whole-exome sequencing

The paper evaluates the NeuroBooster Array's accuracy in detecting GBA1 variants, finding it correctly identifies most carriers but has notable false positives and missed calls.

This paper introduces a variant filtering framework called SMART filtering to improve diagnostic outcomes in genome sequencing by prioritizing non-coding and regulatory variants.

This study analyzes genetic variation in older Lebanese adults to distinguish reference sampling biases from true allele frequency differences and genotype expectations.

The paper identifies rare genetic variants in DYM causing Dyggve-Melchior-Clausen disease through reanalysis of whole-exome sequencing data from affected individuals.

The paper calibrates AlphaGenome Variant Impact (AVI) and SpliceAI2 scores for variant classification, showing their performance across different variant classes and comparison methods.

This study uses exome sequencing to identify genetic variants in the Mexican Jewish Community, finding higher rates of carrier status and novel alleles compared to standard panels.

An AI-assisted C++17 port of VarDictJava gives byte-identical calls on five exome samples while running 3.7-4.8 times faster on one core and needing 8-17 times less memory.

This paper benchmarks the AlphaGenome Variant Impact score against SpliceAI on post-release ClinVar classifications and experimental splicing assays, finding AVI performs well but not outperforms splicing predictors on AUROC.

IVA uses a small language model to perform local genomic variant interpretation, achieving high sensitivity but lower precision in identifying pathogenic variants.

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

The paper proposes a weighted estimation method to correct for imperfect mutation detection in tumor sequencing due to intra-tumor heterogeneity, reducing bias and type I error.

Organoids grew from 13 of 27 resected hepatocellular carcinomas. The sequenced lines kept parental mutations, and solid rather than cystic growth marked shorter progression-free survival (HR 13.91).

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 55 individuals with pathogenic PTEN variants in a population-based cohort, revealing higher prevalence and broader clinical features of PHTS than previously recognized.

NYX provides fast, lossless compression for common omics data formats, achieving better compression ratios and speed than existing codecs.

The paper identifies a KIAA0586 c.1815G>A founder allele associated with short-rib polydactyly syndrome type IV in Romani families and reports its higher frequency in Hungarian Romani individuals.

SCAR introduces controlled mutations, fragmentation, and damage to sequencing data for benchmarking analyses affected by these factors.

This study examines genetic and immune heterogeneity in HCC, finding significant discordance in genetic and immune profiles between multifocal tumours.

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.

The paper identifies recurrent copy-number alterations in RCC brain metastases and shows their association with poor prognosis and metastatic potential across multiple cancers.

T-Rex provides a standardized, no-programming-required tool for analyzing whole-exome sequencing trio data, achieving high precision and sensitivity in variant calling and filtering.

Genomize-SEQ is a web-based platform for genomic variant classification and prioritization, achieving high accuracy in identifying causative variants for rare diseases.

The paper develops a scalable framework to generate harmonized mtDNA datasets from existing sequencing data across biobanks, enabling population-scale mitochondrial genomics without new sequencing.

The paper presents a machine learning model that predicts pathogenic DNA variants using a semantic approach combined with CRF and BiLSTM, achieving state-of-the-art performance.

This study evaluates methods to correct cytosine deamination artifacts in FFPE sequencing, finding enzymatic repair is most effective and FFPErase is the best computational method.

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.

This paper presents a scalable workflow for producing high-purity circular single-stranded DNA using an M13 phagemid system, achieving yields of 120-195 µg from 300 mL culture.

STR-PG provides a scalable framework for short-read STR genotyping by decoupling locus representation from allele content, reducing computational costs while maintaining accuracy.

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