This study aims to establish a two-dimensional PCR (2D-PCR) methodology capable of simultaneously identifying HLA-A*31:01, HLA-B*15:02, HLA-B*57:01, and HLA-B*58:01 alleles to prevent adverse drug reactions (ADRs) and guide safe clinical medication use. To achieve this goal, key nucleotide sites were first selected through multiple sequence alignment for the purpose of identifying HLA alleles: c.243T and c.290T for HLA-A*31:01; c.206C, c.256G, and c.285G for HLA-B*58:01; c.362T and c.419C for...

Structural variants are critical to genetic diversity and disease, yet their detection remains challenging with conventional cytogenetic techniques, including karyotyping, fluorescence in situ hybridization, and chromosome microarray analysis. These methods often lack the resolution and sensitivity needed for comprehensive characterization of chromosomal aberrations. To address these limitations, we implemented genomic proximity mapping (GPM), a genome-wide chromosome conformation capture tec...

This study evaluated an ultraviolet (UV) mutational signature classifier applied to circulating tumor DNA (ctDNA) in cell-free DNA (cfDNA) liquid biopsies, using the FoundationOne Liquid CDx (F1LCDx) platform. Among 73,790 samples, 12.9% (9,527) met the variant threshold for signature analysis, with UV signatures detected in 3.8% (365) of cases. Of these, 51.5% (188) were initially submitted as cutaneous, 8.5% (31) as unspecified primary, and 40.0% (146) as extra-cutaneous tumors. The UV clas...

Clinical implementation of whole genome and whole exome sequencing by next generation sequencing (NGS) allows for comprehensive detection of genomic alterations. However, with the growing number of clinically relevant genes and variants there is an urgent and growing need for reference materials to optimize, validate, and quality control NGS tests. This pilot study documents the paucity of physical reference materials for widely tested genes and demonstrates the utility of in silico mutageniz...

Homologous recombination deficiency (HRD) affects 50% of ovarian cancers (OC) and influences PARP inhibitors efficacy. While one-third of HRD tumours harbour a deleterious BRCA1/2 mutation, these mutations are not the sole cause of HRD. Promoter methylation of BRCA1 and RAD51C contributes to 19% and 2% of cases, respectively.A cohort of 224 ovarian cancer (OC) patients tested for HRD validated our droplet digital PCR (ddPCR) technique. DNA was extracted from FFPE tissue, and the Genomic Insta...