whole-exome sequencing

The paper identifies latitudinal clines in gene variants related to defence and reproductive pathways in Norway spruce, suggesting local adaptation to climate conditions.

The paper analyzes somatic mutations and gene expression in TP53/PTEN DKO murine glioblastoma cell lines using WES and RNA-seq to reveal early genomic instability and later replication-driven mutations associated with malignancy and TMZ resistance.

The paper integrates exome and transcriptome data from a schizophrenia case with low polygenic risk to identify potential variants and transcriptomic abnormalities, revealing biological alterations linked to cerebrovascular disease.

The paper uses pseudo-observations of longevity to identify resilience-associated genes in rhesus macaques exposed to radiation and aging challenges.

The paper analyzes reproductive outcomes in individuals with LPA loss-of-function variants to assess the safety of Lp(a) lowering therapies.

DoAggregate performs rare-variant aggregation tests across genes, pathways, and GO terms, providing detailed cohort-level results and visualizations.

This study identifies ultra-rare damaging variants in schizophrenia risk genes and shows they are associated with earlier hospitalizations, greater childhood adversity, and poorer neuropsychological outcomes across psychotic disorders.

The paper introduces KASM to integrate functional annotations and estimate heritability of rare protein coding variants across 786,871 exomes, finding higher heritability than previous estimates.

The paper evaluates SABLE-MO's performance in identifying shared factors in multi-omics data, finding that stricter retention reduces errors but does not eliminate them.

This study identifies genomic subtypes and immune features of mucosal melanoma, linking CD163+ macrophages to immune resistance and suggesting TIM-3 blockade as a therapeutic target.

The paper identifies KCNA5 mutations under positive selection in colorectal cancer and shows they disrupt channel structure and function, affecting tumor pathways.

The paper introduces the Probability of Necessity (PN) to assess genetic diagnosis, showing it differs from penetrance and can resolve variant classification ambiguity in diseases like ischemic heart disease and Parkinson's.

The paper identifies multiple genetic variants associated with childhood apraxia of speech through whole-exome sequencing and functional analysis, proposing four novel candidate genes.

The paper identifies pervasive somatic NF1 mutations in oligodendrocyte precursors in NF-1 patients, showing clonal selection and spatial bias, and links CDKN2A loss to tumor progression.

The paper identifies a founder variant in ADAP1 associated with increased risk of schizophrenia and bipolar disorder in a Colombian genetic isolate.

iDriver improves cancer driver discovery by accounting for patient-specific mutation burden, identifying known and novel drivers across coding and noncoding regions and outperforming existing methods.

This paper uses genomic foundation models to assess how somatic mutations disrupt cancer biology and clinical outcomes across multiple cancer types.

The paper identifies deep intronic mutational hotspots using in silico mutagenesis and demonstrates that a single antisense oligonucleotide can correct multiple variants causing X-linked Alport syndrome.

The paper identifies de novo pathogenic variants in syndromic genes associated with thoracic aortic disease beyond established aortopathy genes.

This study identifies key oncogenic pathways and targetable genes in MEN1-wild-type low-grade pancreatic NETs that drive metastasis, offering a therapeutic strategy based on pathway intensity rather than mutation count.

This paper shows that tumour telomere length is influenced by patient-specific telomere length, replicating this across two cancer cohorts.

This study identifies HER2 as a prognostic marker in GCA and suggests anti-inflammatory and immune checkpoint inhibition as therapeutic strategies for HER2-negative patients.

The paper develops FunBurd to analyze gene dosage effects on 43 traits in UK-Biobank, finding pleiotropy and non-monotonic responses linked to genetic constraint and brain-specific mechanisms.

SIEVE is a deep-learning framework for variant and gene prioritization in exome studies, achieving strong discrimination and recovering known associations across diseases.

This study uses genomic data from 11,084 patients to build a variant database and identify disease-associated signals, leading to molecular diagnoses in 32 unsolved rare disease cases.

Homozygosity for hypomorphic IL23R variants (G149R, G300V, R381Q) partly impairs IL-23-dependent IFN-γ production in patient cells; with L372F (effect inferred), they are enriched in tuberculosis, not MSMD or CMC patients.

PIMO improves multi-omics integration by modeling pathway-based interactions, enhancing survival analysis and interpretability in cancer datasets.

This study introduces pseudo-haplotype analysis to characterize multi-variant configurations in BAF chromatin remodeling genes, revealing common and rare variant co-occurrence patterns across populations.

This study analyzes a diverse glioma cohort to show ancestry influences on survival, somatic alterations, and mutational processes in diffuse gliomas.