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Jacques Fellay

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Related publications (185)

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Impact of Genetic and Nongenetic Factors on Body Mass Index and Waist-Hip Ratio Change in HIV-Infected Individuals Initiating Antiretroviral Therapy

Jacques Fellay, Christian Axel Wandall Thorball, Christian Hammer

Objective. There is limited data on abdominal obesity and the influence of genetics on weight change after ant iretroviral therapy (ART) initiation. We assessed body mass index (BMI) and waist hip ration (WHR) change over time in the Swiss HIV Cohort study ...

OXFORD UNIV PRESS INC2020

Granulysin Antimicrobial Activity Promotes Dormancy in Mycobacterium tuberculosis

Jacques Fellay

Human tuberculosis (TB) caused by Mycobacterium tuberculosis (Mtb) remains a global public health threat. Granulomas constitute a hallmark of TB pathogenesis that can clear, contain, or exacerbate an infection. Containment is exploited by Mtb as a hideout ...

2025

Analysis of Stop-Gain and Frameshift Variants in Human Innate Immunity Genes

Jacques Fellay, Paul Jack Mc Laren, Istvan Bartha

Loss-of-function variants in innate immunity genes are associated with Mendelian disorders in the form of primary immunodeficiencies. Recent resequencing projects report that stop-gains and frameshifts are collectively prevalent in humans and could be resp ...

Public Library Science2014

Disentangling human tolerance and resistance against HIV

Jacques Fellay, Paul Jack Mc Laren

In ecology, "disease tolerance" is defined as an evolutionary strategy of hosts against pathogens, characterized by reduced or absent pathogenesis despite high pathogen load. To our knowledge, tolerance has to date not been quantified and disentangled from ...

Public Library Science2014

Variability of Primary Sjogren's Syndrome Is Driven by Interferon alpha and Interferon alpha Blood Levels Are Associated With the Class II HLA-DQ Locus

Jacques Fellay, Christian Axel Wandall Thorball

Objective Primary Sjogren's syndrome (SS) is the second most frequent systemic autoimmune disease, affecting 0.1% of the general population. To characterize the molecular and clinical variabilities among patients with primary SS, we integrated transcriptom ...

WILEY2022

HIV-1 and human genetic variation

Jacques Fellay

Over the past four decades, research on the natural history of HIV infection has described how HIV wreaks havoc on human immunity and causes AIDS. HIV host genomic research, which aims to understand how human genetic variation affects our response to HIV i ...

NATURE RESEARCH2021

Human genetic variation in HIV disease: beyond genome-wide association studies

Jacques Fellay, Paul Jack Mc Laren

PURPOSE OF REVIEW: Rapid expansion of genomic technologies has resulted in an unprecedented ability to interrogate the impact of human genetic variation on disease. HIV-1 infection is a unique model for studying this impact because host genetic variation i ...

Lippincott Williams & Wilkins2015

Telomere Length Declines in Persons With Human Immunodeficiency Virus Before Antiretroviral Therapy Start but Not After Viral Suppression: A Longitudinal Study Over >17 Years

Jacques Fellay

A total of 107 Swiss HIV Cohort Study participants contributed longitudinal samples. During untreated chronic HIV infection (median observation time, 7.7 years) but not during suppressive antiretroviral therapy (median observation time, 9.8 years), we reco ...

OXFORD UNIV PRESS INC2021

HIV-phyloTSI: subtype-independent estimation of time since HIV-1 infection for cross-sectional measures of population incidence using deep sequence data

Jacques Fellay

Background Estimating the time since HIV infection (TSI) at population level is essential for tracking changes in the global HIV epidemic. Most methods for determining TSI give a binary classification of infections as recent or non-recent within a window o ...

Springer Science and Business Media LLC2025

Viral Genetic Determinants of Prolonged Respiratory Syncytial Virus Infection Among Infants in a Healthy Term Birth Cohort

Jacques Fellay, Thomas Junier, Zhi Ming Xu, Dylan Lawless

Background. Respiratory syncytial virus (RSV) is associated with acute respiratory infection. We sought to identify RSV variants associated with prolonged infection. ...

OXFORD UNIV PRESS INC2023

Self-reported neurocognitive complaints in the Swiss HIV Cohort Study: a viral genome-wide association study

Jacques Fellay

People with HIV may report neurocognitive complaints, with or without associated neurocognitive impairment, varying between individuals and populations. While the HIV genome could play a major role, large systematic viral genome-wide screens to date are la ...

Oxford University Press2024

Genome-to-genome analysis reveals associations between human and mycobacterial genetic variation in tuberculosis patients from Tanzania

Simon Sie-Mon Tang, Jacques Fellay, Zhi Ming Xu, Dylan Lawless, Olivier Noël Marie Naret, Sina Rüeger

The risk and prognosis of tuberculosis (TB) are influenced by a complex interplay between human and bacterial genetic factors. While previous genomic studies have largely examined human and bacterial genomes separately, we adopted an integrated approach to ...

Springer Science and Business Media LLC2025

Blacklisting variants common in private cohorts but not in public databases optimizes human exome analysis

Jacques Fellay, Alessandro Borghesi

Computational analyses of human patient exomes aim to filter out as many nonpathogenic genetic variants (NPVs) as possible, without removing the true disease-causing mutations. This involves comparing the patient's exome with public databases to remove rep ...

National Academy of Sciences2019

European genetic diversity and susceptibility to pathogens

Jacques Fellay, Paul Jack Mc Laren

Infectious diseases, both in their endemic and epidemic forms, have shaped the human genome. Ecology has also contributed to geographically constrained pressures on human populations. There are now multiple examples of population-specific genetic variants ...

2013

Genetics of human susceptibility to active and latent tuberculosis: present knowledge and future perspectives

Jacques Fellay, Nimisha Chaturvedi

Tuberculosis is an ancient human disease, estimated to have originated and evolved over thousands of years alongside modern human populations. Despite considerable advances in disease control, tuberculosis remains one of the world's deadliest communicable ...

2018

CD38 Expression by Antigen-Specific CD4 T Cells Is Significantly Restored 5 Months After Treatment Initiation Independently of Sputum Bacterial Load at the Time of Tuberculosis Diagnosis

Jacques Fellay

T cell activation markers (TAM) expressed by antigen-specific T cells constitute promising candidates to attest the presence of an active infection by Mycobacterium tuberculosis (Mtb). Reciprocally, their modulation may be used to assess antibiotic treatme ...

FRONTIERS MEDIA SA2022

Differential immunodominance hierarchy of CD8+ T cell responses in HLA-B27:05 and B27:02-mediated control of HIV-1 infection

Jacques Fellay

The well-characterised association between HLA-B27:05 and protection against HIV disease progression has been linked to immunodominant HLA-B27:05-restricted CD8+ T-cell responses towards the conserved Gag 263-272 ('KK10') and Pol 901-909 'KY9' epitopes. ...

American Society for Microbiology2018

Epistatic interaction between ERAP2 and HLA modulates HIV-1 adaptation and disease outcome in an Australian population

Jacques Fellay

A strong genetic predictor of outcome following untreated HIV-1 infection is the carriage of specific alleles of human leukocyte antigens (HLAs) that present viral epitopes to T cells. Residual variation in outcome measures may be attributed, in part, to v ...

2024

Smoking changes adaptive immunity with persistent effects

Jacques Fellay

Individuals differ widely in their immune responses, with age, sex and genetic factors having major roles in this inherent variability1–6. However, the variables that drive such differences in cytokine secretion—a crucial component of the host response to ...

2024

Whole-exome Sequencing for the Identification of Rare Variants in Primary Immunodeficiency Genes in Children With Sepsis: A Prospective, Population-based Cohort Study

Jacques Fellay, Christian Axel Wandall Thorball, Alessandro Borghesi, Nimisha Chaturvedi, Samira Asgari

Background. The role of primary immunodeficiencies (PID) in susceptibility to sepsis remains unknown. It is unclear whether children with sepsis benefit from genetic investigations. We hypothesized that sepsis may represent the first manifestation of under ...

OXFORD UNIV PRESS INC2020