A Rare Case of X-Linked Four-Way Philadelphia Chromosome Translocation with Therapeutic Challenges and Clonal Evolution.

BACKGROUND: Chronic myeloid leukemia (CML), a myeloproliferative neoplasm defined by the BCR::ABL1 fusion gene arising from the Philadelphia chromosome (Ph) translocation t(9:22)(q34;q11), exhibits diverse clinical courses often influenced by additional chromosomal aberrations (ACAs). This report presents a case of CML har-boring a novel four-way Ph translocation involving the X chromosome, offering insights into the interplay between complex karyotypes and treatment response and emphasizing the need for further research into the role of ACAs in CML management. METHODS: A 42-year-old man diagnosed with CML in the accelerated phase presented a novel four-way Ph translocation involving chromosomes X, 5, 9, and 22: 46,Y,t(X;5;9;22)(q26;q15;q34;q11.2). Despite achieving a major molecular response initially with imatinib and nilotinib, BCR::ABL1 levels (international scale) increased up to 24.0%, which prompted the use of second-line nilotinib. RESULTS: Follow-up bone marrow (BM) studies revealed clonal evolution with trisomy 8 and an unclassified ABL1 mutation (E292V), potentially contributing to resistance. Though a transient major molecular response (MMR) occurred after a switch to third-line dasatinib, this change failed to achieve a deep molecular response, and BCR-ABL1 levels were elevated above the MMR. CONCLUSIONS: This case highlights the challenge of ACAs impacting CML treatment response and prognosis. Limited knowledge exists on complex Ph translocations involving the X chromosome, but this report contributes data for further research. Understanding ACA effects on therapeutic response and prognosis requires a detailed study of such complex chromosomal aberrations.

Comparison of Xpert Xpress SARS-CoV-2 Assay Compared with Standard M nCoV Real-Time PCR: Prospective Study.

BACKGROUND: Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), can be diagnosed using rapid real-time polymerase chain reaction (PCR), real-time reverse transcription PCR (rRT-PCR), or rapid antigen testing. Among these, rRT-PCR is considered the gold standard assay. The Xpert Xpress SARS-CoV-2 assay is a rapid, real-time PCR test; approved by the Korean Disease Control and Prevention Agency in 2020. Current performance of the Xpert assay (Xpert) with the STANDARD M nCoV Real-Time Detection kit (SD) were determined. METHODS: All samples used by the SD test team were immediately transferred to the Xpert test team within 24 hours. Both tests were conducted between April 2023 and July 2023. Exclusion criteria were studies which show either inconclusive, invalid, or erroneous results. Positive rate, sensitivity, specificity, overall concordance rate, positive concordance rate, discordance rate, false-positive rate, and false-negative rates of the Xpert assay with the STANDARD M nCoV Real-Time Detection kit were determined. RESULTS: Samples from 347 patients (174 men and 173 women) with a median age of 60 years (range; 6 - 90 years) were included. Positive rate, sensitivity, specificity, overall concordance rate, positive concordance rate, discordance rate, false-positive rate, and false-negative rates of the Xpert assay were 11.2%, 82.1%, 95.0%, 93.9%, 6.6%, 6.1%, 41.0%, and 1.6%, respectively. CONCLUSIONS: COVID-19 results from Xpert should be confirmed through rRT-PCR because of low sensitivity (82.1%) and high false-positive rate (41.0%).

Comparison of Positive/Inconclusive Xpert Xpress SARS-CoV-2 with the Standard M nCoV Real-Time Detection.

BACKGROUND: COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), can be diagnosed using rapid real-time PCR, real-time reverse transcription PCR (rRT-PCR), or rapid antigen testing. Among these, rRT-PCR is considered the gold standard assay. The Xpert Xpress SARS-CoV-2 assay is a rapid real-time PCR test, approved by the Korean Disease Control and Prevention Agency in 2020. The overall concordance and positive concordance rates of the Xpert assay with the STANDARD M nCoV Real-Time Detection kit were determined. METHODS: All samples with positive or inconclusive Xpert test results from July 2021 to February 2023 that underwent confirmatory testing using the reference rRT-PCR assay were included in the analysis. RESULTS: Samples from 224 patients (93 men and 131 women) with a median age of 59 years (range 15 - 90 years) were included. Of 212 samples that tested positive using Xpert, 112 (52.8%) were true positves and 100 (47.2%) were false positives on rRT-PCR testing. The overall concordance and positive concordance rates were 52.8% (112/212) and 54.5% (112/224), respectively. In the Xpert positive group, the samples had a lower Ct value for the E gene than the N2 gene. The Ct values for the E and N2 genes were significantly lower in the positive group than in the inconclusive group. CONCLUSIONS: Positive or inconclusive Xpert results should be confirmed by the gold standard rRT-PCR for early control of this disease. Furthermore, Korea's policy should be reconsidered given the high false-positive rate of the rapid real-time PCR Xpert Xpress SARS-CoV-2 assay.

The Usefulness of the Ratio of Antigen-Autoantibody Immune Complexes to Their Free Antigens in the Diagnosis of Non-Small Cell Lung Cancer.

Autoantibodies against specific lung cancer-associated antigens have been suggested for the performance of lung cancer diagnosis. This study aimed to evaluate the diagnostic performance of the antigen-autoantibody immune complex (AIC) against its free antigens for CYFRA21-1, ProGRP, neutrophil gelatinase-associated lipocalin (NGAL), and neuron-specific enolase (NSE) in non-small cell lung cancer (NSCLC). In total, 85 patients with NSCLC and 120 healthy controls (HCs) were examined using a 9-guanine DNA chip method. The ratios of AICs to their antigens and the combinations of ratios consisting of two to four markers were calculated. The levels of AICs for CYFRA21-1, ProGRP, NGAL, and NSE were higher than those for their free antigens in all participants. The levels of each free antigens distinguished patients with NSCLC from the HCs. The ratios of the AIC to its antigen and seven combinations of two to four ratios were significantly higher in patients with NSCLC than in the HCs. Excellent diagnostic performance was observed for all combination ratios (C4-1), with 85.9% sensitivity and 86.7% specificity at a 3.51 cut-off. Higher sensitivity was observed in the early stages (0-I) and adenocarcinoma than in stages II-IV and other pathological types. Combining all ratios of AICs and their antigens for all four markers was useful when diagnosing NSCLC.

Analytical Performance and Comparability of Three New Coagulation Analyzers.

BACKGROUND: Analytical performance should be evaluated before a new coagulation analyzer is adopted in a clinical laboratory. The objective of this study was to evaluate analytical performances of three new coagulation analyzers (STA-R Max3, CN-6000, and Cobas t511) and compare them based on the following four coagulation parameters: prothrombin time (PT), activated partial thromboplastin time (aPTT), fibrinogen, and D-dimer. METHODS: A total of 427 plasma samples, including fresh and frozen/thawed plasma spanning wide ranges. Each of the manufacturers' quality control samples were used for the evaluation. Analytical performances were evaluated. Parameters considered were precision, carryover, verification of analytical measurement range, auto-dilution, and reference range according to the CLSI guidelines (H57-A). The results of each parameter were compared between STA-R compact (currently in use) and three new analyzers using fresh plasma. The results were compared among three new analyzers using fresh and frozen/thawed plasma, and samples with interferences of hemolysis/icterus/ lipemia (H/I/L). RESULTS: Analytical performances were excellent for all analyzers within each manufacturer's target based on results of precision, carryover, linearity, and verifications of auto-dilution, and reference range. Results for four parameters (PT/aPTT/fibrinogen/D-dimer) with the three new analyzers using fresh samples were well-correlated with those of STA-R Compact except for D-dimer tests (Pearson's r: 0.84 to 1.00). Good correlations were observed between the new analyzers with the total samples (fresh and frozen/thawed samples) (Pearson's r, 0.86 to 0.97). However, weaker correlation and/or higher mean bias% were observed for aPTT and D-dimer with total samples and for four parameters with normal samples rather than abnormal samples across the three analyzers. Differences were more prominent with H/I/L samples, especially between STA-R Max3 and CN-6000 or Cobas t511 for PT, aPTT, and D-dimers. CONCLUSIONS: With excellent analytical performances, the three new coagulation analyzers demonstrated good correlations, although high variabilities were seen for aPTT and D-dimers. High variability in comparison analysis might be mainly attributed to differences in reference and reportable ranges of each parameter across the three different analyzers.

9G TestTM Cancer/Lung: A Desirable Companion to LDCT for Lung Cancer Screening.

A complimentary biomarker test that can be used in combination with LDCT for lung cancer screening is highly desirable to improve the diagnostic capacity of LDCT and reduce the false-positive rates. Most importantly, the stage I lung cancer detection rate can be dramatically increased by the simultaneous use of a biomarker test with LDCT. The present study was conducted to evaluate 9G testTM Cancer/Lung's sensitivity and specificity in detecting Stage 0~IV lung cancer. The obtained results indicate that the 9G testTM Cancer/Lung can detect lung cancer with overall sensitivity and specificity of 75.0% (69.1~80.3) and 97.3% (95.0~98.8), respectively. The detection of stage I, stage II, stage III, and stage IV cancers with sensitivities of 77.5%, 78.1%, 67.4%, and 33.3%, respectively, at the specificity of 97.3% have never been reported before. The receiver operating characteristic curve analysis allowed us to determine the population-weighted AUC of 0.93 (95% CI, 0.91-0.95). These results indicate that the 9G testTM Cancer/Lung can be used in conjunction with LDCT to screen lung cancer. Furthermore, obtained results indicate that the use of 9G testTM Cancer/Lung with LDCT for lung cancer screening can increase stage I cancer detection, which is crucial to improve the currently low 5-year survival rates.

Correction: Quantification of CYFRA 21-1 and a CYFRA 21-1-anti-CYFRA 21-1 autoantibody immune complex for detection of early stage lung cancer.

Correction for 'Quantification of CYFRA 21-1 and a CYFRA 21-1-anti-CYFRA 21-1 autoantibody immune complex for detection of early stage lung cancer' by Keum-Soo Song et al., Chem. Commun., 2019, 55, 10060-10063.

Quantification of CYFRA 21-1 and a CYFRA 21-1-anti-CYFRA 21-1 autoantibody immune complex for detection of early stage lung cancer.

Population-based screening of stage 0-I lung cancer is crucial to save lives. In this article, we describe the development of a method for the detection of a CYFRA 21-1-autoantibody complex and CYFRA 21-1 in plasma samples. The CIC/CYFRA 21-1 ratio allows the detection of stage I-IV lung cancer with 76.0% sensitivity and 87.5% specificity.

Utilization of Archived Plasma to Detect Epidermal Growth Factor Receptor Mutation in Non-Small Cell Lung Cancer Patients.

Precision medicine has received increased attention as an effective approach for the treatment of cancer patients. Because of challenges associated with the availability of archived tissue, liquid biopsies are often performed to detect cancer-specific mutations. One of the major advantages of the liquid biopsy is that the treatment can be monitored longitudinally, even after the tumor tissue is no longer available. In a clinical setting, one component of precision medicine is the detection of cancer-specific mutations using archived samples. In this study, we evaluated the epidermal growth factor receptor (EGFR) mutation status of samples of lung cancer patients stored before introduction of the plasma EGFR test at our institution. The aim of this study was to validate the utility of archived plasma samples for detection of the EGFR mutation in nonsmall cell lung cancer (NSCLC) patients. The Cobas® EGFR Mutation Test v2 was the first liquid biopsy test approved as a companion diagnostic test for patients with NSCLC treated with tyrosine kinase inhibitors. We tested for the EGFR mutation in 116 plasma samples archived in the biobank, and the results were compared with those obtained in the tissue or cytology EGFR mutation test. The EGFR mutation-positive rate from archived plasma was lower than that determined from tissue or cytology at 19.0% and 53.4%, respectively, and the concordance rate between the two tests was 58.6%. Of interest, five (4.3%) samples showed the T790M mutation in the plasma test, whereas this mutation was only detected in two (1.7%) tissue/cytology samples. Five (4.3%) samples were additionally positive in the plasma test. Overall, these results indicate that archived plasma samples can serve as an alternative source for the plasma EGFR mutation test when tissue samples are not available, and can improve precision medicine and long-term follow-up in a noninvasive manner.

Clinical utility of the Xpert MRSA assay for early detection of methicillin-resistant Staphylococcus aureus.

Methicillin-resistant Staphylococcus aureus (MRSA) is responsible for many nosocomial and community-acquired infections, resulting in significant morbidity and mortality. A practical way to limit the spread of MRSA is early detection and proper treatment. However, screening culture for MRSA typically requires 2-3 days. The Xpert MRSA assay (Cepheid, Sunnyvale, CA, USA) is a real-time polymerase chain reaction-based assay developed for screening an MRSA-specific DNA sequence within the staphylococcal cassette chromosome in 2 h. Lower respiratory tract specimens, such as transtracheal aspirates (TTAs) and bronchoalveolar lavage fluid (BALF), are commonly obtained from intubated patients. Therefore, using the lower respiratory tract specimens with the Xpert MRSA assay may be a practical tool for patient care. We performed the Xpert MRSA assay on 108 TTA and 21 BALF specimens from 92 patients and compared the results to those obtained by culture. The two assays showed concordant results in 120 (93.0%) cases and discordant results in 9 (7.0%) cases, which were culture­negative and Xpert MRSA-positive. Among the discordant cases, 5 patients developed culture-positive samples 2-15 days after the Xpert MRSA detected MRSA. We conclude that the Xpert MRSA assay is a rapid, sensitive and clinically useful test, particularly for the early detection of MRSA.

[Development of indicators to assess the stability of remnant blood samples stored in a biobank: experience at one institution].

BACKGROUND: One of the major concerns with biobanking is the absence of standard operating procedures to eliminate pre-analytical variation arising from sample collection, preparation, and storage. Currently, there is a lack of tools to carry out quality control procedures for stored blood samples. The aim of this study is to assess the quality of stored blood samples in our biobank and to suggest appropriate indicators for their quality control. METHODS: The stored blood samples that we tested have been registered into our biobank since 2003. These were transferred to our biobank after carrying out routine requested tests, because the samples would have otherwise been discarded. For the purpose of quality control, we analyzed the concentrations and the integrity of DNA and RNA extracted from the stored samples and tested the levels of several serum proteins; the results were compared with the corresponding pre-storage levels. RESULTS: A total of 19 samples were stored from 2006 to 2009. Of the 22 samples stored between 2003 and 2005, 50% showed complete DNA integrity. However, sufficient RNA integrity was noted in only 1 sample stored as recently as 2009. High blood urea nitrogen levels were also noted in the stored sera, but the increase did not correlate to the duration of storage. CONCLUSIONS: The amount and integrity of nucleic acids extracted from stored blood samples are potential indicators that can be used for quality control. A guideline for the quality assessment of stored blood samples in a biobank is urgently needed.