whole-exome sequencing

Latent-Factor Stability Is Not Sufficient: Evaluating SABLE-MO in Simulated and Cancer Multi-Omics Data

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.

Genomic classification and immune profiling define mucosal melanoma

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.

A versatile set of computational tools for inference of genetic ancestry from human molecular data

The paper introduces RAIDS, a toolset for inferring genetic ancestry from various sequence data, including cancer and low-coverage scenarios.

Integrated Clinical-Genomic Reanalysis Identifies Diagnostic Gaps and Candidate Genes in a Pediatric Rare Disease Cohort

Analysis of Rare Coding Variation Identifies New Genetic Contributors to Schizophrenia

Ultra-rare damaging coding variants in 87,959 schizophrenia cases and 150,587 controls implicate 40 genes (16 exome-wide, 24 at 5% FDR), half overlapping autism, developmental delay or bipolar genes.

Genomic foundation model-derived disruption profiling links somatic mutations to cancer biology and clinical outcomes

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

Genomic and Transcriptomic Landscapes of MEN1-Wild-Type Low-Grade Metastatic Pancreatic NETs Uncover Key Oncogenic Drivers and Targetable Pathways

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.

Patient-Derived Glioma Models Preserve Tumor Heterogeneity and Identify Stearoyl-CoA Desaturase1 (SCD1) as a Candidate Biomarker for Precision Immunotherapy

HER2 Prognostic Significance and Therapeutic Implications in Gastric Cardia Adenocarcinoma: Insights from Multi-Omics Profiling

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.

Identification of pre-existing ubiquitous neoantigen-reactive tumor-infiltrating T-cells in a patient with metastatic pancreatic neuroendocrine tumor

This study identifies a ubiquitous neoantigen-reactive T-cell response across multiple metastatic sites in a patient with pancreatic neuroendocrine tumor, supporting the use of mutation-sharing status for neoantigen selection in immunotherapy.

clinTALL: machine learning-driven multimodal subtypeclassification and treatment outcome prediction in pediatric T-ALL

clinTALL is a deep learning framework that classifies pediatric T-ALL subtypes and predicts treatment outcomes using multimodal data, achieving high accuracy and concordance indices.

Interpretable variant effect prediction from genomic foundation model embeddings

A low-rank covariance probe on Evo 2 embeddings predicts ClinVar pathogenicity across SNVs and indels, while annotation probes plus an LLM produce mechanistic hypotheses; scores released for 4.2 million variants.

Humans homozygous for rare or common hypomorphic IL23R variants are prone to tuberculosis

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: Pathway-based Interpretable Multi-Omics interactions for multi-omics integration

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

Pan-Cancer Driver Mutation Signatures Define a Molecular Taxonomy of Tumors

This paper defines driver mutation signatures across cancers to classify tumors molecularly and link driver mutations to therapeutic vulnerabilities.

Stratified evaluation of blood RNA sequencing in a rare disease cohort

This study evaluates RNA-seq's diagnostic utility in three patient groups with non-diagnostic exome sequencing, finding higher yields in groups with candidate variants.

Characterization of the somatic landscape and transcriptional profile of breast tumors from 748 Hispanic/Latina women in California

The paper analyzes somatic mutations and transcriptional profiles in breast tumors from 748 Hispanic/Latina women, finding differences in tumor immune microenvironment ecotypes linked to ancestry and APOBEC3A/B copy-number deletions.

Tumour neoantigen repertoire computational predictions in malignant peripheral nerve sheath tumours define potential targets for immunotherapy

This study predicts neoantigen repertoires in MPNSTs and identifies immune-related differences between PRC2-Loss and PRC2-WT subtypes, highlighting potential immunotherapy targets.

Archetype analysis of lung adenocarcinoma premalignancy links heterogeneity in premalignant lesions to diverging features of invasive disease

This study identifies four molecular archetypes of lung adenocarcinoma premalignant lesions using bulk RNA and exome sequencing, linking proliferation-associated features to aggressive tumor outcomes.

Uncovering Latent Structure in Gliomas Using Multi-Omics Factor Analysis

This study uses multi-omics factor analysis to identify molecular profiles and biomarkers in gliomas, revealing relationships between methylation, genetics, and transcriptional patterns.

Clustering Digestive Tract Tumors Using Transcriptomic and Mutation Data

The paper develops a method called Newmanization to reduce tissue signals in transcriptomic data and applies it to digestive tract cancer samples, showing improved clustering and separation compared to mutation data.

Integrative immune subtyping of HNSCC reveals clinically relevant phenotypes and treatment-associated transitions

This study identifies four immune subtype clusters in HNSCC using multi-omics data and shows their association with treatment response and survival.

Integrating Epstein-Barr virus (EBV) status into diffuse large B cell lymphoma (DLBCL) genetics

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.

Integrating 730,947 exome sequences with clinical literature improves gene discovery

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.

From Single-Cell Emergent Behaviors to Clinical Outcome: PTEN-driven Migratory Efficiency as a Potential New Vulnerability in Glioblastoma

This study identifies PTEN gain-of-function mutations as linked to increased migratory efficiency in glioblastoma cells, correlating with poorer patient survival.

Multi-modal benchmarking of the Ultima UG100 and Illumina NovaSeq sequencing platforms using clinically relevant FFPE tissues

This paper benchmarks the Ultima UG100 and Illumina NovaSeq platforms on FFPE tissues for various sequencing modalities, finding they produce comparable results with subtle discrepancies in non-coding transcripts.

Co-evolution of Oncogenic KRAS Signaling and LILRBhigh Macrophages Drives Pancreatic Cancer Recurrence

This study identifies a co-evolved tumor-immune interaction involving KRAS signaling and LILRBhigh macrophages that drives PDAC recurrence and presents a therapeutic strategy targeting this axis.

Spatially Integrated Multi-Omics reveals the Multicellular Landscape of Progenitor-Driven Glioblastoma Progression

This study integrates multi-omic data from glioblastoma patients to identify a high-risk progenitor phenotype linked to poor survival and spatially defined tumor progression.

NRF2 pathway activation and SPP1⁺TREM2⁺ macrophages drive chemoradiotherapy resistance in esophageal squamous cell carcinoma

This study identifies NRF2 pathway activation and SPP1⁺TREM2⁺ macrophages as drivers of chemoradiotherapy resistance in ESCC through multi-omics analysis of clinical trial data.

OncoBERT: Context-Aware Modeling of Somatic Mutations for Precision Oncology

OncoBERT models somatic mutations in cancer to identify patient-specific subtypes and improve prediction of treatment response by integrating mutational context with clinical biomarkers.