Publications related to Genotype-first approach

Back-to-Africa introductions of Mycobacterium tuberculosis as the main cause of tuberculosis in Dar es Salaam, Tanzania

In settings with high tuberculosis (TB) endemicity, distinct genotypes of the Mycobacterium tuberculosis complex (MTBC) often differ in prevalence. However, the factors leading to these differences remain poorly understood. Here we studied the MTBC populat ...

PUBLIC LIBRARY SCIENCE2023

Selective elimination of enterovirus genotypes by activated sludge and chlorination

Tamar Kohn, Shotaro Torii

Enteroviruses, which are commonly circulating viruses shed in the stool, are released into the sewage system and only partially removed or inactivated, resulting in the discharge of infectious enteroviruses into the environment. Activated sludge and chlori ...

2023

Genomic Diversity of Torque Teno Virus in Blood Samples from Febrile Paediatric Outpatients in Tanzania: A Descriptive Cohort Study

Mary-Anne Hartley

Torque teno virus (TTV) is considered to be an ubiquitous member of the commensal human blood virome commonly reported in mixed genotype co-infections. This study investigates the genomic diversity of TTV in blood samples from 816 febrile Tanzanian childre ...

MDPI2022

Using population-specific add-on polymorphisms to improve genotype imputation in underrepresented populations

Jacques Fellay, Zhi Ming Xu, Sina Rüeger

Genome-wide association studies rely on the statistical inference of untyped variants, called imputation, to increase the coverage of genotyping arrays. However, the results are often suboptimal in populations underrepresented in existing reference panels ...

Public Library Science2022

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

Olivier Noël Marie Naret

The focus of the work presented in this thesis is the exploration of the genetic architecture of complex human traits - at the dawn of genomic medicine. The underlying mechanisms explaining the enormously polygenic nature of most human complex traits are ...

EPFL2021

Automated phenotyping of Caenorhabditis elegans embryos with a high-throughput-screening microfluidic platform

Martinus Gijs, Matteo Cornaglia, Raphaël Etienne Jean Trouillon, Hüseyin Baris Atakan, Tunç Alkanat

The nematode Caenorhabditis elegans has been extensively used as a model multicellular organism to study the influence of osmotic stress conditions and the toxicity of chemical compounds on developmental and motility-associated phenotypes. However, the sev ...

2020

Population Genomics of Mycobacterium leprae Reveals a New Genotype in Madagascar and the Comoros

Stewart Cole, Stefanie Boy-Röttger, Andrej Benjak, Charlotte Avanzi, Philippe Busso, Pushpendra Singh, Thyago Leal Calvo

Human settlement of Madagascar traces back to the beginning of the first millennium with the arrival of Austronesians from Southeast Asia, followed by migrations from Africa and the Middle East. Remains of these different cultural, genetic, and linguistic ...

Frontiers Media SA2020

Elucidating regulatory mechanisms shaping the transcriptome and proteome of the gut immune response in Drosophila melanogaster

Michael Vincent Frochaux

Work on Drosophila melanogaster paved the way to our current understanding of modern genetics. Since then, this model organism has contributed greatly to various fields such as neurobiology, development, and immunology. The discovery and analysis of the va ...

EPFL2019

The phenotypic impact of naturally occurring genetic and molecular mitochondrial variation in a Drosophila Genetic Reference Population

Roel Paulus Josephus Bevers

Genome-wide association (GWA) studies aim to dissect the relationship between genotype and phenotype. So far, the focus has been on nuclear genetic determinants as variation in the mitochondrial genome is often low in the study cohorts. Despite this observ ...

EPFL2018

Strain-level diversity drives alternative community types in millimetre-scale granular biofilms

Christof Holliger

Microbial communities are often highly diverse in their composition, both at a coarse-grained taxonomic level, such as genus, and at a highly resolved level, such as strains, within species. This variability can be driven by either extrinsic factors such a ...

NATURE PUBLISHING GROUP2018

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

Jacques Fellay, Istvan Bartha, Paul Jack Mc Laren

Previous genetic association studies of human immunodeficiency virus-1 (HIV-1) progression have focused on common human genetic variation ascertained through genome-wide genotyping. ...

Oxford Univ Press Inc2017

De-anonymizing Genomic Databases Using Phenotypic Traits

Jean-Pierre Hubaux, Joachim Ludovic Hugonot, Kévin Clément Huguenin, Erman Ayday, Mathias Jacques Jean-Marc Humbert

People increasingly have their genomes sequenced and some of them share their genomic data online. They do so for various purposes, including to find relatives and to help advance genomic research. An individual's genome carries very sensitive, private inf ...

2015

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

Paul Jack Mc Laren

The outcome after infection with the human immunodeficiency virus type 1 (HIV-1) is a complex phenotype determined by interactions among the pathogen, the human host and the surrounding environment. An impact of host genetic variation on HIV-1 susceptibili ...

Nature Publishing Group2015

Genome-wide association study of virologic response with efavirenz-containing or abacavir-containing regimens in AIDS clinical trials group protocols

Paul Jack Mc Laren

Background Efavirenz and abacavir are components of recommended first-line regimens for HIV-1 infection. We used genome-wide genotyping and clinical data to explore genetic associations with virologic failure among patients randomized to efavirenz-containi ...

Lippincott Williams & Wilkins2015

Resistance to Diet-Induced Obesity and Associated Metabolic Perturbations in Haploinsufficient Monocarboxylate Transporter 1 Mice

Pierre Magistretti, Sylvain Eric Lengacher, Luc Pellerin

The monocarboxylate transporter 1 (MCT1 or SLC16A1) is a carrier of short-chain fatty acids, ketone bodies, and lactate in several tissues. Genetically modified C57BL/6J mice were produced by targeted disruption of the mct1 gene in order to understand the ...

Public Library of Science2013

Metabolic modeling and experimental studies on carbon and energy metabolism of Mycobacterium tuberculosis

Muhittin Emre Özdemir

Tuberculosis is an ancient human disease affecting millions of people every year. The common causative agent, Mycobacterium tuberculosis, is a peculiar pathogen that can persist in the host tissues for decades. Many of the key attributes of M. tuberculosis ...

EPFL2013

Inference about the number of contributors to a DNA mixture: Comparative analyses of a Bayesian network approach and the maximum allele count method

Kjell Konis

In the forensic examination of DNA mixtures, the question of how to set the total number of contributors (N) presents a topic of ongoing interest. Part of the discussion gravitates around issues of bias, in particular when assessments of the number of cont ...

Elsevier2012

Genotyping Microarray for CSNB-Associated Genes

PURPOSE. Congenital stationary night blindness (CSNB) is a clinically and genetically heterogeneous retinal disease. Although electroretinographic (ERG) measurements can discriminate clinical subgroups, the identification of the underlying genetic defects ...

2009

Stress, genotype and norepinephrine in the prediction of mouse behavior using reinforcement learning

Maria del Carmen Sandi Perez, Wulfram Gerstner, Gediminas Luksys

Individual behavioral performance during learning is known to be affected by modulatory factors, such as stress and motivation, and by genetic predispositions that influence sensitivity to these factors. Despite numerous studies, no integrative framework i ...

Nature Publishing Group2009

The Notch signaling pathway : hair graying and pigment cell homeostasis

Karine Schouwey

In animals, pigment cells are essential for coloration, as seen in feathers, fur, skin and eyes. In mammals, neural crest-derived melanocytes constitute the major population of pigment cells that is located mainly in the skin epidermis, as well as in hair ...

EPFL2009