Publications related to Exome | EPFL Graph Search

A Biallelic Truncating Variant in the TPR Domain of GEMIN5 Associated with Intellectual Disability and Cerebral Atrophy

GEMIN5 is a multifunctional RNA-binding protein required for the assembly of survival motor neurons. Several bi-allelic truncating and missense variants in this gene are reported to cause a neurodevelopmental disorder characterized by cerebellar atrophy, i ...

2023

Variants in USP48 encoding ubiquitin hydrolase are associated with autosomal dominant non-syndromic hereditary hearing loss

Nicolas Jean Philippe Guex

Non-Syndromic Hereditary Hearing Loss (NSHHL) is a genetically heterogeneous sensory disorder with about 120 genes already associated. Through exome sequencing (ES) and data aggregation, we identified a family with six affected individuals and one unrelate ...

Oxford University Press2021

Genomic Instability Profiles at the Single Cell Level in Mouse Colorectal Cancers of Defined Genotypes

Maxim Norkin, Jörg Hülsken, Paloma Ordonez Moran

The genomes of many human CRCs have been sequenced, revealing a large number of genetic alterations. However, the molecular mechanisms underlying the accumulation of these alterations are still being debated. In this study, we examined colorectal tumours t ...

2021

Integrated proteogenomic deep sequencing and analytics accurately identify non-canonical peptides in tumor immunopeptidomes

Didier Trono, George Coukos, Marion Leleu, Evaristo Jose Planet Letschert, Markus Müller, Florian Huber, Laia Simo Riudalbas, Delphine Yvette L Grun, Ioannis Xenarios, Lin Zhang, Alexandre Harari, Marion Arnaud

Efforts to precisely identify tumor human leukocyte antigen (HLA) bound peptides capable of mediating T cell-based tumor rejection still face important challenges. Recent studies suggest that non-canonical tumor-specific HLA peptides derived from annotated ...

Nature Research2020

Genetic spectrum of retinal dystrophies in Tunisia

Imen Habibi

We report the molecular basis of the largest Tunisian cohort with inherited retinal dystrophies (IRD) reported to date, identify disease-causing pathogenic variants and describe genotype-phenotype correlations. A subset of 26 families from a cohort of 73 f ...

Nature Research2020

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

Jacques Fellay, Christian Axel Wandall Thorball, Alessandro Borghesi

Background: The primary hurdle for the eradication of HIV-1 is the establishment of a latent viral reservoir early after primary infection. Here, we investigated the potential influence of human genetic variation on the HIV-1 reservoir size and its decay r ...

LIPPINCOTT WILLIAMS & WILKINS2020

Mutations in VSX2, SOX2, and FOXE3 Identified in Patients with Micro-/Anophthalmia

Imen Habibi

Anophthalmia and microphthalmia (A/M) are rare distinct phenotypes that represent a continuum of structural developmental eye defects. Here, we describe three probands from an Egyptian population with various forms of A/M: two patients with bilateral anoph ...

2019

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

Jacques Fellay, Christian Hammer, Nimisha Chaturvedi, Petar Scepanovic, Samira Asgari

Acute liver failure (ALF) or fulminant hepatitis is a rare, yet severe outcome of infection with hepatitis B virus (HBV) that carries a high mortality rate. The occurrence of a life-threatening condition upon infection with a prevalent virus in individuals ...

2019

Detection and benchmarking of somatic mutations in cancer genomes using RNA-seq data

Philipp Bucher, Alexandre Coudray

To detect functional somatic mutations in tumor samples, whole-exome sequencing (WES) is often used for its reliability and relative low cost. RNA-seq, while generally used to measure gene expression, can potentially also be used for identification of soma ...

2018

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

Jacques Fellay, Istvan Bartha, Samira Asgari, Christoph Berger, Paul Jack Mc Laren, Richard Wong

One out of three pediatric sepsis deaths in high income countries occur in previously healthy children. Primary immunodeficiencies (PIDs) have been postulated to underlie fulminant sepsis, but this concept remains to be confirmed in clinical practice. Pseu ...

Frontiers Media Sa2016

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

Evolutionary dynamics of coding and non-coding transcriptomes

Anamaria Necsulea

Gene expression changes may underlie much of phenotypic evolution. The development of high-throughput RNA sequencing protocols has opened the door to unprecedented large-scale and cross-species transcriptome comparisons by allowing accurate and sensitive a ...

Nature Publishing Group2014

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

Jacques Fellay, Amalio Telenti, 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

ALDH1A3 loss of function causes bilateral anophthalmia/microphthalmia and hypoplasia of the optic nerve and optic chiasm

The major active retinoid, all-trans retinoic acid, has long been recognized as critical for the development of several organs, including the eye. Mutations in STRA6, the gene encoding the cellular receptor for vitamin A, in patients with MatthewWood syndr ...

Oxford University Press2013

Assessment of transcript reconstruction methods for RNA-seq

We evaluated 25 protocol variants of 14 independent computational methods for exon identification, transcript reconstruction and expression-level quantification from RNA-seq data. Our results show that most algorithms are able to identify discrete transcri ...

Nature Publishing Group2013

IROme, a New High-Throughput Molecular Tool for the Diagnosis of Inherited Retinal Dystrophies

Tatiana Favez, Pascal Escher, Alexandra Iouranova

The molecular diagnosis of retinal dystrophies is difficult because of the very important number of genes implicated and is rarely helped by genotype-phenotype correlations. This prompted us to develop IROme, a custom designed in solution-based targeted ex ...

Hindawi Publishing Corporation2013

Whole-Exome Sequencing Identifies Mutations in GPR179 Leading to Autosomal-Recessive Complete Congenital Stationary Night Blindness

Congenital stationary night blindness (CSNB) is a heterogeneous retinal disorder characterized by visual impairment under low light conditions. This disorder is due to a signal transmission defect from rod photoreceptors to adjacent bipolar cells in the re ...

2012

Analysis of HIV-1 Expression Level and Sense of Transcription by High-Throughput Sequencing of the Infected Cell

Jacques Rougemont, Amalio Telenti

Next-generation sequencing offers an unprecedented opportunity to jointly analyze cellular and viral transcriptional activity without prerequisite knowledge of the nature of the transcripts. SupT1 cells were infected with a vesicular stomatitis virus G env ...

American Society for Microbiology2011