Publications de Amalio Telenti

Functional characterization of 3D protein structures informed by human genetic diversity

Amalio Telenti, Julia di Iulio, Istvan Bartha

Sequence variation data of the human proteome can be used to analyze 3D protein structures to derive functional insights. We used genetic variant data from nearly 140,000 individuals to analyze 3D positional conservation in 4,715 proteins and 3,951 homolog ...

National Academy of Sciences2019

GenoShare: Supporting Privacy-Informed Decisions for Sharing Exact Genomic Data

Jean-Pierre Hubaux, Mathias Jacques Jean-Marc Humbert, Amalio Telenti, Jean Louis Raisaro, Carmela González Troncoso

The academic community has proposed many solutions to address the privacy concerns associated with genomic-data sharing. However, practitioners have not adopted these solutions due to their impact on the data utility. To address this problem, we introduce ...

EPFL infoscience2018

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

Thomas Junier, Amalio Telenti, Samira Asgari, Jacques Fellay, Istvan Bartha, Paul Jack Mc Laren, Christian Hammer

Viral respiratory infections are usually mild and self-limiting; still they exceptionally result in life-threatening infections in previously healthy children. To investigate a potential genetic cause, we recruited 120 previously healthy children requiring ...

Natl Acad Sciences2017

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

Amalio Telenti, Jacques Fellay, Istvan Bartha, Paul Jack Mc Laren

We evaluated the fraction of variation in HIV-1 set point viral load attributable to viral or human genetic factors by using joint host/pathogen genetic data from 541 HIV infected individuals. We show that viral genetic diversity explains 29% of the variat ...

Public Library of Science2017

Privacy-enhancing technologies for medical tests using genomic data

Jean-Pierre Hubaux, Mathias Jacques Jean-Marc Humbert, Jacques Rougemont, Amalio Telenti, Jacques Fellay, Erman Ayday, Jean Louis Raisaro

In this invention, we propose privacy-enhancing technologies for medical tests and personalized medicine methods, which utilize patients' genomic data. Assuming the whole genome sequencing is done by a certified institution, we propose to store patients' g ...

2016

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

Jean-Pierre Hubaux, Amalio Telenti, Jacques Fellay, Erman Ayday, Istvan Bartha, Paul Jack Mc Laren, Jean Louis Raisaro

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

Nature Publishing Group2016

Method for privacy-preserving medical risk test

Jean-Pierre Hubaux, Amalio Telenti, Erman Ayday, Paul Jack Mc Laren, Jean Louis Raisaro

A privacy-preserving method for performing a disease susceptibility test on a patient, said method comprising: (I) performing homomorphic computations, (J) obtaining a test result which is partly decrypted with a first part (prk1 resp. prk2) of a private k ...

2016

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

Amalio Telenti, Jacques Fellay, Paul Jack Mc Laren

Siglec-1/CD169 is a myeloid-cell surface receptor critical for HIV-1 capture and infection of bystander target cells. To dissect the role of SIGLEC1 in natura, we scan a large population genetic database and identify a loss-of-function variant (Glu88Ter) t ...

Nature Publishing Group2016

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

Amalio Telenti, Jérémie Perreaud, Danielle Thompson, Paul Jack Mc Laren, Daniel Sauter

Background: Known antiretroviral restriction factors are encoded by genes that are under positive selection pressure, induced during HIV-1 infection, up-regulated by interferons, and/or interact with viral proteins. To identify potential novel restriction ...

Biomed Central Ltd2015

Polymorphisms of large effect explain the majority of the host genetic contribution to variation of HIV-1 virus load

Amalio Telenti, Jacques Fellay, Istvan Bartha, Paul Jack Mc Laren

Previous genome-wide association studies (GWAS) of HIV-1-infected populations have been underpowered to detect common variants with moderate impact on disease outcome and have not assessed the phenotypic variance explained by genome-wide additive effects. ...

National Academy of Sciences2015

The Genomic Signature of Population Reconnection Following Isolation: From Theory to HIV

Séverine Vuilleumier Varisco, Amalio Telenti, Jeffrey David Jensen

Ease of worldwide travel provides increased opportunities for organisms not only to colonize new environments but also to encounter related but diverged populations. Such events of reconnection and secondary contact of previously isolated populations are w ...

Genetics Society of America2015

The Characteristics of Heterozygous Protein Truncating Variants in the Human Genome

Amalio Telenti, Jacques Fellay, Istvan Bartha, Paul Jack Mc Laren, Nimisha Chaturvedi

Sequencing projects have identified large numbers of rare stop-gain and frameshift variants in the human genome. As most of these are observed in the heterozygous state, they test a gene's tolerance to haploinsufficiency and dominant loss of function. We a ...

Public Library Science2015

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

Amalio Telenti, Jacques Fellay, Istvan Bartha

Systemic immune activation, a major determinant of human immunodeficiency virus (HIV) disease progression, is the result of a complex interplay between viral replication, dysregulation of the immune system, and microbial translocation due to gut mucosal da ...

Oxford University Press2015

On Non-cooperative Genomic Privacy

Jean-Pierre Hubaux, Mathias Jacques Jean-Marc Humbert, Amalio Telenti, Erman Ayday

Over the last few years, the vast progress in genome sequencing has highly increased the availability of genomic data. Today, individuals can obtain their digital genomic sequences at reasonable prices from many online service providers. Individuals can st ...

2015

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

Amalio Telenti, Jacques Fellay, Istvan Bartha, Paul Jack Mc Laren

Background: There is an ever-increasing volume of data on host genes that are modulated during HIV infection, influence disease susceptibility or carry genetic variants that impact HIV infection. We created GuavaH (Genomic Utility for Association and Viral ...

BioMed Central2014

Disentangling human tolerance and resistance against HIV

Amalio Telenti, Jacques Fellay, Paul Jack Mc Laren

In ecology, "disease tolerance" is defined as an evolutionary strategy of hosts against pathogens, characterized by reduced or absent pathogenesis despite high pathogen load. To our knowledge, tolerance has to date not been quantified and disentangled from ...

Public Library Science2014

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

Amalio Telenti, Julia di Iulio, Jacques Fellay, Istvan Bartha, Christian Axel Wandall Thorball

HIV latency is a major obstacle to curing infection. Current strategies to eradicate HIV aim at increasing transcription of the latent provirus. In the present study we observed that latently infected CD4+ T cells from HIV-infected individuals failed to pr ...

Public Library Science2014

Reconciling Utility with Privacy in Genomics

Jean-Pierre Hubaux, Mathias Jacques Jean-Marc Humbert, Amalio Telenti, Erman Ayday

Direct-to-consumer genetic testing makes it possible for everyone to learn their genome sequences. In order to contribute to medical research, a growing number of people publish their genomic data on the Web, sometimes under their real identities. However, ...

2014

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

Amalio Telenti, Jacques Fellay, Istvan Bartha, Paul Jack Mc Laren, Ioannis Xenarios

Loss-of-function variants in innate immunity genes are associated with Mendelian disorders in the form of primary immunodeficiencies. Recent resequencing projects report that stop-gains and frameshifts are collectively prevalent in humans and could be resp ...

Public Library Science2014

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

Amalio Telenti, Jacques Fellay, Xuan Li

Background. Persons infected with human immunodeficiency virus (HIV) have increased rates of coronary artery disease (CAD). The relative contribution of genetic background, HIV-related factors, antiretroviral medications, and traditional risk factors to CA ...

Oxford University Press2013