Mutation Testing Research Articles

IN SILICO AND IN VITRO ASSESSMENT OF ANTI-Leishmania infantum ACTIVITY OF A NOVEL CYCLOHEXYL-1,2,4-OXADIAZOLE DERIVATIVE.

Globally, an estimated 1 billion people reside in endemic areas, and over 12 million individuals are infected with leishmaniasis. Despite its prevalence, leishmaniasis continues to be a neglected disease, mainly affecting underdeveloped countries. In Brazil, the available treatments are pentavalent antimonials and Amphotericin B, which are outdated, toxic, require prolonged parenteral administration and have limited efficacy. The heterocyclic ring oxadiazole has been documented in the literature to possess various biological activities, including leishmanicidal properties, thus positioning it as a potential candidate for further investigation. This study aims to evaluate the in vitro leishmanicidal activity of an oxadiazole compound (2i), explore its mechanism of action through enzymatic inhibition and molecular docking, assess its antioxidant activity, and conduct an in silico pharmacokinetic prediction. Pharmacokinetic predictions via ADME/TOX modeling revealed that the 2i molecule exhibits good intestinal absorption (92%), is water-insoluble (-4 log.mol/L) and demonstrates high permeability in Caco-2 cells (1.35log.Papp10-6cm/s), suggesting potential for oral administration. Metabolic studies indicated that oxadiazole 2i is an inhibitor of cytochrome P450 enzymes CYP1A2 and CYP2C19, necessitating further evaluation of potential drug interactions. Additionally, it did not exhibit hepatotoxicity or cardiotoxicity; however, it demonstrated mutagenic potential in the salmonella reverse mutation test (AMES), which is a genetic method that detects mutagenic chemical agents, thus justifying more complex confirmatory studies. In vitro assays showed that oxadiazole 2i has DPPH (2,2-diphenyl-1-picrylhydrazyl) radical reducing activity, indicating potential antioxidant properties with an IC50 of 12.10µg/mL. Concerning its leishmanicidal mechanism of action, molecular docking simulations at the active site of acetylcholinesterase demonstrated that the 2i molecule had superior binding energy values compared to the reference drug physostigmine (-7.39kcal/mol versus -6.66kcal/mol, respectively). However, the pharmacophore map revealed that physostigmine had more molecular interactions than oxadiazole 2i. In acetylcholinesterase inhibition assays, the 2i molecule exhibited significant inhibitory activity with an IC50 of 11.91µg/mL, suggesting a mechanism of action that compromises the parasitic membrane. Moreover, the 2i molecule demonstrated significant leishmanicidal activity against L. infantum with an IC50 of 30.86μM. Cytotoxicity assays on RAW 264.7 macrophages revealed a high CC50 value of 485.5µM and a selectivity index (SI) of 17.86. Based on these findings, oxadiazole 2i emerges as a promising candidate for further study, offering prospects for more affordable, selective, and less toxic leishmanicidal agents.

Immunolipid magnetic bead-based circulating tumor cell sorting: a novel approach for pathological staging of colorectal cancer

ObjectiveThis study aimed to assess whether circulating tumor cells (CTCs) from colorectal cancer (CRC) could be used as an alternative to tissue samples for genetic mutation testing, overcoming the challenge of difficult tumor tissue acquisition.MethodsWe developed an immunolipid magnetic bead (IMB) system modified with antibodies against epithelial cell adhesion molecule (EpCAM) and vimentin to efficiently separate CTCs. We prepared EpCAM-modified IMBs (Ep-IMBs) and vimentin-modified IMBs (Vi-IMBs). The separation efficiency of the system was evaluated via in vitro experiments and by capturing and counting CTCs in blood samples from 23 CRC patients and 20 healthy controls. Hotspot mutations in patient tissue samples were identified via next-generation sequencing (NGS), whereas mutations in blood CTCs were detected via Sanger sequencing. The concordance between hotspot mutations in tumor tissue and blood CTCs was analyzed.ResultsThe CTC sorting system exhibited good dispersion, stability, and low cytotoxicity, with a specificity of 90.54% and a sensitivity of 89.07%. CRC patients had an average of 8.39 CTCs per 7.5 mL of blood, whereas healthy controls had 0.09 per 7.5 mL of blood. The consistency of gene mutations was as follows: TP53 (91.31%), PIK3CA (76.00%), KRAS (85.36%), BRAF (51.00%), APC (65.67%), and EGFR (74.00%), with an overall gene mutation consistency of 85.06%.ConclusionOur CTC sorting system, which is based on Ep-IMBs and Vi-IMBs, effectively captures CTCs in the peripheral blood of CRC patients and enables clinical hotspot gene mutation testing via these enriched CTCs. This system partially solves the problem of difficult tumor tissue sample collection and provides a reference for gene mutation testing in early diagnosis, therapeutic efficacy evaluation, prognosis assessment, and minimal metastasis detection in CRC patients, showing significant potential for clinical application, especially in targeted therapy gene testing for CRC.

A decade of AGO QS-Mamma – Adherence to the Recommendations of The AGO Breast Committee for Diagnosis and Treatment in EBC in Routine Therapy in Germany

Introduction: The cure for Early Breast Cancer (EBC) is increasing over the last decades due to the improvement of diagnosis and therapy. Individualization of cancer treatment in EBC requires constant optimization by implementing current guidelines. The AGO (working group gynecologic oncology) QS-Mamma initiative, a quality assurance program (QS) of the AGO Breast Committee, was introduced to provide insight in guideline adherence in real world practice in Germany. We evaluated 10 years of QS-Mamma data to identify gaps and trends implementing those guidelines. Methods: QS-Mamma is a retrospective sample survey providing a representative overview of the treatment landscape for the treatment of breast cancer in Germany. The last six cohorts were analyzed over a period of ten years. Across all cohorts, an average of 264 centers documented a total of n=4,577 patients with EBC. Results: Testing for BRCA mutations in triple-negative patients increased significantly. Breast conserving surgery has been standard of care since the start of data collection; choice of surgical procedure depends primarily on tumor size and nodal status according to the patient´s preference, if possible. Axillary intervention has shifted towards SLNE or targeted axillary procedures in patients with negative preoperative nodal staging. Neoadjuvant systemic therapy (NAST) in operable EBC is established. Anthracycline administration in the adjuvant setting decreases. We noted an uptake on using platinum-containing CTx in TNBC, corresponding to AGO recommendations. Dual HER2 blockade is established in HER2 positive EBC with increased risk of relapse. Changes in guidelines are reflected in real-world data. Conclusion: Guideline adherence in breast cancer care is high and new treatments and diagnostic options are implemented promptly. Finally, escalation and de-escalation of treatment is depending on individual tumor characteristics resulting in the individual risk of recurrence. Guidelines should be flanked by real-world evidence to ensure and survey their impact.

BRCA Mutation Testing in Men with Metastatic Castration-Resistant Prostate Cancer: Practical Guidance for Australian Clinical Practice.

Some patients with metastatic castration-resistant prostate cancer (mCRPC) possess germline or acquired defects in the DNA damage repair (DDR) genes BRCA1 and BRCA2. Tumors with BRCA mutations exhibit sensitivity to poly-ADP ribose polymerase inhibitors (PARPi) such as olaparib and rucaparib. As a result, molecular diagnostic testing to identify patients with BRCA mutations eligible for the PARPi therapy has become an integral component of managing patients with mCRPC. There are practical challenges in the current molecular testing pathway in Australia that can compromise testing success. Testing success is often contingent on quality of tissue handling and laboratory processing techniques to minimize DNA degradation and suboptimal sequencing data quality. Greater adoption of best testing practices in Australia can be facilitated with education and greater awareness of expert recommendations. Here, we provide expert recommendations on how to optimize BRCA molecular diagnostic testing in patients with mCRPC. Optimization and standardization of molecular diagnostic testing will support health care providers and institutes in establishing more efficient testing pathways, enabling access to targeted therapies such as PARPi, and improving patient outcomes.

High-impact trials with genetic and -omics information focus on cancer mutations, are industry-funded and less transparent.

To assess how genetics and -omics information is used in the most cited recent clinical trials, and to evaluate industry involvement and transparency patterns. This is a meta-research evaluation using a previously constructed database of the 600 most cited clinical trials published from 2019 to 2022. Trials that utilized genetic or -omics characterization of participants in the trial design, analysis, and results were considered eligible. 132 (22%) trials used genetic or -omics information, predominantly for detection of cancer mutations (n=101). Utilization included eligibility criteria (n=59), subgroup analysis (n=82), and stratification factor in randomization (n=14). Authors addressed the relevance in the conclusions in 82 studies (62%). 102 studies (77%) provided data availability statements and 6 had data already available. Most studies had industry funding (n=111 [84.0%]). Oncology trials were more likely to be industry-funded (90.1% vs 64.5%, p=0.001), to have industry-affiliated analysts (43.6% vs 22.6%, p=0.036) and to favor industry-sponsored interventions (83.2% vs 58.1% p=0.004). When compared to other trials, genetic and -omics trials were more likely to be funded by industry (84% vs 63.9%, p<0.001) and tended to be less likely to have full protocols (p=0.018) and statistical plans (p=0.04) available. Our study highlights the current underutilization of genetic and -omics technologies beyond testing for cancer mutations. Industry involvement in these trials appears to be more substantial and transparency is more limited, raising concerns about potential bias.

Comparison of tissue-based and plasma-based testing for EGFR mutation in non-small cell lung cancer patients.

Epidermal growth factor receptor (EGFR) gene mutation testing is crucial for the administration of tyrosine kinase inhibitors to treat non-small cell lung cancer. In addition to traditional tissue-based tests, liquid biopsies using plasma are increasingly utilized, particularly for detecting T790M mutations. This study compared tissue- and plasma-based EGFR testing methods. A total of 248 patients were tested for EGFR mutations using tissue and plasma samples from 2018 to 2023 at Pusan National University Yangsan Hospital. Tissue tests were performed using PANAmutyper, and plasma tests were performed using the Cobas EGFR Mutation Test v2. All 248 patients underwent tissue-based EGFR testing, and 245 (98.8%) showed positive results. Of the 408 plasma tests, 237 (58.1%) were positive. For the T790M mutation, tissue biopsies were performed 87 times in 69 patients, and 30 positive cases (38.6%) were detected. Plasma testing for the T790M mutation was conducted 333 times in 207 patients, yielding 62 positive results (18.6%). Of these, 57 (27.5%) were confirmed to have the mutation via plasma testing. Combined tissue and plasma tests for the T790M mutation were positive in nine patients (13.4%), while 17 (25.4%) were positive in tissue only and 12 (17.9%) in plasma only. This mutation was not detected in 28 patients (43.3%). Although the tissue- and plasma-based tests showed a sensitivity of 37.3% and 32.8%, respectively, combined testing increased the detection rate to 56.7%. Thus, neither test demonstrated superiority, rather, they were complementary.

Physician knowledge, use, and perceptions of genetic biomarker testing for the management of patients with newly diagnosed advanced ovarian cancer: an international physician survey.

To explore physician-reported knowledge, use, and perceptions of genetic testing for advanced ovarian cancer management. Gynecology/oncology specialists (n = 390) in the US, Europe, Canada, Japan, and Australia completed an online survey spanning March 2021 to April 2022. Physician-reported breast cancer gene mutation (BRCAm) testing rates increased over the 2 years before the survey; most patients underwent testing in the preceding 6 months. Homologous recombination deficiency (HRD) genomic instability testing rates and physicians' confidence interpreting results remained relatively low. Genetic testing was driven by the associated treatment implications of the findings. Poor performance status, inadequate tissue, and patients' willingness to undergo testing were reported barriers to testing. Findings indicate that there is a need to improve both access to and information about HRD testing.

Deficient Mismatch Repair and BRAF Mutations in Metastatic Colorectal Cancer in the South Island of New Zealand.

Manatū Hauora, the Ministry of Health of New Zealand (NZ), published minimum standards for molecular testing of colorectal cancers (CRCs) in June 2018. These included mismatch repair (MMR) testing at diagnosis and BRAFV600E mutation analysis on newly diagnosed stage IV CRCs. This study aimed to determine the proportion of patients with CRC in the South Island of NZ with metastatic deficient mismatch repair (dMMR) CRC, the proportion of metastatic CRCs and dMMR CRCs that have a BRAFV600E mutation, and audit testing for BRAF mutations and appropriate referral to genetics services. People from the South Island with histologically diagnosed colorectal adenocarcinoma between July 1, 2018, and June 30, 2019, were identified by the National Cancer Registry. Data points extracted from the electronic medical record included staging, MMR status, BRAF mutation testing, and genetics referral. A total of 845 patients met the inclusion criteria; 166 of 845 (19.6%) had dMMR CRC, and of these 130 (78%) had BRAF mutation, 256 patients developed metastatic disease by data cut-off, 20 (7.8%) had dMMR, and 41 (22.2%) had BRAF mutation. When indicated, 275 of 330 (83.3%) were tested for BRAF mutation and 32 of 45 (71.1%) referred to genetics. Compared with other populations, South Island CRC patients had higher rates of dMMR and BRAF mutation. Less than 10% of patients (n = 20) had metastatic dMMR CRC. These patients could be considered candidates for immune checkpoint inhibitor therapy, a small number that would not significantly burden the NZ health system if funded. The vast majority of dMMR CRC was sporadic. Rates of testing could be improved.

Variations in wheat water requirement and climatic causes in arid regions of northwest China.

Analysis of crop water requirement and its influencing factors are important for optimal allocation of water resources. However, research on variations of climatic factors and their contribution to wheat water requirement in Xinjiang is insufficient. In our study, daily meteorological data during 1961‒2017 in Xinjiang was collected. Penman-Monteith formula and crop coefficient method was adopted to calculate wheat water requirement. Mann-Kendall mutation test and grey correlation degree analysis were used to investigate variation characteristics and correlation degree between climatic factors and wheat water requirement. The results showed that wheat water requirement ranged from 511 to 548mm (average = 529.5mm). Spatial distribution of wheat water requirement in Xinjiang presented a pattern of "southeast > Northwest, east > west". Wheat water requirement in most areas of Xinjiang showed a decreasing trend. During the whole growth period of wheat, the top five climatic factors affecting wheat water requirement in Xinjiang were ET0, Tmax, Tmean, sunshine duration, and Umean. Precipitation and relative humidity negatively impacted wheat water requirement, while reference crop evapotranspiration (ET0), mean wind speed (Umean), mean temperature (Tmean), maximum temperature (Tmax), minimum temperature, and sunshine duration had positive effects. This study provides a comprehensive basis for the decision making of efficient agricultural water use and irrigation measures in Xinjiang.

Assessing the impact of different solvents in the bacterial reverse mutation test.

The bacterial reverse mutation test is essential for identifying the mutagenic potential of chemicals. The solubility of the test substance is vital for achieving the recommended assay concentration. Preferred solvents like dimethyl sulfoxide and water are chosen for their compatibility and historical data. Selecting a compatible solvent with Salmonella typhimurium and Escherichia coli WP2 uvrA strains, considering a maximum cytotoxic concentration or the limit of 5 mg/plate, can be challenging. This study assessed various solvents, including N,N-dimethylformamide, acetone, acetonitrile, ethyl acetate, 95% ethanol, diethylene glycol monomethyl ether, methanol, P-dioxane, tetrahydrofuran, and dimethylacetamide, as alternative solvents in the AMES test. Results showed all solvents, except tetrahydrofuran, were compatible at concentrations up to 100 μL/plate or more, as they did not inhibit S9 enzymes, bacterial growth, or alter bacterial revertant colony counts, making them suitable for the bacterial reverse mutation test.

Retrospective detection of ITGB7 gene mutation in a Holstein calf with chronic diarrhea that was suspected of hereditary cholesterol deficiency.

A homozygous individual for ITGB7 gene mutation, an autosomal recessive congenital disorder in Holstein cattle, was retrospectively identified by genotyping of 195 stored blood from patients less than 12 months of age. Other 24 patients (12.3%) showed heterozygous. The homozygous individual was a 107-day-old female calf born on March 2017, who presented with chronic diarrhea and severe hypocholesterolemia suggesting hereditary cholesterol deficiency (CD), but genotyping analysis showed negative for CD. The patient showed watery diarrhea, dehydration, and extreme emaciation. Necropsy revealed no apparent cause of chronic diarrhea. Histopathological examination revealed mild mucosal inflammation from the jejunum to the colon. Seven years after the patient's death, the availability of ITGB7 gene mutation testing revealed the patient to be homozygous.

The Chinese Society of Clinical Oncology (CSCO): Clinical guidelines for the diagnosis and treatment of colorectal cancer, 2024 update.

The 2024 updates of the Chinese Society of Clinical Oncology (CSCO) Clinical Guidelines for the diagnosis and treatment of colorectal cancer emphasize standardizing cancer treatment in China, highlighting the latest advancements in evidence-based medicine, healthcare resource access, and precision medicine in oncology. These updates address disparities in epidemiological trends, clinicopathological characteristics, tumor biology, treatment approaches, and drug selection for colorectal cancer patients across diverse regions and backgrounds. Key revisions include adjustments to evidence levels for intensive treatment strategies, updates to regimens for deficient mismatch repair (dMMR)/ microsatellite instability-high (MSI-H) patients, proficient mismatch repair (pMMR)/ microsatellite stability (MSS) patients who have failed standard therapies, and rectal cancer patients with low recurrence risk. Additionally, recommendations for digital rectal examination and DNA polymerase epsilon (POLE)/ DNA polymerase delta 1 (POLD1) gene mutation testing have been strengthened. The 2024 CSCO Guidelines are based on both Chinese and international clinical research, as well as expert consensus, ensuring their relevance and applicability in clinical practice, while maintaining a commitment to scientific rigor, impartiality, and timely updates.

An Empirical Study of Testing Machine Learning in the Wild

Background : Recently, machine and deep learning (ML/DL) algorithms have been increasingly adopted in many software systems. Due to their inductive nature, ensuring the quality of these systems remains a significant challenge for the research community. Traditionally, software systems were constructed deductively, by writing explicit rules that govern the behavior of the system as program code. However, ML/DL systems infer rules from training data i.e., they are generated inductively. Recent research in ML/DL quality assurance has adapted concepts from traditional software testing, such as mutation testing, to improve reliability. However, it is unclear if these proposed testing techniques are adopted in practice, or if new testing strategies have emerged from real-world ML deployments. There is little empirical evidence about the testing strategies. Aims : To fill this gap, we perform the first fine-grained empirical study on ML testing in the wild to identify the ML properties being tested, the testing strategies, and their implementation throughout the ML workflow. Method : We conducted a mixed-methods study to understand ML software testing practices. We analyzed test files and cases from 11 open-source ML/DL projects on GitHub. Using open coding, we manually examined the testing strategies, tested ML properties, and implemented testing methods to understand their practical application in building and releasing ML/DL software systems. Results : Our findings reveal several key insights: (1) The most common testing strategies, accounting for less than 40%, are Grey-box and White-box methods, such as Negative Testing , Oracle Approximation , and Statistical Testing . (2) A wide range of \(17\) ML properties are tested, out of which only 20% to 30% are frequently tested, including Consistency , Correctness , and Efficiency . (3) Bias and Fairness is more tested in Recommendation (6%) and Computer Vision (CV) (3.9%) systems, while Security and Privacy is tested in CV (2%), Application Platforms (0.9%), and NLP (0.5%). (4) We identified 13 types of testing methods, such as Unit Testing , Input Testing , and Model Testing . Conclusions : This study sheds light on the current adoption of software testing techniques and highlights gaps and limitations in existing ML testing practices.

BRCA Gene Mutation Testing in Ovarian Cancer Patients and Its Impact on Targeted Therapy

Ovarian cancer is a highly fatal gynecological malignancy, with its early symptoms being subtle, resulting in most patients being diagnosed at an advanced stage. Studies have shown that BRCA gene mutations hold significant clinical importance in ovarian cancer patients. Mutations in the BRCA1 and BRCA2 genes are not only closely linked to the onset of ovarian cancer but also play a crucial role in its progression and treatment. The advancement of gene sequencing technology has provided more efficient and accurate methods for detecting BRCA mutations, particularly with the application of next-generation sequencing (NGS), which has greatly improved both detection rates and accuracy. In the field of targeted therapy, PARP inhibitors, as a novel treatment strategy, have been widely applied to ovarian cancer patients with BRCA mutations. These inhibitors work by suppressing the DNA repair pathway, inducing apoptosis in cancer cells, thereby significantly extending patient survival. However, resistance to PARP inhibitors in some patients remains a key challenge in current research. With the deepening of individualized treatment concepts, BRCA mutation testing not only assists doctors in assessing patient sensitivity to PARP inhibitors but also provides critical insights for developing personalized treatment plans. This paper reviews the clinical applications of BRCA gene mutations in ovarian cancer, explores gene testing technologies and their impact on targeted therapy, and emphasizes the analysis of the mechanisms and resistance issues associated with PARP inhibitors, aiming to provide theoretical support for precision medicine in ovarian cancer patients.

Pheochromocytoma in von Hippel-Lindau Disease: Clinical Features and Comparison With Sporadic Pheochromocytoma.

Pheochromocytomas and paragangliomas (PPGLs) are manifestations of von Hippel-Lindau (VHL) disease. This study aims to describe the clinical features of PPGLs in VHL patients and the distinctions between VHL disease-related PPGLs and sporadic PPGLs. The study included all patients with VHL disease and PPGLs treated in a single centre from 2007 to 2023. A total of 145 patients were included in the sporadic PPGLs group. Their clinical data were retrospectively reviewed. Genetic testing for VHL mutation was conducted using Sanger sequencing. Statistical analysis was performed using SPSS 22. Fifty-nine (65.6%) of the 90 VHL disease patients had PPGLs (male: female, 38:21; age at diagnosis, 25.0 ± 13.3 years). 42 (71.2%) patients had lesions only in the adrenal gland, and 16 (27.1%) patients had lesions both in and out of the adrenal gland. 45 (76.3%) patients had multiple lesions. Eighteen (45.0%) patients developed recurrence after surgery. Fifty-eight patients with PPGLs underwent genetic testing and had pathogenic or likely pathogenic mutations in the VHL gene. Fifty-three (91.4%) patients had missense mutations, 34 of which were located in the Elongin-C binding domain. The hotspot mutation sites were codon 161 and codon 167. Five novel mutations were identified. The clinical characteristics showed no significant differences between groups with different mutation sites. Compared to sporadic PPGLs, VHL disease-related PPGLs were more frequently located in the adrenal gland (71.2% vs. 49.0%, p < 0.001), had a higher prevalence of multiple lesions (76.3% vs. 11.0%, p < 0.001), and secreted noradrenaline (80.4% vs. 43.2%, p < 0.001). They were also more likely to relapse after surgery (45.0% vs. 15.3%, p < 0.001). VHL disease-related PPGLs were often multifocal and noradrenergic, and more likely to relapse compared with sporadic PPGLs. No relationships were identified between the mutation sites and the clinical characteristics of PPGLs.

Cell-free tumor DNA analysis in advanced or metastatic breast cancer patients: mutation frequencies, testing intention, and clinical impact.

Circulating cell-free tumor DNA (ctDNA) provides a non-invasive approach for assessing somatic alterations. The German PRAEGNANT registry study aims to explore molecular biomarkers and investigate their integration into clinical practice. In this context, ctDNA testing was included to understand the motivations of clinicians to initiate testing, to identify somatic alterations, and to assess the clinical impact of the results obtained. Patients with advanced/metastatic breast cancer were prospectively enrolled in the Prospective Academic Translational Research Network for the Optimization of Oncological Health Care Quality in the Adjuvant and Advanced/Metastatic Setting (PRAEGNANT study; NCT02338167). The FDA-approved and CE-marked GUARDANT360 CDx test was used to assess somatic alterations. A ctDNA-analysis report was provided to the treating physician along with a questionnaire about the intent for testing and the clinical implications of test results. ctDNA from 49 patients was analyzed prospectively: 37 (76%) had at least one somatic alteration in the analyzed geneset; 14 patients (29%) harbored alterations in TP53, 12 (24%) in PIK3CA, and 6 (12%) in ESR1. Somatic mutations in BRCA1 or BRCA2 were detected in 3 (6%) and 4 (8%) patients, respectively, and 59% of patients had hormone receptor-positive, human epidermal growth factor receptor 2-negative breast cancer. Questionnaires regarding test intentions and clinical impact were completed for 48 (98%) patients. These showed that ctDNA testing influenced treatment decisions for 35% of patients. The high prevalence of somatic alterations in TP53, PIK3CA, ESR1, and BRCA1/2 genes, identified by ctDNA genotyping, highlights their potential as biomarkers for targeted therapies. Detection of specific mutations affected treatment decisions, such as eligibility for alpelisib, and might further facilitate treatment with e.g. elacestrant or capiversatib in future treatment lines.

Deep Learning for Hyperspectral Image Classification: A Critical Evaluation via Mutation Testing

Recently, there has been a surge in the adoption of deep learning (DL) techniques, especially convolutional neural networks (CNNs), to perform hyperspectral image (HSI) classification. Although deep learners have been shown to achieve impressive performance in HSI classification, they are known to be extremely sensitive to even slight perturbations to their inputs and models. When applied in safety-critical applications, it is crucial to know how robust they really are against perturbations. However, there is still limited tool support for DL testing in terms of their robustness, nor are the existing RGB testing approaches able to address the HSI-specific challenges. In this paper, we propose a mutation analysis framework specialized for DL models trained to classify HSIs, which facilitates a critical evaluation of the robustness of DL-based HSI classifiers. First, we introduce a set of mutation operators to inject faults into the inputs and models to simulate distortions of remote sensing HSI classifiers. By utilizing the mutation testing technique, we implement a novel framework which supports the multidimensional evaluation of individual DL-based classifiers. Finally, a comparative study of the robustness of seven popular CNN-based HSI classifiers (i.e., 3D-CNN, FDSSC, HybridSN, MCNN, FC3DCNN, DWTDENSE, and Tri-CNN) on six HSI datasets is provided. Results show that FDSSC and Tri-CNN achieve higher robustness in the presence of distortions, and FDSSC maintains a relatively stable level of robustness even with few training samples. These empirical findings can be partly explained by the characteristics of the classifiers’ architectures. The results substantiate the efficacy of our evaluation framework in assessing the robustness of HSI classifiers and thus confirm its contribution to the field of remote sensing image classification.

COMPARISON OF NANOPORE AND CLASSICAL SANGER SEQUENCING TO IDENTIFY MOSQUITO BLOODMEAL HOSTS.

The tools available to vector control districts (VCDs) to collect mosquito surveillance data are constantly evolving. As more VCDs obtain real-time polymerase chain reaction (PCR) instruments and the costs associated with computing power and next-generation sequencing continue to decrease, the option of generating useful molecular data in-house becomes more viable. Measures such as arbovirus testing and genotyping for insecticide resistance mutations using RT-qPCR, and identifying species used for mosquito bloodmeals with next-generation sequencing or Sanger sequencing are examples. In this study we identify mosquito host bloodmeal species using Nanopore sequencing from Oxford Nanopore Technologies. We used MinION and Flongle flow cells and a Mk1C device to sequence 96 barcoded amplicon samples in a single sequencing run, and share details of data analysis using the free-to-use Galaxy bioinformatics platform. After sequencing the same samples with Sanger sequencing, we conclude that Nanopore sequencing is better at identifying species in mixed bloodmeals. This work demonstrates a potential use of nanopore sequencing by VCDs with basic biology laboratory and computing equipment.

Definitive Radiotherapy for Oligometastatic and Oligoprogressive Thyroid Cancer: A Potential Strategy for Systemic Therapy Deferral.

Definitive radiotherapy (dRT) has been shown to be an effective option for patients with oligometastatic and oligoprogressive cancers; however, this approach has not been well-studied in metastatic thyroid cancer. This retrospective cohort included 119 patients with oligometastatic (34%) and oligoprogressive (66%) metastatic thyroid cancer treated from 2005 to 2024 with 207 dRT courses for 344 sites (50% thoracic, 37% bone, 7.5% brain, 4% abdominopelvic, and 1.5% neck/skull base). Histologies included 61% papillary, 15% poorly differentiated, 13% follicular, and 10% oncocytic, and 114 (96%) patients had radioiodine-refractory disease prior to dRT. Each course involved 1 to 5 sites, with prescriptions intended for definitive control (median BED10, 72 Gy), and palliative RT was excluded. Somatic mutation testing for oncologic drivers was performed in 103 (87%) patients. Each patient had an average of 3 sites (range, 1-23) treated over 2 courses (range, 1-9). Follow-up from first dRT was a median 2.5 years, with overall survival at 3 and 5 years of 81.5% and 70%, respectively. Actuarial local control per site was 91% at 3 years. Median progression-free survival (PFS) after first course was 17 months (95% CI, 10-24 months), with poorly differentiated histology associated with worse outcomes (hazard ratio [HR], 2.20; 95% CI, 1.24-3.90; P=.007), BRAF mutation with improved PFS (HR, 0.59; 95% CI, 0.37-0.95; P=.029), and no significant findings with respect to systemic therapy. At initial dRT, 92 (77%) patients were not on systemic therapy; and after first dRT, freedom from systemic therapy escalation was a median 4.1 years (95% CI, 1.7-6.5 years), with 2- and 5-year continued deferral rates of 73% and 46%, respectively. Grade 3 toxicities were noted for 1.5% of courses, with no grade 4-5 events observed. This study underscores the potential of dRT as a feasible strategy for deferring systemic therapy escalation in patients with oligometastatic and oligoprogressive metastatic thyroid cancer, demonstrating that sequential dRT courses impart excellent local control and are safe to deliver repeatedly for multiple distant sites. Further studies are warranted to validate these findings and elucidate the full benefit of dRT as part of a multidisciplinary approach for metastatic thyroid cancer.

Craniofrontonasal syndrome in a patient with an inv(X)(p22.2q13.1), separating EFNB1 from its enhancer.

Craniofrontonasal syndrome (CFNS) is an X-linked developmental disorder caused by loss of function variants (LOFVs) in the ephrin B1 (EFNB1) gene located on Xq13.1. In CFNS, unlike in other X-linked disorders, females with heterozygous EFNB1 pathogenic variants (PVs) have a severe phenotype, whereas males carrying hemizygous EFNB1 PVs have a mild phenotype. Here we report a female CFNS patient who was diagnosed with the typical features of CFNS as a new-born. Chromosomal analysis revealed a de novo pericentric inversion of one X chromosome; inv(X)(p22q13). Molecular testing for EFNB1 mutations and a SNP-array test for genomic imbalances returned negative results. We identified the inversion breakpoints using whole genome sequencing (WGS). One of the breakpoints was about 97 kbp downstream of the 3' end of the EFNB1 gene, separating a potential EFNB1 enhancer region from the EFNB1 gene. To our knowledge, this is the first case of CFNS caused by a large structural variant, altering the genomic and regulatory context of EFNB1.