations assume that all individuals are exchangeable and do not take population stratification (PS), a known confounding factor in ... ...

Abstract	Many methods for rare variant association studies require permutations to assess the significance of tests. Standard permutations assume that all individuals are exchangeable and do not take population stratification (PS), a known confounding factor in genetic studies, into account. We propose a novel strategy, LocPerm, in which individual phenotypes are permuted only with their closest ancestry-based neighbors. We performed a simulation study, focusing on small samples, to evaluate and compare LocPerm with standard permutations and classical adjustment on first principal components. Under the null hypothesis, LocPerm was the only method providing an acceptable type I error, regardless of sample size and level of stratification. The power of LocPerm was similar to that of standard permutation in the absence of PS, and remained stable in different PS scenarios. We conclude that LocPerm is a method of choice for taking PS and/or small sample size into account in rare variant association studies.
MeSH term(s)	Computer Simulation ; Genetic Association Studies ; Genetics, Population ; Humans ; Models, Genetic ; Sample Size
Language	English
Publishing date	2021-08-17
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	605785-8
ISSN	1098-2272 ; 0741-0395
ISSN (online)	1098-2272
ISSN	0741-0395
DOI	10.1002/gepi.22426
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Article ; Online: The dissection of complex susceptibility to infectious disease: bacterial, viral and parasitic infections.

Abel, Laurent / Alcaïs, Alexandre / Schurr, Erwin

Current opinion in immunology

2014 Volume 30, Page(s) 72–78

Abstract: Infectious diseases are the result of the exposure of susceptible hosts to pathogenic microbes. Genetic factors are important determinants of host susceptibility and efforts are being made to establish the molecular identity of such genetic ... ...

Abstract	Infectious diseases are the result of the exposure of susceptible hosts to pathogenic microbes. Genetic factors are important determinants of host susceptibility and efforts are being made to establish the molecular identity of such genetic susceptibility variants by genome-wide association studies. Results obtained to date partly confirm already known genetic vulnerabilities, but also point to new and unexpected mechanisms of susceptibility that extend from classical innate and acquired immunity to weaknesses in constitutional resistance. These studies also revealed an overlap in genetic control between infectious disease and other common immune and inflammatory disorders.
MeSH term(s)	Animals ; Bacterial Infections/immunology ; Disease Susceptibility ; Genome-Wide Association Study ; Humans ; Parasitic Diseases/immunology ; Virus Diseases/immunology
Language	English
Publishing date	2014-10
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	1035767-1
ISSN	1879-0372 ; 0952-7915
ISSN (online)	1879-0372
ISSN	0952-7915
DOI	10.1016/j.coi.2014.07.002
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Article ; Online: Genetic diagnosis of primary immunodeficiencies: A survey of the French national registry.

Mahlaoui, Nizar / Picard, Capucine / Bach, Perrine / Costes, Laurence / Courteille, Virginie / Ranohavimparany, Anja / Alcaïs, Alexandre / Jais, Jean-Philippe / Fischer, Alain

The Journal of allergy and clinical immunology

2019 Volume 143, Issue 4, Page(s) 1646–1649.e10

MeSH term(s)	France ; Genetic Testing/statistics & numerical data ; Humans ; Primary Immunodeficiency Diseases/diagnosis ; Primary Immunodeficiency Diseases/genetics ; Registries ; Retrospective Studies
Language	English
Publishing date	2019-01-09
Publishing country	United States
Document type	Letter ; Research Support, Non-U.S. Gov't
ZDB-ID	121011-7
ISSN	1097-6825 ; 1085-8725 ; 0091-6749
ISSN (online)	1097-6825 ; 1085-8725
ISSN	0091-6749
DOI	10.1016/j.jaci.2018.12.994
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Article ; Online: A general efficient and flexible approach for genome-wide association analyses of imputed genotypes in family-based designs.

Cobat, Aurélie / Abel, Laurent / Alcaïs, Alexandre / Schurr, Erwin

Genetic epidemiology

2014 Volume 38, Issue 6, Page(s) 560–571

Abstract: Genotype imputation is a critical technique for following up genome-wide association studies. Efficient methods are available for dealing with the probabilistic nature of imputed single nucleotide polymorphisms (SNPs) in population-based designs, but not ...

Abstract	Genotype imputation is a critical technique for following up genome-wide association studies. Efficient methods are available for dealing with the probabilistic nature of imputed single nucleotide polymorphisms (SNPs) in population-based designs, but not for family-based studies. We have developed a new analytical approach (FBATdosage), using imputed allele dosage in the general framework of family-based association tests to bridge this gap. Simulation studies showed that FBATdosage yielded highly consistent type I error rates, whatever the level of genotype uncertainty, and a much higher power than the best-guess genotype approach. FBATdosage allows fast linkage and association testing of several million of imputed variants with binary or quantitative phenotypes in nuclear families of arbitrary size with arbitrary missing data for the parents. The application of this approach to a family-based association study of leprosy susceptibility successfully refined the association signal at two candidate loci, C1orf141-IL23R on chromosome 1 and RAB32-C6orf103 on chromosome 6.
MeSH term(s)	Alleles ; Chromosomes, Human, Pair 1 ; Chromosomes, Human, Pair 6 ; Disease Susceptibility ; Genetic Linkage ; Genetic Loci ; Genome-Wide Association Study ; Genotype ; Humans ; Leprosy/genetics ; Leprosy/pathology ; Models, Genetic ; Nuclear Family ; Phenotype ; Polymorphism, Single Nucleotide ; Receptors, Interleukin/genetics ; rab GTP-Binding Proteins/genetics
Chemical Substances	IL23R protein, human ; Receptors, Interleukin ; Rab32 protein, human (EC 3.6.1.-) ; rab GTP-Binding Proteins (EC 3.6.5.2)
Language	English
Publishing date	2014-09
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	605785-8
ISSN	1098-2272 ; 0741-0395
ISSN (online)	1098-2272
ISSN	0741-0395
DOI	10.1002/gepi.21842
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Article ; Online: Allele-dependent interaction of LRRK2 and NOD2 in leprosy.

Dallmann-Sauer, Monica / Xu, Yong Zhong / da Costa, Ana Lúcia França / Tao, Shao / Gomes, Tiago Araujo / Prata, Rhana Berto da Silva / Correa-Macedo, Wilian / Manry, Jérémy / Alcaïs, Alexandre / Abel, Laurent / Cobat, Aurélie / Fava, Vinicius M / Pinheiro, Roberta Olmo / Lara, Flavio Alves / Probst, Christian M / Mira, Marcelo T / Schurr, Erwin

PLoS pathogens

2023 Volume 19, Issue 3, Page(s) e1011260

Abstract: Leprosy, caused by Mycobacterium leprae, rarely affects children younger than 5 years. Here, we studied a multiplex leprosy family that included monozygotic twins aged 22 months suffering from paucibacillary leprosy. Whole genome sequencing identified ... ...

Abstract	Leprosy, caused by Mycobacterium leprae, rarely affects children younger than 5 years. Here, we studied a multiplex leprosy family that included monozygotic twins aged 22 months suffering from paucibacillary leprosy. Whole genome sequencing identified three amino acid mutations previously associated with Crohn's disease and Parkinson's disease as candidate variants for early onset leprosy: LRRK2 N551K, R1398H and NOD2 R702W. In genome-edited macrophages, we demonstrated that cells expressing the LRRK2 mutations displayed reduced apoptosis activity following mycobacterial challenge independently of NOD2. However, employing co-immunoprecipitation and confocal microscopy we showed that LRRK2 and NOD2 proteins interacted in RAW cells and monocyte-derived macrophages, and that this interaction was substantially reduced for the NOD2 R702W mutation. Moreover, we observed a joint effect of LRRK2 and NOD2 variants on Bacillus Calmette-Guérin (BCG)-induced respiratory burst, NF-κB activation and cytokine/chemokine secretion with a strong impact for the genotypes found in the twins consistent with a role of the identified mutations in the development of early onset leprosy.
MeSH term(s)	Child ; Humans ; Alleles ; Genetic Predisposition to Disease ; Genotype ; Leprosy/genetics ; Mutation ; Nod2 Signaling Adaptor Protein/genetics ; Leucine-Rich Repeat Serine-Threonine Protein Kinase-2/genetics
Chemical Substances	Nod2 Signaling Adaptor Protein ; NOD2 protein, human ; LRRK2 protein, human (EC 2.7.11.1) ; Leucine-Rich Repeat Serine-Threonine Protein Kinase-2 (EC 2.7.11.1)
Language	English
Publishing date	2023-03-27
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2205412-1
ISSN	1553-7374 ; 1553-7374
ISSN (online)	1553-7374
ISSN	1553-7374
DOI	10.1371/journal.ppat.1011260
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Article: Age-Dependent Association of

Fava, Vinicius M / Sales-Marques, Carolinne / Alcaïs, Alexandre / Moraes, Milton O / Schurr, Erwin

Frontiers in immunology

2017 Volume 8, Page(s) 155

Abstract: A current major challenge in leprosy control is the prevention of permanent disabilities. Host pathological inflammatory responses termed type 1 reaction (T1R) are a leading cause of nerve damage for leprosy patients. The environmental or inherited ... ...

Abstract	A current major challenge in leprosy control is the prevention of permanent disabilities. Host pathological inflammatory responses termed type 1 reaction (T1R) are a leading cause of nerve damage for leprosy patients. The environmental or inherited factors that predispose leprosy cases to undergo T1R are not known. However, studies have shown an important contribution of host genetics for susceptibility to T1R. We have previously identified variants encompassing the
Language	English
Publishing date	2017-02-14
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2606827-8
ISSN	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2017.00155
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Article ; Online: Deep resequencing identifies candidate functional genes in leprosy GWAS loci.

Fava, Vinicius M / Dallmann-Sauer, Monica / Orlova, Marianna / Correa-Macedo, Wilian / Van Thuc, Nguyen / Thai, Vu Hong / Alcaïs, Alexandre / Abel, Laurent / Cobat, Aurélie / Schurr, Erwin

PLoS neglected tropical diseases

2021 Volume 15, Issue 12, Page(s) e0010029

Abstract: Leprosy is the second most prevalent mycobacterial disease globally. Despite the existence of an effective therapy, leprosy incidence has consistently remained above 200,000 cases per year since 2010. Numerous host genetic factors have been identified ... ...

Abstract	Leprosy is the second most prevalent mycobacterial disease globally. Despite the existence of an effective therapy, leprosy incidence has consistently remained above 200,000 cases per year since 2010. Numerous host genetic factors have been identified for leprosy that contribute to the persistently high case numbers. In the past decade, genetic epidemiology approaches, including genome-wide association studies (GWAS), identified more than 30 loci contributing to leprosy susceptibility. However, GWAS loci commonly encompass multiple genes, which poses a challenge to define causal candidates for each locus. To address this problem, we hypothesized that genes contributing to leprosy susceptibility differ in their frequencies of rare protein-altering variants between cases and controls. Using deep resequencing we assessed protein-coding variants for 34 genes located in GWAS or linkage loci in 555 Vietnamese leprosy cases and 500 healthy controls. We observed 234 nonsynonymous mutations in the targeted genes. A significant depletion of protein-altering variants was detected for the IL18R1 and BCL10 genes in leprosy cases. The IL18R1 gene is clustered with IL18RAP and IL1RL1 in the leprosy GWAS locus on chromosome 2q12.1. Moreover, in a recent GWAS we identified an HLA-independent signal of association with leprosy on chromosome 6p21. Here, we report amino acid changes in the CDSN and PSORS1C2 genes depleted in leprosy cases, indicating them as candidate genes in the chromosome 6p21 locus. Our results show that deep resequencing can identify leprosy candidate susceptibility genes that had been missed by classic linkage and association approaches.
MeSH term(s)	Adolescent ; Adult ; B-Cell CLL-Lymphoma 10 Protein/genetics ; Female ; Genetic Linkage ; Genetic Predisposition to Disease ; Genome-Wide Association Study ; High-Throughput Nucleotide Sequencing ; Humans ; Interleukin-18 Receptor alpha Subunit/genetics ; Interleukin-18 Receptor beta Subunit/genetics ; Leprosy/genetics ; Male ; Young Adult
Chemical Substances	B-Cell CLL-Lymphoma 10 Protein ; BCL10 protein, human ; IL18R1 protein, human ; IL18RAP protein, human ; Interleukin-18 Receptor alpha Subunit ; Interleukin-18 Receptor beta Subunit
Language	English
Publishing date	2021-12-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	2429704-5
ISSN	1935-2735 ; 1935-2735
ISSN (online)	1935-2735
ISSN	1935-2735
DOI	10.1371/journal.pntd.0010029
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Article ; Online: Controlling for human population stratification in rare variant association studies.

Bouaziz, Matthieu / Mullaert, Jimmy / Bigio, Benedetta / Seeleuthner, Yoann / Casanova, Jean-Laurent / Alcais, Alexandre / Abel, Laurent / Cobat, Aurélie

Scientific reports

2021 Volume 11, Issue 1, Page(s) 19015

Abstract: Population stratification is a confounder of genetic association studies. In analyses of rare variants, corrections based on principal components (PCs) and linear mixed models (LMMs) yield conflicting conclusions. Studies evaluating these approaches ... ...

Abstract	Population stratification is a confounder of genetic association studies. In analyses of rare variants, corrections based on principal components (PCs) and linear mixed models (LMMs) yield conflicting conclusions. Studies evaluating these approaches generally focused on limited types of structure and large sample sizes. We investigated the properties of several correction methods through a large simulation study using real exome data, and several within- and between-continent stratification scenarios. We considered different sample sizes, with situations including as few as 50 cases, to account for the analysis of rare disorders. Large samples showed that accounting for stratification was more difficult with a continental than with a worldwide structure. When considering a sample of 50 cases, an inflation of type-I-errors was observed with PCs for small numbers of controls (≤ 100), and with LMMs for large numbers of controls (≥ 1000). We also tested a novel local permutation method (LocPerm), which maintained a correct type-I-error in all situations. Powers were equivalent for all approaches pointing out that the key issue is to properly control type-I-errors. Finally, we found that power of analyses including small numbers of cases can be increased, by adding a large panel of external controls, provided an appropriate stratification correction was used.
MeSH term(s)	Computer Simulation ; Exome/genetics ; Genetic Association Studies/methods ; Genetic Variation/genetics ; Genetics, Population ; Genome-Wide Association Study ; Humans ; Linear Models ; Principal Component Analysis ; Rare Diseases/genetics ; Sample Size
Language	English
Publishing date	2021-09-24
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-021-98370-5
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Article ; Online: Genome-wide association study of Buruli ulcer in rural Benin highlights role of two LncRNAs and the autophagy pathway.

Manry, Jeremy / Vincent, Quentin B / Johnson, Christian / Chrabieh, Maya / Lorenzo, Lazaro / Theodorou, Ioannis / Ardant, Marie-Françoise / Marion, Estelle / Chauty, Annick / Marsollier, Laurent / Abel, Laurent / Alcaïs, Alexandre

Communications biology

2020 Volume 3, Issue 1, Page(s) 177

Abstract: Buruli ulcer, caused by Mycobacterium ulcerans and characterized by devastating necrotizing skin lesions, is the third mycobacterial disease worldwide. The role of host genetics in susceptibility to Buruli ulcer has long been suggested. We conduct the ... ...

Abstract	Buruli ulcer, caused by Mycobacterium ulcerans and characterized by devastating necrotizing skin lesions, is the third mycobacterial disease worldwide. The role of host genetics in susceptibility to Buruli ulcer has long been suggested. We conduct the first genome-wide association study of Buruli ulcer on a sample of 1524 well characterized patients and controls from rural Benin. Two-stage analyses identify two variants located within LncRNA genes: rs9814705 in ENSG00000240095.1 (P = 2.85 × 10
MeSH term(s)	Adolescent ; Adult ; Autophagy/genetics ; Autophagy-Related Proteins/genetics ; Benin ; Buruli Ulcer/diagnosis ; Buruli Ulcer/genetics ; Buruli Ulcer/microbiology ; Case-Control Studies ; Child ; Female ; Genetic Predisposition to Disease ; Genome-Wide Association Study ; Host-Pathogen Interactions ; Humans ; Male ; Mutation, Missense ; Mycobacterium ulcerans/pathogenicity ; Phenotype ; Polymorphism, Single Nucleotide ; RNA, Long Noncoding/genetics ; Risk Assessment ; Risk Factors ; Young Adult
Chemical Substances	ATG16L1 protein, human ; Autophagy-Related Proteins ; RNA, Long Noncoding
Language	English
Publishing date	2020-04-20
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2399-3642
ISSN (online)	2399-3642
DOI	10.1038/s42003-020-0920-6
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