Mathieu Bourgey

This paper benchmarks sequencing technologies and variant callers for detecting SNPs, indels, and SVs, finding that SRS is optimal for small variants while LRS excels in SV detection and complex regions.

The paper investigates the evolution of chromosome 4p loss in basal breast cancer, identifying C4orf19 as a novel gene that suppresses proliferation and is part of a kinase module.

WEGS combines low-depth whole genome and high-depth whole exome sequencing to reduce costs while maintaining variant detection accuracy in genetic studies.

The paper evaluates variant calling in difficult genomic regions using short- and long-read sequencing, showing improved performance with new methods and multi-technology approaches.

The paper investigates the association of rare loss-of-function variants in type I IFN immunity genes with severe COVID-19 and finds no significant association.

This study uses cell-free DNA methylation profiling in plasma to identify organ-specific injury and predict COVID-19 severity in hospitalized patients.

The paper identifies a batch effect in 1000 Genomes Project data causing spurious mutation calls and affecting GWAS results, suggesting legacy data may need to be retired or upgraded.

GenPipes provides a scalable framework for genomic analyses, offering pre-built pipelines and flexibility for custom workflows.

The paper uses single-cell RNA-seq to show glioblastoma recapitulates normal brain development, identifying a conserved trilineage hierarchy with glial progenitor-like cells as the origin of cancer heterogeneity and therapeutic targets.

The paper identifies NOTCH1 variants as a major genetic contributor to non-syndromic Tetralogy of Fallot, with 6% of patients carrying deleterious variants.