Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

English How to set up a Journal club? Tips for first time visits and starting a journal club for radiographers.

Abstract Journal clubs are getting more and more popular and are seen in many variations. A classic journal club is a structured educational meeting for a group of people to discuss, debate, and examine published articles. Journal clubs can be used to gain the latest knowledge in new areas of interest. It is important to educate radiographers and students to use a critical approach when discussing research. This may or may not lead to a new standard of practice. &nbsp; Journal club meetings can be initiated from e.g., clinical departments, educational institutions, groups with special interests e.g., statistics, modality, or by established research groups. The workload is typically reading one or two articles as preparation for each meeting and pointing out a presenter with the task of recapitulating the study aim, method, result, and conclusion. However, it is not expected that the journal club members read the paper(s) thoroughly. The interesting part is the presenter’s perspective and interpretation of the selected paper and the discussion followed by the rest of the group members. This tutorial presents how to start a journal club and explains simple steps to consider before the first meeting

The sonographer dilemma: Ultrasound follow-up in patients with small gallbladder polyps: The sonographer dilemma

What should sonographers recommend to patients diagnosed with small gallbladder polyps? Is follow-up always the solution? And for how many years should we encourage patients to participate in a follow-up ultrasound program? This tutorial discusses current research and guidelines.&nbsp

Can Ultrasound Elastography Discriminate between Rectal Adenoma and Cancer? A Systematic Review

Background: Rectal cancer is a common malignancy. Since the introduction of bowel-screening programs, the number of patients with advanced adenomas and early rectal cancer has increased. Despite improved diagnostics, the discrimination between rectal adenomas and early rectal cancer (i.e., pT1–T2) remains challenging. The purpose of this systematic review was to evaluate the diagnostic performance of endorectal ultrasound (ERUS) elastography in discriminating rectal adenomas from cancer. Method: Using PRISMA guidelines, a systematic search was performed on PubMed, Embase, and MEDLINE databases. Studies evaluating the primary staging of rectal adenomas and cancer using ERUS elastography were included. Results: Six studies were identified; three evaluated the discrimination between adenomas and cancer; two evaluated adenomas and early rectal cancer (i.e., pT1–T2); one evaluated performance on different T categories. All studies reported increased diagnostic accuracy of ERUS elastography compared to ERUS. Sensitivity, specificity and accuracy ranged 0.93–1.00, 0.83–1.00 and 0.91–1.00, respectively, when discriminating adenomas from cancer. In the differentiation between adenomas and early rectal cancer, the sensitivity, specificity and accuracy were 0.82–1.00, 0.86–1.00 and 0.84–1.00, respectively. Conclusion: Elastography increases the accuracy of ERUS and may provide valuable information on malignant transformation of rectal lesions

Diffusion-Weighted MRI in Patients with Testicular Tumors&mdash;Intra- and Interobserver Variability

In general, magnetic resonance (MR) diffusion-weighted imaging (DWI) has shown potential in clinical settings. In testicles parenchyma, the DW imaging helps differentiate and characterize benign from malignant lesions. Placement and size of the region of interest (ROI) may affect the ADC value. Therefore, the aim of this study was to investigate the intra- and interobserver variability in testicular tumors when measuring ADC using various types of regions of interest (ROI). Two observers performed the ADC measurements in testicular lesions based on three ROI methods: (1) whole volume, (2) round, and (3) small sample groups. Intra- and interobserver variability was analyzed for all ROI methods using intraclass correlation coefficients (ICC) and bland-altman plots. The two observers performed the measurements twice, three months apart. A total of 26 malignant testicle tumors were included. Interobserver agreement was excellent in tumor length (ICC = 0.98) and tumor width (ICC = 0.98). In addition, intraobserver agreement was excellent in tumor length (ICC = 0.98) and tumor width (ICC = 0.99). The whole volume interobserver agreement in the first reading was excellent (ICC = 0.93). Round ADC had an excellent (ICC = 0.93) and fair (ICC = 0.58) interobserver agreement, in the first and second reading, respectively. Interobserver agreement in ADC small ROIs was good (ICC = 0.87), and good (ICC = 0.78), in the first and second reading, respectively. Intraobserver agreement varied from fair, good to excellent agreement. The ROI method showed varying inter- and intraobserver agreement in ADC measurement. Using multiple small ROI conceded the highest interobserver variability, and, thus, the whole volume or round seem to be the preferable methods