Fields of expertise
MissionHuman genetic variation plays a key role in determining individual outcomes after exposure to infectious agents.
The mission of our laboratory is to contribute to a better understanding of inter-individual differences in response to infections, using a range of contemporary genomic tools. Approaches include genome-wide genotyping and association analysis, exome/genome sequencing and transcriptomics.
BiographyJacques Fellay is a medical scientist with expertise in infectious diseases and human genomics. He obtained his MD from the University of Lausanne in 2002 and his PhD from University of Utrecht. After a clinical training in infectious diseases in Switzerland and a 4-years postdoctoral fellowship at Duke University, he joined the EPFL in April 2011 with an SNF Professorship.
On top of his EPFL affiliation, Jacques is also Head of Precision Medicine at the University Hospital (CHUV) in Lausanne, Group Leader at the Swiss Institute of Bioinformatics, and Co-director of the Health2030 Genome Center at Campus Biotech in Geneva.
Revolutionizing Medical Data Sharing Using Advanced Privacy-Enhancing Technologies: Technical, Legal, and Ethical SynthesisJournal Of Medical Internet Research. 2021-02-25. DOI : 10.2196/25120.
The influence of human genetic variation on Epstein–Barr virus sequence diversityScientific Reports. 2021-02-25. DOI : 10.1038/s41598-021-84070-7.
The genetic architecture of complex human traits at the dawn of genomic medicineLausanne, EPFL, 2021. DOI : 10.5075/epfl-thesis-8464.
Dissemination of Mycobacterium tuberculosis is associated to a SIGLEC1 null variant that limits antigen exchange via trafficking extracellular vesiclesJournal Of Extracellular Vesicles. 2021-01-01. DOI : 10.1002/jev2.12046.
Genome-to-genome analysis identifies an Asian-specific variant in the gene encoding NTCP that leads to specific HBV escape mutations during chronic infection2020-12-01. p. 316-317.
Human genomics of the humoral response against polyomaviruses2020-12-01. p. 312-313.
An indel in the promoter region of NFKB1 confers protection against infection but increases risk of allergy2020-12-01. p. 311-312.
Using reference-fixed principal components to improve polygenic risk score prediction2020-12-01. p. 134-135.
Host Genomics of the HIV-1 Reservoir Size and Its Decay Rate During Suppressive Antiretroviral TreatmentJaids-Journal Of Acquired Immune Deficiency Syndromes. 2020-12-01. DOI : 10.1097/QAI.0000000000002473.
Whole-exome Sequencing for the Identification of Rare Variants in Primary Immunodeficiency Genes in Children With Sepsis: A Prospective, Population-based Cohort StudyClinical Infectious Diseases. 2020-11-15. DOI : 10.1093/cid/ciaa290.
HLA tapasin independence: broader peptide repertoire and HIV controlProceedings Of The National Academy Of Sciences Of The United States Of America. 2020-11-10. DOI : 10.1073/pnas.2013554117.
Heritability of the HIV-1 reservoir size and decay under long-term suppressive ARTNature Communications. 2020-11-02. DOI : 10.1038/s41467-020-19198-7.
Virosaurus A Reference to Explore and Capture Virus Genetic DiversityViruses-Basel. 2020-11-01. DOI : 10.3390/v12111248.
Inborn errors of type I IFN immunity in patients with life-threatening COVID-19Science. 2020-10-23. DOI : 10.1126/science.abd4570.
Designing a Tanzanian Specific SNP Array Add-On to Capture Population-Specific Genetic Variations and to Improve Genotype Imputation2020-07-01. 48th European Mathematical Genetics Meeting (EMGM), Lausanne, SWITZERLAND, Apr 16-17, 2020. p. 227-227. DOI : 10.1159/000507248.
Susceptibility to infection in early life: a growing role for human geneticsHuman Genetics. 2020-06-01. DOI : 10.1007/s00439-019-02109-2.
Exploring the interactions between the human and viral genomesHuman Genetics. 2020-06-01. DOI : 10.1007/s00439-019-02089-3.
Assessing the impact of non-pharmaceutical interventions on SARS-CoV-2 transmission in SwitzerlandSwiss Medical Weekly. 2020-05-30. DOI : 10.4414/smw.20295.
COVID-19 epidemic in Switzerland: on the importance of testing, contact tracing and isolationSwiss Medical Weekly. 2020-03-19. DOI : 10.4414/smw.2020.20225.
HLA Heterozygote Advantage against HIV-1 Is Driven by Quantitative and Qualitative Differences in HLA Allele-Specific Peptide PresentationMolecular Biology And Evolution. 2020-03-01. DOI : 10.1093/molbev/msz249.
Contribution of Genetic Background and Data Collection on Adverse Events of Anti-human Immunodeficiency Virus (HIV) Drugs (D:A:D) Clinical Risk Score to Chronic Kidney Disease in Swiss HIV-infected Persons With Normal Baseline Estimated Glomerular Filtration RateClinical Infectious Diseases. 2020-03-01. DOI : 10.1093/cid/ciz280.
Data protection and ethics requirements for multisite research with health data: a comparative examination of legislative governance frameworks and the role of data protection technologiesJournal Of Law And The Biosciences. 2020-01-01. DOI : 10.1093/jlb/lsaa010.
Contact networks across ages: computational analysis of epidemiological dynamicsLausanne, EPFL, 2020. DOI : 10.5075/epfl-thesis-7482.
Impact of Genetic and Nongenetic Factors on Body Mass Index and Waist-Hip Ratio Change in HIV-Infected Individuals Initiating Antiretroviral TherapyOpen Forum Infectious Diseases. 2020-01-01. DOI : 10.1093/ofid/ofz464.
HIV host genomics in the era of effective antiretroviral therapyLausanne, EPFL, 2020. DOI : 10.5075/epfl-thesis-10132.
Gender medicine and oncology: report and consensus of an ESMO workshopAnnals Of Oncology. 2019-12-01. DOI : 10.1093/annonc/mdz414.
Systems Biology in 874 Patients with Primary Sjogren's Syndrome Indicates the Predominant Role of Interferon Alpha Compared to Interferon Gamma, Its Association with Systemic Complications, and a New Aspect of the Genetic Contribution of HLA2019-10-01.
Genome-to-genome analysis of Epstein-Barr virus infection2019-10-01. 52nd Conference of the European-Society-of-Human-Genetics (ESHG), Gothenburg, SWEDEN, Jun 15-18, 2019. p. 1365-1365.
Rare variants in antiviral response genes drive severe viral respiratory infections in children2019-10-01. 52nd Conference of the European-Society-of-Human-Genetics (ESHG), Gothenburg, SWEDEN, Jun 15-18, 2019. p. 1374-1375.
Human genetic determinants of chronic low-grade inflammation in the general population2019-10-01. 52nd Conference of the European-Society-of-Human-Genetics (ESHG), Gothenburg, SWEDEN, Jun 15-18, 2019. p. 1747-1748.
Predicting the Occurrence of Variants in RAG1 and RAG2Journal Of Clinical Immunology. 2019-10-01. DOI : 10.1007/s10875-019-00670-z.
A comprehensive assessment of demographic, environmental, and host genetic associations with gut microbiome diversity in healthy individualsMicrobiome. 2019-09-13. DOI : 10.1186/s40168-019-0747-x.
Adaptation of hepatitis C virus to interferon lambda polymorphism across multiple viral genotypesElife. 2019-09-03. DOI : 10.7554/eLife.42542.
HIV Transmission Chains Exhibit Greater HLA-B Homogeneity Than Randomly ExpectedJaids-Journal Of Acquired Immune Deficiency Syndromes. 2019-08-15. DOI : 10.1097/QAI.0000000000002077.
Determinants of HIV-1 reservoir size and long-term dynamics during suppressive ARTNature Communications. 2019-07-19. DOI : 10.1038/s41467-019-10884-9.
Effect of Fc Receptor Genetic Diversity on HIV-1 Disease PathogenesisFrontiers In Immunology. 2019-05-09. DOI : 10.3389/fimmu.2019.00970.
Associations between usual diet and gut microbiota composition: results from the Milieu Interieur cross-sectional studyAmerican Journal Of Clinical Nutrition. 2019-05-01. DOI : 10.1093/ajcn/nqz029.
Human genomics of acute liver failure due to hepatitis B virus infection: An exome sequencing study in liver transplant recipientsJournal Of Viral Hepatitis. 2019-02-01. DOI : 10.1111/jvh.13019.
Blacklisting variants common in private cohorts but not in public databases optimizes human exome analysisProceedings Of The National Academy Of Sciences Of The United States Of America. 2019-01-15. DOI : 10.1073/pnas.1808403116.
HIV peptidome-wide association study reveals patient-specific epitope repertoires associated with HIV controlProceedings Of The National Academy Of Sciences Of The United States Of America. 2019-01-15. DOI : 10.1073/pnas.1812548116.
A viral vector based in vivo model of tauopathy to explore therapeutic strategies against tau pathologyLausanne, EPFL, 2019. DOI : 10.5075/epfl-thesis-9532.
Exploring on Protein-DNA interactionsLausanne, EPFL, 2019. DOI : 10.5075/epfl-thesis-9426.
HIV-1 Vpu is a potent transcriptional suppressor of NF-κB-elicited antiviral immune responseseLife. 2019. DOI : 10.7554/eLife.41930.
Virucidal nanomaterials against influenzaLausanne, EPFL, 2019. DOI : 10.5075/epfl-thesis-9114.
Interferon lambda 3/4 polymorphisms are associated with AIDS-related Kaposi's sarcomaAids. 2018-11-28. DOI : 10.1097/QAD.0000000000002004.
Human genetic variants and age are the strongest predictors of humoral immune responses to common pathogens and vaccinesGenome Medicine. 2018-07-27. DOI : 10.1186/s13073-018-0568-8.
Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiverVirus Evolution. 2018-05-18. DOI : 10.1093/ve/vey007.
Killer cell immunoglobulin–like receptor 3DL1 variation modifies HLA-B*57 protection against HIV-1Journal of Clinical Investigation. 2018-05-01. DOI : 10.1172/JCI98463.
Natural variation in the parameters of innate immune cells is preferentially driven by genetic factorsNature Immunology. 2018-03-19. DOI : 10.1038/s41590-018-0049-7.
Detection of novel astroviruses MLB1 and MLB2 in the sera of febrile Tanzanian childrenEmerging Microbes & Infections. 2018-03-14. DOI : 10.1038/s41426-018-0025-1.
Are privacy-enhancing technologies for genomic data ready for the clinic? A survey of medical experts of the Swiss HIV Cohort StudyJournal of Biomedical Informatics. 2018-03-01. DOI : 10.1016/j.jbi.2017.12.013.
Elevated HLA-A expression impairs HIV control through inhibition of NKG2A-expressing cellsScience. 2018-01-05. DOI : 10.1126/science.aam8825.
Visual masking deficits in schizophrenia: A view into the genetics of the disease through an endophenotype2018. Annual meeting of the American Society of Human Genetics (ASHG), San Diego, USA, October 16-20, 2018.
Genetic determinants of healthy human immune variance: from humoral response to microbiome diversityLausanne, EPFL, 2018. DOI : 10.5075/epfl-thesis-8955.
Correcting for Population Stratification Reduces False Positive and False Negative Results in Joint Analyses of Host and Pathogen GenomesFrontiers in Genetics. 2018. DOI : 10.3389/fgene.2018.00266.
Computational and Statistical analyses of Molecular Evolution and Demography using Large-scale Sequencing DataLausanne, EPFL, 2018. DOI : 10.5075/epfl-thesis-8748.
Genomics: a Swiss army knife to fight leprosyLausanne, EPFL, 2018. DOI : 10.5075/epfl-thesis-8482.
On Secure Cloud Computing for Genomic Data: From Storage to AnalysisLausanne, EPFL, 2018. DOI : 10.5075/epfl-thesis-8367.
Dissecting HIV Virulence: Heritability of Setpoint Viral Load, CD4 T Cell Decline and Per-Parasite PathogenicityMolecular biology and evolution. 2018. DOI : 10.1093/molbev/msx246.
Differential immunodominance hierarchy of CD8 T cell responses in HLA-B*27:05 and B*27:02-mediated control of HIV-1 infectionJournal of virology. 2018. DOI : 10.1128/JVI.01685-17.
Genetics of human susceptibility to active and latent tuberculosis: present knowledge and future perspectivesThe Lancet. Infectious Diseases. 2018. DOI : 10.1016/S1473-3099(17)30623-0.
HLA-B*14:02-Restricted Env-Specific CD8 T-Cell Activity Has Highly Potent Antiviral Efficacy Associated with Immune Control of HIV InfectionJournal of virology. 2017. DOI : 10.1128/JVI.00544-17.
Evaluating the Impact of Functional Genetic Variation on HIV-1 ControlThe Journal of infectious diseases. 2017. DOI : 10.1093/infdis/jix470.
Distinctive roles of age, sex, and genetics in shaping transcriptional variation of human immune responses to microbial challengesProceedings of the National Academy of Sciences of the United States of America. 2017. DOI : 10.1073/pnas.1714765115.
Viral genetic variation accounts for a third of variability in HIV-1 set-point viral load in EuropePlos Biology. 2017. DOI : 10.1371/journal.pbio.2001855.
Severe viral respiratory infections in children with IFIH1 loss-of-function mutationsProceedings of the National Academy of Sciences of the United States of America. 2017. DOI : 10.1073/pnas.1704259114.
SQC: Secure Quality Control for Meta-Analysis of Genome-Wide Association StudiesBioinformatics. 2017. DOI : 10.1093/bioinformatics/btx193.
Genome-to-genome analysis highlights the effect of the human innate and adaptive immune systems on the hepatitis C virusNature Genetics. 2017. DOI : 10.1038/ng.3835.
Estimating the Respective Contributions of Human and Viral Genetic Variation to HIV ControlPLoS Computational Biology. 2017. DOI : 10.1371/journal.pcbi.1005339.
Neonatal Group B Streptococcal Disease in Otherwise Healthy Infants: Failure of Specific Neonatal Immune ResponsesFrontiers In Immunology. 2017. DOI : 10.3389/fimmu.2017.00215.
No Evidence for Association of beta-Defensin Genomic Copy Number with HIV Susceptibility, HIV Load during Clinical Latency, or Progression to AIDSAnnals Of Human Genetics. 2017. DOI : 10.1111/ahg.12182.
A privacy-preserving solution for compressed storage and selective retrieval of genomic dataGenome Research. 2016-10-27. DOI : 10.1101/gr.206870.116.
Contribution of Genetic Background and Clinical Risk Factors to Low-Trauma Fractures in Human Immunodeficiency Virus (HIV)-Positive Persons: The Swiss HIV Cohort StudyOpen Forum Infectious Diseases. 2016-04-01. DOI : 10.1093/ofid/ofw101.
Privacy-enhancing technologies for medical tests using genomic dataEP2895980 ; US9536047 ; US2016224735 ; US9306443 ; US9270446 ; US2015236849 ; EP2895980 ; CN103677065 ; WO2014040964 ; US2014077757 ; EP2709028 ; TW201411310 . 2016.
Exome Sequencing Reveals Primary Immunodeficiencies in Children with Community-Acquired Pseudomonas aeruginosa SepsisFrontiers In Immunology. 2016. DOI : 10.3389/fimmu.2016.00357.
Multiple HCV Amino Acid Variants Associate with Interferon Lambda Polymorphism in Genotype 1a, 1b and 3a Infections2016. 67th Annual Meeting of the American-Association-for-the-Study-of-Liver-Diseases (AASLD), Boston, MA, NOV 11-15, 2016. p. 33A-33A.
Familial segregation of group B streptococcal infection in a consanguineous kindredInternational Journal Of Infectious Diseases. 2016. DOI : 10.1016/j.ijid.2016.08.010.
Determinants of HIV-1 broadly neutralizing antibody inductionNature Medicine. 2016. DOI : 10.1038/nm.4187.
Corrigendum: Exome Sequencing reveals Primary immunodeficiencies in Children with Community-Acquired Pseudomonas aeruginosa Sepsis (vol 7, 357, 2016)Frontiers In Immunology. 2016. DOI : 10.3389/fimmu.2016.00447.
Identification of Siglec-1 null individuals infected with HIV-1Nature Communications. 2016. DOI : 10.1038/ncomms12412.
The Drosophila gut response to infectionLausanne, EPFL, 2016. DOI : 10.5075/epfl-thesis-7151.
Role of APOBEC3F Gene Variation in HIV-1 Disease Progression and Pneumocystis PneumoniaPlos Genetics. 2016. DOI : 10.1371/journal.pgen.1005921.
Privacy-preserving genomic testing in the clinic: a model using HIV treatmentGenetics in medicine : official journal of the American College of Medical Genetics. 2016. DOI : 10.1038/gim.2015.167.
Host and pathogen genomics of severe pediatric infectionsLausanne, EPFL, 2016. DOI : 10.5075/epfl-thesis-6656.
Amino Acid Variation in HLA Class II Proteins Is a Major Determinant of Humoral Response to Common VirusesAmerican Journal Of Human Genetics. 2015. DOI : 10.1016/j.ajhg.2015.09.008.
Polymorphisms of large effect explain the majority of the host genetic contribution to variation of HIV-1 virus loadProceedings Of The National Academy Of Sciences Of The United States Of America. 2015. DOI : 10.1073/pnas.1514867112.
The Characteristics of Heterozygous Protein Truncating Variants in the Human GenomePlos Computational Biology. 2015. DOI : 10.1371/journal.pcbi.1004647.
The Interplay Between Host Genetic Variation, Viral Replication, and Microbial Translocation in Untreated HIV-Infected IndividualsThe Journal of infectious diseases. 2015. DOI : 10.1093/infdis/jiv089.
Privacy in the Genomic EraACM Computing Surveys. 2015. DOI : 10.1145/2767007.
Adaptation on a genomic scaleeLife. 2015. DOI : 10.7554/eLife.06193.
Human genetic variation in HIV disease: beyond genome-wide association studiesCurrent opinion in HIV and AIDS. 2015. DOI : 10.1097/COH.0000000000000133.
Quantifying Genomic Privacy via Inference Attack with High-Order SNV Correlations2015. 2nd International Workshop on Genome Privacy and Security (in conjunction with IEEE S&P 2015), San Jose, CA, USA, May 21, 2015.
GenoGuard: Protecting Genomic Data against Brute-Force Attacks2015. 36th IEEE Symposium on Security and Privacy (S&P 2015), San Jose, CA, USA, May 18-20, 2015.
GenoGuard: Protecting Genomic Data Against Brute-Force Attacks2015
Valparaíso en 02h01. Promenade d'un port à l'autre2014
Médecine génomique et Maladies infectieuses [Genomic medicine and infectious diseases]Praxis. 2014. DOI : 10.1024/1661-8157/a001658.
A Novel Acute Retroviral Syndrome Severity Score Predicts the Key Surrogate Markers for HIV-1 Disease ProgressionPlos One. 2014. DOI : 10.1371/journal.pone.0114111.
HLA class I and KIR genes do not protect against HIV type 1 infection in highly exposed uninfected individuals with hemophilia AThe Journal of infectious diseases. 2014. DOI : 10.1093/infdis/jiu214.
Disentangling human tolerance and resistance against HIVPLoS biology. 2014. DOI : 10.1371/journal.pbio.1001951.
Practical Solutions for Protecting Individual Genomic PrivacyAmerican Society of Human Genetics (ASHG), San Diego, CA, USA, October 2014.
Teaching & PhD
Life Sciences Engineering