whole-exome sequencing

EXaCT-2 is a whole exome sequencing platform that detects various cancer-related genomic features with high accuracy and sensitivity, outperforming standard assays in detecting sub-clonal mutations and molecular metrics.

The paper introduces a genome browser for Parkinson's disease genomic data, integrating WGS and CES samples with variant annotations and ancestry stratification.

This study calibrates in-frame indel variant effect predictors for clinical classification, showing they reach multiple evidence levels but perform worse than missense predictors.

This paper introduces SubNetDL, a deep learning model that uses subclonal mutation profiles and protein-protein interaction networks to predict cancer therapy response, achieving strong performance across multiple cancer types and treatment modalities.

The paper introduces LongevityBench, a benchmark to evaluate LLMs' ability to understand aging biology and predict age-related outcomes from biodata.

This study identifies inherited genetic risk factors in young-onset lung cancer, finding higher burdens of rare pathogenic variants in DDR and cilia-related genes and elevated polygenic risk scores.

The paper evaluates six somatic variant callers on high coverage tumour-only amplicon sequencing data, finding FreeBayes, VarScan, MuTect2, and Pisces perform best.

The paper investigates the effect of rare coding variants in schizophrenia-associated genes on generalised cognition in the UK Biobank using exome-sequencing data.

This study identifies RAS mutations as a key driver of extramedullary acute myeloid leukemia, showing their role in promoting leukemic cell migration and infiltration through the JAML-PI3K/AKT pathway.

The paper identifies biases in estimating heritability from ultra-rare variants and shows that accounting for these biases reveals significant heritability estimates for several traits.

Berrylyzer is a variant prioritization system for prenatal genetic diagnosis that outperforms existing tools in ranking diagnostic variants and recall rates.

This study integrates EBV status into DLBCL genetics by analyzing sequencing data and cell lines, finding EBV-positive DLBCL is heterogeneous and current cell lines poorly model tumor complexity.

This study evaluates cancer risk and mortality in individuals with PALB2 pathogenic variants using genomic data from two cohorts, finding increased cancer odds and mortality.

The paper introduces muat, a transformer-based tool for tumour classification using somatic variants, achieving high accuracy across different cohorts without retraining.

OncoMORPHIA provides an interactive web platform for visualizing and annotating cancer mutations using 3D structures and clinical data from multiple sources.

OncoVI is a Python-based tool that automates oncogenicity classification of somatic variants using guidelines, achieving 80% accuracy on test data and 79% agreement with expert assessments.

This study benchmarks somatic mutation detection using the human pangenome reference and finds improved accuracy, especially in East Asian individuals.

This study uses spatial multi-omics to show cSCLC has a monoclonal origin, lineage plasticity, and distinct microenvironment niches, leading to a new diagnostic assay.

This paper introduces GroupSig, a framework to overcome sparsity in clinical targeted-panel sequencing data, identifying inherited determinants of mutational signatures in cancer.

This paper improves variant effect predictors by calibrating them gene- and domain-aware, increasing evidence assignment and accuracy for variant classification.

This study identifies a germline BRIP1 variant linked to childhood cancer, showing it causes genomic instability and creates therapeutic vulnerabilities.

This study investigates genomic imprinting in Scots pine using haploid megagametophyte tissue to resolve parental alleles, finding no evidence of imprinting in conifers.

The paper performs whole exome sequencing on 44,028 British South Asians to identify gene-phenotype associations and knockout genes, finding novel links and implications for drug development.

gnomAD v4 (730,947 exomes) brings LOFTEE-2 loss-of-function annotation (0.90 precision, strict mode), missense-aware constraint, and LLM-mined literature evidence combined with constraint to rank disease genes.

CanVar-UK is a web platform that supports collaborative interpretation of germline variants in cancer susceptibility genes by integrating variant data, clinical information, and expert discussions.

This study shows that thermal adaptation across yeast species involves convergent changes in conserved regulatory networks, despite divergent phenotypic outcomes.

This study implements whole-exome sequencing in Algeria for neurodevelopmental disorders, achieving molecular diagnoses in 8/14 cases and highlighting challenges in variant interpretation and database underrepresentation.

COBT is a gene-based rare variant burden test for case-only studies that outperforms existing methods and identifies novel candidate variants in rare diseases.

This study identifies digenic inheritance of SPG7 and AFG3L2 mutations as a cause of motor neuron and cerebellar disorders in 17 patients.