Genome-wide methylome analysis using MethylCap-seq uncovers 4 hypermethylated markers with high sensitivity for both adeno- and squamous-cell cervical carcinoma

Background: Cytology-based screening methods for cervical adenocarcinoma (ADC) and to a lesser extent squamous-cell carcinoma (SCC) suffer from low sensitivity. DNA hypermethylation analysis in cervical scrapings may improve detection of SCC, but few methylation markers have been described for ADC. We aimed to identify novel methylation markers for the early detection of both ADC and SCC. Results: Genome-wide methylation profiling for 20 normal cervices, 6 ADC and 6 SCC using MethylCap-seq yielded 53 candidate regions hypermethylated in both ADC and SCC. Verification and independent validation of the 15 most significant regions revealed 5 markers with differential methylation between 17 normals and 13 cancers. Quantitative methylation-specific PCR on cervical cancer scrapings resulted in detection rates ranging between 80% and 92% while between 94% and 99% of control scrapings tested negative. Four markers (SLC6A5, SOX1, SOX14 and TBX20) detected ADC and SCC with similar sensitivity. In scrapings from women referred with an abnormal smear (n = 229), CIN3+ sensitivity was between 36% and 71%, while between 71% and 93% of adenocarcinoma in situ (AdCIS) were detected; and CIN0/1 specificity was between 88% and 98%. Compared to hrHPV, the combination SOX1/SOX14 showed a similar CIN3+ sensitivity (80% vs. 75%, respectively, P>0.2), while specificity improved (42% vs. 84%, respectively, P < 10(-5)). Conclusion: SOX1 and SOX14 are methylation biomarkers applicable for screening of all cervical cancer types

An anthropomorphic thyroid phantom for ultrasound-guided radiofrequency ablation of nodules

Background: Needle-based procedures such as fine needle aspiration (FNA) and thermal ablation, are often applied for thyroid nodule diagnosis and therapeutic purposes, respectively. With blood vessels and nerves nearby, these procedures can pose risks in damaging surrounding critical structures. Purpose: The development and validation of innovative strategies to manage these risks require a test object with well-characterized physical properties. For this work, we focus on the application of ultrasound-guided thermal radio-frequency ablation (RFA). Methods: We have developed an anthropomorphic phantom mimicking the thyroid and surrounding anatomical and physiological structures that are relevant to ultrasound-guided thermal ablation. The phantom was composed of a mixture of polyacrylamide, water, and egg white extract and was cast using molds in multiple steps. The thermal, acoustical, and electrical characteristics were experimentally validated. The ablation zones were analyzed via non-destructive T2-weighted MRI scans utilizing the relaxometry changes of coagulated egg albumen, and the temperature distribution was monitored using an array of fiber Bragg sensors. Results: The physical properties of the phantom were verified both on ultrasound as well as its response to thermal ablation. The final temperature achieved (92{\deg}C), the median percentage of the nodule ablated (82.1%), the median volume ablated outside the nodule (0.8 mL), and the median number of critical structures affected (0) were quantified. Conclusion: An anthropomorphic phantom that can provide a realistic model for development and training in ultrasound-guided needle-based thermal interventions for thyroid nodules has been presented. In the future, this model can also be extended to novel needle-based diagnostic procedures.Comment: 19 pages, 10 figures, 3 table

External Validation of a Measurement Tool to Assess Systematic Reviews (AMSTAR)

BACKGROUND: Thousands of systematic reviews have been conducted in all areas of health care. However, the methodological quality of these reviews is variable and should routinely be appraised. AMSTAR is a measurement tool to assess systematic reviews. METHODOLOGY: AMSTAR was used to appraise 42 reviews focusing on therapies to treat gastro-esophageal reflux disease, peptic ulcer disease, and other acid-related diseases. Two assessors applied the AMSTAR to each review. Two other assessors, plus a clinician and/or methodologist applied a global assessment to each review independently. CONCLUSIONS: The sample of 42 reviews covered a wide range of methodological quality. The overall scores on AMSTAR ranged from 0 to 10 (out of a maximum of 11) with a mean of 4.6 (95% CI: 3.7 to 5.6) and median 4.0 (range 2.0 to 6.0). The inter-observer agreement of the individual items ranged from moderate to almost perfect agreement. Nine items scored a kappa of >0.75 (95% CI: 0.55 to 0.96). The reliability of the total AMSTAR score was excellent: kappa 0.84 (95% CI: 0.67 to 1.00) and Pearson's R 0.96 (95% CI: 0.92 to 0.98). The overall scores for the global assessment ranged from 2 to 7 (out of a maximum score of 7) with a mean of 4.43 (95% CI: 3.6 to 5.3) and median 4.0 (range 2.25 to 5.75). The agreement was lower with a kappa of 0.63 (95% CI: 0.40 to 0.88). Construct validity was shown by AMSTAR convergence with the results of the global assessment: Pearson's R 0.72 (95% CI: 0.53 to 0.84). For the AMSTAR total score, the limits of agreement were -0.19+/-1.38. This translates to a minimum detectable difference between reviews of 0.64 'AMSTAR points'. Further validation of AMSTAR is needed to assess its validity, reliability and perceived utility by appraisers and end users of reviews across a broader range of systematic reviews

Barrett's lesion detection using a minimal integer-based neural network for embedded systems integration

Embedded processing architectures are often integrated into devices to develop novel functions in a cost-effective medical system. In order to integrate neural networks in medical equipment, these models require specialized optimizations for preparing their integration in a high-efficiency and power-constrained environment. In this paper, we research the feasibility of quantized networks with limited memory for the detection of Barrett’s neoplasia. An Efficientnet-lite1+Deeplabv3 architecture is proposed, which is trained using a quantization-aware training scheme, in order to achieve an 8-bit integer-based model. The performance of the quantized model is comparable with float32 precision models. We show that the quantized model with only 5-MB memory is capable of reaching the same performance scores with 95% Area Under the Curve (AUC), compared to a fullprecision U-Net architecture, which is 10× larger. We have also optimized the segmentation head for efficiency and reduced the output to a resolution of 32×32 pixels. The results show that this resolution captures sufficient segmentation detail to reach a DICE score of 66.51%, which is comparable to the full floating-point model. The proposed lightweight approach also makes the model quite energy-efficient, since it can be real-time executed on a 2-Watt Coral Edge TPU. The obtained low power consumption of the lightweight Barrett’s esophagus neoplasia detection and segmentation system enables the direct integration into standard endoscopic equipment

Discovery of new methylation markers to improve screening for cervical intraepithelial neoplasia grade 2/3

Background: Assessment of DNA promoter methylation markers in cervical scrapings for the detection of cervical intraepithelial neoplasia (CIN) and cervical cancer is feasible, but finding methylation markers with both high sensitivity as well as high specificity remains a challenge. In this study, we aimed to identify new methylation markers for the detection of high-grade CIN (CIN2/3 or worse, CIN2+) by using innovative genome-wide methylation analysis (MethylCap-seq). We focused on diagnostic performance of methylation markers with high sensitivity and high specificity considering any methylation level as positive. Results: MethylCap-seq of normal cervices and CIN2/3 revealed 176 differentially methylated regions (DMRs) comprising 164 genes. After verification and validation of the 15 best discriminating genes with methylation-specific PCR (MSP), 9 genes showed significant differential methylation in an independent cohort of normal cervices versus CIN2/3 lesions (p < 0.05). For further diagnostic evaluation, these 9 markers were tested with quantitative MSP (QMSP) in cervical scrapings from 2 cohorts: (1) cervical carcinoma versus healthy controls and (2) patients referred from population-based screening with an abnormal Pap smear in whom also HPV status was determined. Methylation levels of 8/9 genes were significantly higher in carcinoma compared to normal scrapings. For all 8 genes, methylation levels increased with the severity of the underlying histological lesion in scrapings from patients referred with an abnormal Pap smear. In addition, the diagnostic performance was investigated, using these 8 new genes and 4 genes (previously identified by our group: C13ORF18, JAM3, EPB41L3, and TERT). In a triage setting (after a positive Pap smear), sensitivity for CIN2+ of the best combination of genes (C13ORF18/JAM3/ANKRD18CP) (74 %) was comparable to hrHPV testing (79 %), while specificity was significantly higher (76 % versus 42 %, p <= 0.05). In addition, in hrHPV-positive scrapings, sensitivity and specificity for CIN2+ of this best-performing combination was comparable to the population referred with abnormal Pap smear. Conclusions: We identified new CIN2/3-specific methylation markers using genome-wide DNA methylation analysis. The diagnostic performance of our new methylation panel shows higher specificity, which should result in prevention of unnecessary colposcopies for women referred with abnormal cytology. In addition, these newly found markers might be applied as a triage test in hrHPV-positive women from population-based screening. The next step before implementation in primary screening programs will be validation in population-based cohorts

Determining sensitivity and specificity of HER2 testing in breast cancer using a tissue micro-array approach

INTRODUCTION: Overexpression of the human epidermal growth factor receptor 2 (HER2) as a result of HER2 gene amplification is associated with a relatively poor prognosis in breast cancer and is predictive of HER2-targeting therapy response. False-positive rates of up to 20% for HER2 testing have been described. HER2-testing laboratories are therefore encouraged to participate in external quality control schemes in order to improve HER2-testing standardization. METHODS: This study investigated the feasibility of retesting large numbers of invasive breast cancers for HER2 status on tissue micro-array (TMA) as part of a quality control scheme. For this assessment different HER2 testing methods were used including HER2 detecting antibodies SP3, 4B5, Herceptest and mono color silver in situ hybridization (SISH) and dual color SISH. Final HER2 status for each tumor on the TMA was compared to the local testing result for the same tumor. Discordances between these two results were investigated further by staining whole tumor sections. RESULTS: For this study, 1,210 invasive breast carcinomas of patients treated in six hospitals between 2006 and 2008 were evaluated. Results from the three immunohistochemistry (IHC) and two in situ hybridization (ISH) assays performed on the TMAs were compared. The final HER2 status on TMA was determined with SP3, 4B5 and mono color SISH. Concordance between local HER2 test results and TMA retesting was 98.0%. Discordant results between local and TMA retesting were found in 20 tumors (2.0%). False positive HER2 IHC results were identified in 13 (1.3%) tumors; false negative IHC results in seven (0.7%) tumors. CONCLUSIONS: Retesting large volumes of HER2 classified breast carcinomas was found to be feasible and can be reliably performed by staining TMAs with SP3, 4B5 and mono color SISH in combination with full-sized slides for discordant cases. The frequency of false-positive results was lower than previously reported in the literature. This method is now offered to other HER2-testing laboratories

External quality assessment of SARS-CoV-2-sequencing: An ESGMD-SSM pilot trial across 15 European laboratories

Objective: This first pilot on external quality assessment (EQA) of SARS-CoV-2 whole genome sequencing, initiated by the ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD) and Swiss Society for Microbiology (SSM), aims to build a framework between laboratories in order to improve pathogen surveillance sequencing.Methods: Ten samples with varying viral loads were sent out to 15 clinical laboratories who had free choice of sequencing methods and bioinformatic analyses. The key aspects on which the individual centres were compared on were identification of 1) SNPs and indels, 2) Pango lineages, and 3) clusters between samples.Results: The participating laboratories used a wide array of methods and analysis pipelines. Most were able to generate whole genomes for all samples. Genomes were sequenced to varying depth (up to 100-fold difference across centres). There was a very good consensus regarding the majority of reporting criteria, but there were a few discrepancies in lineage and cluster assignment. Additionally, there were inconsistencies in variant calling. The main reasons for discrepancies were missing data, bioinformatic choices, and interpretation of data.Conclusions: The pilot EQA was an overall success. It was able to show the high quality of participating labs and provide valuable feedback in cases where problems occurred, thereby improving the sequencing setup of laboratories. A larger follow-up EQA should, however, improve on defining the variables and format of the report. Additionally, contamination and/or minority variants should be a further aspect of assessment.</p

Ultrasound imaging in thyroid nodule diagnosis, therapy, and follow‐up: Current status and future trends

Ultrasound, the primary imaging modality in thyroid nodule management, suffers from drawbacks including: high inter- and intra-observer variability, limited field-of-view and limited functional imaging. Developments in ultrasound technologies are taking place to overcome these limitations, including three-dimensional-Doppler, -elastography, -nodule characteristics-extraction, and novel machine-learning algorithms. For thyroid ablative treatments and biopsies, perioperative use of three-dimensional ultrasound opens a new field of research. This review provides an overview of the current and future applications of ultrasound, and discusses the potential of new developments and trends that may improve the diagnosis, therapy, and follow-up of thyroid nodules