Mark F. Bennett

This paper uses automated patch-clamp assays to reclassify SCN1A missense variants, changing classifications for 50% of tested variants.

The paper evaluates ddPCR as a primary diagnostic tool for vascular anomalies, finding it detects 51% of pathogenic variants in a cohort, with an overall diagnostic yield of 75% when combined with NGS.

nf-cavalier automates variant annotation, filtering, and reporting for rare Mendelian diseases using customizable criteria and generates user-friendly outputs for clinical teams.

This study uses deep sequencing to identify genetic variants in focal cortical dysplasias, finding pathogenic variants in 71% of cases and highlighting the importance of somatic variants in FCDIIb.

This paper introduces KIML, a machine learning framework that integrates experimental data with biological knowledge to improve disease gene prioritisation, showing better performance than existing methods.

Genome sequencing improves diagnostic yield for developmental and epileptic encephalopathies by identifying structural and non-coding variants missed by exome or gene panel testing.

The paper introduces a computational model to quantify tandem repeat instability using long-read sequencing data and applies it to identify unstable alleles in 256 HPRC cell lines.

The paper reports a novel complex structural variant at the FBRSL1 locus causing a dominant-negative mechanism, leading to a severe developmental and epileptic encephalopathy in a patient with additional congenital abnormalities.

The paper identifies RNU2-2 variants as a frequent cause of neurodevelopmental disorders, both dominant and recessive, in a large cohort of individuals with rare disorders.

The paper introduces a new TR catalog, TRExplorer v1.0, containing 4.86 million loci, designed for both short-read and long-read analyses and includes variation clusters identified using long-read HiFi data.

The paper constructs TRCompDB, a database of 4.4 million tandem repeat loci across 832 human genomes, revealing mutation rates and dynamics influenced by recombination and duplication context.

This study identifies a novel intronic GAA repeat expansion in FGF14 as a cause of autosomal dominant adult-onset ataxia, with (GAA)>335 being fully penetrant and (GAA)>250 likely pathogenic.

This study identifies 18 high-confidence genetic variants in 26% of childhood apraxia of speech cases, expanding the list of candidate genes and highlighting shared pathways with other neurodevelopmental disorders.

REViewer visualizes sequencing data around long repeat expansions by reconstructing haplotypes and aligning reads, improving the assessment of repeat genotype calls and detecting interruptions.

iLINCS provides a web-based platform for analyzing omics signatures of diseases and cellular perturbations through integrative analytics and visualization tools.

The paper introduces superSTR, an ultrafast alignment-free method for detecting repeat expansions in DNA and RNA sequencing data, identifying known and novel mutations in human and mouse datasets.

The paper identifies loss-of-function KCNH2 variants as enriched in SUDEP patients compared to epilepsy controls, suggesting a genetic biomarker for SUDEP risk.

ExpansionHunter Denovo detects known and novel repeat expansions in short-read sequencing data without requiring predefined repeat catalogs.

This study validates new bioinformatic tools to identify expanded repeats, discovering a novel intronic pentamer expansion in RFC1 causing CANVAS.

The paper introduces exSTRa, a method to detect repeat expansions in WES and WGS data, showing superior performance for WES compared to existing methods.