Jacques Fellay
EPFL SV GHI UPFELLAY
AAB 2 40 (Bâtiment AAB)
Station 19
CH-1015 Lausanne
+41 21 693 72 32
+41 21 693 18 49
Office: AAB 2 40
EPFL › SV › GHI › UPFELLAY
Website: https://fellay-lab.epfl.ch
+41 21 693 18 49
EPFL › VPA › VPA-AVP-DLE › AVP-DLE-EDOC › EDCB-GE
Website: https://go.epfl.ch/phd-edcb
+41 21 693 18 49
EPFL › VPA › VPA-FAC › ASC
+41 21 693 18 49
EPFL › VPA › VPA-AVP-DLE › AVP-DLE-EDOC › CDOCT
+41 21 693 18 49
EPFL › SV › SV-DEC › SV-DIR
+41 21 693 18 49
EPFL › VPA › VPA-FAC › HREC
Expertise
Human genomics of infectious diseases - Immunogenetics - Virus-host interactions - Translational genomics - Personalized health
Mission
Human genetic variation plays a key role in modulating immunity and 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.
Jacques Fellay is a medical scientist with expertise in human genomics, infectious diseases, and personalized health. 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 position, Jacques is also Head of Precision Medicine at the University Hospital (CHUV) in Lausanne, Group Leader at the Swiss Institute of Bioinformatics (SIB), Faculty member at the Swiss School of Public Health (SSPH ), and Chief Scientist at the Health2030 Genome Center at Campus Biotech in Geneva.
Awards
National Latsis Prize
Latsis foundation
2012
Leenaards Prize for translational medical research
Leenaards foundation
2015
Excellence in Basic Research Award
Swiss Society for Infectious Diseases
2017
« Divisionnaire F.-K. Rünzi » Foundation Award
2013
Infoscience
Joint host-pathogen genomic analysis identifies hepatitis B virus mutations associated with human NTCP and HLA class I variation
American Journal Of Human Genetics. 2024-06-06. DOI : 10.1016/j.ajhg.2024.04.013.Diagnostic accuracy of a sequence-specific Mtb-DNA hybridization assay in urine: a case-control study including subclinical TB cases
Microbiology Spectrum. 2024-05-08. DOI : 10.1128/spectrum.00426-24.Bacterial diversity dominates variable macrophage responses of tuberculosis patients in Tanzania
Scientific Reports. 2024-04-23. DOI : 10.1038/s41598-024-60001-0.A common NFKB1 variant detected through antibody analysis in UK Biobank predicts risk of infection and allergy
American Journal Of Human Genetics. 2024-02-01. DOI : 10.1016/j.ajhg.2023.12.013.Rare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-19 (vol 15, 22, 2023)
Genome Medicine. 2024-01-06. DOI : 10.1186/s13073-023-01278-0.Prevalence of actionable pharmacogenetic variants in a Swiss hospital cohort
2024-01-01. 56th Annual Conference of the European-Society-of-Human-Genetics (ESHG), Glasgow, SCOTLAND, JUN 10-13, 2023. p. 700-700.Inborn errors of type I interferon immunity in patients with severe acute hepatitis E
2024-01-01. 56th Annual Conference of the European-Society-of-Human-Genetics (ESHG), Glasgow, SCOTLAND, JUN 10-13, 2023. p. 451-451.Prevalence of clonal hematopoiesis in people living with HIV
2024-01-01. 56th Annual Conference of the European-Society-of-Human-Genetics (ESHG), Glasgow, SCOTLAND, JUN 10-13, 2023. p. 443-444.The impact of human genetics on Mycobacterium tuberculosis intra-host evolution
2024-01-01. 56th Annual Conference of the European-Society-of-Human-Genetics (ESHG), Glasgow, SCOTLAND, JUN 10-13, 2023. p. 346-346.The HLA-B*57:01 allele corresponds to a very large MHC haploblock likely explaining its massive effect for HIV-1 elite control
Frontiers In Immunology. 2023-12-11. DOI : 10.3389/fimmu.2023.1305856.Inborn errors of type I interferon immunity in patients with symptomatic acute hepatitis E
Hepatology. 2023-12-08. DOI : 10.1097/HEP.0000000000000701.Predicting type 2 diabetes risk before and after solid organ transplantation using polygenic scores in a Danish cohort
Frontiers In Molecular Biosciences. 2023-12-07. DOI : 10.3389/fmolb.2023.1282412.Cytokine-armed dendritic cell progenitors for antigen-agnostic cancer immunotherapy
Nature Cancer. 2023-11-23. DOI : 10.1038/s43018-023-00668-y.Autoantibodies against type I IFNs in humans with alternative NF-κB pathway deficiency
Nature. 2023-11-08. DOI : 10.1038/s41586-023-06717-x.Inborn Errors of Type I Interferon Immunity in Patients with Severe Acute Hepatitis E
2023-09-11. p. 14S-14S.Africa-specific human genetic variation near CHD1L associates with HIV-1 load
Nature. 2023-08-02. DOI : 10.1038/s41586-023-06370-4.Variation in African genomes linked to control of HIV
Nature. 2023-08-02. DOI : 10.1038/d41586-023-02277-2.A metagenome-wide association study of HIV disease progression in HIV controllers
Iscience. 2023-07-21. DOI : 10.1016/j.isci.2023.107214.Autoantibodies neutralizing type I IFNs underlie West Nile virus encephalitis in & SIM;40% of patients
Journal Of Experimental Medicine. 2023-06-22. DOI : 10.1084/jem.20230661.Multiancestry sex-stratified genomic associations with HIV viral load and controller status from the ICGH
Jci Insight. 2023-06-08. DOI : 10.1172/jci.insight.170068.Association of a Polygenic Risk Score With Osteoporosis in People Living With HIV: The Swiss HIV Cohort Study
Journal Of Infectious Diseases. 2023-05-24. DOI : 10.1093/infdis/jiad179.A polygenic risk score to predict sudden cardiac arrest in patients with cardiovascular disease
2023-05-11. 55th European-Society-of-Human-Genetics (ESHG) Conference, Vienna, AUSTRIA, JUN 11-14, 2022. p. 691-691.Host genomic susceptibility to severe respiratory syncytial virus infection
2023-05-11. 55th European-Society-of-Human-Genetics (ESHG) Conference, Vienna, AUSTRIA, JUN 11-14, 2022. p. 163-164.A polygenic risk score improves the prediction of cardiovascular risk associated with obstructive sleep-apnoea
2023-05-11. 55th European-Society-of-Human-Genetics (ESHG) Conference, Vienna, AUSTRIA, JUN 11-14, 2022. p. 145-146.Secondary structure of the human mitochondrial genome affects formation of deletions
Bmc Biology. 2023-05-08. DOI : 10.1186/s12915-023-01606-1.Viral Genetic Determinants of Prolonged Respiratory Syncytial Virus Infection Among Infants in a Healthy Term Birth Cohort
Journal Of Infectious Diseases. 2023-05-01. DOI : 10.1093/infdis/jiac442.Epigenetic ageing accelerates before antiretroviral therapy and decelerates after viral suppression in people with HIV in Switzerland: a longitudinal study over 17 years
Lancet Healthy Longevity. 2023-05-01. DOI : 10.1016/S2666-7568(23)00037-5.Rare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-19
Genome Medicine. 2023-04-05. DOI : 10.1186/s13073-023-01173-8.Back-to-Africa introductions of Mycobacterium tuberculosis as the main cause of tuberculosis in Dar es Salaam, Tanzania
Plos Pathogens. 2023-04-01. DOI : 10.1371/journal.ppat.1010893.Associations of genetic and infectious risk factors with coronary heart disease
Elife. 2023-02-14. DOI : 10.7554/eLife.79742.Leukocyte Count and Coronary Artery Disease Events in People With Human Immunodeficiency Virus: A Longitudinal Study
Clinical Infectious Diseases. 2023-01-23. DOI : 10.1093/cid/ciad033.Combining European and US risk prediction models with polygenic risk scores to refine cardiovascular prevention: the CoLaus|PsyCoLaus Study
European Journal Of Preventive Cardiology. 2023-01-18. DOI : 10.1093/eurjpc/zwad012.Multivalent Virucidal Antivirals: Synthesis, Mechanisms of Action, and Immune-stimulating Effects
Lausanne, EPFL, 2023. DOI : 10.5075/epfl-thesis-10366.Genetic features and genomic targets of human KRAB-zinc finger proteins
Genome Research. 2023. DOI : 10.1101/gr.277722.123.Host-Pathogen Interactions Through the Genomic Lens
Lausanne, EPFL, 2023. DOI : 10.5075/epfl-thesis-10351.Visual masking deficits in schizophrenia: a view into the genetics of the disease through an endophenotype
Translational Psychiatry. 2022-12-31. DOI : 10.1038/s41398-022-02275-4.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
Arthritis & Rheumatology. 2022-11-02. DOI : 10.1002/art.42265.The combined impact of persistent infections and human genetic variation on C-reactive protein levels
Bmc Medicine. 2022-11-01. DOI : 10.1186/s12916-022-02607-7.A mitochondria-specific mutational signature of aging: increased rate of A > G substitutions on the heavy strand
Nucleic Acids Research. 2022-09-21. DOI : 10.1093/nar/gkac779.Polygenic Risk Scores for Prediction of Subclinical Coronary Artery Disease in Persons Living With HIV: The Swiss HIV Cohort Study
Clinical Infectious Diseases. 2022-09-13. DOI : 10.1093/cid/ciac758.A Phylogeny-aware GWAS Framework to Correct for Heritable Pathogen Effects on Infectious Disease Traits
Molecular Biology And Evolution. 2022-08-03. DOI : 10.1093/molbev/msac163.A Baseline Cellular Antiviral State Is Maintained by cGAS and Its Most Frequent Naturally Occurring Variant rs610913
Journal Of Immunology. 2022-08-01. DOI : 10.4049/jimmunol.2100685.Improving polygenic prediction with genetically inferred ancestry
Human Genetics And Genomics Advances. 2022-07-14. DOI : 10.1016/j.xhgg.2022.100109.Host genomics of SARS-CoV-2 infection
European Journal Of Human Genetics. 2022-06-30. DOI : 10.1038/s41431-022-01136-4.The risk of COVID-19 death is much greater and age dependent with type I IFN autoantibodies
Proceedings Of The National Academy Of Sciences Of The United States Of America. 2022-05-24. DOI : 10.1073/pnas.2200413119.Identifying and Characterizing Trans Women in the Swiss HIV Cohort Study as an Epidemiologically Distinct Risk Group (vol 74, pg 1468, 2022)
Clinical Infectious Diseases. 2022-04-27. DOI : 10.1093/cid/ciac242.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
Frontiers In Medicine. 2022-04-15. DOI : 10.3389/fmed.2022.821776.Phylogenetic estimation of the viral fitness landscape of HIV-1 set-point viral load
Virus Evolution. 2022-04-07. DOI : 10.1093/ve/veac022.A polygenic risk score to predict sudden cardiac arrest in patients with cardiovascular disease
2022-04-01. 50th European Mathematical Genetics Meeting (EMGM), Univ Cambridge, MRC Biostatist Unit, Cambridge, ENGLAND, April 21-22, 2022. p. 28-28.Risk of mitochondrial deletions is affected by the global secondary structure of the mitochondrial genome
2022-04-01. p. 438-439.Increased CHIP prevalence amongst people living with HIV
2022-04-01. p. 75-75.A billion-year trend of amino acid substitutions in the mitochondrial genome
2022-04-01. p. 535-535.Mitochondrial mutational spectrum in human cancers is sensitive to cellular hypoxia
2022-04-01. p. 413-414.A highly virulent variant of HIV-1 circulating in the Netherlands
Science. 2022-02-04. DOI : 10.1126/science.abk1688.Increased prevalence of clonal hematopoiesis of indeterminate potential amongst people living with HIV
Scientific Reports. 2022-01-12. DOI : 10.1038/s41598-021-04308-2.Using population-specific add-on polymorphisms to improve genotype imputation in underrepresented populations
Plos Computational Biology. 2022-01-01. DOI : 10.1371/journal.pcbi.1009628.The interplay between human genetic variation, chronic inflammation and persistent infection: relevance for cardiovascular morbidity
Lausanne, EPFL, 2022. DOI : 10.5075/epfl-thesis-9518.Identifying and Characterizing Trans Women in the Swiss HIV Cohort Study as an Epidemiologically Distinct Risk Group
Clinical Infectious Diseases. 2022. DOI : 10.1093/cid/ciab628.A global effort to dissect the human genetic basis of resistance to SARS-CoV-2 infection
Nature Immunology. 2022. DOI : 10.1038/s41590-021-01030-z.Telomere Length Declines in Persons With Human Immunodeficiency Virus Before Antiretroviral Therapy Start but Not After Viral Suppression: A Longitudinal Study Over >17 Years
Journal Of Infectious Diseases. 2021-12-16. DOI : 10.1093/infdis/jiab603.Human genomics of the humoral immune response against polyomaviruses
Virus Evolution. 2021-12-01. DOI : 10.1093/ve/veab058.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
Clinical Infectious Diseases. 2021-11-01. DOI : 10.1093/cid/ciab521.Viral genome wide association study identifies novel hepatitis C virus polymorphisms associated with sofosbuvir treatment failure
Nature Communications. 2021-10-20. DOI : 10.1038/s41467-021-25649-6.Truly privacy-preserving federated analytics for precision medicine with multiparty homomorphic encryption
Nature Communications. 2021-10-11. DOI : 10.1038/s41467-021-25972-y.A high-resolution HLA reference panel capturing global population diversity enables multi-ancestry fine-mapping in HIV host response
Nature Genetics. 2021-10-01. DOI : 10.1038/s41588-021-00935-7.Immunological lessons from genome-wide association studies of infections
Current Opinion In Immunology. 2021-10-01. DOI : 10.1016/j.coi.2021.03.017.Autoantibodies neutralizing type I IFNs are present in similar to 4% of uninfected individuals over 70 years old and account for similar to 20% of COVID-19 deaths
Science Immunology. 2021-08-01. DOI : 10.1126/sciimmunol.abl4340.Genetic variation near CXCL12 is associated with susceptibility to HIV-related non-Hodgkin lymphoma
Haematologica. 2021-08-01. DOI : 10.3324/haematol.2020.247023.HIV-1 and human genetic variation
Nature Reviews Genetics. 2021-06-24. DOI : 10.1038/s41576-021-00378-0.Rapid Progression of Kidney Dysfunction in People Living With HIV: Use of Polygenic and Data Collection on Adverse Events of Anti-HIV Drugs (D:A:D) Risk Scores
Journal Of Infectious Diseases. 2021-06-15. DOI : 10.1093/infdis/jiaa695.Systematic screening of viral and human genetic variation identifies antiretroviral resistance and immune escape link
Elife. 2021-06-01. DOI : 10.7554/eLife.67388.Revolutionizing Medical Data Sharing Using Advanced Privacy-Enhancing Technologies: Technical, Legal, and Ethical Synthesis
Journal Of Medical Internet Research. 2021-02-25. DOI : 10.2196/25120.The influence of human genetic variation on Epstein–Barr virus sequence diversity
Scientific Reports. 2021-02-25. DOI : 10.1038/s41598-021-84070-7.Blood virosphere in febrile Tanzanian children
Emerging Microbes & Infections. 2021-01-01. DOI : 10.1080/22221751.2021.1925161.The genetic architecture of complex human traits at the dawn of genomic medicine
Lausanne, 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 vesicles
Journal Of Extracellular Vesicles. 2021-01-01. DOI : 10.1002/jev2.12046.On the use of applied machine learning and digital infrastructure to leverage social media data in health and epidemiology
Lausanne, EPFL, 2021. DOI : 10.5075/epfl-thesis-8283.Genome-to-genome analysis identifies an Asian-specific variant in the gene encoding NTCP that leads to specific HBV escape mutations during chronic infection
2020-12-01. p. 316-317.Human genomics of the humoral response against polyomaviruses
2020-12-01. p. 312-313.An indel in the promoter region of NFKB1 confers protection against infection but increases risk of allergy
2020-12-01. p. 311-312.Using reference-fixed principal components to improve polygenic risk score prediction
2020-12-01. p. 134-135.Host Genomics of the HIV-1 Reservoir Size and Its Decay Rate During Suppressive Antiretroviral Treatment
Jaids-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 Study
Clinical Infectious Diseases. 2020-11-15. DOI : 10.1093/cid/ciaa290.HLA tapasin independence: broader peptide repertoire and HIV control
Proceedings 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 ART
Nature Communications. 2020-11-02. DOI : 10.1038/s41467-020-19198-7.Virosaurus A Reference to Explore and Capture Virus Genetic Diversity
Viruses-Basel. 2020-11-01. DOI : 10.3390/v12111248.Inborn errors of type I IFN immunity in patients with life-threatening COVID-19
Science. 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 Imputation
2020-07-01. 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 genetics
Human Genetics. 2020-06-01. DOI : 10.1007/s00439-019-02109-2.Exploring the interactions between the human and viral genomes
Human Genetics. 2020-06-01. DOI : 10.1007/s00439-019-02089-3.Assessing the impact of non-pharmaceutical interventions on SARS-CoV-2 transmission in Switzerland
Swiss Medical Weekly. 2020-05-30. DOI : 10.4414/smw.20295.HLA Heterozygote Advantage against HIV-1 Is Driven by Quantitative and Qualitative Differences in HLA Allele-Specific Peptide Presentation
Molecular 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 Rate
Clinical Infectious Diseases. 2020-03-01. DOI : 10.1093/cid/ciz280.SPHN/PHRT - MedCo in Action: Empowering the Swiss Molecular Tumor Board with Privacy-Preserving and Real-Time Patient Discovery
2020-01-01. 30th Medical Informatics Europe (MIE) Conference, Geneva, SWITZERLAND, Apr, 2020. p. 1161-1162. DOI : 10.3233/SHTI200345.GenoShare: Supporting Privacy-Informed Decisions for Sharing Individual-Level Genetic Data
2020-01-01. 30th Medical Informatics Europe (MIE) Conference, Geneva, SWITZERLAND, Apr, 2020. p. 238-241. DOI : 10.3233/SHTI200158.Data protection and ethics requirements for multisite research with health data: a comparative examination of legislative governance frameworks and the role of data protection technologies
Journal Of Law And The Biosciences. 2020-01-01. DOI : 10.1093/jlb/lsaa010.Contact networks across ages: computational analysis of epidemiological dynamics
Lausanne, 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 Therapy
Open Forum Infectious Diseases. 2020-01-01. DOI : 10.1093/ofid/ofz464.COVID-19 epidemic in Switzerland: on the importance of testing, contact tracing and isolation
Swiss Medical Weekly. 2020-03-19. DOI : 10.4414/smw.2020.20225.HIV host genomics in the era of effective antiretroviral therapy
Lausanne, EPFL, 2020. DOI : 10.5075/epfl-thesis-10132.Teaching & PhD
PhD Students
Lisa Mathilde Julia Fournier, Valeriia Timonina, Chaimae El Houjjaji, Mariam Ait Oumelloul, Simon Tang, Emmanuelle Marie Mohbat, Miranda Linnéa Carlsson
Past EPFL PhD Students
Samira Asgari, Petar Scepanovic, Christian Axel Wandall Thorball, Olivier Naret, Flavia Aurelia Hodel, Zhi Ming Xu, Ali Saadat Varnosfaderanii
Past EPFL PhD Students as codirector
Courses
Genomic solutions to sustainable development
BIO-312
The course explores how genomic technologies can contribute to achieving the UN Sustainable Development Goals. Students will learn how genomics impacts healthcare, agriculture, energy, and environmental conservation through lectures, case studies, and practical projects.
New tools & research strategies in personalized health
BIO-491
This course introduces the concept of personalized health, exploring its foundational technologies as well as the technological, legal, and ethical challenges the field currently faces. Strategies and approaches used to address these challenges will also be discussed.