Journal of Molecular Diagnostics最新文献

A noninvasive test for earlier detection of pancreatic cancer in individuals at higher risk is currently unavailable. To fill this void, we devised PancSure, a laboratory developed test in compliance with clinical regulations. PancSure is based on the protein biomarkers LYVE1 and REG1B, measured in urine by enzyme-linked immunosorbent assay, and commonly utilized serum/plasma CA19.9, with an updated version of the PancRISK algorithm for data interpretation. The test was validated in a cohort of 565 patients: 117 (21%) asymptomatic patients without any known pancreatic condition or malignancies, 242 (43%) symptomatic patients with benign pancreatic diseases and 206 (36%) confirmed cancers; 161 (77.5%) stages I-II and 45 (22.5%) stages III-IV. PancSure passed all specifications during analytical validation and distinguishes early-stage resectable cancer from asymptomatic individuals with AUC of 0.93 (0.89-0.97, 95% CI) and 85-90% sensitivity (SN) and 78-87% specificity (SP); from symptomatic patients with AUC of 0.86 (0.81-0.91, 95% CI) and 83-85% SN and 72-83% SP; and from all non-cancer patients (pooled controls) with AUC of 0.89 (0.84-0.93, 95% CI) and 83-85% SN and 78-87% SP. PancSure is a noninvasive clinical-grade test with a 48-hour turnover, ready for implementation without any costly instrumentation, thus providing a viable solution for the earlier detection of pancreatic cancer in at risk groups for improved patient care.

Testing for somatic mutations in JAK2, MPL, and CALR genes is a crucial element in the diagnosis of myeloproliferative neoplasms (MPNs). This may have inadvertently led to increased requests for testing to rule out MPN, including clinical situations with low pretest probability. This article examines JAK2, MPL, and CALR testing by next-generation sequencing (NGS) with the goal of formulating practical guidelines to make test use more efficient and effective. NGS results from 1482 patients tested between 2015 and March 2022 were retrieved, along with corresponding bone marrow biopsies and complete blood cell count results performed within 90 days before NGS, and 245 cases (16.5%) were positive for pathogenic variants in JAK2, MPL, or CALR genes. The findings showed an increase in the proportion of positive cases with patient age, and a statistically significant difference in red blood cell counts and platelet counts among patients with positive versus negative results. Using these factors, simple algorithms were constructed to predict positive results with a maximum sensitivity of 91%, while potentially eliminating 28% of negative test results. However, these models still failed to identify approximately 9% of patients with MPNs. Among these missed patients, many had either primary myelofibrosis or myelodysplastic syndrome/MPN. Considering a simple triage model to help guide MPN testing could represent a more cost-effective approach, particularly if missed patients could be further reduced.

Circulating tumor DNA (ctDNA) quantification surpasses cancer antigen 15 to 3 for metastatic breast cancer surveillance. Clinical translation, however, is limited because of uncertainties about the optimal method and clinically valid ctDNA decision thresholds. Plasma-SeqSensei Breast Cancer IVD kit (PSS) is a novel assay for ctDNA molecular counting, detecting ≥0.06% variant allele fractions in AKT1, ERBB2, ESR1, KRAS, PIK3CA, and TP53. PSS was validated against droplet digital PCR (ddPCR) in 201 samples from 16 subjects with PIK3CA/TP53-mutated cancers, longitudinally sampled for a median of 93 (range, 18 to 113) weeks, three to five weekly. PSS and ddPCR ctDNA levels correlate significantly (Spearman ρ, 0.923; 95% CI, 0.898-0.941) across 0% to 43% variant allele frequency (VAF) range. PSS predicts 12-week progression with high clinical accuracy (area under the curve, 0.848; 95% CI, 0.790-0.894). PSS validates a previously developed ddPCR classifier: <10 copies/mL (0.25% VAF); excludes >100 copies/mL (2.5% VAF); and confirms progression, with negative predictive value (95% CI) of 83% (76%-88%) and positive predictive value (95% CI) of 91% (81%-96%) (weighted κ, 0.856; 95% CI, 0.797-0.915). PSS thus confirms robust clinical thresholds (10 to 100 copies/mL, 0.25% to 2.5% VAF) for metastatic breast cancer surveillance, using absolute molecular counting.

An amplicon-based targeted next-generation sequencing (NGS) assay for the detection of gene fusions in sarcomas was developed, validated, and implemented. This assay can detect fusions in targeted regions of 138 genes and BCOR internal tandem duplications. This study reviews our experience with testing on the first 652 patients analyzed. Gene fusions were detected in 238 (36.5%) of 652 cases, including 83 distinct fusions in the 238 fusion-positive cases, 10 of which had not been previously described. Among the 238 fusion-positive cases, the results assisted in establishing a diagnosis for 137 (58%) cases, confirmed a suspected diagnosis in 66 (28%) cases, changed a suspected diagnosis in 25 (10%) cases, and were novel fusions with unknown clinical significance in 10 (4%) cases. Twenty-six cases had gene fusions (ALK, ROS1, NTRK1, NTRK3, and COL1A1::PDGFB) for which there are targetable therapies. BCOR internal tandem duplications were identified in 6 (1.2%) of 485 patients. Among the 138 genes in the panel, 66 were involved in one or more fusions, and 72 were not involved in any fusions. There was little overlap between the genes involved as 5'-partners (31 different genes) and 3'-partners (37 different genes). This study shows the clinical utility of a next-generation sequencing gene fusion detection assay for the diagnosis and treatment of sarcomas.