Publications associées à Zygosity

Variant-specific pathophysiological mechanisms of AFF3 differently influence transcriptome profiles

Giovanna Ambrosini, Nicolas Jean Philippe Guex, Christian Iseli

Background: We previously described the KINSSHIP syndrome, an autosomal dominant disorder associated with intellectual disability (ID), mesomelic dysplasia and horseshoe kidney,caused by de novo variants in the degron of AFF3. Mouse knock-ins and overexpre ...

BMC2024

Environment-dependent epistasis increases phenotypic diversity in gene regulatory networks

Florence Gauye, Florian Baier

Mutations to gene regulatory networks can be maladaptive or a source of evolutionary novelty. Epistasis con-founds our understanding of how mutations affect the expression patterns of gene regulatory networks, a chal-lenge exacerbated by the dependence of ...

AMER ASSOC ADVANCEMENT SCIENCE2023

Reanalysis of mtDNA mutations of human primordial germ cells (PGCs) reveals NUMT contamination and suggests that selection in PGCs may be positive

Konstantin Popadin

The resilience of the mitochondrial genome (mtDNA) to a high mutational pressure depends, in part, on negative purifying selection in the germline. A paradigm in the field has been that such selection, at least in part, takes place in primordial germ cells ...

Elsevier Sci Ltd2023

The SNP-Based Profiling of Montecristo Feral Goat Populations Reveals a History of Isolation, Bottlenecks, and the Effects of Management

Elia Vajana

The Montecristo wild goat is an endangered feral population that has been on the homonymous island in the Tuscan Archipelago since ancient times. The origins of Montecristo goats are still debated, with authors dating their introduction either back to Neol ...

MDPI2022

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

Konstantin Popadin

The A-to-G point mutation at position 3243 in the human mitochondrial genome (m.3243A > G) is the most common pathogenic mtDNA variant responsible for disease in humans. It is widely accepted that m.3243A > G levels decrease in blood with age, and an age c ...

Oxford University Press2022

Ultrafast homomorphic encryption models enable secure outsourcing of genotype imputation

Jean-Pierre Hubaux, Juan Ramón Troncoso-Pastoriza, David Jules Froelicher, Jean-Philippe Léonard Bossuat, Yiping Ma

Genotype imputation is a fundamental step in genomic data analysis, where missing variant genotypes are predicted using the existing genotypes of nearby "tag"variants. Although researchers can outsource genotype imputation, privacy concerns may prohibit ge ...

CELL PRESS2021

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

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

Jacques Fellay

Pathogen-mediated balancing selection is regarded as a key driver of host immunogenetic diversity. A hallmark for balancing selection in humans is the heterozygote advantage at genes of the human leukocyte antigen (HLA), resulting in improved HIV-1 control ...

OXFORD UNIV PRESS2020

Mutation update: TGFBI pathogenic and likely pathogenic variants in corneal dystrophies

Human transforming growth factor beta-induced (TGFBI), is a gene responsible for various corneal dystrophies. TGFBI produces a protein called TGFBI, which is involved in cell adhesion and serves as a recognition sequence for integrins. An alteration in cel ...

2019

Feature Learning of Virus Genome Evolution With the Nucleotide Skip-Gram Neural Network

Hyunjin Shim

Recent studies reveal that even the smallest genomes such as viruses evolve through complex and stochastic processes, and the assumption of independent alleles is not valid in most applications. Advances in sequencing technologies produce multiple time-poi ...

2019

Novel PDE6B Mutation Presenting with Retinitis Pigmentosa - A Case Series of Three Patients

Imen Habibi

Background Retinitis pigmentosa (RP) affects 2.5 million people worldwide. Increased identification of causative gene defects and the increasing possibility of treatment necessitates better knowledge of phenotype-genotype correlations to help identify pati ...

2019

Analysis of Inherited Optic Neuropathies

Background Inherited optic neuropathies (IONs) cover a spectrum of clinically and genetically heterogenic conditions. Genetic evaluation of patients with IONs may enable their better clinico-diagnostic assessment and management of the disease. The aim of t ...

2019

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

Identifying mutations in Tunisian families with retinal dystrophy

Imen Habibi

Retinal dystrophies (RD) are a rare genetic disorder with high genetic heterogeneity. This study aimed at identifying disease-causing variants in fifteen consanguineous Tunisian families. Full ophthalmic examination was performed. Index patients were subje ...

Nature Research2016

Mutations in the polyglutamylase geneTTLL5, expressed in photoreceptor cells and spermatozoa, are associated with cone-rod degeneration and reduced male fertility

Hereditary retinal degenerations encompass a group of genetic diseases characterized by extreme clinical variability. Following next-generation sequencing and autozygome-based screening of patients presenting with a peculiar, recessive form of cone-dominat ...

Oxford University Press2016

A Novel Recessive RPGRIP1 Mutation Causing Leber Congenital Amaurosis

Background: Leber congenital amaurosis is an early-onset childhood severe retinal dystrophy, of significant genetic heterogeneity. RPGRIP1 is ubiquitously expressed, but mutations in RPGRIP1 lead to a retina-restricted phenotype, such as Leber congenital a ...

Georg Thieme Verlag Kg2016

Detecting and Quantifying Changing Selection Intensities from Time-Sampled Polymorphism Data

Jeffrey David Jensen, Matthieu Foll, Sebastian Matuszewski, Hyunjin Shim, Stefan Jean Laurent

During his well-known debate with Fisher regarding the phenotypic dataset of Panaxia dominula, Wright suggested fluctuating selection as a potential explanation for the observed change in allele frequencies. This model has since been invoked in a number of ...

Genetics Society of America2016

Catch Me if You Can: Adaptation from Standing Genetic Variation to a Moving Phenotypic Optimum

Sebastian Matuszewski

Adaptation lies at the heart of Darwinian evolution. Accordingly, numerous studies have tried to provide a formal framework for the description of the adaptive process. Of these, two complementary modeling approaches have emerged: While so-called adaptive- ...

2015

The Characteristics of Heterozygous Protein Truncating Variants in the Human Genome

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

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

Effects of ploidy and sex-locus genotype on gene expression patterns in the fire ant Solenopsis invicta

Chitsanu Khurewathanakul, Oksana Riba Grognuz, Laurent Keller

Males in many animal species differ greatly from females in morphology, physiology and behaviour. Ants, bees and wasps have a haplodiploid mechanism of sex determination whereby unfertilized eggs become males while fertilized eggs become females. However, ...

Royal Soc2014