Mathieu Bourgey
A5003541054- Immunodeficiency and Autoimmune Disorders
- Cancer Genomics and Diagnostics
- Genomics and Rare Diseases
- Genetic Associations and Epidemiology
- Epigenetics and DNA Methylation
- Immune Cell Function and Interaction
- SARS-CoV-2 and COVID-19 Research
- interferon and immune responses
- T-cell and B-cell Immunology
- Gene expression and cancer classification
- Genetic factors in colorectal cancer
- Plant Virus Research Studies
- Chromatin Remodeling and Cancer
- Genomics and Phylogenetic Studies
- Cancer-related molecular mechanisms research
- Congenital heart defects research
- Celiac Disease Research and Management
- COVID-19 Clinical Research Studies
- Single-cell and spatial transcriptomics
- Congenital Heart Disease Studies
- Pancreatic and Hepatic Oncology Research
- Glioma Diagnosis and Treatment
- Genetics, Bioinformatics, and Biomedical Research
- Fetal and Pediatric Neurological Disorders
- Scientific Computing and Data Management
McGill University
2018-2025
McGill Genome Centre
2018-2024
Mila - Quebec Artificial Intelligence Institute
2023-2024
Ontario Genomics
2018-2023
Concordia University
2022
McGill University and Génome Québec Innovation Centre
2012-2020
University of Manchester
2019
Manchester Metropolitan University
2019
Barwon Health
2014
Medical University of Graz
2014
Pediatric glioblastomas (GBM) including diffuse intrinsic pontine gliomas (DIPG) are devastating brain tumors with no effective therapy. Here, we investigated clinical and biological impacts of histone H3.3 mutations. Forty-two DIPGs were tested for Wild-type versus mutated (K27M-H3.3) subgroups compared HIST1H3B, IDH, ATRX TP53 mutations, copy number alterations outcome. K27M-H3.3 occurred in 71 %, mutations 77 % 9 DIPGs. more frequent older children (p < 0.0001). No G34V/R-H3.3, IDH1/2 or...
Cancer stem cells are critical for cancer initiation, development, and treatment resistance. Our understanding of these processes, how they relate to glioblastoma heterogeneity, is limited. To overcome limitations, we performed single-cell RNA sequencing on 53586 adult 22637 normal human fetal brain cells, compared the lineage hierarchy developing transcriptome cells. We find a conserved neural tri-lineage centered around glial progenitor-like also that this progenitor population contains...
With the decreasing cost of sequencing and rapid developments in genomics technologies protocols, need for validated bioinformatics software that enables efficient large-scale data processing is growing.Here we present GenPipes, a flexible Python-based framework facilitates development deployment multi-step workflows optimized high-performance computing clusters cloud. GenPipes already implements 12 scalable pipelines various applications, including RNA sequencing, chromatin...
Familial recurrence studies provide strong evidence for a genetic component to the predisposition sporadic, nonsyndromic Tetralogy of Fallot (TOF), most common cyanotic congenital heart disease phenotype. Rare variants have been identified as important contributors risk disease, but relatively small numbers TOF cases studied date.We used whole exome sequencing assess prevalence unique, deleterious in largest cohort patients reported date.Eight hundred twenty-nine underwent sequencing. The...
The precisionFDA Truth Challenge V2 aimed to assess the state of art variant calling in challenging genomic regions. Starting with FASTQs, 20 challenge participants applied their variant-calling pipelines and submitted 64 call sets for one or more sequencing technologies (Illumina, PacBio HiFi, Oxford Nanopore Technologies). Submissions were evaluated following best practices benchmarking small variants updated Genome a Bottle benchmark genome stratifications. submissions included numerous...
Inborn errors of human IFN-γ-dependent macrophagic immunity underlie mycobacterial diseases, whereas inborn IFN-α/β-dependent intrinsic viral diseases. Both types IFNs induce the transcription factor IRF1. We describe unrelated children with inherited complete IRF1 deficiency and early-onset, multiple, life-threatening diseases caused by weakly virulent mycobacteria related intramacrophagic pathogens. These have no history severe disease, despite exposure to many viruses, including...
Abstract Perivascular space (PVS) burden is an emerging, poorly understood, magnetic resonance imaging marker of cerebral small vessel disease, a leading cause stroke and dementia. Genome-wide association studies in up to 40,095 participants (18 population-based cohorts, 66.3 ± 8.6 yr, 96.9% European ancestry) revealed 24 genome-wide significant PVS risk loci, mainly the white matter. These were associated with matter already young adults ( N = 1,748; 22.1 2.3 yr) enriched early-onset...
Abstract: Coeliac disease is an enteropathy due to intolerance gluten. The association between HLA‐DQ genes and CD well established. majority of patients carry the heterodimer encoded by DQA1*05/DQB1*02 , either in cis or trans . remaining part DQ DQA1*03‐DQB1*0302 aim study was estimate risks associated with different genotypes European populations. HLA information available for 470 trio families from four countries: France (117), Italy (128), Norway Sweden (225). Five DQA1‐DQB1 haplotypes...
A recent report found that rare predicted loss-of-function (pLOF) variants across 13 candidate genes in TLR3- and IRF7-dependent type I IFN pathways explain up to 3.5% of severe COVID-19 cases. We performed whole-exome or whole-genome sequencing 1,864 cases (713 with 1,151 mild disease) 15,033 ancestry-matched population controls 4 independent biobanks. tested whether pLOF these were associated COVID-19. identified only 1 mutation among 713 observed no enrichment pLOFs compared evidence...
Host genetics is a key determinant of COVID-19 outcomes. Previously, the Genetics Initiative genome-wide association study used common variants to identify multiple loci associated with However, largest impact on outcomes are expected be rare in population. Hence, studying may provide additional insights into disease susceptibility and pathogenesis, thereby informing therapeutics development. Here, we combined whole-exome whole-genome sequencing from 21 cohorts across 12 countries performed...
The basal breast cancer subtype is enriched for triple-negative (TNBC) and displays consistent large chromosomal deletions. Here, we characterize evolution maintenance of chromosome 4p (chr4p) loss in cancer. Analysis Cancer Genome Atlas data shows recurrent deletion chr4p Phylogenetic analysis a panel 23 primary tumor/patient-derived xenograft cancers reveals early deletion. Mechanistically show that associated with enhanced proliferation. Gene function studies identify an unknown gene,...
<b>Background:</b> Several studies have shown an elevated prevalence of coeliac disease (CD) in sibs patients (risk 8–12%). <b>Aim and method:</b> We evaluated the risk that children with CD will also develop CD. This cohort 188 Italian families was composed probands CD, at least one sib both parents. status determined human leucocyte antigen (HLA)-DQ genotyping performed all family members. The study used a dataset triads (127 their parents) genotyped for HLA-DQ. <b>Results:</b> overall...
Although childhood acute lymphoblastic leukemia is the most common pediatric cancer, its etiology remains poorly understood. In an attempt to replicate findings of 2 recent genome-wide association studies in a French-Canadian cohort, we confirmed 5 SNPs [rs7073837 (P=4.2 × 10−4), rs10994982 (P=3.8 rs10740055 (P=1.6 10−5), rs10821936 (P=1.7 10−7) and rs7089424 (P=3.6 10−7)] ARID5B gene with leukemia. We also selective effect for B-cell hyperdiploidy report putative gender-specific on risk...
Summary The precisionFDA Truth Challenge V2 aimed to assess the state-of-the-art of variant calling in difficult-to-map regions and Major Histocompatibility Complex (MHC). Starting with FASTQ files, 20 challenge participants applied their pipelines submitted 64 callsets for one or more sequencing technologies (~35X Illumina, ~35X PacBio HiFi, ~50X Oxford Nanopore Technologies). Submissions were evaluated following best practices benchmarking small variants new GIAB benchmark sets genome...
Cerebral white matter hyperintensities on MRI are markers of cerebral small vessel disease, a major risk factor for dementia and stroke. Despite the successful identification multiple genetic variants associated with this highly heritable condition, its architecture remains incompletely understood. More specifically, role DNA methylation has received little attention. We investigated association between hyperintensity burden in blood at ∼450 000 cytosine-phosphate-guanine (CpG) sites 9732...
Abstract Whole genome sequencing (WGS) at high-depth (30X) allows the accurate discovery of variants in coding and non-coding DNA regions helps elucidate genetic underpinnings human health diseases. Yet, due to prohibitive cost WGS, most large-scale association studies use genotyping arrays or whole exome (WES). Here we propose a cost-effective method which call “Whole Exome Genome Sequencing” (WEGS), that combines low-depth WGS WES with up 8 samples pooled sequenced simultaneously...
Abstract Brain regions drive multiple physiological functions through specific gene expression patterns that adapt to environmental influences, drug treatments and disease conditions. To generate a detailed atlas of the brain transcriptome in context diabetes, we carried out RNA sequencing hypothalamus, hippocampus, brainstem striatum Goto-Kakizaki (GK) rat model spontaneous type 2 which was applied identify transcription adaptation improved glycemic control following vertical sleeve...
The kidney and upper urinary tract develop through reciprocal interactions between the ureteric bud surrounding mesenchyme. Ureteric branching forms arborized collecting duct system of kidney, while tips promote nephron formation from dedicated progenitor cells. While cells are relatively well characterized, origin progenitors has received little attention so far. It is established that induced nephric duct, an epithelial derived intermediate mesoderm embryo. However, cell state transitions...