Search results for: Sophie Limou

Items from 1 to 16 out of 16 results

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A multi‐ethnic reference panel to impute HLA classical and non‐classical class I alleles in admixed samples: Testing imputation accuracy in an admixed sample from Brazil

Nayane S. B. Silva, Sonia Bourguiba‐Hachemi, Viviane A. O. Ciriaco, Stefan H. Y. Knorst, more

HLA > 103 > 6 > n/a - n/a

The MHC class I region contains crucial genes for the innate and adaptive immune response, playing a key role in susceptibility to many autoimmune and infectious diseases. Genome‐wide association studies have identified numerous disease‐associated SNPs within this region. However, these associations do not fully capture the immune‐biological relevance of specific HLA alleles. HLA imputation techniques...

article

18th International HLA and Immunogenetics Workshop: Report on the SNP‐HLA Reference Consortium (SHLARC) component

Nayane S. B. Silva, Sonia Bourguiba‐Hachemi, Venceslas Douillard, Satu Koskela, more

HLA > 103 > 1 > n/a - n/a

The SNP‐HLA Reference Consortium (SHLARC), a component of the 18th International HLA and Immunogenetics Workshop, is aimed at collecting diverse and extensive human leukocyte antigen (HLA) data to create custom reference panels and enhance HLA imputation techniques. Genome‐wide association studies (GWAS) have significantly contributed to identifying genetic associations with various diseases. The...

article

Optimal population‐specific HLA imputation with dimension reduction

Venceslas Douillard, Nayane Santos Brito Silva, Sonia Bourguiba‐Hachemi, Michel S. Naslavsky, more

HLA > 103 > 1 > n/a - n/a

Human genomics has quickly evolved, powering genome‐wide association studies (GWASs). SNP‐based GWASs cannot capture the intense polymorphism of HLA genes, highly associated with disease susceptibility. There are methods to statistically impute HLA genotypes from SNP‐genotypes data, but lack of diversity in reference panels hinders their performance. We evaluated the accuracy of the 1000 Genomes data...

article

Immunogenetics of HLA‐B: SNP, allele, and haplotype diversity in populations from different continents and ancestry backgrounds

Nayane dos Santos Brito Silva, Andreia da Silva Souza, Heloisa de Souza Andrade, Raphaela Neto Pereira, more

HLA > 101 > 6 > 634 - 646

HLA‐B is among the most variable gene in the human genome. This gene encodes a key molecule for antigen presentation to CD8+ T lymphocytes and NK cell modulation. Despite the myriad of studies evaluating its coding region (with an emphasis on exons 2 and 3), few studies evaluated introns and regulatory sequences in real population samples. Thus, HLA‐B variability is probably underestimated. We applied...

article

HLA‐EPI: A new EPIsode in exploring donor/recipient epitopic compatibilities

Estelle Geffard, Léo Boussamet, Alexandre Walencik, Florent Delbos, more

HLA > 99 > 2 > 79 - 92

The HLA system plays a pivotal role both in transplantation and immunology. While classical HLA genotypes matching is made at the allelic level, recent progresses were developed to explore antibody–antigen recognition by studying epitopes. Donor to recipient matching at the epitopic level is becoming a trending topic in the transplantation research field because anti‐HLA antibodies are epitope‐specific...

article

Transcriptional meta‐analysis of regulatory B cells

Florian Dubois, Sophie Limou, Mélanie Chesneau, Nicolas Degauque, more

European Journal of Immunology > 50 > 11 > 1757 - 1769

Regulatory B cells (Bregs) have the ability to regulate inflammation in various pathological situations, making them key players in immune regulation. Several mechanisms have been described and we recently identified a GZMB expressing Breg population in kidney transplanted patients who tolerate a kidney graft. To further investigate their biology and mechanisms, we conducted a transcriptomic analysis...

article

Cover Image

Nicolas Vince, Venceslas Douillard, Estelle Geffard, Diogo Meyer, more

Genetic Epidemiology > 44 > 7 > i - i

Front Cover Caption: The cover image is based on the Original Article SNP‐HLA Reference Consortium (SHLARC): HLA and SNP data sharing for promoting MHC‐centric analyses in genomics by Nicolas Vince et al., https://doi.org/10.1002/gepi.22334.

article

SNP‐HLA Reference Consortium (SHLARC): HLA and SNP data sharing for promoting MHC‐centric analyses in genomics

Nicolas Vince, Venceslas Douillard, Estelle Geffard, Diogo Meyer, more

Genetic Epidemiology > 44 > 7 > 733 - 740

Genome‐wide associations studies have repeatedly identified the major histocompatibility complex genomic region (6p21.3) as key in immune pathologies. Researchers have also aimed to extend the biological interpretation of associations by focusing directly on human leukocyte antigen (HLA) polymorphisms and their combination as haplotypes. To circumvent the effort and high costs of HLA typing, statistical...

article

Chronic kidney disease and HIV in the era of antiretroviral treatment: findings from a 10-year cohort study in a west African setting

Nongodo Firmin Kaboré, Armel Poda, Jacques Zoungrana, Ollo Da, more

BMC Nephrology > 2019 > 20 > 1 > 1-10

Background It has been reported that people living with HIV in West Africa exhibited the highest risks for chronic kidney disease (CKD) in the world. Here, we aimed at determining the CKD frequency and changes in kidney function during antiretroviral treatment (ART) in a large cohort of HIV-patients followed in Burkina Faso. Methods We included ART-naive adults who initiated ART at the Day Care...

article

Renal cortical volume: High correlation with pre- and post-operative renal function in living kidney donors

Edouard Gardan, Lola Jacquemont, Christophe Perret, Pierre-Marie Heudes, more

European Journal of Radiology > 2018 > 99 > C > 118-123

CT volumetry has previously been proposed as an alternative to scintigraphy for the evaluation of pre-donation split renal function and the prediction of post-donation renal function in living kidney donors. The aim of our study was to retrospectively assess the relevance of three CT volumetry techniques for estimating pre-donation kidney function and predicting the risk for chronic kidney disease...

article

P103 SNP-HLA reference consortium: HLA and SNP data sharing for promoting HLA centric analyses in genomics

Nicolas Vince, Alexandre Walencik, Estelle Geffard, Sophie Limou, more

Human Immunology > 2017 > 78 > S > 129

To build large panels of reference for HLA imputation from SNP genotypes including worldwide datasets.Recently, the Haplotype Reference Consortium aggregated over 20 studies to create a very large reference panel of human haplotypes where ∼50M genetic variants are observed from >31,500 sequenced whole genomes (http://www.haplotype-reference-consortium.org/). Based on this model we propose to use...

article

Multidimensional reduction of multicentric cohort heterogeneity: An alternative method to increase statistical power and robustness

Caroline Le Gall, Julie Laurent, Nicolas Vince, Antoine Lizee, more

Human Immunology > 2016 > 77 > 11 > 1024-1029

Modern clinical research takes advantage of multicentric cohorts to increase sample size and gain in statistical power. However, combining individuals from different recruitment centers provides heterogeneity in the dataset that needs to be accounted for to obtain robust results. Sophisticated statistical multivariate models adjusting for center effect can be implemented, but they can become unstable...

article

Variants in CXCR4 associate with juvenile idiopathic arthritis susceptibility

Terri H. Finkel, Jin Li, Zhi Wei, Wei Wang, more

BMC Medical Genetics > 2016 > 17 > 1 > 1-9

Background Juvenile idiopathic arthritis (JIA) is the most common chronic rheumatic disease among children, the etiology of which involves a strong genetic component, but much of the underlying genetic determinants still remain unknown. Our aim was to identify novel genetic variants that predispose to JIA. Methods We performed a genome-wide association study (GWAS) and replication in a total of...

article

APOL1 Kidney Disease Risk Variants: An Evolving Landscape

Patrick D. Dummer, Sophie Limou, Avi Z. Rosenberg, Jurgen Heymann, more

Seminars in Nephrology > 2015 > 35 > 3 > 222-236

Apolipoprotein L1 (APOL1) genetic variants account for much of the excess risk of chronic and end-stage kidney disease, which results in a significant global health disparity for persons of African ancestry. We estimate the lifetime risk of kidney disease in APOL1 dual-risk allele individuals to be at least 15%. Experimental evidence suggests a direct role of APOL1 in pore formation, cellular injury,...

article

APOL1 Kidney Risk Alleles: Population Genetics and Disease Associations

Sophie Limou, George W. Nelson, Jeffrey B. Kopp, Cheryl A. Winkler

Advances in Chronic Kidney Disease > 2014 > 21 > 5 > 426-433

APOL1 kidney disease is a unique case in the field of the genetics of common disease: 2 variants (termed G1 and G2) with high population frequency have been repeatedly associated with nondiabetic CKDs, with very strong effect size (odds ratios 3-29) in populations of sub-Saharan African descent. This review provides an update on the spectrum of APOL1 kidney disease and on the worldwide distribution...

article

Exploration of associations between phospholipase A2 gene family polymorphisms and AIDS progression using the SNPlex™ method

Sophie Limou, Cédric Coulonges, Mario Foglio, Simon Heath, more

Biomedicine & Pharmacotherapy > 2008 > 62 > 1 > 31-40

Members of the secreted phospholipase A2 (PLA2) protein family can inhibit HIV-1 virus replication in vitro. To evaluate the impact of PLA2 gene polymorphisms on AIDS disease development, we studied 12 family members using SNPlex™ technology that permitted simultaneous typing of 70 tagging Single Nucleotide Polymorphisms (tagSNPs). The study utilized HIV-1 seropositive donors with slow progressor...

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Keywords

HLA (3)
CHRONIC KIDNEY DISEASE (2)
HIV (2)
HLA IMPUTATION (2)
IMPUTATION (2)
REFERENCE PANEL (2)
SNP (2)
18TH INTERNATIONAL HLA AND IMMUNOGENETICS WORKSHOP (1)
ADMIXED POPULATION (1)
ADMIXED POPULATIONS (1)
AFRICA (1)
AFRICAN ADMIXTURE (1)
AIDS (1)
ANTIRETROVIRAL TREATMENT (1)
APOL1 (1)
APOL1 DEMOGRAPHICS (1)
APOLIPOPROTEIN L1 (1)
B CELLS (1)
BREGS (1)
BURKINA FASO (1)
CKD (1)
COMPUTED TOMOGRAPHY SCAN (1)
CONSORTIUM (1)
CXCR4 (1)
DIMENSION REDUCTION (1)
DISEASE (1)
EPIDEMIOLOGY (1)
EPITOPIC COMPATIBILITY (1)
EVOLUTIONARY ASPECTS (1)
FOCAL SEGMENTAL GLOMERULOSCLEROSIS (1)
GENE EXPRESSION (1)
GENETIC ASSOCIATION (1)
GENOME-WIDE ASSOCIATION STUDY (1)
GENOMIC (1)
GLOMERULAR DISEASE (1)
GRANZYME B (1)
HAPLOTYPES (1)
HEALTH DISPARITIES (1)
HEMATOPOIETIC STEM CELL TRANSPLANTATION (1)
HETEROGENEITY (1)
HLA CLASS I (1)
HLA EPITOPE (1)
HLA EPLET (1)
HLA‐B (1)
HSCT (1)
IMMUNOGENOMICS (1)
INNATE IMMUNITY (1)
ISOTOPIC MEASURES (1)
JUVENILE IDIOPATHIC ARTHRITIS (1)
KIDNEY FUNCTION (1)
LIVING KIDNEY DONOR (1)
META‐ANALYSIS (1)
MULTICENTRIC COHORT (1)
MULTIDIMENSIONAL REDUCTION (1)
MULTIPLE CORRESPONDENCE ANALYSES (1)
NGS (1)
PATHOGENESIS (1)
PLA2 (1)
POLYMORPHISM (1)
PREDICTION (1)
PROGRESSION (1)
RENAL CORTICAL VOLUME (1)
SHLARC (1)
SOLID ORGAN TRANSPLANTATION (1)
TARGETED RESEQUENCING (1)
VARIABILITY (1)
WORLDWIDE POPULATIONS (1)
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