Journal Articles

Africa-specific human genetic variation near CHD1L associates with HIV-1 load

P. J. J. McLaren; I. Porreca; G. Iaconis; H. P. Mok; S. Mukhopadhyay et al. 

Nature. 2023-08-02. DOI : 10.1038/s41586-023-06370-4.

Variation in African genomes linked to control of HIV

P. J. McLaren; J. Fellay 

Nature. 2023-08-02. DOI : 10.1038/d41586-023-02277-2.

A metagenome-wide association study of HIV disease progression in HIV controllers

L. M. Real; M. E. Saez; A. Corma-Gomez; A. Gonzalez-Perez; C. Thorball et al. 

Iscience. 2023-07-21. Vol. 26, num. 7, p. 107214. DOI : 10.1016/j.isci.2023.107214.

Prevalence of CFTR variants in primary immunodeficiency patients with bronchiectasis is an important modifying cofactor

D. Lawless; H. L. Allen; J. E. D. Thaventhiran; S. Goddard; O. S. Burren et al. 

Journal Of Allergy And Clinical Immunology. 2023-07-01. Vol. 152, num. 1, p. 257-265. DOI : 10.1016/j.jaci.2023.01.035.

Autoantibodies neutralizing type I IFNs underlie West Nile virus encephalitis in & SIM;40% of patients

A. Gervais; F. Rovida; M. A. Avanzini; S. Croce; A. Marchal et al. 

Journal Of Experimental Medicine. 2023-06-22. Vol. 220, num. 9, p. e20230661. DOI : 10.1084/jem.20230661.

Multiancestry sex-stratified genomic associations with HIV viral load and controller status from the ICGH

C. Vergara; J. F. Tuff; J. Int Collaboration Genomics HIV ICGH; J. Fellay; P. Duggal et al. 

Jci Insight. 2023-06-08. Vol. 8, num. 11, p. 170068. DOI : 10.1172/jci.insight.170068.

Association of a Polygenic Risk Score With Osteoporosis in People Living With HIV: The Swiss HIV Cohort Study

J. M. Schwenke; C. W. Thorball; I. C. Schoepf; L. Ryom; B. Hasse et al. 

Journal Of Infectious Diseases. 2023-05-24. DOI : 10.1093/infdis/jiad179.

Secondary structure of the human mitochondrial genome affects formation of deletions

V. Shamanskiy; A. A. Mikhailova; E. O. Tretiakov; K. Ushakova; A. G. Mikhailova et al. 

Bmc Biology. 2023-05-08. Vol. 21, num. 1, p. 103. DOI : 10.1186/s12915-023-01606-1.

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

D. Lawless; C. G. McKennan; S. R. Das; T. Junier; Z. M. Xu et al. 

Journal Of Infectious Diseases. 2023-05-01. Vol. 227, num. 10, p. 1194-1202. 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

I. C. Schoepf; A. Esteban-Cantos; C. W. Thorball; B. Rodes; P. Reiss et al. 

Lancet Healthy Longevity. 2023-05-01. Vol. 4, num. 5, p. E211-E218. 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

D. Matuozzo; E. Talouarn; A. Marchal; P. Zhang; J. Manry et al. 

Genome Medicine. 2023-04-05. Vol. 15, num. 1, p. 22. 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

M. Zwyer; L. Rutaihwa; E. Windels; J. Hella; F. Menardo et al. 

Plos Pathogens. 2023-04-01. Vol. 19, num. 4, p. e1010893. DOI : 10.1371/journal.ppat.1010893.

Live Birth of a Healthy Child in a Couple with Identical mtDNA Carrying a Pathogenic c.471_477delTTTAAAAinsG Variant in the MOCS2 Gene

M. Tofilo; N. Voronova; L. Nigmatullina; E. Kuznetsova; V. Timonina et al. 

Genes. 2023-03-01. Vol. 14, num. 3, p. 720. DOI : 10.3390/genes14030720.

Associations of genetic and infectious risk factors with coronary heart disease

F. Hodel; Z. M. Xu; C. W. Thorball; R. de la Harpe; P. Letang-Mathieu et al. 

Elife. 2023-02-14. Vol. 12, p. e79742. DOI : 10.7554/eLife.79742.

Leukocyte Count and Coronary Artery Disease Events in People With Human Immunodeficiency Virus: A Longitudinal Study

E. F. Avery; J. N. Kleynhans; B. Ledergerber; I. C. Schoepf; C. W. Thorball et al. 

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

R. de La Harpe; C. W. Thorball; C. Redin; S. Fournier; O. Mueller et al. 

European Journal Of Preventive Cardiology. 2023-01-18. DOI : 10.1093/eurjpc/zwad012.

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

J. de Tribolet-Hardy; C. W. Thorball; R. Forey; E. Planet; J. Duc et al. 

Genome Research. 2023. DOI : 10.1101/gr.277722.123.


Host-Pathogen Interactions Through the Genomic Lens

Z. M. Xu / J. Fellay (Dir.)  

Lausanne, EPFL, 2023. 


Journal Articles

Visual masking deficits in schizophrenia: a view into the genetics of the disease through an endophenotype

A. Shaqiri; F. Hodel; J. R. da Cruz; M. Roinishvili; E. Chkonia et al. 

Translational Psychiatry. 2022-12-31. Vol. 12, num. 1, p. 1-10, 529. 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

D. Trutschel; P. Bost; X. Mariette; V. Bondet; A. Llibre et al. 

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

F. Hodel; O. Naret; C. Bonnet; N. Brenner; N. Bender et al. 

Bmc Medicine. 2022-11-01. Vol. 20, num. 1, p. 416. DOI : 10.1186/s12916-022-02607-7.

A mitochondria-specific mutational signature of aging: increased rate of A > G substitutions on the heavy strand

A. G. Mikhailova; A. A. Mikhailova; K. Ushakova; E. O. Tretiakov; D. Iliushchenko et al. 

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

I. C. Schoepf; C. W. Thorball; H. Kovari; B. Ledergerber; R. R. Buechel et al. 

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

S. Nadeau; C. W. Thorball; R. Kouyos; H. F. Guenthard; J. Boeni et al. 

Molecular Biology And Evolution. 2022-08-03. Vol. 39, num. 8, p. msac163. DOI : 10.1093/molbev/msac163.

A Baseline Cellular Antiviral State Is Maintained by cGAS and Its Most Frequent Naturally Occurring Variant rs610913

J. Kazmierski; C. Elsner; K. Doehner; S. Xu; A. Ducroux et al. 

Journal Of Immunology. 2022-08-01. Vol. 209, num. 3, p. 535-547. DOI : 10.4049/jimmunol.2100685.

Dynamics of the most common pathogenic mtDNA variant m.3243A > G demonstrate frequency-dependency in blood and positive selection in the germline

M. Franco; S. J. Pickett; Z. Fleischmann; M. Khrapko; A. Cote-L’Heureux et al. 

Human Molecular Genetics. 2022-07-15. DOI : 10.1093/hmg/ddac149.

Improving polygenic prediction with genetically inferred ancestry

O. Naret; Z. Kutalik; F. Hodel; Z. M. Xu; P. Marques-Vidal et al. 

Human Genetics And Genomics Advances. 2022-07-14. Vol. 3, num. 3, p. 100109. DOI : 10.1016/j.xhgg.2022.100109.

The risk of COVID-19 death is much greater and age dependent with type I IFN autoantibodies

J. Manry; P. Bastard; A. Gervais; T. Le Voyer; J. Rosain et al. 

Proceedings Of The National Academy Of Sciences Of The United States Of America. 2022-05-24. Vol. 119, num. 21, p. e2200413119. DOI : 10.1073/pnas.2200413119.

Mitochondrial Pseudogenes Suggest Repeated Inter-Species Hybridization among Direct Human Ancestors

K. Popadin; K. Gunbin; L. Peshkin; S. Annis; Z. Fleischmann et al. 

Genes. 2022-05-01. Vol. 13, num. 5, p. 810. DOI : 10.3390/genes13050810.

Autoantibodies against type I IFNs in patients with Ph-negative myeloproliferative neoplasms

O. Borsani; P. Bastard; J. Rosain; A. Gervais; E. Sant’Antonio et al. 

Blood. 2022-04-28. Vol. 139, num. 17, p. 2716-2720. DOI : 10.1182/blood.2021014890.

Identifying and Characterizing Trans Women in the Swiss HIV Cohort Study as an Epidemiologically Distinct Risk Group (vol 74, pg 1468, 2022)

H. Nguyen; B. Hampel; D. G. Nunez; M. Battegay; A. Hachfeld et al. 

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

H. Hiza; J. Hella; A. Arbues; M. Sasamalo; V. Misana et al. 

Frontiers In Medicine. 2022-04-15. Vol. 9, p. 821776. DOI : 10.3389/fmed.2022.821776.

Phylogenetic estimation of the viral fitness landscape of HIV-1 set-point viral load

L. Zhao; C. Wymant; F. Blanquart; T. Golubchik; A. Gall et al. 

Virus Evolution. 2022-04-07. Vol. 8, num. 1, p. veac022. DOI : 10.1093/ve/veac022.

Incomplete Recovery of Zebrafish Retina Following Cryoinjury

D. Dzulova; D. Lawless; G. G. Pinton; N. A. Renner; D. F. Schorderet 

Cells. 2022-04-01. Vol. 11, num. 8, p. 1373. DOI : 10.3390/cells11081373.

A highly virulent variant of HIV-1 circulating in the Netherlands

C. Wymant; D. Bezemer; F. Blanquart; L. Ferretti; A. Gall et al. 

Science. 2022-02-04. Vol. 375, num. 6580, p. 540-545. DOI : 10.1126/science.abk1688.

Increased prevalence of clonal hematopoiesis of indeterminate potential amongst people living with HIV

A. G. Bick; K. Popadin; C. W. Thorball; M. M. Uddin; M. Zanni et al. 

Scientific Reports. 2022-01-12. Vol. 12, num. 1, p. 577. DOI : 10.1038/s41598-021-04308-2.

Identifying and Characterizing Trans Women in the Swiss HIV Cohort Study as an Epidemiologically Distinct Risk Group

Huyen Nguyen; B. Hampel; D. G. Nunez; M. Battegay; A. Hachfeld et al. 

Clinical Infectious Diseases. 2022. Vol. 74, num. 8, p. 1468–1475. DOI : 10.1093/cid/ciab628.

PUS3-related disorder: Report of a novel patient and delineation of the phenotypic spectrum

A. Borghesi; M. Plumari; E. Rossi; C. Vigano; R. M. Cerbo et al. 

American Journal Of Medical Genetics Part A. 2022. Vol. 188, num. 2, p. 635-641. DOI : 10.1002/ajmg.a.62547.

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

E. Andreakos; L. Abel; D. C. Vinh; E. Kaja; B. A. Drolet et al. 

Nature Immunology. 2022. Vol. 23, p. 159–164. DOI : 10.1038/s41590-021-01030-z.

Conference Papers

A polygenic risk score to predict sudden cardiac arrest in patients with cardiovascular disease

E. Porcu; C. Thorball; A. P. Porretta; E. Pruvot; K. Wiskott et al. 

2022-04-01.  p. 28-28.

Risk of mitochondrial deletions is affected by the global secondary structure of the mitochondrial genome

V. Shamanskiy; A. A. Mikhailova; K. Ushakova; A. G. Mikhailova; S. Oreshkov et al. 

2022-04-01.  p. 438-439.

Increased CHIP prevalence amongst people living with HIV

K. Popadin; A. G. Bick; C. W. Thorball; M. M. Uddin; M. Zanni et al. 

2022-04-01.  p. 75-75.

A billion-year trend of amino acid substitutions in the mitochondrial genome

A. A. Mikhailova; A. G. Mikhailova; V. Shamanskiy; K. Ushakova; A. Galieva et al. 

2022-04-01.  p. 535-535.

Mitochondrial mutational spectrum in human cancers is sensitive to cellular hypoxia

A. G. Mikhailova; P. Lisitsa; A. A. Mikhailova; K. Ushakova; E. Tretiakov et al. 

2022-04-01.  p. 413-414.


How to: Diagnose inborn errors of intrinsic and innate immunity to viral, bacterial, mycobacterial, and fungal infections

F. Conti; M. Moratti; M. Giannella; S. Ferrari; A. Borghesi 

Clinical Microbiology And Infection. 2022-11-01. Vol. 28, num. 11, p. 1441-1448. DOI : 10.1016/j.cmi.2022.07.021.

Host genomics of SARS-CoV-2 infection

C. Redin; C. W. Thorball; J. Fellay 

European Journal Of Human Genetics. 2022-06-30. Vol. 30, p. 908–914. DOI : 10.1038/s41431-022-01136-4.

Neonatal Manifestations of Chronic Granulomatous Disease: MAS/HLH and Necrotizing Pneumonia as Unusual Phenotypes and Review of the Literature

A. Marzollo; F. Conti; L. Rossini; B. Rivalta; L. Leonardi et al. 

Journal Of Clinical Immunology. 2022. Vol. 42, p. 299–311. DOI : 10.1007/s10875-021-01159-4.


The interplay between human genetic variation, chronic inflammation and persistent infection: relevance for cardiovascular morbidity

F. A. S. Hodel / J. Fellay (Dir.)  

Lausanne, EPFL, 2022. 


Journal Articles

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

I. C. Schoepf; C. W. Thorball; B. Ledergerber; N. A. Kootstra; P. Reiss et al. 

Journal Of Infectious Diseases. 2021-12-16. Vol. 225, num. 9, p. 1581-1591. DOI : 10.1093/infdis/jiab603.

Biallelic mutations in calcium release activated channel regulator 2A (CRACR2A) cause a primary immunodeficiency disorder

B. Wu; L. Rice; J. Shrimpton; D. Lawless; K. Walker et al. 

Elife. 2021-12-15. Vol. 10, p. e72559. DOI : 10.7554/eLife.72559.

Human genomics of the humoral immune response against polyomaviruses

F. Hodel; A. Y. Chong; P. Scepanovic; Z. M. Xu; O. Naret et al. 

Virus Evolution. 2021-12-01. Vol. 7, num. 2, p. veab058. 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

I. C. Schoepf; C. W. Thorball; B. Ledergerber; T. Engel; M. Raffenberg et al. 

Clinical Infectious Diseases. 2021-11-01. Vol. 73, num. 9, p. 1597-1604. DOI : 10.1093/cid/ciab521.

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

D. A. Smith; A. Magri; R. Bowden; N. Chaturvedi; J. Fellay et al. 

Nature Communications. 2021-10-20. Vol. 12, num. 1, p. 6105. DOI : 10.1038/s41467-021-25649-6.

Truly privacy-preserving federated analytics for precision medicine with multiparty homomorphic encryption

D. Froelicher; J. R. Troncoso-Pastoriza; J. L. Raisaro; M. A. Cuendet; J. S. Sousa et al. 

Nature Communications. 2021-10-11. Vol. 12, num. 1, p. 5910. 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

Y. Luo; M. Kanai; W. Choi; X. Li; S. Sakaue et al. 

Nature Genetics. 2021-10-01. Vol. 53, num. 10, p. 1504-1516. DOI : 10.1038/s41588-021-00935-7.

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

P. Bastard; A. Gervais; T. Le Voyer; J. Rosain; Q. Philippot et al. 

Science Immunology. 2021-08-01. Vol. 6, num. 62, p. eabl4340. DOI : 10.1126/sciimmunol.abl4340.

Genetic variation near CXCL12 is associated with susceptibility to HIV-related non-Hodgkin lymphoma

C. W. Thorball; T. Oudot-Mellakh; N. Ehsan; C. Hammer; F. A. Santoni et al. 

Haematologica. 2021-08-01. Vol. 106, num. 8, p. 2233-2241. DOI : 10.3324/haematol.2020.247023.

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

L. G. Dietrich; C. W. Thorball; L. Ryom; F. Burkhalter; B. Hasse et al. 

Journal Of Infectious Diseases. 2021-06-15. Vol. 223, num. 12, p. 2145-2153. DOI : 10.1093/infdis/jiaa695.

Systematic screening of viral and human genetic variation identifies antiretroviral resistance and immune escape link

H. Nguyen; C. W. Thorball; J. Fellay; J. Boni; S. Yerly et al. 

Elife. 2021-06-01. Vol. 10, p. e67388. DOI : 10.7554/eLife.67388.

Neonatal-Onset Familial Mediterranean Fever in an Infant with Human Parainfluenza Virus-4 Infection

A. Michev; A. Borghesi; C. Tretti; M. Martella; A. Di Comite et al. 

Neonatology. 2021-03-31. Vol. 118, num. 3, p. 359–363. DOI : 10.1159/000514694.

Revolutionizing Medical Data Sharing Using Advanced Privacy-Enhancing Technologies: Technical, Legal, and Ethical Synthesis

J. Scheibner; J. R. Troncoso-Pastoriza; M. Ienca; J. Fellay; E. Vayena et al. 

Journal Of Medical Internet Research. 2021-02-25. Vol. 23, num. 2, p. e25120. DOI : 10.2196/25120.

The influence of human genetic variation on Epstein–Barr virus sequence diversity

S. Rüeger; C. Hammer; A. Loetscher; P. J. McLaren; D. Lawless et al. 

Scientific Reports. 2021-02-25. Vol. 11, num. 1, p. 4586. DOI : 10.1038/s41598-021-84070-7.

Blood virosphere in febrile Tanzanian children

S. Cordey; F. Laubscher; M-A. Hartley; T. Junier; K. Keitel et al. 

Emerging Microbes & Infections. 2021-01-01. Vol. 10, num. 1, p. 982-993. DOI : 10.1080/22221751.2021.1925161.

Dissemination of Mycobacterium tuberculosis is associated to a SIGLEC1 null variant that limits antigen exchange via trafficking extracellular vesicles

S. Benet; C. Galvez; F. Drobniewski; I. Kontsevaya; L. Arias et al. 

Journal Of Extracellular Vesicles. 2021-01-01. Vol. 10, num. 3, p. e12046. DOI : 10.1002/jev2.12046.


Immunological lessons from genome-wide association studies of infections

C. W. Thorball; J. Fellay; A. Borghesi 

Current Opinion In Immunology. 2021-10-01. Vol. 72, p. 119-125. DOI : 10.1016/j.coi.2021.03.017.

HIV-1 and human genetic variation

P. J. McLaren; J. Fellay 

Nature Reviews Genetics. 2021-06-24. Vol. 22, p. 645–657. DOI : 10.1038/s41576-021-00378-0.


The genetic architecture of complex human traits at the dawn of genomic medicine

O. N. M. Naret / J. Fellay (Dir.)  

Lausanne, EPFL, 2021. 


Journal Articles

Host Genomics of the HIV-1 Reservoir Size and Its Decay Rate During Suppressive Antiretroviral Treatment

C. W. Thorball; A. Borghesi; N. Bachmann; C. Von Siebenthal; V. Vongrad et al. 

Jaids-Journal Of Acquired Immune Deficiency Syndromes. 2020-12-01. Vol. 85, num. 4, p. 517-524. 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

A. Borghesi; J. Trueck; S. Asgari; V. Sancho-Shimizu; P. K. A. Agyeman et al. 

Clinical Infectious Diseases. 2020-11-15. Vol. 71, num. 10, p. E614-E623. DOI : 10.1093/cid/ciaa290.

HLA tapasin independence: broader peptide repertoire and HIV control

A. A. Bashirova; M. Viard; V. Naranbhai; A. Grifoni; W. Garcia-Beltran et al. 

Proceedings Of The National Academy Of Sciences Of The United States Of America. 2020-11-10. Vol. 117, num. 45, p. 28232-28238. DOI : 10.1073/pnas.2013554117.

Heritability of the HIV-1 reservoir size and decay under long-term suppressive ART

C. Wan; N. Bachmann; V. Mitov; F. Blanquart; S. P. Cespedes et al. 

Nature Communications. 2020-11-02. Vol. 11, num. 1, p. 5542. DOI : 10.1038/s41467-020-19198-7.

Virosaurus A Reference to Explore and Capture Virus Genetic Diversity

A. Gleizes; F. Laubscher; N. Guex; C. Iseli; T. Junier et al. 

Viruses-Basel. 2020-11-01. Vol. 12, num. 11, p. 1248. DOI : 10.3390/v12111248.

Inborn errors of type I IFN immunity in patients with life-threatening COVID-19

Q. Zhang; P. Bastard; Z. Liu; J. Le Pen; M. Moncada-Velez et al. 

Science. 2020-10-23. Vol. 370, num. 6515, p. 422. DOI : 10.1126/science.abd4570.

Polygenic modelling of treatment effect heterogeneity

Z. M. Xu; S. Burgess 

Genetic Epidemiology. 2020-08-10. Vol. 44, num. 8, p. 868-879. DOI : 10.1002/gepi.22347.

Assessing the impact of non-pharmaceutical interventions on SARS-CoV-2 transmission in Switzerland

J. C. Lemaitre; F. J. Perez-Saez; A. S. Azman; A. Rinaldo; J. Fellay 

Swiss Medical Weekly. 2020-05-30. Vol. 150, p. w20295. DOI : 10.4414/smw.20295.

HLA Heterozygote Advantage against HIV-1 Is Driven by Quantitative and Qualitative Differences in HLA Allele-Specific Peptide Presentation

J. Arora; F. Pierini; P. J. McLaren; M. Carrington; J. Fellay et al. 

Molecular Biology And Evolution. 2020-03-01. Vol. 37, num. 3, p. 639-650. 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

L. G. Dietrich; C. Barcelo; C. W. Thorball; L. Ryom; F. Burkhalter et al. 

Clinical Infectious Diseases. 2020-03-01. Vol. 70, num. 5, p. 890-897. 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 technologies

J. Scheibner; M. Ienca; S. Kechagia; J. R. Troncoso-Pastoriza; J. L. Raisaro et al. 

Journal Of Law And The Biosciences. 2020-01-01. Vol. 7, num. 1, p. lsaa010. DOI : 10.1093/jlb/lsaa010.

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

C. Barcelo; M. Guidi; C. W. Thorball; C. Hammer; A. Chaouch et al. 

Open Forum Infectious Diseases. 2020-01-01. Vol. 7, num. 1, p. ofz464. DOI : 10.1093/ofid/ofz464.

Conference Papers

Genome-to-genome analysis identifies an Asian-specific variant in the gene encoding NTCP that leads to specific HBV escape mutations during chronic infection

Z. Xu; S. Rueger; P. Shea; M. Buti; H. L. Y. Chan et al. 

2020-12-01.  p. 316-317.

Human genomics of the humoral response against polyomaviruses

F. Hodel; A. Y. Chong; P. Scepanovic; C. W. Thorball; Z. M. Xu et al. 

2020-12-01.  p. 312-313.

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

A. Y. Chong; N. Brenner; A. Jimenez Kaufmann; A. Cortes; R. Almond et al. 

2020-12-01.  p. 311-312.

Using reference-fixed principal components to improve polygenic risk score prediction

O. Naret; J. Fellay 

2020-12-01.  p. 134-135.

Designing a Tanzanian Specific SNP Array Add-On to Capture Population-Specific Genetic Variations and to Improve Genotype Imputation

Z. Xu; S. Rueeger; U. Portevin; S. Gagneux; J. Fellay 

2020-07-01. 48th European Mathematical Genetics Meeting (EMGM), Lausanne, SWITZERLAND, Apr 16-17, 2020. p. 227-227. DOI : 10.1159/000507248.

Is Competition for Resource between Genes a Driving Force of the Omnigenic Architecture?

O. Naret 

2020-07-01. 48th European Mathematical Genetics Meeting (EMGM), Lausanne, SWITZERLAND, Apr 16-17, 2020. p. 217-218.

SPHN/PHRT – MedCo in Action: Empowering the Swiss Molecular Tumor Board with Privacy-Preserving and Real-Time Patient Discovery

J. L. Raisaro; J. R. Troncoso-Pastoriza; S. Pradervand; M. Cuendet; M. Misbach et al. 

2020-01-01. 30th Medical Informatics Europe (MIE) Conference, Geneva, SWITZERLAND, Apr, 2020. p. 1161-1162. DOI : 10.3233/SHTI200345.


Susceptibility to infection in early life: a growing role for human genetics

A. Borghesi; A. Marzollo; A. Michev; J. Fellay 

Human Genetics. 2020-06-01. Vol. 139, num. 6-7, p. 733-743. DOI : 10.1007/s00439-019-02109-2.

Exploring the interactions between the human and viral genomes

J. Fellay; V. Pedergnana 

Human Genetics. 2020-06-01. Vol. 139, num. 6-7, p. 777-781. DOI : 10.1007/s00439-019-02089-3.


HIV host genomics in the era of effective antiretroviral therapy

C. A. W. Thorball / J. Fellay; D. Trono (Dir.)  

Lausanne, EPFL, 2020. 


Journal Articles

Predicting the Occurrence of Variants in RAG1 and RAG2

D. Lawless; H. L. Allen; J. Thaventhiran; F. Hodel; R. Anwar et al. 

Journal Of Clinical Immunology. 2019-10-01. Vol. 39, num. 7, p. 688-701. DOI : 10.1007/s10875-019-00670-z.

A comprehensive assessment of demographic, environmental, and host genetic associations with gut microbiome diversity in healthy individuals

P. Scepanovic; F. Hodel; S. Mondot; V. Partula; A. Byrd et al. 

Microbiome. 2019-09-13. Vol. 7, num. 1, p. 130. DOI : 10.1186/s40168-019-0747-x.

Adaptation of hepatitis C virus to interferon lambda polymorphism across multiple viral genotypes

N. Chaturvedi; E. S. Svarovskaia; H. Mo; A. O. Osinusi; D. M. Brainard et al. 

Elife. 2019-09-03. Vol. 8, p. e42542. DOI : 10.7554/eLife.42542.

HIV Transmission Chains Exhibit Greater HLA-B Homogeneity Than Randomly Expected

Huyen Nguyen; C. W. Thorball; J. Fellay; J. Boni; S. Yerly et al. 

Jaids-Journal Of Acquired Immune Deficiency Syndromes. 2019-08-15. Vol. 81, num. 5, p. 508-515. DOI : 10.1097/QAI.0000000000002077.

Determinants of HIV-1 reservoir size and long-term dynamics during suppressive ART

N. Bachmann; C. von Siebenthal; V. Vongrad; T. Turk; K. Neumann et al. 

Nature Communications. 2019-07-19. Vol. 10, p. 3193. DOI : 10.1038/s41467-019-10884-9.

Associations between usual diet and gut microbiota composition: results from the Milieu Interieur cross-sectional study

V. Partula; S. Mondot; M. J. Torres; E. Kesse-Guyot; M. Deschasaux et al. 

American Journal Of Clinical Nutrition. 2019-05-01. Vol. 109, num. 5, p. 1472-1483. DOI : 10.1093/ajcn/nqz029.

Human genomics of acute liver failure due to hepatitis B virus infection: An exome sequencing study in liver transplant recipients

S. Asgari; N. Chaturvedi; P. Scepanovic; C. Hammer; N. Semmo et al. 

Journal Of Viral Hepatitis. 2019-02-01. Vol. 26, num. 2, p. 271-277. DOI : 10.1111/jvh.13019.

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

P. Maffucci; B. Bigio; F. Rapaport; A. Cobat; A. Borghesi et al. 

Proceedings Of The National Academy Of Sciences Of The United States Of America. 2019-01-15. Vol. 116, num. 3, p. 950-959. DOI : 10.1073/pnas.1808403116.

HIV peptidome-wide association study reveals patient-specific epitope repertoires associated with HIV control

J. Arora; P. J. McLare; N. Chaturvedi; M. Carrington; J. Fellay et al. 

Proceedings Of The National Academy Of Sciences Of The United States Of America. 2019-01-15. Vol. 116, num. 3, p. 944-949. DOI : 10.1073/pnas.1812548116.

HIV-1 Vpu is a potent transcriptional suppressor of NF-κB-elicited antiviral immune responses

S. Langer; C. Hammer; K. Hopfensperger; L. Klein; D. Hotter et al. 

eLife. 2019. Vol. 8, p. e41930. DOI : 10.7554/eLife.41930.

Conference Papers

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 HLA

P. Bost; X. Mariette; V. Bondet; A. Llibre; C. Posseme et al. 


Genome-to-genome analysis of Epstein-Barr virus infection

S. Rueger; C. Hammer; A. Loetscher; E. Zdobnov; J. Fellay 

2019-10-01. 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 children

D. Lawless; S. Asgari; L. Schlapbach; J. Fellay 

2019-10-01. 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 population

F. Hodel; P. Marques-Vidal; P. Vollenweider; J. Fellay 

2019-10-01. 52nd Conference of the European-Society-of-Human-Genetics (ESHG), Gothenburg, SWEDEN, Jun 15-18, 2019. p. 1747-1748.


Gender medicine and oncology: report and consensus of an ESMO workshop

A. D. Wagner; S. Oertelt-Prigione; A. Adjei; T. Buclin; V. Cristina et al. 

Annals Of Oncology. 2019-12-01. Vol. 30, num. 12, p. 1914-1924. DOI : 10.1093/annonc/mdz414.

Effect of Fc Receptor Genetic Diversity on HIV-1 Disease Pathogenesis

D. E. Geraghty; C. W. Thorball; J. Fellay; R. Thomas 

Frontiers In Immunology. 2019-05-09. Vol. 10, p. 970. DOI : 10.3389/fimmu.2019.00970.


Journal Articles

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

S. Bibert; A. Wojtowicz; P. Taffe; P. E. Tarr; E. Bernasconi et al. 

Aids. 2018-11-28. Vol. 32, num. 18, p. 2759-2765. DOI : 10.1097/QAD.0000000000002004.

Memory B Cells Activate Brain-Homing, Autoreactive CD4(+) T Cells in Multiple Sclerosis

I. Jelcic; F. Al Nimer; J. Wang; V. Lentsch; R. Planas et al. 

Cell. 2018-09-20. Vol. 175, num. 1, p. 100.e1. DOI : 10.1016/j.cell.2018.08.011.

Human genetic variants and age are the strongest predictors of humoral immune responses to common pathogens and vaccines

P. Scepanovic; C. Alanio; C. Hammer; F. Hodel; J. Bergstedt et al. 

Genome Medicine. 2018-07-27. Vol. 10, num. 1, p. 59. DOI : 10.1186/s13073-018-0568-8.

Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver

C. Wymant; F. Blanquart; T. Golubchik; A. Gall; M. Bakker et al. 

Virus Evolution. 2018-05-18. Vol. 4, num. 1, p. vey007. DOI : 10.1093/ve/vey007.

Killer cell immunoglobulin–like receptor 3DL1 variation modifies HLA-B*57 protection against HIV-1

M. P. Martin; V. Naranbhai; P. R. Shea; Y. Qi; V. Ramsuran et al. 

Journal of Clinical Investigation. 2018-05-01. Vol. 128, num. 5, p. 1903-1912. DOI : 10.1172/JCI98463.

Natural variation in the parameters of innate immune cells is preferentially driven by genetic factors

E. Patin; M. Hasan; J. Bergstedt; V. Rouilly; V. Libri et al. 

Nature Immunology. 2018-03-19. Vol. 19, num. 3, p. 302-314. DOI : 10.1038/s41590-018-0049-7.

Detection of novel astroviruses MLB1 and MLB2 in the sera of febrile Tanzanian children

S. Cordey; M-A. Hartley; K. Keitel; F. Laubscher; F. Brito et al. 

Emerging Microbes & Infections. 2018-03-14. Vol. 7, num. 1, p. 1-3. 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 Study

J-L. Raisaro; P. J. McLaren; J. Fellay; M. Cavassini; C. Klersy et al. 

Journal of Biomedical Informatics. 2018-03-01. Vol. 79, p. 1-6. DOI : 10.1016/j.jbi.2017.12.013.

Elevated HLA-A expression impairs HIV control through inhibition of NKG2A-expressing cells

V. Ramsuran; V. Naranbhai; A. Horowitz; Y. Qi; M. P. Martin et al. 

Science. 2018-01-05. Vol. 359, num. 6371, p. 86-90. DOI : 10.1126/science.aam8825.

The human noncoding genome defined by genetic diversity

J. di Iulio; I. Bartha; E. Wong; H. Yu; V. Lavrenko et al. 

Nature Genetics. 2018. Vol. 50, num. 3, p. 333-337. DOI : 10.1038/s41588-018-0062-7.

Correcting for Population Stratification Reduces False Positive and False Negative Results in Joint Analyses of Host and Pathogen Genomes

O. Naret; N. Chaturvedi; I. Bartha; C. Hammer; J. Fellay 

Frontiers in Genetics. 2018. Vol. 9, p. 266. DOI : 10.3389/fgene.2018.00266.

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

F. Bertels; A. Marzel; G. Leventhal; V. Mitov; J. Fellay et al. 

Molecular biology and evolution. 2018. Vol. 35, num. 1, p. 27-37. 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 infection

E. Adland; M. Hill; N. Lavandier; A. Csala; A. Edwards et al. 

Journal of virology. 2018. Vol. 92, num. 4, p. e01685-17. DOI : 10.1128/JVI.01685-17.

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

L. Abel; J. Fellay; D. W. Haas; E. Schurr; G. Srikrishna et al. 

The Lancet. Infectious Diseases. 2018. Vol. 18, num. 3, p. E64-E75. DOI : 10.1016/S1473-3099(17)30623-0.

Conference Papers

B – T cell interactions activate and maintain brain-homing T cells in multiple sclerosis.

I. Jelcic; F. Al Nimer; J. Wang; V. Lentsch; R. Planas et al. 

2018-10-01. 34th Congress of the European-Committee-for-Treatment-and-Research-in-Multiple-Sclerosis (ECTRIMS), Berlin, GERMANY, Oct 10-12, 2018. p. 56-56.

The Serotonin receptor 3E subunit variant HTR3E c.*76G> A is confirmed as a risk factor for IBS-D in females

B. Niesler; N. Hattensperger; C. Martinez; S. Schmitteckert; L. A. Houghton et al. 



Genetic determinants of healthy human immune variance: from humoral response to microbiome diversity

P. Scepanovic / J. Fellay; B. Deplancke (Dir.)  

Lausanne, EPFL, 2018. 


Journal Articles

HLA-B*14:02-Restricted Env-Specific CD8+ T-Cell Activity Has Highly Potent Antiviral Efficacy Associated with Immune Control of HIV Infection

E. M. Leitman; C. B. Willberg; M-H. Tsai; H. Chen; S. Buus et al. 

Journal of virology. 2017. Vol. 91, num. 22, p. e00544-17. DOI : 10.1128/JVI.00544-17.

Evaluating the Impact of Functional Genetic Variation on HIV-1 Control

P. J. McLaren; S. L. Pulit; D. Gurdasani; I. Bartha; P. R. Shea et al. 

The Journal of infectious diseases. 2017. Vol. 216, num. 9, p. 1063-1069. DOI : 10.1093/infdis/jix470.

Distinctive roles of age, sex, and genetics in shaping transcriptional variation of human immune responses to microbial challenges

B. Piasecka; D. Duffy; A. Urrutia; H. Quach; E. Patin et al. 

Proceedings of the National Academy of Sciences of the United States of America. 2017. Vol. 115, num. 3, p. E488-E497. DOI : 10.1073/pnas.1714765115.

Viral genetic variation accounts for a third of variability in HIV-1 set-point viral load in Europe

F. Blanquart; C. Wymant; M. Cornelissen; A. Gall; M. Bakker et al. 

Plos Biology. 2017. Vol. 15, num. 6, p. e2001855. DOI : 10.1371/journal.pbio.2001855.

Severe viral respiratory infections in children with IFIH1 loss-of-function mutations

S. Asgari; L. J. Schlapbach; S. Anchisi; C. Hammer; I. Bartha et al. 

Proceedings of the National Academy of Sciences of the United States of America. 2017. Vol. 114, num. 31, p. 8342-8347. DOI : 10.1073/pnas.1704259114.

SQC: Secure Quality Control for Meta-Analysis of Genome-Wide Association Studies

Z. Huang; H. Lin; J. Fellay; Z. Kutalik; J-P. Hubaux 

Bioinformatics. 2017. Vol. 33, num. 15, p. 2273-2280. DOI : 10.1093/bioinformatics/btx193.

Genome-to-genome analysis highlights the effect of the human innate and adaptive immune systems on the hepatitis C virus

M. A. Ansari; V. Pedergnana; C. L. C. Ip; A. Magri; A. Von Delft et al. 

Nature Genetics. 2017. Vol. 49, num. 5, p. 666-+. DOI : 10.1038/ng.3835.

Estimating the Respective Contributions of Human and Viral Genetic Variation to HIV Control

I. Bartha; P. J. Mclaren; C. Brumme; R. Harrigan; A. Telenti et al. 

PLoS Computational Biology. 2017. Vol. 13, num. 2, p. e1005339. DOI : 10.1371/journal.pcbi.1005339.

Neonatal Group B Streptococcal Disease in Otherwise Healthy Infants: Failure of Specific Neonatal Immune Responses

A. Borghesi; M. Stronati; J. Fellay 

Frontiers In Immunology. 2017. Vol. 8, p. 215. 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 AIDS

R. Abujaber; P. R. Shea; P. J. Mclaren; S. Lakhi; J. Gilmour et al. 

Annals Of Human Genetics. 2017. Vol. 81, num. 1, p. 27-34. DOI : 10.1111/ahg.12182.


Journal Articles

A privacy-preserving solution for compressed storage and selective retrieval of genomic data

Z. Huang; E. Ayday; H. Lin; R. S. Aiyar; A. Molyneaux et al. 

Genome Research. 2016-10-27. Vol. 26, num. 12, p. 1687-1696. 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 Study

T. Junier; M. Rotger; E. Biver; B. Ledergerber; C. Barcelo et al. 

Open Forum Infectious Diseases. 2016-04-01. Vol. 3, num. 2, p. ofw101. DOI : 10.1093/ofid/ofw101.

Exome Sequencing Reveals Primary Immunodeficiencies in Children with Community-Acquired Pseudomonas aeruginosa Sepsis

S. Asgari; P. J. Mclaren; J. Peake; M. Wong; R. Wong et al. 

Frontiers In Immunology. 2016. Vol. 7, p. 357. DOI : 10.3389/fimmu.2016.00357.

Familial segregation of group B streptococcal infection in a consanguineous kindred

F. Licciardi; D. Montin; A. Versace; G. Migliore; C. Tzialla et al. 

International Journal Of Infectious Diseases. 2016. Vol. 51, p. 22-24. DOI : 10.1016/j.ijid.2016.08.010.

Determinants of HIV-1 broadly neutralizing antibody induction

P. Rusert; R. D. Kouyos; C. Kadelka; H. Ebner; M. Schanz et al. 

Nature Medicine. 2016. Vol. 22, num. 11, p. 1260-1267. DOI : 10.1038/nm.4187.

Corrigendum: Exome Sequencing reveals Primary immunodeficiencies in Children with Community-Acquired Pseudomonas aeruginosa Sepsis (vol 7, 357, 2016)

S. Asgari; P. J. Mclaren; J. Peake; M. Wong; R. Wong et al. 

Frontiers In Immunology. 2016. Vol. 7, p. 447. DOI : 10.3389/fimmu.2016.00447.

Identification of Siglec-1 null individuals infected with HIV-1

J. Martinez-Picado; P. J. Mclaren; I. Erkizia; M. P. Martin; S. Benet et al. 

Nature Communications. 2016. Vol. 7, p. 12412. DOI : 10.1038/ncomms12412.

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

P. An; S. Penugonda; C. W. Thorball; I. Bartha; J. J. Goedert et al. 

Plos Genetics. 2016. Vol. 12, num. 3, p. e1005921. DOI : 10.1371/journal.pgen.1005921.

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

P. J. McLaren; J. L. Raisaro; M. Aouri; M. Rotger; E. Ayday et al. 

Genetics in medicine : official journal of the American College of Medical Genetics. 2016. Vol. 18, p. 814-822. DOI : 10.1038/gim.2015.167.

Conference Papers

Multiple HCV Amino Acid Variants Associate with Interferon Lambda Polymorphism in Genotype 1a, 1b and 3a Infections

N. Chaturvedi; R. K. Chodavarapu; E. S. Svarovskaia; H. Mo; A. O. Osinusi et al. 

2016. 67th Annual Meeting of the American-Association-for-the-Study-of-Liver-Diseases (AASLD), Boston, MA, NOV 11-15, 2016. p. 33A-33A.


Host and pathogen genomics of severe pediatric infections

S. Asgari / J. Fellay (Dir.)  

Lausanne, EPFL, 2016. 


Method for privacy-preserving medical risk test

J. L. Raisaro; E. Ayday; P. Mclaren; J-p. Hubaux; A. Telenti et al. 

US9524370; US2016125141; EP3016011.



Journal Articles

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

C. Hammer; M. Begemann; P. J. Mclaren; I. Bartha; A. Michel et al. 

American Journal Of Human Genetics. 2015. Vol. 97, num. 5, p. 738-743. 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 load

P. J. Mclaren; C. Coulonges; I. Bartha; T. L. Lenz; A. J. Deutsch et al. 

Proceedings Of The National Academy Of Sciences Of The United States Of America. 2015. Vol. 112, num. 47, p. 14658-14663. DOI : 10.1073/pnas.1514867112.

The Characteristics of Heterozygous Protein Truncating Variants in the Human Genome

I. Bartha; A. Rausell; P. J. Mclaren; P. Mohammadi; M. Tardaguila et al. 

Plos Computational Biology. 2015. Vol. 11, num. 12, p. e1004647. DOI : 10.1371/journal.pcbi.1004647.

Identification of potential HIV restriction factors by combining evolutionary genomic signatures with functional analyses

P. J. Mclaren; A. Gawanbacht; N. Pyndiah; C. Krapp; D. Hotter et al. 

Retrovirology. 2015. Vol. 12, p. 41. DOI : 10.1186/s12977-015-0165-5.

The Interplay Between Host Genetic Variation, Viral Replication, and Microbial Translocation in Untreated HIV-Infected Individuals

M. R. Perkins; I. Bartha; J. K. Timmer; J. C. Liebner; D. Wollinsky et al. 

The Journal of infectious diseases. 2015. Vol. 212, num. 4, p. 578-84. DOI : 10.1093/infdis/jiv089.

Privacy in the Genomic Era

M. Naveed; E. Ayday; E. Clayton; J. Fellay; C. Gunter et al. 

ACM Computing Surveys. 2015. Vol. 48, num. 1, p. 6. DOI : 10.1145/2767007.

Adaptation on a genomic scale

I. Bartha; J. Fellay 

eLife. 2015. Vol. 4, p. e06193. DOI : 10.7554/eLife.06193.

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

P. J. McLaren; J. Fellay 

Current opinion in HIV and AIDS. 2015. Vol. 10, num. 2, p. 110-5. DOI : 10.1097/COH.0000000000000133.

Conference Papers

Quantifying Genomic Privacy via Inference Attack with High-Order SNV Correlations

S. Samani; Z. Huang; E. Ayday; M. Elliot; J. Fellay et al. 

2015. 2nd International Workshop on Genome Privacy and Security (in conjunction with IEEE S&P 2015), San Jose, CA, USA, May 21, 2015. p. 32-40. DOI : 10.1109/SPW.2015.21.

GenoGuard: Protecting Genomic Data against Brute-Force Attacks

Z. Huang; E. Ayday; J. Fellay; J-P. Hubaux; A. Juels 

2015. 36th IEEE Symposium on Security and Privacy (S&P 2015), San Jose, CA, USA, May 18-20, 2015. p. 447-462. DOI : 10.1109/SP.2015.34.


The impact of host genetic variation on infection with HIV-1

P. J. Mclaren; M. Carrington 

Nature Immunology. 2015. Vol. 16, num. 6, p. 577-583. DOI : 10.1038/ni.3147.


GenoGuard: Protecting Genomic Data Against Brute-Force Attacks

Z. Huang; E. Ayday; J. Fellay; J-P. Hubaux; A. Juels 



Journal Articles

Médecine génomique et Maladies infectieuses [Genomic medicine and infectious diseases]

J. Fellay 

Praxis. 2014. Vol. 103, num. 10, p. 587-90. DOI : 10.1024/1661-8157/a001658.

A Novel Acute Retroviral Syndrome Severity Score Predicts the Key Surrogate Markers for HIV-1 Disease Progression

D. L. Braun; R. Kouyos; C. Oberle; C. Grube; B. Joos et al. 

Plos One. 2014. Vol. 9, num. 12, p. e114111. 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 A

N. Vince; A. A. Bashirova; A. Lied; X. Gao; L. Dorrell et al. 

The Journal of infectious diseases. 2014. Vol. 210, num. 7, p. 1047-51. DOI : 10.1093/infdis/jiu214.

Disentangling human tolerance and resistance against HIV

R. R. Regoes; P. J. McLaren; M. Battegay; E. Bernasconi; A. Calmy et al. 

PLoS biology. 2014. Vol. 12, num. 9, p. e1001951. DOI : 10.1371/journal.pbio.1001951.

Dynamics of HIV Latency and Reactivation in a Primary CD4+T Cell Model

P. Mohammadi; J. Di Iulio; M. Munoz; R. Martinez; I. Bartha et al. 

Plos Pathogens. 2014. Vol. 10, num. 5, p. e1004156. DOI : 10.1371/journal.ppat.1004156.

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

A. Rausell; P. Mohammadi; P. J. Mclaren; I. Bartha; I. Xenarios et al. 

Plos Computational Biology. 2014. Vol. 10, num. 7, p. e1003757. DOI : 10.1371/journal.pcbi.1003757.

LILRB2 Interaction with HLA Class I Correlates with Control of HIV-1 Infection

A. A. Bashirova; E. Martin-Gayo; D. C. Jones; Y. Qi; R. Apps et al. 

Plos Genetics. 2014. Vol. 10, num. 3, p. e1004196. DOI : 10.1371/journal.pgen.1004196.

GuavaH: a compendium of host genomic data in HIV biology and disease

I. Bartha; P. J. Mclaren; A. Ciuffi; J. Fellay; A. Telenti 

Retrovirology. 2014. Vol. 11, p. 6. DOI : 10.1186/1742-4690-11-6.


Practical Solutions for Protecting Individual Genomic Privacy

J. Fellay; J. L. Raisaro; Z. Huang; M. Humbert; E. Ayday et al. 

American Society of Human Genetics (ASHG), San Diego, CA, USA, October 2014.


Journal Articles

On stand by: host genetics of HIV control

M. Carrington; A. A. Bashirova; P. J. Mclaren 

Aids. 2013. Vol. 27, num. 18, p. 2831-2839. DOI : 10.1097/01.aids.0000432536.85335.c8.

A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control

I. Bartha; J. M. Carlson; C. J. Brumme; P. J. Mclaren; Z. L. Brumme et al. 

Elife. 2013. Vol. 2, p. e01123. DOI : 10.7554/eLife.01123.

Genetic interplay between HLA-C and MIR148A in HIV control and Crohn disease

S. Kulkarni; Y. Qi; C. O’Huigin; F. Pereyra; V. Ramsuran et al. 

Proceedings Of The National Academy Of Sciences Of The United States Of America. 2013. Vol. 110, num. 51, p. 20705-20710. DOI : 10.1073/pnas.1312237110.

A genome-wide association study of resistance to HIV infection in highly exposed uninfected individuals with hemophilia A

J. Lane; P. J. Mclaren; L. Dorrell; K. V. Shianna; A. Stemke et al. 

Human Molecular Genetics. 2013. Vol. 22, num. 9, p. 1903-1910. DOI : 10.1093/hmg/ddt033.

Contribution of Genetic Background, Traditional Risk Factors, and HIV-Related Factors to Coronary Artery Disease Events in HIV-Positive Persons

M. Rotger; T. R. Glass; T. Junier; J. Lundgren; J. D. Neaton et al. 

Clinical Infectious Diseases. 2013. Vol. 57, num. 1, p. 112-121. DOI : 10.1093/cid/cit196.

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

P. J. Mclaren; C. Coulonges; S. Ripke; L. Van Den Berg; S. Buchbinder et al. 

PLoS Pathogens. 2013. Vol. 9, num. 7, p. e1003515. DOI : 10.1371/journal.ppat.1003515.

Influence of HLA-C Expression Level on HIV Control

R. Apps; Y. Qi; J. M. Carlson; H. Chen; X. Gao et al. 

Science. 2013. Vol. 340, num. 6128, p. 87-91. DOI : 10.1126/science.1232685.

Conference Papers

Privacy-Preserving Computation of Disease Risk by Using Genomic, Clinical, and Environmental Data

E. Ayday; J. L. Raisaro; M. Laren; P. Jack; J. Fellay et al. 

2013. USENIX Security Workshop on Health Information Technologies (HealthTech ’13), Washington, DC, USA, August.


European genetic diversity and susceptibility to pathogens

P. J. McLaren; J. Fellay; A. Telenti 

Human heredity. 2013. Vol. 76, num. 3-4, p. 187-93. DOI : 10.1159/000357758.


Privacy-Preserving Computation of Disease Risk by Using Genomic, Clinical, and Environmental Data (poster version)

E. Ayday; J. L. Raisaro; M. Laren; P. Jack; J. Fellay et al. 

USENIX Security Workshop on Health Information Technologies (HealthTech ’13), Washington, DC, USA, August, 2013.


Journal Articles

Role of retroviral restriction factors in the interferon- -mediated suppression of HIV-1 in vivo

S. K. Pillai; M. Abdel-Mohsen; J. Guatelli; M. Skasko; A. Monto et al. 

Proceedings of the National Academy of Sciences. 2012. Vol. 109, num. 8, p. 3035-3040. DOI : 10.1073/pnas.1111573109.

HLA-Bw4 identifies a population of HIV-infected patients with an increased capacity to control viral replication after structured treatment interruption

M. Stern; K. Czaja; A. Rauch; M. Rickenbach; H. F. Günthard et al. 

HIV Medicine. 2012. Vol. 13, num. 10, p. 589-595. DOI : 10.1111/j.1468-1293.2012.01019.x.

Interleukin 28B polymorphisms are the only common genetic variants associated with low-density lipoprotein cholesterol (LDL-C) in genotype-1 chronic hepatitis C and determine the association between LDL-C and treatment response

P. J. Clark; A. J. Thompson; M. Zhu; D. M. Vock; Q. Zhu et al. 

Journal of viral hepatitis. 2012. Vol. 19, num. 5, p. 332-40. DOI : 10.1111/j.1365-2893.2011.01553.x.

The association of genetic variants with hepatic steatosis in patients with genotype 1 chronic hepatitis C infection

P. J. Clark; A. J. Thompson; Q. Zhu; D. M. Vock; M. Zhu et al. 

Digestive diseases and sciences. 2012. Vol. 57, num. 8, p. 2213-21. DOI : 10.1007/s10620-012-2171-y.


Journal Articles

Copy Number Variation of KIR Genes Influences HIV-1 Control

K. Pelak; A. C. Need; J. Fellay; K. V. Shianna; S. Feng et al. 

Plos Biology. 2011. Vol. 9, num. 11, p. e1001208. DOI : 10.1371/journal.pbio.1001208.

Mapping of positive selection sites in the HIV-1 genome in the context of RNA and protein structural constraints

J. Snoeck; J. Fellay; I. Bartha; D. C. Douek; A. Telenti 

Retrovirology. 2011. Vol. 8, p. 87. DOI : 10.1186/1742-4690-8-87.

A polymorphism in the leptin gene promoter is associated with anemia in patients with HIV disease

G. J. Vanasse; J-Y. Jeong; J. Tate; H. Bathulapalli; D. Anderson et al. 

Blood. 2011. Vol. 118, p. 5401-5408. DOI : 10.1182/blood-2011-06-362194.

Comparative transcriptomics of extreme phenotypes of human HIV-1 infection and SIV infection in sooty mangabey and rhesus macaque

M. Rotger; J. Dalmau; A. Rauch; P. McLaren; S. Bosinger et al. 

The Journal of clinical investigation. 2011. Vol. 121, num. 6, p. 2391-2400. DOI : 10.1172/JCI45235.

Personalized hepatitis C therapy: opportunities and pitfalls

A. Rauch; J. Fellay 

Expert review of molecular diagnostics. 2011. Vol. 11, num. 2, p. 127-9. DOI : 10.1586/erm.10.116.

Inosine triphosphate protects against ribavirin-induced adenosine triphosphate loss by adenylosuccinate synthase function

Y. Hitomi; E. T. Cirulli; J. Fellay; J. G. McHutchison; A. J. Thompson et al. 

Gastroenterology. 2011. Vol. 140, num. 4, p. 1314-21. DOI : 10.1053/j.gastro.2010.12.038.

Common human genetic variants and HIV-1 susceptibility: a genome-wide survey in a homogeneous African population

S. Petrovski; J. Fellay; K. V. Shianna; N. Carpenetti; J. Kumwenda et al. 

AIDS. 2011. Vol. 25, num. 4, p. 513-8. DOI : 10.1097/QAD.0b013e328343817b.

Genome-wide association study identifies single nucleotide polymorphism in DYRK1A associated with replication of HIV-1 in monocyte-derived macrophages

S. M. Bol; P. D. Moerland; S. Limou; Y. van Remmerden; C. Coulonges et al. 

PloS One. 2011. Vol. 6, num. 2, p. e17190. DOI : 10.1371/journal.pone.0017190.

Host genetic determinants of T cell responses to the MRKAd5 HIV-1 gag/pol/nef vaccine in the step trial

J. Fellay; N. Frahm; K. V. Shianna; E. T. Cirulli; D. R. Casimiro et al. 

The Journal of infectious diseases. 2011. Vol. 203, num. 6, p. 773-9. DOI : 10.1093/infdis/jiq125.

Estimating the net contribution of IL28B variation to spontaneous hepatitis C virus clearance

J. di Iulio; A. Ciuffi; K. Fitzmaurice; D. Kelleher; M. Rotger et al. 

Hepatology. 2011. Vol. 53, num. 5, p. 1446-1454. DOI : 10.1002/hep.24263.

Impact of Phenotype Definition on Genome-Wide Association Signals: Empirical Evaluation in Human Immunodeficiency Virus Type 1 Infection

E. Evangelou; J. Fellay; S. Colombo; J. Martinez-Picado; N. Obel et al. 

American Journal of Epidemiology. 2011. Vol. 173, num. 11, p. 1336-1342. DOI : 10.1093/aje/kwr024.


Hepatitis C pharmacogenetics: state of the art in 2010

N. H. Afdhal; J. G. McHutchison; S. Zeuzem; A. Mangia; J-M. Pawlotsky et al. 

Hepatology. 2011. Vol. 53, num. 1, p. 336-45. DOI : 10.1002/hep.24052.


Journal Articles

How the human genome can predict response to Hepatitis C therapy

A. J. Thompson; J. Fellay; J. G. McHutchison 

Current Hepatitis Reports. 2010. Vol. 9, num. 1, p. 1-8. DOI : 10.1007/s11901-010-0029-3.

Young and Early Career Investigators: Report from a Global HIV Vaccine Enterprise Working Group

D. H. Barouch; T. Ndung’u; G. Alter; T. Cardozo; B. Chohan et al. 

Nature Precedings. 2010. DOI : 10.1038/npre.2010.4800.2.

A polymorphism in the HCP5 gene associated with HLA-B*5701 does not restrict HIV-1 in vitro

W. Yoon; B-J. Ma; J. Fellay; W. Huang; S-M. Xia et al. 

AIDS. 2010. Vol. 24, num. 1, p. 155-7. DOI : 10.1097/QAD.0b013e32833202f5.

Hepatitis C trials that combine investigational agents with pegylated interferon should be stratified by interleukin-28B genotype

A. J. Thompson; A. J. Muir; M. S. Sulkowski; K. Patel; H. L. Tillmann et al. 

Hepatology. 2010. Vol. 52, num. 6, p. 2243-4. DOI : 10.1002/hep.23826.

Role of human leukocyte antigen class I alleles in progressive multifocal leukoencephalopathy

S. Gheuens; J. Fellay; D. B. Goldstein; I. J. Koralnik 

Journal of neurovirology. 2010. Vol. 16, num. 1, p. 41-7. DOI : 10.3109/13550280903552438.

Host determinants of HIV-1 control in African Americans

K. Pelak; D. B. Goldstein; N. M. Walley; J. Fellay; D. Ge et al. 

The Journal of infectious diseases. 2010. Vol. 201, num. 8, p. 1141-9. DOI : 10.1086/651382.

Genome-wide mRNA expression correlates of viral control in CD4+ T-cells from HIV-1-infected individuals

M. Rotger; K. K. Dang; J. Fellay; E. L. Heinzen; S. Feng et al. 

PLoS pathogens. 2010. Vol. 6, num. 2, p. e1000781. DOI : 10.1371/journal.ppat.1000781.

ITPA gene variants protect against anaemia in patients treated for chronic hepatitis C

J. Fellay; A. J. Thompson; D. Ge; C. E. Gumbs; T. J. Urban et al. 

Nature. 2010. Vol. 464, num. 7287, p. 405-8. DOI : 10.1038/nature08825.

Interleukin-28B polymorphism improves viral kinetics and is the strongest pretreatment predictor of sustained virologic response in genotype 1 hepatitis C virus

A. J. Thompson; A. J. Muir; M. S. Sulkowski; D. Ge; J. Fellay et al. 

Gastroenterology. 2010. Vol. 139, num. 1, p. 120-9. DOI : 10.1053/j.gastro.2010.04.013.

Counteraction of HLA-C-mediated immune control of HIV-1 by Nef

A. Specht; A. Telenti; R. Martinez; J. Fellay; E. Bailes et al. 

Journal of virology. 2010. Vol. 84, num. 14, p. 7300-11. DOI : 10.1128/JVI.00619-10.

Variants in the ITPA gene protect against ribavirin-induced hemolytic anemia and decrease the need for ribavirin dose reduction

A. J. Thompson; J. Fellay; K. Patel; H. L. Tillmann; S. Naggie et al. 

Gastroenterology. 2010. Vol. 139, num. 4, p. 1181-9. DOI : 10.1053/j.gastro.2010.06.016.

Evidence of dysregulation of dendritic cells in primary HIV infection

R. L. Sabado; M. O’Brien; A. Subedi; L. Qin; N. Hu et al. 

Blood. 2010. Vol. 116, num. 19, p. 3839-52. DOI : 10.1182/blood-2010-03-273763.

The characterization of twenty sequenced human genomes

K. Pelak; K. V. Shianna; D. Ge; J. M. Maia; M. Zhu et al. 

PLoS genetics. 2010. Vol. 6, num. 9, p. e1001111. DOI : 10.1371/journal.pgen.1001111.

IL28B genotype is associated with differential expression of intrahepatic interferon-stimulated genes in patients with chronic hepatitis C

T. J. Urban; A. J. Thompson; S. S. Bradrick; J. Fellay; D. Schuppan et al. 

Hepatology. 2010. Vol. 52, num. 6, p. 1888-96. DOI : 10.1002/hep.23912.


Host genetics and HIV-1: the final phase?

J. Fellay; K. V. Shianna; A. Telenti; D. B. Goldstein 

PLoS pathogens. 2010. Vol. 6, num. 10, p. e1001033. DOI : 10.1371/journal.ppat.1001033.


Journal Articles

Challenges facing young investigators

G. Alter; J. Brenchley; J. Fellay 

IAVI report. 2009. Vol. 13, num. 1, p. 14-7.

CCL3L1 and HIV/AIDS susceptibility

T. J. Urban; A. C. Weintrob; J. Fellay; S. Colombo; K. V. Shianna et al. 

Nature medicine. 2009. Vol. 15, num. 10, p. 1110-2. DOI : 10.1038/nm1009-1110.

The Duffy antigen receptor for chemokines null promoter variant does not influence HIV-1 acquisition or disease progression

N. M. Walley; B. Julg; S. P. Dickson; J. Fellay; D. Ge et al. 

Cell host & microbe. 2009. Vol. 5, num. 5, p. 408-10. DOI : 10.1016/j.chom.2009.04.011.

HLA-C cell surface expression and control of HIV/AIDS correlate with a variant upstream of HLA-C

R. Thomas; R. Apps; Y. Qi; X. Gao; V. Male et al. 

Nature genetics. 2009. Vol. 41, num. 12, p. 1290-4. DOI : 10.1038/ng.486.

X chromosomal variation is associated with slow progression to AIDS in HIV-1-infected women

R. A. Siddiqui; U. Sauermann; J. Altmüller; E. Fritzer; M. Nothnagel et al. 

American journal of human genetics. 2009. Vol. 85, num. 2, p. 228-39. DOI : 10.1016/j.ajhg.2009.07.013.

Genetic variation in IL28B predicts hepatitis C treatment-induced viral clearance

D. Ge; J. Fellay; A. J. Thompson; J. S. Simon; K. V. Shianna et al. 

Nature. 2009. Vol. 461, num. 7262, p. 399-401. DOI : 10.1038/nature08309.

Common genetic variation and the control of HIV-1 in humans

J. Fellay; D. Ge; K. V. Shianna; S. Colombo; B. Ledergerber et al. 

PLoS genetics. 2009. Vol. 5, num. 12, p. e1000791. DOI : 10.1371/journal.pgen.1000791.


Host genetics influences on HIV type-1 disease

J. Fellay 

Antiviral therapy. 2009. Vol. 14, num. 6, p. 731-8. DOI : 10.3851/IMP1253.


Journal Articles

The HCP5 single-nucleotide polymorphism: a simple screening tool for prediction of hypersensitivity reaction to abacavir

S. Colombo; A. Rauch; M. Rotger; J. Fellay; R. Martinez et al. 

The Journal of infectious diseases. 2008. Vol. 198, num. 6, p. 864-7. DOI : 10.1086/591184.

WGAViewer: software for genomic annotation of whole genome association studies

D. Ge; K. Zhang; A. C. Need; O. Martin; J. Fellay et al. 

Genome research. 2008. Vol. 18, num. 4, p. 640-3. DOI : 10.1101/gr.071571.107.


Journal Articles

Host genetics: fine-tuning innate signaling

J. Fellay; D. B. Goldstein 

Current biology. 2007. Vol. 17, num. 13, p. R516-8. DOI : 10.1016/j.cub.2007.04.052.

Adverse events to antiretrovirals in the Swiss HIV Cohort Study: effect on mortality and treatment modification

O. Keiser; J. Fellay; M. Opravil; H. H. Hirsch; B. Hirschel et al. 

Antiviral therapy. 2007. Vol. 12, num. 8, p. 1157-64.

Efficacy and safety of universal valganciclovir prophylaxis combined with a tacrolimus/mycophenolate-based regimen in kidney transplantation

O. Manuel; J-P. Venetz; J. Fellay; J-B. Wasserfallen; N. Sturzenegger et al. 

Swiss medical weekly. 2007. Vol. 137, num. 47-48, p. 669-676. DOI : 10.4414/smw.2007.11961.

A whole-genome association study of major determinants for host control of HIV-1

J. Fellay; K. V. Shianna; D. Ge; S. Colombo; B. Ledergerber et al. 

Science. 2007. Vol. 317, num. 5840, p. 944-7. DOI : 10.1126/science.1143767.


Journal Articles

HIV and solid organ transplantation: the Swiss experience

N. J. Müller; H. Furrer; L. Kaiser; B. Hirschel; M. Cavassini et al. 

Swiss medical weekly. 2006. Vol. 136, num. 11-12, p. 194-6. DOI : 10.4414/smw.2006.11356.


[HIV-AIDS: answers to new questions]

J. Fellay; M. Cavassini 

Revue médicale suisse. 2006. Vol. 2, num. 60, p. 912-7.


Journal Articles

Treatment of cytomegalovirus infection or disease in solid organ transplant recipients with valganciclovir

J. Fellay; J-P. Venetz; M. Pascual; J-D. Aubert; C. Seudoux et al. 

American journal of transplantation. 2005. Vol. 5, num. 7, p. 1781-2. DOI : 10.1111/j.1600-6143.2005.00936.x.

Variations of CYP3A activity induced by antiretroviral treatment in HIV-1 infected patients

J. Fellay; C. Marzolini; L. Decosterd; K. P. Golay; P. Baumann et al. 

European journal of clinical pharmacology. 2005. Vol. 60, num. 12, p. 865-73. DOI : 10.1007/s00228-004-0855-8.


Journal Articles

CYP3A activity measured by the midazolam test is not related to 3435 C >T polymorphism in the multiple drug resistance transporter gene

C. B. Eap; J. Fellay; T. Buclin; G. Bleiber; K. P. Golay et al. 

Pharmacogenetics. 2004. Vol. 14, num. 4, p. 255-60. DOI : 10.1097/00008571-200404000-00005.


Journal Articles

Population pharmacokinetics and effects of efavirenz in patients with human immunodeficiency virus infection

C. Csajka; C. Marzolini; K. Fattinger; L. A. Décosterd; J. Fellay et al. 

Clinical pharmacology and therapeutics. 2003. Vol. 73, num. 1, p. 20-30. DOI : 10.1067/mcp.2003.22.


Journal Articles

HIV lipoatrophy and mosquito bites

G. Greub; J. Fellay; A. Telenti 

Clinical infectious diseases. 2002. Vol. 34, num. 2, p. 288-9. DOI : 10.1086/323014.

Multidrug resistance and response to antiretroviral treatment

J. Fellay; D. Back; A. H. Schinkel; C. B. Eap; A. Telenti 

Lancet. 2002. Vol. 359, num. 9323, p. 2114-5. DOI : 10.1016/S0140-6736(02)08922-5.

Response to antiretroviral treatment in HIV-1-infected individuals with allelic variants of the multidrug resistance transporter 1: a pharmacogenetics study

J. Fellay; C. Marzolini; E. R. Meaden; D. J. Back; T. Buclin et al. 

Lancet. 2002. Vol. 359, num. 9300, p. 30-6. DOI : 10.1016/S0140-6736(02)07276-8.


Journal Articles

Prevalence of adverse events associated with potent antiretroviral treatment: Swiss HIV Cohort Study

J. Fellay; K. Boubaker; B. Ledergerber; E. Bernasconi; H. Furrer et al. 

Lancet. 2001. Vol. 358, num. 9290, p. 1322-7. DOI : 10.1016/S0140-6736(01)06413-3.