Standard Molecular Testing Research Articles

Cancer of Unknown Primary Site: A New Era of Practice-Changing Approaches to Diagnosis, Staging, and Precision Therapy

The enigmatic syndrome of metastatic cancer of unknown primary (CUP) site has frustrated physicians and patients for decades. There has been debate whether CUP is a single biologically distinct cancer or a constellation of many different cancers with clinically undetectable anatomic primary sites. For the past 40 years, the diagnosis of a specific cancer type for most patients was indeterminate, and fit patients were usually treated as a single cancer with the same empiric chemotherapy (EC) regimens with poor overall results. The aggregate data from autopsies, clinical observations, specialized standard pathology, molecular testing, and several clinical trials support CUP as a multitude of clinically occult invasive primary tumors requiring different site-specific therapies (SSTs). In the past several years, improved genomic testing has been used, and the addition of molecular-guided therapies (MGTs) and immunotherapy (IO) has been shown to be superior for many different advanced cancers. Two older randomized prospective trials conducted before the advent of IO and most MGT failed to show a better outcome for patients with molecularly diagnosed cancers who received SST (tailored chemotherapy regimens) versus EC, although patients with more responsive tumor types appeared to benefit. Two recently reported randomized trials documented the clinical relevance of molecular diagnosis and comprehensive genomic profiling. The administration of improved precision SST guided by molecular diagnosis and characterization revealed significantly improved outcomes compared with EC. The management of patients with CUP is undergoing rapid change including the diagnosis of the presumed primary tumors, TNM staging for selected patients, molecular profiling, and an expanded improved role of precision therapies highlighting the rapid emergent new era of practice changing standards of care.

Scenario analysis and multi-criteria decision analysis to explore alternative reimbursement pathways for whole genome sequencing for blood cancer patients

BackgroundWhole genome sequencing (WGS) has transformative potential for blood cancer management, but reimbursement is hindered by uncertain benefits relative to added costs. This study employed scenario planning and multi-criteria decision analysis (MCDA) to evaluate stakeholders’ preferences for alternative reimbursement pathways, informing future health technology assessment (HTA) submission of WGS in blood cancer. MethodsKey factors influencing WGS reimbursement in blood cancers were identified through a literature search. Hypothetical scenarios describing various evidential characteristics of WGS for HTA were developed using the morphological approach. An online survey, incorporating MCDA weights, was designed to gather stakeholder preferences (consumers/patients, clinicians/health professionals, industry representatives, health economists, and HTA committee members) for these scenarios. The survey assessed participants' approval of WGS reimbursement for each scenario, and scenario preferences were determined using the geometric mean method, applying an algorithm to improve reliability and precision by addressing inconsistent responses. ResultsNineteen participants provided complete survey responses, primarily clinicians or health professionals (n = 6; 32 %), consumers/patients and industry representatives (both at n = 5; 26 %). “Clinical impact of WGS results on patient care" was the most critical criterion (criteria weight of 0.25), followed by "diagnostic accuracy of WGS" (0.21), "cost-effectiveness of WGS" (0.19), "availability of reimbursed treatment after WGS" (0.16), and "eligibility criteria for reimbursed treatment based on actionable WGS results" and "cost comparison of WGS" (both at 0.09). Participants preferred a scenario with substantial clinical evidence, high access to reimbursed targeted treatment, cost-effectiveness below $50,000 per quality-adjusted life year (QALY) gained, and affordability relative to standard molecular tests. Reimbursement was initially opposed until criteria such as equal cost to standard tests and better treatment accessibility were met. ConclusionPayers commonly emphasize acceptable cost-effectiveness, but strong clinical evidence for many variants and comparable costs to standard tests are likely to drive positive reimbursement decisions for WGS.

Deep Learning Artificial Intelligence Predicts Homologous Recombination Deficiency and Platinum Response From Histologic Slides.

Cancers with homologous recombination deficiency (HRD) can benefit from platinum salts and poly(ADP-ribose) polymerase inhibitors. Standard diagnostic tests for detecting HRD require molecular profiling, which is not universally available. We trained DeepHRD, a deep learning platform for predicting HRD from hematoxylin and eosin (H&E)-stained histopathological slides, using primary breast (n = 1,008) and ovarian (n = 459) cancers from The Cancer Genome Atlas (TCGA). DeepHRD was compared with four standard HRD molecular tests using breast (n = 349) and ovarian (n = 141) cancers from multiple independent data sets, including platinum-treated clinical cohorts with RECIST progression-free survival (PFS), complete response (CR), and overall survival (OS) endpoints. DeepHRD predicted HRD from held-out H&E-stained breast cancer slides in TCGA with an AUC of 0.81 (95% CI, 0.77 to 0.85). This performance was confirmed in two independent primary breast cancer cohorts (AUC, 0.76 [95% CI, 0.71 to 0.82]). In an external platinum-treated metastatic breast cancer cohort, samples predicted as HRD had higher complete CR (AUC, 0.76 [95% CI, 0.54 to 0.93]) with 3.7-fold increase in median PFS (14.4 v 3.9 months; P = .0019) and hazard ratio (HR) of 0.45 (P = .0047). There were no significant differences in nonplatinum treatment outcome by predicted HRD status in three breast cancer cohorts, including CR (AUC, 0.39) and PFS (HR, 0.98, P = .95) in taxane-treated metastatic breast cancer. Through transfer learning to high-grade serous ovarian cancer, DeepHRD-predicted HRD samples had better OS after first-line (HR, 0.46; P = .030) and neoadjuvant (HR, 0.49; P = .015) platinum therapy in two cohorts. DeepHRD can predict HRD in breast and ovarian cancers directly from routine H&E slides across multiple external cohorts, slide scanners, and tissue fixation variables. When compared with molecular testing, DeepHRD classified 1.8- to 3.1-fold more patients with HRD, which exhibited better OS in high-grade serous ovarian cancer and platinum-specific PFS in metastatic breast cancer.

Abstract LB391: Deep learning AI predicts HRD and platinum response from histologic slides

Abstract Background: Cancers with homologous recombination deficiency (HRD) can benefit from platinum salts and PARP inhibitors. Standard diagnostic tests, including FDA-approved companion diagnostics, for detecting HRD require molecular profiling, which is not universally available with global testing rates lowest among minority, rural, and other underserved populations. Methods: We trained DeepHRD, a deep-learning platform for predicting HRD from hematoxylin and eosin (H&E)-stained histopathological slides, using primary breast (n=1,008) and ovarian (n=459) cancers from The Cancer Genome Atlas (TCGA). DeepHRD was compared to four standard HRD molecular tests using breast (n=349) and ovarian (n=141) cancers from multiple external and independent datasets, including clinical cohorts with platinum complete response, progression-free survival (PFS) and overall survival (OS) endpoints. Results: DeepHRD detected HRD from held-out H&E-stained breast cancer slides in TCGA with an AUC of 0.81 ([0.77-0.85]; 95% confidence interval). This performance was confirmed in two independent primary breast cancer cohorts (AUC=0.76; [0.71-0.82]). In an external platinum-treated metastatic breast cancer cohort, samples detected as HRD had a higher complete response (AUC=0.76; [0.54-0.93]) with 3.7-fold increase in median PFS (14.4 versus 3.9 months; p-value=0.0019) and hazard ratio (HR) of 0.45 (p=0.0047) after correcting for PAM50 molecular subtype and age at diagnosis. This deep-learning classifier outperformed four genomic HRD tests used in the clinic, including standard HRD score, BRCA1/2, 26-HR gene panel and single-base substitution signature 3 (SBS3). Multiresolution spatial mapping identified morphological features utilized by DeepHRD for detecting HRD, notably enriched for neoplastic and necrotic tissues, and a higher macrophage density. Through transfer learning to high-grade serous-ovarian cancer, DeepHRD-positive samples exhibited better overall survival after TCGA first-line (HR=0.46; p=0.030) and an external neoadjuvant (HR=0.49; p=0.015) platinum-treated cohorts. Conclusion: In summary, DeepHRD exhibits consistent hazard ratios ranging from 0.45 to 0.49 across the three clinical cohorts and captures 1.8- to 3.1-fold more HRD-positive breast and ovarian cancer patients. DeepHRD-positive breast cancer patients that received platinum exhibited better complete response and PFS. Similarly, DeepHRD-positive platinum-treated ovarian cancer patients had a better OS. DeepHRD’s ability to detect HRD from digital H&E slides provides an important precision oncology tool that can be utilized in resource-constrained and underserved areas where genomic testing is generally not existent. Citation Format: Erik N. Bergstrom, Ammal Abbasi, Marcos Diaz-Gay, Loïck Galland, Sylvain Ladoire, Scott M. Lippman, Ludmil B. Alexandrov. Deep learning AI predicts HRD and platinum response from histologic slides [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB391.

Clinical impact of rapid molecular diagnostic tests in patients presenting with viral respiratory symptoms: A systematic literature review.

Molecular tests can detect lower concentrations of viral genetic material over a longer period of respiratory infection than antigen tests. Delays associated with central laboratory testing can result in hospital-acquired transmission, avoidable patient admission, and unnecessary use of antimicrobials, all which may lead to increased cost of patient management. The aim of this study was to summarize comparisons of clinical outcomes associated with rapid molecular diagnostic tests (RMDTs) versus other diagnostic tests for viral respiratory infections. A systematic literature review (SLR) conducted in April 2023 identified studies evaluating clinical outcomes of molecular and antigen diagnostic tests for patients suspected of having respiratory viral infections. The SLR included 21 studies, of which seven and 14 compared RMDTs (conducted at points of care or at laboratories) to standard (non-rapid) molecular tests or antigen tests to detect SARS-CoV-2 and influenza, respectively. In studies testing for SARS-CoV-2, RMDTs led to reductions in time to test results versus standard molecular tests (range of the reported medians: 0.2-3.8 hours versus 4.3-35.9 hours), with similar length of emergency department stay (3.2-8 hours versus 3.7-28.8 hours). Similarly, in studies testing for influenza, RMDTs led to reductions in time to test results versus standard molecular tests (1-3.5 hours versus 18.2-29.2 hours), with similar length of emergency department stay (3.7-11 hours versus 3.8-11.9 hours). RMDTs were found to decrease exposure time of uninfected patients, rate of hospitalization, length of stay at the hospitals, and frequency of unnecessary antiviral and antibacterial therapy, while improving patient flow, compared to other tests. Compared to other diagnostic tests, RMDTs improve clinical outcomes, test turnaround time, and stewardship by decreasing unnecessary use of antibiotics and antivirals. They also reduce hospital admission and length of stay, which may, in turn, reduce unnecessary exposure of patients to hospital-acquired infections and their associated costs.

Reworking the Tao-Mo exchange-correlation functional. II. De-orbitalization.

In Paper I [H. Francisco, A. C. Cancio, and S. B. Trickey, J. Chem. Phys. 159, 214102 (2023)], we gave a regularization of the Tao-Mo exchange functional that removes the order-of-limits problem in the original Tao-Mo form and also eliminates the unphysical behavior introduced by an earlier regularization while essentially preserving compliance with the second-order gradient expansion. The resulting simplified, regularized (sregTM) functional delivers performance on standard molecular and solid state test sets equal to that of the earlier revised, regularized Tao-Mo functional. Here, we address de-orbitalization of that new sregTM into a pure density functional. We summarize the failures of the Mejía-Rodríguez and Trickey de-orbitalization strategy [Phys. Rev. A 96, 052512 (2017)] when used with both versions. We discuss how those failures apparently arise in the so-called z' indicator function and in substitutes for the reduced density Laplacian in the parent functionals. Then, we show that the sregTM functional can be de-orbitalized somewhat well with a rather peculiarly parameterized version of the previously used deorbitalizer. We discuss, briefly, a de-orbitalization that works in the sense of reproducing error patterns but that apparently succeeds by cancelation of major qualitative errors associated with the de-orbitalized indicator functions α and z, hence, is not recommended. We suggest that the same issue underlies the earlier finding of comparatively mediocre performance of the de-orbitalized Tao-Perdew-Staroverov-Scuseri functional. Our work demonstrates that the intricacy of such two-indicator functionals magnifies the errors introduced by the Mejía-Rodríguez and Trickey de-orbitalization approach in ways that are extremely difficult to analyze and correct.

One-plasmid double-expression system for preparation of MS2 virus-like particles packaging SARS-CoV-2 RNA.

COVID-19 is a disease caused by a virus named SARS-CoV-2. SARS-CoV-2 is a single-stranded positive-sense RNA virus. Reverse transcription quantitative PCR (RT-qPCR) assays are the gold standard molecular test for detection of RNA viruses. The aim of this study was to construct an RNA-positive control based on MS2 phage-like particles (MS2 VLPs) to detect SARS-CoV-2 RNA. pCDFDuet-1 was used as a one-plasmid double-expression system to construct MS2 VLPs containing ssRNA of SARS-CoV-2. The sequence encoding one copy of maturase, His-tag and coat protein dimer was cloned and inserted into MCS1 of the plasmid; the fragment encoding protein N and ORF1ab from SARS-CoV-2 was cloned and inserted into MCS2. The prepared plasmid was transformed into Escherichia coli strain BL2 (DE3), and expression of the construct was induced by 1 mM isopropyl-L-thio-D-galactopyranoside (IPTG) at 30°C for 12 hours. MS2 VLPs were purified and collected with Ni-NTA affinity chromatography columns. The size and shape of the MS2 VLPs were verified by transmission electron microscopy, and the stability of MS2 VLP packaged RNA was evaluated by treatment with RNase A. Effects of storage temperature and buffer on MS2 VLP stability were also investigated. The results showed that SARS-CoV-2 MS2 VLPs could be successfully produced by this one-plasmid double-expression system. MS2 VLPs showed high stability and may be used as a positive control in molecular diagnosis of COVID-19.

CRISPR Typing of Clinical Strains of Salmonella spp. Isolated in Tehran, Iran.

Salmonella is one of the most leading causes of food-born infection and death among infants and people with the poor immunity system. Because Salmonella spp. have diversity in the genome composition and pathogenicity, access to rapid identification and genotyping is necessary to control of salmonellosis. The CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) typing is a genotyping method that checks these variable sequences in the bacterial genome in a specific species. This study aimed to differentiate Salmonella strains using CRISPR region. Salmonella isolates, previously identified via standard microbiological and molecular tests, were subjected to the study. Bacterial DNA was extracted and PCR was done using specific primers. The different PCR products were sequenced and the repeats patterns were used to identify additional or degenerate repeat clusters in the CRISPR region. All different sequences were analyzed using CRISPRtionary tool for dendrogram generation using the binary file. Overall, 119 strains of various Salmonella serovars were used. The result showed unique CRISPR and diversity in spacer both in sequence and the number. Analysis of the extracted sequence and band patterns illustrated that, except for S. infantis, both S. enteritidis and S. typhimurium isolates were classified as a separate cluster. CRISPR genotyping could provide serotype/spacers dictionary and it is performed at low cost and high speed in comparison to the other typing methods. Therefore, the assessment of CRISPR and spacer content can be considered as a powerful and practical discriminatory method for subtyping of Salmonella isolates.

Effect of treatment regimen of the rheumatoid arthritis patients on the risk of coronavirus disease 2019 by modulating the inflammatory mediators.

The therapeutic profile of the patients with rheumatoid arthritis (RA) commonly consists of immunosuppressive and anti-inflammatory compounds. Here in this research, we assessed the potential effect of drug treatment in the RA patients in increasing the risk of coronavirus disease 2019 (COVID-19) infection. In this retrospective cross-sectional study, 200 subjects with RA were recruited. The treatment profile of the subjects for the past 6months was collected. The COVID-19 diagnosis was implemented based on the standard molecular tests and clinical examinations. Serum concentration of cytokines was measured using enzyme-linked immunosorbent assay (ELISA). It was detected that there was an increased risk of COVID-19 in RA subjects receiving Etanercept (OR = 3.51, 95% CI 1.19-10.30, P = 0.022). Concentrations of Interleukin (IL)-1β, Interferon (IFN)-γ, Tumor necrosis factor (TNF)-α, IL-6, IL-17A, and IL-23 were significantly higher in the RA patients with COVID-19 relative to RA cases without COVID-19. In RA/COVID-19 cases receiving Etanercept, serum levels of TNF-α, IL-1β, and IL-6 were significantly lower than RA/COVID-19 subjects without Etanercept therapy. It seems that Etanercept therapy in RA cases might increase proneness of the COVID-19 risk in these cases. The mechanism of this increased risk may stem from suppressing a protective immunity state in the RA cases.

Rapid Detection of DNA and RNA Shrimp Viruses Using CRISPR-Based Diagnostics.

Timely detection of persistent and emerging pathogens is critical to controlling disease spread, particularly in high-density populations with increased contact between individuals and limited-to-no ability to quarantine. Standard molecular diagnostic tests for surveying pathogenic microbes have provided the sensitivity needed for early detection, but lag in time-to-result leading to delayed action. On-site diagnostics alleviate this lag, but current technologies are less sensitive and adaptable than lab-based molecular methods. Towards the development of improved on-site diagnostics, we demonstrated the adaptability of a loop-mediated isothermal amplification-CRISPR coupled technology for detecting DNA and RNA viruses that have greatly impacted shrimp populations worldwide; White Spot Syndrome Virus and Taura Syndrome Virus. Both CRISPR-based fluorescent assays we developed showed similar sensitivity and accuracy for viral detection and load quantification to real-time PCR. Additionally, both assays specifically targeted their respective virus with no false positives detected in animals infected with other common pathogens or in certified specific pathogen-free animals. IMPORTANCE The Pacific white shrimp (Penaeus vannamei) is one of the most valuable aquaculture species in the world but has suffered major economic losses from outbreaks of White Spot Syndrome Virus and Taura Syndrome Virus. Rapid detection of these viruses can improve aquaculture practices by enabling more timely action to be taken to combat disease outbreaks. Highly sensitive, specific, and robust CRISPR-based diagnostic assays such as those developed here have the potential to revolutionize disease management in agriculture and aquaculture helping to promote global food security.

A Micro-Macro Markov Chain Monte Carlo Method for Molecular Dynamics using Reaction Coordinate Proposals

We introduce a new micro-macro Markov chain Monte Carlo method to sample invariant distributions of molecular dynamics systems that exhibit a time-scale separation between the microscopic (fast) dynamics, and the macroscopic (slow) dynamics of some low-dimensional set of reaction coordinates. The algorithm enhances exploration of the state space in the presence of metastability by allowing larger proposed moves at the macroscopic level, on which a conditional accept-reject procedure is applied. Only when the macroscopic proposal is accepted, is the full microscopic state reconstructed from the newly sampled reaction coordinate value and is subjected to a second accept/reject procedure. The computational gain stems from the fact that most proposals are rejected at the macroscopic level, at low computational cost, while microscopic states, once reconstructed, are almost always accepted. We analytically show convergence and discuss the rate of convergence of the proposed algorithm, and numerically illustrate its efficiency on two standard molecular test cases.

Feasibility of Comprehensive Genomic Profiling (CGP) in Real-Life Clinical Practice.

In advanced or metastatic settings, Comprehensive Genomic Profiling (CGP) allows the evaluation of thousands of gene alterations with the goal of offering new opportunities for personalized treatment in solid tumors. This study evaluated the CGP Success Rate in a real-life cohort of 184 patients enrolled in a prospective clinical trial. CGP data were compared with the routine molecular testing strategy adopted in-house. Sample age, tumor area, and the percentage of tumor nuclei were recorded for CGP analysis. We found that 150/184 (81.5%) samples resulted in satisfying CGP reports. The CGP Success Rate was higher in samples from surgical specimens (96.7%) and in specimens that had been stored (sample age) for less than six months (89.4%). Among the inconclusive CGP reports, 7/34 (20.6%) were optimal samples, according to CGP sample requirements. Moreover, with the in-house molecular testing approach, we could obtain clinically relevant molecular data in 25/34 (73.5%) samples that had inconclusive CGP reports. In conclusion, despite the fact that CGP offers specific therapeutical options in selected patients, our data suggest that the standard molecular testing strategy should not be replaced in routine molecular profiling.

Evaluation of Antimicrobial Effects of Trona and Alum on Dental Caries Isolates

Trona and alum are chemical substances found abundantly in nature. Dental caries, usually of bacterial origin, is a chronic disease in which microorganisms metabolize sugars from the diet and produce acid which can demineralize enamel, dentine, cementum and inorganic portion of tooth, followed by destruction of organic portions, leading to cavity formation. This research work was aimed at evaluating the antimicrobial effects of trona and alum on microorganisms isolated from dental caries. It was carried out at Microbiology laboratory unit of Nnamdi Azikiwe University, Awka, Nigeria. Eighty-five dental swab specimens were aseptically and properly collected from patients with carious tooth using sterile swab sticks. Microorganisms were isolated and identified using standard macroscopic, microscopic, biochemical and molecular testing methods. The isolates were Streptococcus mutans, Staphylococcus aureus, Bacillus cereus, Lactobacillus spp and Candida albicans. Antimicrobial sensitivity test of trona and alum on the isolates was carried out using the agar-well diffusion method. The results revealed that these isolates were susceptible to the natural compounds as zones of inhibition were observed at different concentrations. Alum showed the highest zone of inhibition of 25mm against Lactobacillus sp. at 200mg while trona showed inhibition of 17mm against Bacillus cereus at 200mg. The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of the compounds were also determined. The MIC and MBC of alum against the isolates ranges between 50mg/ml to 12.5mg/ml; while trona recorded 200mg/ml against all the isolates. The findings provide the scientific basis for use of alum and trona as antimicrobial agents; thus the need for their production at industrial level.

Multiparametric Magnetic Resonance Imaging Correlates of Isocitrate Dehydrogenase Mutation in WHO high-Grade Astrocytomas.

Isocitrate dehydrogenase (IDH) mutation and O-6 methyl guanine methyl transferase (MGMT) methylation are surrogate biomarkers of improved survival in gliomas. This study aims at studying the ability of semantic magnetic resonance imaging (MRI) features to predict the IDH mutation status confirmed by the gold standard molecular tests. The MRI of 148 patients were reviewed for various imaging parameters based on the Visually AcceSAble Rembrandt Images (VASARI) study. Their IDH status was determined using immunohistochemistry (IHC). Fisher's exact or chi-square tests for univariate and logistic regression for multivariate analysis were used. Parameters such as mild and patchy enhancement, minimal edema, necrosis < 25%, presence of cysts, and less rCBV (relative cerebral blood volume) correlated with IDH mutation. The median age of IDH-mutant and IDH-wild patients were 34 years (IQR: 29-43) and 52 years (IQR: 45-59), respectively. Mild to moderate enhancement was observed in 15/19 IDH-mutant patients (79%), while 99/129 IDH-wildtype (77%) had severe enhancement (p-value <0.001). The volume of edema with respect to tumor volume distinguished IDH-mutants from wild phenotypes (peritumoral edema volume < tumor volume was associated with higher IDH-mutant phenotypes; p-value < 0.025). IDH-mutant patients had a median rCBV value of 1.8 (IQR: 1.4-2.0), while for IDH-wild phenotypes, it was 2.6 (IQR: 1.9-3.5) {p-value = 0.001}. On multivariate analysis, a cut-off of 25% necrosis was able to differentiate IDH-mutant from IDH-wildtype (p-value < 0.001), and a cut-off rCBV of 2.0 could differentiate IDH-mutant from IDH-wild phenotypes (p-value < 0.007). Semantic imaging features could reliably predict the IDH mutation status in high-grade gliomas. Presurgical prediction of IDH mutation status could help the treating oncologist to tailor the adjuvant therapy or use novel IDH inhibitors.

Megaconial congenital muscular dystrophy due to novel CHKB variants: a case report and literature review

BackgroundCholine kinase beta (CHKB) catalyzes the first step in the de novo biosynthesis of phosphatidyl choline and phosphatidylethanolamine via the Kennedy pathway. Derangement of this pathway might also influence the homeostasis of mitochondrial membranes.Autosomal recessive CHKB mutations cause a rare form of congenital muscular dystrophy known as megaconial congenital muscular dystrophy (MCMD).Case presentationWe describe a novel proband presenting MCMD due to unpublished CHKB mutations. The patient is a 6-year-old boy who came to our attention for cognitive impairment and slowly progressive muscular weakness. He was the first son of non-consanguineous healthy parents from Sri Lanka. Neurological examination showed proximal weakness at four limbs, weak osteotendinous reflexes, Gowers’ maneuver, and waddling gate. Creatine kinase levels were mildly increased. EMG and brain MRI were normal. Left quadriceps skeletal muscle biopsy showed a myopathic pattern with nuclear centralizations and connective tissue increase. Histological and histochemical staining suggested subsarcolemmal localization and dimensional increase of mitochondria. Ultrastructural analysis confirmed the presence of enlarged (“megaconial”) mitochondria. Direct sequencing of CHKB identified two novel defects: the c.1060G > C (p.Gly354Arg) substitution and the c.448-56_29del intronic deletion, segregating from father and mother, respectively. Subcloning of RT-PCR amplicons from patient’s muscle RNA showed that c.448-56_29del results in the partial retention (14 nucleotides) of intron 3, altering physiological splicing and transcript stability. Biochemical studies showed reduced levels of the mitochondrial fission factor DRP1 and the severe impairment of mitochondrial respiratory chain activity in patient’s muscle compared to controls.ConclusionsThis report expands the molecular findings associated with MCMD and confirms the importance of considering CHKB variants in the differential diagnosis of patients presenting with muscular dystrophy and mental retardation. The clinical outcome of MCMD patients seems to be influenced by CHKB molecular defects. Histological and ultrastructural examination of muscle biopsy directed molecular studies and allowed the identification and characterization of an intronic mutation, usually escaping standard molecular testing.

Is There a Role for Large Exome Sequencing in the Management of Metastatic Non-Small Cell Lung Cancer: A Brief Report of Real Life.

IntroductionNon-small-cell lung cancer (NSCLC) is one of the main causes of death by cancer worldwide. With the rise of targeted therapies, the search for molecular abnormalities is becoming a crucial step in the management of lung cancer. Whole exome sequencing (WES) is developing rapidly and is now accessible in routine care. However, its value, compared to smaller gene panels, remains unclear.MethodsWe conducted a retrospective analysis of all 281 patients with lung carcinoma referred to the Molecular Tumor Board of the Georges-François Leclerc Cancer Center (CGFL) between March 2015 and January 2018. We compared the results of standard molecular testing with the results of WES performed on every patient.ResultsWES highlighted many more mutations than smaller panels (mutations were found in 82 genes, while smaller panels found, at the most, mutations in 12 genes). Most of these mutations were class III or IV according to the ESCAT classification. The exome sensitivity also showed limitations, notably a slightly lower efficiency for common mutations, including classical EGFR mutations.ConclusionSmall, targeted panels could be preferred over WES at the initial diagnosis of metastatic NSCLC. They are more sensitive for the identification of mutations on the most frequently mutated genes, such as ALK, BRAF, EGFR, ERBB2, KRAS or MET. Larger panels or WES could be useful at disease progression, to enlarge treatment possibilities by highlighting uncommon but potentially targetable mutations that are not covered by smaller, targeted panels.

Utility of droplet digital polymerase chain reaction for TERT and BRAF mutational profiling of thyroid nodules

BackgroundMutations involving BRAF and TERT are important predictors of disease severity in thyroid cancer, but molecular testing is limited by cost and lack of adequate tissue sample. This study aimed to assess the utility of BRAFV600E and TERT testing using droplet digital PCR (ddPCR) as a diagnostic and prognostic tool for thyroid fine needle aspirate biopsy (FNAB).MethodsPatients with thyroid nodules were prospectively enrolled from March 2015 to September 2018. Pre-operative FNAB was collected for standard cytology and molecular testing. BRAFV600E and TERT levels were analyzed by ddPCR. Cytology (Bethesda system) and ddPCR results were correlated to surgical pathology.ResultsA total of 222 patients were enrolled, of which 124 received thyroid surgery. Pre-operative cytology alone with Bethesda ≥5 was 100% specific and 70% sensitive for malignancy on final surgical pathology. BRAFV600E positivity or TERT overexpression was 100% specific and 60.0% sensitive. Combining cytology (Bethesda ≥5) with BRAFV600E and TERT testing increased the sensitivity of a malignant diagnosis to 80.0%. High TERT levels and/or BRAFV600E was associated with aggressive or advanced stage pathology.ConclusionsCombining cytology with ddPCR analysis of BRAFV600E and TERT can improve the diagnostic accuracy of thyroid FNAB, and help predict aggressive pathology.

The Impact of Foundation Medicine Testing on Cancer Patients: A Single Academic Centre Experience.

BackgroundThe use of Next-Generation Sequencing (NGS) has recently allowed significant improvements in cancer treatment. Foundation Medicine® (FM) provides a genomic profiling test based on NGS for a variety of cancers. However, it is unclear if the Foundation Medicine test would result in a better outcome than the standard on-site molecular testing. In this retrospective chart review, we identified the FM cases from an academic Canadian hospital and determined whether these test results improved treatment options for those patients.Materials and MethodsA retrospective analysis was performed on patients with solid tumors who had FM testing between May 1, 2014 and May 1, 2018. Clinical factors and outcomes were measured using descriptive statistics using Microsoft Excel® Software.ResultsOut of 66 FM tests, eight patients (= 12%) had a direct change in therapy based on the FM tests. Identified were 285 oncogenic mutations (median 1, range 0–31); where TP53 (n = 31, 10.9%), CDKN2A (n = 19, 6.7%), KRAS (n = 16, 5.6%) and APC (n = 9, 3.2%) were the most common FM mutations identified.ConclusionA small proportion of FM reports identified actionable mutations and led to direct treatment change. FM testing is expensive and a few of the identified mutations are now part of routine on-site testing. NGS testing is likely to become more widespread, but this research suggests that its true clinical impact may be restricted to a minority of patients.

A rapid near-patient detection system for SARS-CoV-2 using saliva

The highly infectious nature of SARS-CoV-2 necessitates the use of widespread testing to control the spread of the virus. Presently, the standard molecular testing method (reverse transcriptase-polymerase chain reaction, RT-PCR) is restricted to the laboratory, time-consuming, and costly. This increases the turnaround time for getting test results. This study sought to develop a rapid, near-patient saliva-based test for COVID-19 (Saliva-Dry LAMP) with similar accuracy to that of standard RT-PCR tests. A lyophilized dual-target reverse transcription-loop-mediated isothermal amplification (RT-LAMP) test with fluorometric detection by the naked eye was developed. The assay relies on dry reagents that are room temperature stable. A device containing a centrifuge, heat block, and blue LED light system was manufactured to reduce the cost of performing the assay. This test has a limit of detection of 1 copy/µL and achieved a positive percent agreement of 100% [95% CI 88.43% to 100.0%] and a negative percent agreement of 96.7% [95% CI 82.78–99.92%] relative to a reference standard test. Saliva-Dry LAMP can be completed in 105 min. Precision, cross-reactivity, and interfering substances analysis met international regulatory standards. The combination of ease of sample collection, dry reagents, visual detection, low capital equipment cost, and excellent analytical sensitivity make Saliva-Dry LAMP particularly useful for resource-limited settings.

COVID-19 Rapid Antigen Test as Screening Strategy at Points of Entry: Experience in Lazio Region, Central Italy, August-October 2020.

COVID-19 pandemic is a dramatic health, social and economic global challenge. There is urgent need to maximize testing capacity. Rapid Antigen Tests (RAT) represent good candidates for point-of-care and mass surveillance testing to rapidly identify SARS-CoV-2-infected people, counterbalancing lower sensitivity vs. gold standard molecular tests with fast results and possible recurrent testing. We describe the results obtained with the testing algorithm implemented at points of entry (airports and ports) in the Lazio Region (Italy), using the STANDARD F COVID-19 Antigen Fluorescence ImmunoAssay (FIA), followed by molecular confirmation of FIA-positive samples. From mid-August to mid-October 2020, 73,643 RAT were reported to the Regional Surveillance Information System for travelers at points of entry in Lazio Region. Of these, 1176 (1.6%) were FIA-positive, and the proportion of RT-PCR-confirmed samples was 40.5%. Our data show that the probability of confirmation was directly dependent from the semi-quantitative FIA results. In addition, the molecularly confirmed samples were those with high levels of virus and that were actually harboring infectious virus. These results support public health strategies based on early mass screening campaigns by RAT in settings where molecular testing is not feasible or easily accessible, such as points of entry. This approach would contribute to promptly controlling viral spread through travel, which is now of particular concern due to the spread of SARS-CoV-2 variants.