Fields of expertise
MissionHuman 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.
BiographyJacques 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.
Africa-specific human genetic variation near CHD1L associates with HIV-1 loadNature. 2023-08-02. DOI : 10.1038/s41586-023-06370-4.
Variation in African genomes linked to control of HIVNature. 2023-08-02. DOI : 10.1038/d41586-023-02277-2.
Autoantibodies neutralizing type I IFNs underlie West Nile virus encephalitis in & SIM;40% of patientsJournal 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 ICGHJci 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 StudyJournal Of Infectious Diseases. 2023-05-24. DOI : 10.1093/infdis/jiad179.
Secondary structure of the human mitochondrial genome affects formation of deletionsBmc Biology. 2023-05-08. DOI : 10.1186/s12915-023-01606-1.
Epigenetic ageing accelerates before antiretroviral therapy and decelerates after viral suppression in people with HIV in Switzerland: a longitudinal study over 17 yearsLancet 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-19Genome 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, TanzaniaPlos Pathogens. 2023-04-01. DOI : 10.1371/journal.ppat.1010893.
Associations of genetic and infectious risk factors with coronary heart diseaseElife. 2023-02-14. DOI : 10.7554/eLife.79742.
Leukocyte Count and Coronary Artery Disease Events in People With Human Immunodeficiency Virus: A Longitudinal StudyClinical 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 StudyEuropean Journal Of Preventive Cardiology. 2023-01-18. DOI : 10.1093/eurjpc/zwad012.
Host-Pathogen Interactions Through the Genomic LensLausanne, EPFL, 2023. DOI : 10.5075/epfl-thesis-10351.
Visual masking deficits in schizophrenia: a view into the genetics of the disease through an endophenotypeTranslational 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 LocusArthritis & Rheumatology. 2022-11-02. DOI : 10.1002/art.42265.
The combined impact of persistent infections and human genetic variation on C-reactive protein levelsBmc 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 strandNucleic 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 StudyClinical Infectious Diseases. 2022-09-13. DOI : 10.1093/cid/ciac758.
A Phylogeny-aware GWAS Framework to Correct for Heritable Pathogen Effects on Infectious Disease TraitsMolecular 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 rs610913Journal Of Immunology. 2022-08-01. DOI : 10.4049/jimmunol.2100685.
Improving polygenic prediction with genetically inferred ancestryHuman Genetics And Genomics Advances. 2022-07-14. DOI : 10.1016/j.xhgg.2022.100109.
Host genomics of SARS-CoV-2 infectionEuropean 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 autoantibodiesProceedings 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 DiagnosisFrontiers In Medicine. 2022-04-15. DOI : 10.3389/fmed.2022.821776.
Phylogenetic estimation of the viral fitness landscape of HIV-1 set-point viral loadVirus Evolution. 2022-04-07. DOI : 10.1093/ve/veac022.
A polygenic risk score to predict sudden cardiac arrest in patients with cardiovascular disease2022-04-01. p. 28-28.
Risk of mitochondrial deletions is affected by the global secondary structure of the mitochondrial genome2022-04-01. p. 438-439.
Increased CHIP prevalence amongst people living with HIV2022-04-01. p. 75-75.
A billion-year trend of amino acid substitutions in the mitochondrial genome2022-04-01. p. 535-535.
Mitochondrial mutational spectrum in human cancers is sensitive to cellular hypoxia2022-04-01. p. 413-414.
A highly virulent variant of HIV-1 circulating in the NetherlandsScience. 2022-02-04. DOI : 10.1126/science.abk1688.
Increased prevalence of clonal hematopoiesis of indeterminate potential amongst people living with HIVScientific Reports. 2022-01-12. DOI : 10.1038/s41598-021-04308-2.
The interplay between human genetic variation, chronic inflammation and persistent infection: relevance for cardiovascular morbidityLausanne, EPFL, 2022. DOI : 10.5075/epfl-thesis-9518.
Identifying and Characterizing Trans Women in the Swiss HIV Cohort Study as an Epidemiologically Distinct Risk GroupClinical Infectious Diseases. 2022. DOI : 10.1093/cid/ciab628.
A global effort to dissect the human genetic basis of resistance to SARS-CoV-2 infectionNature 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 YearsJournal Of Infectious Diseases. 2021-12-16. DOI : 10.1093/infdis/jiab603.
Human genomics of the humoral immune response against polyomavirusesVirus 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 StudyClinical 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 failureNature Communications. 2021-10-20. DOI : 10.1038/s41467-021-25649-6.
Truly privacy-preserving federated analytics for precision medicine with multiparty homomorphic encryptionNature 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 responseNature Genetics. 2021-10-01. DOI : 10.1038/s41588-021-00935-7.
Immunological lessons from genome-wide association studies of infectionsCurrent 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 deathsScience Immunology. 2021-08-01. DOI : 10.1126/sciimmunol.abl4340.
Genetic variation near CXCL12 is associated with susceptibility to HIV-related non-Hodgkin lymphomaHaematologica. 2021-08-01. DOI : 10.3324/haematol.2020.247023.
HIV-1 and human genetic variationNature 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 ScoresJournal 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 linkElife. 2021-06-01. DOI : 10.7554/eLife.67388.
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.
Blood virosphere in febrile Tanzanian childrenEmerging Microbes & Infections. 2021-01-01. DOI : 10.1080/22221751.2021.1925161.
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.
On the use of applied machine learning and digital infrastructure to leverage social media data in health and epidemiologyLausanne, 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 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.
SPHN/PHRT - MedCo in Action: Empowering the Swiss Molecular Tumor Board with Privacy-Preserving and Real-Time Patient Discovery2020-01-01. 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 Data2020-01-01. 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 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.
Teaching & PhD
Life Sciences Engineering