Journal of Molecular Diagnostics最新文献

The TruSight Oncology 500 (TSO500) High-Throughput Assay is a genomic profiling assay, supported by a bioinformatic analysis pipeline to evaluate somatic single-nucleotide variations/deletions/insertions, gene amplification, microsatellite instability, tumor mutational burden (TMB), gene fusion, and splice variants in solid tumors. This study outlines the approach used by the Genomics Laboratory at the Mayo Clinic to evaluate the technical performance of TSO500. The assessment involved 104 DNA and 223 RNA samples extracted from >20 tumor types. The assay demonstrated robust performance using 40 ng of input DNA and RNA, with slightly improved results observed at 60 ng of input DNA. Tumor percentage significantly influenced assay performance, with all variants being detected at 93% and 85% and above at tumor percentage >50% and >20%, respectively. Precision exceeded 93% across all variant types, including single-nucleotide variations and deletions/insertions with a variant allele frequency of ≥5%. Accuracy was ≥97% for all variant types except for TMB, which was 83.3% when compared with the reference method. Most discordant TMB cases had scores in the range of 8 to 12 mutations per megabase. Overall, the TSO500 assay demonstrated strong performance and reliable accuracy in detecting the evaluated markers.

This article examines the frequency distribution of tier 1 pharmacogenetic variants of the Association for Molecular Pathology Pharmacogenomics Working Group Recommendations in two large (>1000 individuals) cohorts of the admixed Brazilian population, and in patients from the Brazilian Public Health System enrolled in pharmacogenetic trials. Three tier 1 variants, all in DPYD, were consistently absent, which may justify their noninclusion in genotyping panels for Brazilians; 13 variants had frequency ≤1.0%, and the remaining 21 variants ranged in frequency from 1.2% (NUDT15∗3) to 76.4% (CYP3A5∗3). The frequency of some CYP2C9, CYP2D6, CYP3A4, and VKORC1 variants differed significantly across the three major race/color categories of the Brazilian Census (White, Brown, and Black), as a consequence of different proportions of individual European and African ancestry. However, it is recommended that selection of variants for inclusion in pharmacogenetic testing panels and implementation of pharmacogenetic-informed dosing guidelines for Brazilians should not be determined by race/color categories. Native Americans (0.4% of the Brazilian population), virtually absent from the study cohorts, display wide interethnic diversity in frequency of some tier 1 variants (eg, NUDT15∗3 and TPMT∗3A) and/or differ markedly from non-Indigenous people in frequency of some variant alleles (eg, CYP2C19∗17). Collectively, the data support the notion that population diversity must be taken into account on the design and implementation of pharmacogenetic testing panels.

Previous studies have reported that mitochondrial DNA copy number (mtDNA-CN) of blood was associated with a series of aging-related diseases. However, it remains unknown whether mtDNA-CN can be a potential biomarker of acute aortic syndromes (AASs). The mtDNA-CN in blood of 190 male patients with AAS and 207 healthy controls were detected by standardized real-time quantitative PCR-based assay. The mtDNA sequencing data of blood and myocardial muscle in 134 individuals were used to analyze mtDNA somatic mutations in blood. mtDNA-CN in peripheral blood was negatively correlated with age of individuals. Further analysis based on next-generation sequencing data demonstrated numbers and heteroplasmy of mtDNA mutations were positively correlated with age. Remarkably, mtDNA-CN of patients with AAS was lower than that of healthy controls. Logistic regression also showed that mtDNA-CN was independently associated with risk of AAS. During follow-up, patients with the lowest mtDNA-CN quartile had a hazard ratio of 2.543 for all-cause-mortality and 1.964 for composite end points compared with the other patients. Moreover, multivariate Cox regression indicated that lowest mtDNA-CN quartile was independently associated with all-cause mortality in patients with AAS. Our study demonstrated a negative correlation between mtDNA-CN and age. Moreover, lower mtDNA-CN in peripheral blood was significantly associated with higher risk and worse prognosis of AAS. It provided crucial evidence supporting the potential of mtDNA-CN as a novel biomarker of AAS.

Achieving a stable deep molecular response with the option to discontinue tyrosine kinase inhibitor treatment is the new therapeutic goal for patients with chronic myeloid leukemia (CML). Several studies have shown that individuals expressing the BCR::ABL1 e14a2 transcript achieve a major molecular response more rapidly than those with the e13a2 transcript. However, technical issues may have confounded these observations, and data for pediatric patients are limited. This study analyzed the distribution of BCR::ABL1 transcript types and their association with baseline hematologic parameters and tyrosine kinase inhibitor treatment response in 102 pediatric patients with CML. Subgroups were compared on the basis of results from routine multiplex PCR and droplet digital PCR (ddPCR). The dynamics of the transcript types under therapy were evaluated in detail in patients and a CML cell line co-expressing e13a2 + e14a2. ddPCR has identified significantly more patients co-expressing e13a2 + e14a2 than classified on the basis of routine diagnostics. This has implications for the categorization of individual subgroups. Comparing transcript dynamics in individuals or a cell line expressing both variants simultaneously revealed no differences in treatment response. When analyzing clinical data based on the transcript classification of patients, it is important to use methods that detect both variants with equal sensitivity. In ddPCR, the transcript variants' ratio is accurately shown because there is no competitive template amplification, as seen in multiplex and quantitative real-time PCR.