Publications by Jacques Fellay

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Genome sequencing technology has advanced at a rapid pace and it is now possible to generate highlydetailed genotypes inexpensively. The collection and analysis of such data has the potential to support various applications, including personalized medical ...

Multiple genome-wide association studies (GWAS) have been performed in HIV-1 infected individuals, identifying common genetic influences on viral control and disease course. Similarly, common genetic correlates of acquisition of HIV-1 after exposure have b ...

SARS-CoV-2 infections display tremendous interindividual variability, ranging from asymptomatic infections to life-threatening disease. Inborn errors of, and autoantibodies directed against, type I interferons (IFNs) account for about 20% of critical COVID ...

The implementation of genomic-based medicine is hindered by unresolved questions regarding data privacy and delivery of interpreted results to health-care practitioners. We used DNA-based prediction of HIV-related outcomes as a model to explore critical is ...

Broadly neutralizing antibodies (bnAbs) are a focal component of HIV-1 vaccine design, yet basic aspects of their induction remain poorly understood. Here we report on viral, host and disease factors that steer bnAb evolution using the results of a systema ...

Background: Kaposi's sarcoma, the most common AIDS-related cancer, represents a major public concern in resource-limited countries. Single nucleotide polymorphisms within the Interferon lambda 3/4 region (IFNL3/4) determine the expression, function of IFNL ...

Background. In people living with human immunodeficiency virus (HIV) (PLWH), individual polygenic risk scores (PRSs) are associated with coronary artery disease (CAD) events. Whether PRSs are associated with subclinical CAD is unknown. ...

The magnitude of the human antibody response to viral antigens is highly variable. To explore the human genetic contribution to this variability, we performed genome-wide association studies of the immunoglobulin G response to 14 pathogenic viruses in 2,36 ...

A variant upstream of human leukocyte antigen C (HLA-C) shows the most significant genome-wide effect on HIV control in European Americans and is also associated with the level of HLA-C expression. We characterized the differential cell surface expression ...

Sofosbuvir is a common therapy in hepatitis C virus infection, which targets the NS5B polymerase. Here, Smith et al. analyze the association between whole genome HCV polymorphisms and sofosbuvir treatment failure and identify three common polymorphisms pre ...

Introduction: We have reanalyzed the genomic data of the International Collaboration for the Genomics of HIV (ICGH), centering on HIV-1 Elite Controllers.Methods: We performed a genome-wide Association Study comparing 543 HIV Elite Controllers with 3,272 u ...

Sequencing the genome of Candida albicans as it evolves in a patient reveals the genetic changes that allow the yeast to adapt to its environment. ...

Krüppel-associated box (KRAB) domain-containing zinc finger proteins (KZFPs) are one of the largest groups of transcription factors encoded by tetrapods, with 378 members in human alone. KZFP genes are often grouped in clusters reflecting amplification by ...

Patients with autoimmune polyendocrinopathy syndrome type 1 (APS-1) caused by autosomal recessive AIRE deficiency produce autoantibodies that neutralize type I interferons (IFNs) 1,2 , conferring a predisposition to life-threatening COVID-19 pneumonia 3 . ...

Human APOBEC3 cytidine deaminases are intrinsic resistance factors to HIV-1. However, HIV-1 encodes a viral infectivity factor (Vif) that degrades APOBEC3 proteins. In vitro APO-BEC3F (A3F) anti-HIV-1 activity is weaker than A3G but is partially resistant ...

Objectives: The risk of diabetes mellitus (DM) is increased in people with HIV. Chronic inflammation contributes to DM risk. High leukocytes are associated with DM in the general population, but in people with HIV, evidence of a leukocyte-DM association is ...

Secure storage of genomic data is of great and increasing importance. The scientific community's improving ability to interpret individuals' genetic materials and the growing size of genetic database populations have been aggravating the potential conseque ...

Background: Coronary artery disease (CAD) is in part genetically determined. Aging is accentuated in people with human immunodeficiency virus (HIV) (PLWH). It is unknown whether genetic CAD event prediction in PLWH is improved by applying individual polyge ...

Pathogen strains may differ in virulence because they attain different loads in their hosts, or because they induce different disease-causing mechanisms independent of their load. In evolutionary ecology, the latter is referred to as" per-parasite pathogen ...

Jacques Fellay

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Privacy in the Genomic Era

Association Study of Common Genetic Variants and HIV-1 Acquisition in 6,300 Infected Cases and 7,200 Controls

A global effort to dissect the human genetic basis of resistance to SARS-CoV-2 infection

Privacy-preserving genomic testing in the clinic: a model using HIV treatment

Determinants of HIV-1 broadly neutralizing antibody induction

Interferon lambda 3/4 polymorphisms are associated with AIDS-related Kaposi's sarcoma

Polygenic Risk Scores for Prediction of Subclinical Coronary Artery Disease in Persons Living With HIV: The Swiss HIV Cohort Study

Amino Acid Variation in HLA Class II Proteins Is a Major Determinant of Humoral Response to Common Viruses

Influence of HLA-C Expression Level on HIV Control

Viral genome wide association study identifies novel hepatitis C virus polymorphisms associated with sofosbuvir treatment failure

The HLA-B*57:01 allele corresponds to a very large MHC haploblock likely explaining its massive effect for HIV-1 elite control

Adaptation on a genomic scale

Genetic features and genomic targets of human KRAB-zinc finger proteins

An indel in the promoter region of NFKB1 confers protection against infection but increases risk of allergy

Autoantibodies against type I IFNs in humans with alternative NF-κB pathway deficiency

Role of APOBEC3F Gene Variation in HIV-1 Disease Progression and Pneumocystis Pneumonia

Leukocyte Count and New-onset Diabetes Mellitus in People with Hiv: a Longitudinal Study

GenoGuard: Protecting Genomic Data against Brute-Force Attacks

Coronary Artery Disease-Associated and Longevity-Associated Polygenic Risk Scores for Prediction of Coronary Artery Disease Events in Persons Living With Human Immunodeficiency Virus: The Swiss HIV Cohort Study

Dissecting HIV Virulence: Heritability of Setpoint Viral Load, CD4+ T Cell Decline and Per-Parasite Pathogenicity