An Exome Capture-Based RNA-Sequencing Assay for Genome-Wide Identification and Prioritization of Clinically Important Fusions in Pediatric Tumors

This study reports the development of an exome capture-based RNA-sequencing assay to detect recurring and novel fusions in hematologic, solid, and central nervous system tumors. The assay used Twist Comprehensive Exome capture with either fresh or formalin-fixed samples and a bioinformatic platform that provides fusion detection, prioritization, and downstream curation. A minimum of 50 million uniquely mapped reads, a consensus read alignment/fusion calling approach using four callers (Arriba, FusionCatcher, STAR-Fusion, and Dragen), and custom software were used to integrate, annotate, and rank the candidate fusion calls. In an evaluation of 50 samples, the number of calls varied substantially by caller, from a mean of 24.8 with STAR-Fusion to 259.6 with FusionCatcher; only 1.1% of calls were made by all four callers. Therefore a filtering and ranking algorithm was developed based on multiple criteria, including number of supporting reads, calling consensus, genes involved, and cross-reference against databases of known cancer-associated or likely false-positive fusions. This approach was highly effective in pinpointing known clinically relevant fusions, ranking them first in 47 of 50 samples (94%). Detection of pathogenic gene fusions in three diagnostically challenging cases highlights the importance of a genome-wide and nontargeted method for fusion detection in pediatric cancer.

Use of real-time immersive digital training and educational technologies to improve patient safety during the processing of reusable medical devices: Quo Vadis?

Hospital acquired infections stemming from contaminated reusable medical devices are of increasing concern. This issue is exaggerated with the introduction of complex medical devices like endoscopes and robotic instrumentation. Although medical device manufacturers validate their cleaning instructions for use, evidence in the literature demonstrates that effective device processing is not being performed consistently within sterile processing departments in clinical settings. The result is increased risks to patient safety. As a solution to this problem, focused one-on-one training increases compliance to the medical device manufacturer's processing instruction. However, often this is not a practical solution for the volume of healthcare staff responsible for device processing activities. This constitutes the first paper to address the blended use of educational and digital technologies to address these challenges and as a result inform safety and sustainability for the medical device sector. Cognitive learning theory is an evidence-based framework for learning. It supports the use of immersive educational experiences using emerging extended reality technologies (e.g., virtual or augmented reality) to increase learning comprehension. The delivery of educational content via these technologies provides an innovative option for repeatable leaning and training outcomes. The motivation is to decrease patient risk of contaminated reusable medical devices. The proposed approach while primary motivated by safety can also enhance sustainability and efficiency enabled by artificial intelligence and robotic instrumentation.

Lessons learned from regional training of paediatric nephrology fellows in Africa

BACKGROUND

Access to care for children with kidney disease is limited in less well-resourced regions of the world and paediatric nephrology (PN) workforce development with good practical skills is critical.

METHODS

Retrospective review of a PN training program and trainee feedback from 1999 to 2021, based at Red Cross War Memorial Children's Hospital (RCWMCH), University of Cape Town.

RESULTS

A regionally appropriate 1-2-year training program enrolled 38 fellows with an initial 100% return rate to their country of origin. Program funding included fellowships from the International Pediatric Nephrology Association (IPNA), International Society of Nephrology (ISN), International Society of Peritoneal Dialysis (ISPD), and the African Paediatric Fellowship Program (APFP). Fellows were trained on both in- and out-patient management of infants and children with kidney disorders. "Hands-on skills" training included examination, diagnosis and management skills, practical insertion of peritoneal dialysis catheters for management of acute kidney injury and kidney biopsies. Of 16 trainees who completed > 1 year of training, 14 (88%) successfully completed subspecialty exams and 9 (56%) completed a master's degree with a research component. PN fellows reported that their training was appropriate and enabled them to make a difference in their respective communities.

CONCLUSIONS

This training program has successfully equipped African physicians with the requisite knowledge and skills to provide PN services in resource-constrained areas for children with kidney disease. The provision of funding from multiple organizations committed to paediatric kidney disease has contributed to the success of the program, along with the fellows' commitment to build PN healthcare capacity in Africa. A higher resolution version of the Graphical abstract is available as Supplementary information.

Mitochondrial DNA haplogroup, genetic ancestry, and susceptibility to Ewing sarcoma

Based on current studies, the incidence of Ewing sarcoma (ES) varies significantly by race and ethnicity, with the disease being most common in patients of European ancestry. However, race/ethnicity has generally been self-reported rather than formally evaluated at a population level using DNA evidence. Additionally, mitochondrial dysfunction is a hallmark of ES, yet there have been no reported studies of mitochondrial genetics in ES. Thus, we evaluated both the mitochondrial and nuclear ancestries of 420 pediatric ES patients in the United States using whole-genome sequencing. We found that the mitochondrial DNA (mtDNA) genomes of only six (1.4 %) patients belonged to African L haplogroups, while those of 90 % of the patients belonged to macrohaplogroup R, which includes haplogroup H, the most common maternal lineage in Europe. Compared to the general US population, European haplogroups were significantly enriched in ES patients (p < 2.2e-16) and the African haplogroups are significantly impoverished (p < 4.6e-16). Using the ancestry informative markers defined in a National Genographic study, the vast majority of patients exhibited significant nuclear ancestry originating from the Mediterranean, Northern Europe, and Southwest Asia, including all six patients with African L mtDNAs. Very few had primarily African nuclear ancestry. This is the first genomic epidemiology study to simultaneously interrogate the mitochondrial and nuclear ancestries of ES patients. While supporting previous findings of enriched European ancestry in ES patients, these results also suggest alternative hypotheses for the significant contribution of mitochondrial ancestry in ES patients, as well as the protective role of African ancestry.

Non-Invasive Profiling of Advanced Prostate Cancer via Multi-Parametric Liquid Biopsy and Radiomic Analysis

Integrating liquid biopsies of circulating tumor cells (CTCs) and cell-free DNA (cfDNA) with other minimally invasive measures may yield more comprehensive disease profiles. We evaluated the feasibility of concurrent cellular and molecular analysis of CTCs and cfDNA combined with radiomic analysis of CT scans from patients with metastatic castration-resistant PC (mCRPC). CTCs from 22 patients were enumerated, stained for PC-relevant markers, and clustered based on morphometric and immunofluorescent features using machine learning. DNA from single CTCs, matched cfDNA, and buffy coats was sequenced using a targeted amplicon cancer hotspot panel. Radiomic analysis was performed on bone metastases identified on CT scans from the same patients. CTCs were detected in 77% of patients and clustered reproducibly. cfDNA sequencing had high sensitivity (98.8%) for germline variants compared to WBC. Shared and unique somatic variants in PC-related genes were detected in cfDNA in 45% of patients (MAF > 0.1%) and in CTCs in 92% of patients (MAF > 10%). Radiomic analysis identified a signature that strongly correlated with CTC count and plasma cfDNA level. Integration of cellular, molecular, and radiomic data in a multi-parametric approach is feasible, yielding complementary profiles that may enable more comprehensive non-invasive disease modeling and prediction.

Adherence to Choosing Wisely Campaign Guidelines at Three Health Systems

Introduction/Objective

With rising healthcare costs in the United States, there has been a push for lab stewardship to improve the quality of patient care while reducing costs. To optimize the use of clinical laboratory testing, the ASCP working with other medical specialty organizations, developed the Choosing Wisely Campaign to promulgate evidence-based guidelines to optimize clinical laboratory testing.

Methods/Case Report

We examined adherence to three Choosing Wisely guidelines over a four-year period (2017- 2020), through queries of internal cost accounting databases to return aggregate volumes as well as variable and total costs at three large academic health systems. We measured concurrent orders for: 1) erythrocyte sedimentation rate (ESR) with C-reactive protein (CRP), 2) serum/plasma amylase with lipase, and 3) free thyroxine (FT4) and/or total triiodothyronine (TT3) with thyroid stimulating hormone (TSH) when the TSH is within the reference range (using an frequency estimate of 85% based on other studies). We also examined another guideline for concurrent orders for serum aldolase with creatine kinase (CK). We also quantified aggregate variable costs for the non-recommended test in each Choosing Wisely guideline (amylase, ESR, FT4 and/or TT3), and for serum aldolase when ordered with CK.

Results (if a Case Study enter NA)

Over the four-year period, there were 322,853 unnecessary tests based on these four guidelines (120,587 ESR and CRP, 30,444 amylase and lipase, 164,818 FT4 and/or TT3 with TSH, and 7,004 aldolase). Overall, unnecessary testing decreased between 2017 and 2020 for amylase with lipase, remained essentially unchanged for aldolase, and increased for the other two test guideline scenarios. The largest changes were concurrent orders for amylase and lipase at one health system (38% decrease), and orders for TT3 with a normal TSH result at another health system (324% increase). The four-year variable cost of these unnecessary tests was $1,215,309 ($303,827 mean annual cost), resulting in potential annual variable cost savings of $101,276 for each health system for the four guidelines we examined. Variable costs for unnecessary testing increased by 16.5% ($45,571) over the four-year period.

Conclusion

Guideline-based unnecessary testing remains as a target to improve laboratory diagnostic testing. There is potential to realize significant achievable cost savings if guidelines are implemented and maintained.

495 Audit on Blood Ordering Requests in Mastectomies: The Need for a Routine Group and Hold

Aim

A group and hold (G&H) forms part of the pretransfusion compatibility testing and is commonly requested in anticipation of a possible blood transfusion. Requests made in the context of elective procedures with a low transfusion probability, such as a mastectomy, are associated with added financial burden and increases workload in a healthcare system. This audit aims to analyse the cost-benefit associated with the routine request for a preoperative G&H in patients undergoing mastectomies.

Method

A total of 100 patients undergoing mastectomies from the period of September 2019 to October 2020 were included in the audit. Data regarding blood order requests, units of blood transfused, perioperative haemoglobin and the type of mastectomy (right, left or bilateral) were collected.

Results

All patients had a routine G&H as part of their preoperative assessment. The average age in this cohort was 60.3. Right-sided mastectomy was the commonest procedure in this cohort (N = 52). The average preoperative haemoglobin was 13.0g/dL. 2/100 patients received post-operative blood transfusions. The transfusion probability in this cohort was 2%. Only 15% of the cohort had a post-operative haemoglobin level checked. The average drop in haemoglobin in this cohort was 2.3g/dL.

Conclusions

This audit demonstrates the low prevalence of blood transfusions in patients undergoing mastectomies, consistent with current literature. The projected cost savings associated with selective requests for G&H are significant. However, the implementation of a safe and targeted blood ordering approach in patients with high bleeding risks will require a validated stratification system.

cGAS-mediated induction of type I interferon due to inborn errors of histone pre-mRNA processing

Inappropriate stimulation or defective negative regulation of the type I interferon response can lead to autoinflammation. In genetically uncharacterized cases of the type I interferonopathy Aicardi-Goutières syndrome, we identified biallelic mutations in LSM11 and RNU7-1, which encode components of the replication-dependent histone pre-mRNA-processing complex. Mutations were associated with the misprocessing of canonical histone transcripts and a disturbance of linker histone stoichiometry. Additionally, we observed an altered distribution of nuclear cyclic guanosine monophosphate-adenosine monophosphate synthase (cGAS) and enhanced interferon signaling mediated by the cGAS-stimulator of interferon genes (STING) pathway in patient-derived fibroblasts. Finally, we established that chromatin without linker histone stimulates cyclic guanosine monophosphate-adenosine monophosphate (cGAMP) production in vitro more efficiently. We conclude that nuclear histones, as key constituents of chromatin, are essential in suppressing the immunogenicity of self-DNA.

Abstract 5379: Non-invasive profiling of advanced prostate cancer via multi-parametric liquid biopsy and radiomics

Introduction: Biomarkers of treatment response in advanced prostate cancer (PC) are urgently needed. Liquid biopsy profiling and radiomic imaging enable non-invasive, repeatable tumor profiling, and combining these modalities could yield powerful new predictive tools. We tested the feasibility of concurrent, multi-parametric molecular analysis of circulating tumor cells (CTCs) and matched plasma cell-free DNA (cfDNA), combined with radiomic analysis of CT scans from the same patients.

Methods: Under IRB-approved informed consent, blood was collected from 23 patients with metastatic castrate resistant PC (mCRPC). CTCs were enumerated using the RareCyte and CellSearch platforms, and individual single CTCs and white blood cells (WBCs) were retrieved using RareCyte's integrated robotic micropipette. DNA was extracted from single cells (scDNA), as well as from matched cfDNA and buffy coats (bcDNA), then sequenced using Ampliseq HD Pan-cancer panel. Concurrent radiomic analysis was performed on bone metastatic lesions identified on CT scans from the same patients, and manually segmented regions of interest were queried for a variety of texture metrics.

Results: Of 19 patients with both CellSearch and RareCyte enumeration, CTCs were detected in 12 by CellSearch (63%; median: 3/7.5 mL; range 1-343/ 7.5 mL) and in 14 by RareCyte (74%; median: 1/7.5 mL; range 1-363/7.5 mL). Using matched bcDNA as a gold standard, sensitivity and positive predictive value of germline SNP detection were 74% and 93% for scDNA, and 98% and 99% for cfDNA. A total of 48 and 18 somatic alterations were identified across the cohort in CTCs and cfDNA, respectively, including mutations in AR, TP53, CCND3, FGFR1, ALK, and ROS1. Of 14 patients whose single CTCs were recovered by RareCyte, 12 (86%) had detectable somatic mutations in scDNA, and 7 (50%) had detectable somatic mutations in matched cfDNA. While some mutations were concordant between matched scDNA and cfDNA, most were distinct. Radiomic entropy in CT scans was associated with CellSearch CTC-counts (AUC of 0.74) using the FDA-cleared prognostic threshold of &lt;5 vs. ≥5 CTCs/7.5ml.

Conclusion: We successfully piloted an integrated, multi-parametric analysis of matched single CTCs, WBCs, plasma cfDNA, and buffy coats, along with matched radiomic analysis of CT scans in patients with mCRPC. Germline variants were detected more readily in cfDNA, whereas somatic mutations in commonly altered genes were detected more frequently in CTCs. CellSearch CTC count, an FDA cleared prognostic biomarker, correlated with radiomic entropy, the first such association to our knowledge between liquid biopsy and radiographic readouts. The results demonstrate the feasibility of this approach and its potential to generate comprehensive molecular data and new biomarker profiles. Prospective validation in a large PC cohort is underway.

Citation Format: Gareth J. Morrison, Jonathan Buckley, D. Gigi Ostrow, Bino Varghese, Nolan Ericson, Steven Cen, Alexander Cunha, Yi-Tsung Lu, Tad George, Jeffrey Smith, David Quinn, Vinay Duddalwar, Timothy Triche, Amir Goldkorn. Non-invasive profiling of advanced prostate cancer via multi-parametric liquid biopsy and radiomics [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5379.

The Healthy Champions program in Pennsylvania schools: Assessment, awareness, and improvement of school wellness

Schools are important environments for promotion of healthy behaviors to reduce childhood obesity; however, many barriers prevent schools from sustaining wellness programs. The goal of the Healthy Champions program was to assist schools with identifying areas for improvement through a nutrition and activity-focused assessment, and delivery of a customized score report and welcome kit with materials to promote healthful behavior change. In this study, we aimed to describe participation and assessment results for this program across a five-year period. Enrollment in the Healthy Champions program was open to private and public K-12 schools across Pennsylvania beginning in 2013. School staff completed an assessment that scored aspects of the wellness environment and was used to enroll schools in the program. Schools were awarded star status (0–5) based upon responses and provided a tailored response to improve ratings, and with re-enrollment, became a simple way for schools to track progress. From 2013 to 2018, 592 schools enrolled for at least one year, representing 58 out of 67 counties (87%) in Pennsylvania. Mean star status at baseline was 2.89 out of 5; however, schools enrolled for multiple years (51%) saw significant improvement in star status, independent of school size and rural/urban status.

Adherence to a Mediterranean Diet Is Not Associated with Risk of Sarcopenic Symptomology: A Cross-Sectional Analysis of Overweight and Obese Older Adults in Australia

Adherence to a Mediterranean Diet (MedDiet) is inversely associated with sarcopenia. The aim of this study was to examine the association between adherence to a MedDiet and sarcopenic symptomology in obese older adults. For confirmation of sarcopenia, low appendicular skeletal muscle (ASM: males, ≤7.25kg/m2; females, ≤5.5kg/m2) accompanied low handgrip strength (males, ≤30kg; females, ≤20kg) or low physical performance (Short Physical Performance Battery [SPPB]: ≤8; or gait speed: ≤0.8m/sec). Adherence to a MedDiet was determined using the Mediterranean Diet Adherence Screener (MEDAS). Sixty-five older adults were included. Adherence to a MedDiet was not associated with a decreased risk of sarcopenic symptomology (SPPB: OR = 0.20; 95% CI: 0.01-3.1; P = 0.234; Muscle strength: OR = 1.81; 95% CI: 0.32-10.15; P = 0.499; Gait speed: OR = 0.58; 95% CI: 0.13-2.50; P = 0.468). Future research should investigate whether a Mediterranean-style intervention can prevent or improve sarcopenic symptomology, including in non-Mediterranean populations.

Automated monitoring of behaviour in zebrafish after invasive procedures

Fish are used in a variety of experimental contexts often in high numbers. To maintain their welfare and ensure valid results during invasive procedures it is vital that we can detect subtle changes in behaviour that may allow us to intervene to provide pain-relief. Therefore, an automated method, the Fish Behaviour Index (FBI), was devised and used for testing the impact of laboratory procedures and efficacy of analgesic drugs in the model species, the zebrafish. Cameras with tracking software were used to visually track and quantify female zebrafish behaviour in real time after a number of laboratory procedures including fin clipping, PIT tagging, and nociceptor excitation via injection of acetic acid subcutaneously. The FBI was derived from activity and distance swum measured before and after these procedures compared with control and sham groups. Further, the efficacy of a range of drugs with analgesic properties to identify efficacy of these agents was explored. Lidocaine (5 mg/L), flunixin (8 mg/L) and morphine (48 mg/L) prevented the associated reduction in activity and distance swum after fin clipping. From an ethical perspective, the FBI represents a significant refinement in the use of zebrafish and could be adopted across a wide range of biological disciplines.

OncoKids: A Comprehensive Next-Generation Sequencing Panel for Pediatric Malignancies

The OncoKids panel is an amplification-based next-generation sequencing assay designed to detect diagnostic, prognostic, and therapeutic markers across the spectrum of pediatric malignancies, including leukemias, sarcomas, brain tumors, and embryonal tumors. This panel uses low input amounts of DNA (20 ng) and RNA (20 ng) and is compatible with formalin-fixed, paraffin-embedded and frozen tissue, bone marrow, and peripheral blood. The DNA content of this panel covers the full coding regions of 44 cancer predisposition loci, tumor suppressor genes, and oncogenes; hotspots for mutations in 82 genes; and amplification events in 24 genes. The RNA content includes 1421 targeted gene fusions. We describe the validation of this panel by using a large cohort of 192 unique clinical samples that included a wide range of tumor types and alterations. Robust performance was observed for analytical sensitivity, reproducibility, and limit of detection studies. The results from this study support the use of OncoKids for routine clinical testing of a wide variety of pediatric malignancies.

The Predictive Ability of Pre-Operative Magnetic Resonance Imaging to Detect Pathological Outcomes in Prostate Cancer

Aims Accurate preoperative knowledge of tumour stage is important in preoperative planning at radical prostatectomy (RP). The aim of this study was to assess the predictive ability of multiparametric MRI for detecting pathological outcomes. Methods A retrospective review was performed of all patients who underwent RP over a 4 year period. Results Preoperative MRI was reported as showing T3 or T4 disease in 26(17.9%) out of 145 patients undergoing RP. Of these, 10(6.9%) had ECE (extra-capsular extension) and 1(0.7%) had SVI (seminal vesicle invasion) on final histology. The sensitivity and specificity of MRI for detecting ECE were 27.3% and 87.6%, respectively. The sensitivity and specificity of MRI for detecting SVI were 11.1% and 97.8%, respectively. The positive predictive values for determining ECE and SVI were 45.5% and 25%, respectively and negative predictive values were 75.9% and 94.4%. Conclusion MRI has good specificity but poor and heterogeneous sensitivity for predicting T3 disease in RP specimen.

A randomised controlled intervention study investigating the efficacy of carotenoid-rich fruits and vegetables and extra-virgin olive oil on attenuating sarcopenic symptomology in overweight and obese older adults during energy intake restriction: protocol paper

Background

Weight loss interventions have not been advocated for overweight/obese older adults due to potential loss of skeletal muscle and strength impacting on physical function with potential loss of independence. Carotenoids and polyphenols are inversely associated with sarcopenic symptomology. This paper reports the protocol of a study evaluating the efficacy of a high-protein, energy restricted diet rich in carotenoids and polyphenols on body composition, muscle strength, physical performance and quality of life in overweight and obese older adults.

Methods

This randomised controlled clinical trial will recruit community-dwelling, healthy overweight and obese older adults (≥60 years) for a 12-week weight loss intervention. Seventy-three participants will be recruited and randomized to an energy restricted (~30% restriction), isocaloric diet (30% protein; 30% carbohydrate; 40% fat) enriched with either: a) 375 g/d of high carotenoid vegetables, 300 g/d high carotenoid fruit, and 40-60 ml extra-virgin olive oil (EVOO); or b) 375 g/d of lower carotenoid vegetables, 300 g/d lower carotenoid fruit, and 40-60 ml Polyunsaturated fatty acid (PUFA) based oil. All participants will receive individual dietary counselling each fortnight for the duration of the study and will be asked to maintain their habitual level of physical activity throughout the study. The primary outcome will be appendicular skeletal muscle (ASM) assessed by dual energy X-ray absorptiometry (DXA). Secondary outcomes will include body weight, fat-free mass (FFM), fat mass (FM), muscle strength (Isometric hand-grip strength), physical performance (Short Physical Performance Battery), physical activity (International Physical Activity Questionnaire) and health related quality of life (SF-36). Outcomes will be measured at baseline and at week 12.

Discussion

The results of this study will provide a novel insight relating to the potential influence of high carotenoid and polyphenol intakes on attenuation of ASM during dietary energy-restricted weight loss in overweight and obese older adults.

Trial registration

The trial was registered on the Australia New Zealand Clinical Trials Register (ACTRN12616001400459); Trial registration date: 10th October, 2016.

Generation and characterization of tamoxifen-inducible Pax9-CreER knock-in mice using CrispR/Cas9

Pax9 encodes a paired-box homeodomain (Pax) transcription factor and is critical for the development of multiple organs. Using CrispR/Cas9-mediated homologous directed repair (HDR), we generated a new Pax9-CreER knock-in mouse line in which the CreER(T2) fusion protein is produced after synthesis of endogenous Pax9 protein. We found that tdTomato reporter expression in Pax9-CreER;tdTomato reporter mice is detectable in a similar pattern to the endogenous Pax9 expression, faithfully recapitulating the Pax9 expression domains throughout the embryo and in the adult mouse. At early embryonic stages, the tdTomato reporter is expressed first in the pharyngeal pouch region and later in the craniofacial mesenchyme, somites, limbs, and lingual papillae in the adult tongue. These results demonstrate that this new Pax9-CreER knock-in mouse line can be used for lineage tracing and genetic targeting of Pax9-expressing cells and their progeny in a temporally and spatially controlled manner during development and organogenesis.

Abstract 1546: Differential gene expression analysis by NGS of primary tumor xenograft cells, circulating tumor cells, and metastasis cells purified from the same mouse hosts to identify drivers of cancer dissemination

Introduction: Cancer dissemination involves ongoing dynamic transit of tumor cells between primary and metastatic sites via a hematogenous or “liquid phase”. To identify molecular mechanisms related to the liquid phase of cancer dissemination, we developed a tractable mouse xenograft model wherein GFP-labeled pure primary tumor (PT) cells, circulating tumor cells (CTCs) and lung metastasis (LM) cells are isolated and characterized from the same host.

Methods: GFP+ MDA-MB-231 human breast cancer cells were inoculated subcutaneously into NOD/SCID/IL2r-γnull (NSG) mice. When a 1cm diameter primary tumor xenograft formed, 500 μl blood were collected by intracardiac puncture, and CTCs were enriched by wbc/rbc depletion (StemCell Tech). PT and LM samples were fluorescence microdissected from the same mouse hosts and disaggregated into single cell suspensions. Using a micromanipulator pipette, matched PT, CTC, and LM samples (100 pure GFP+ cells each) were isolated, lysed for RNA extraction (Ambion), and analyzed using the Ion AmpliSeq Transcriptome Human Gene Expression workflow for library preparation and pooled sequencing (Ion Proton). Sequence data from biologic triplicates was aligned and curated using the Genetrix bioinformatics suite, and candidate genes were further analyzed using Ingenuity Pathway Analysis (IPA).

Results: The sequence panel provides gene-level expression information from over 20,000 genes covering &gt; 95% of the RefSeq gene database. Initially, we focused on genes that were up- or down- regulated in CTCs compared with both PT and LM (i.e. differentially expressed in the liquid phase: 402 genes, 184 up-regulated in CTCs, 218 down-regulated in CTCs, fold change range 1.2x-22x). After further filtering for false discovery, 4 up-regulated and 39 down-regulated genes were selected for IPA analysis, which revealed associations with cellular movement pathways (16 genes) and cancer pathways (24 genes). Of these, the top-ranked 12 differentially expressed genes in CTCs relative to PT and LM (9 down-regulated and 3 up-regulated) were selected for validation by qPCR and further functional characterization in the mouse xenograft model.

Conclusions: Here we leveraged new techniques for pure CTC capture, AmpliSeq transcriptome amplification and sequencing to identify and validate new candidate drivers of cancer dissemination. This model holds the potential to uncover key mechanisms engaged by cells that leave the primary and metastatic tumor niche and enter the cancer's liquid phase. Further validation and functional analysis of these candidates in vitro, in vivo and in patient samples may identify new therapeutic targets that specifically disrupt cancer dissemination.

Citation Format: Tong Xu, Gareth Morrison, Yucheng Xu, Timothy Triche, Jonathan Buckley, Amir Goldkorn. Differential gene expression analysis by NGS of primary tumor xenograft cells, circulating tumor cells, and metastasis cells purified from the same mouse hosts to identify drivers of cancer dissemination. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1546.

Effects of Low-Fat Diets Differing in Protein and Carbohydrate Content on Cardiometabolic Risk Factors during Weight Loss and Weight Maintenance in Obese Adults with Type 2 Diabetes

Despite evidence for the benefits of higher-protein (HP) diets in weight loss, their role in type 2 diabetes mellitus (T2DM) management and weight maintenance is not clear. This randomised study compared the effects of a HP diet (38% carbohydrate, 30% protein, 29% fat) to a isocaloric higher-carbohydrate diet (HC: 53%:21%:23%) on cardiometabolic risk factors for 12 weeks in energy restriction (~30% reduction) followed by 12 weeks of energy balance whilst performing regular exercise. Outcomes were measured at baseline and the end of each phase. Sixty-one overweight/obese adults (BMI (body mass index) 34.3 ± 5.1 kg/m², aged 55 ± 8 years) with T2DM who commenced the study were included in the intention-to-treat analysis including the 17 participants (HP n = 9, HC n = 8) who withdrew. Following weight loss (M ± SEM: −7.8 ± 0.6 kg), there were significant reductions in HbA1c (−1.4% ± 0.1%, p < 0.001) and several cardiometabolic health risk factors. Improvements were sustained for 12 weeks when weight was stabilised and weight loss maintained. Both the HP and HC dietary patterns with concurrent exercise may be effective strategies for weight loss and weight maintenance in T2DM although further studies are needed to determine the longer term effects of weight maintenance.

A Rapid and Sensitive Next-Generation Sequencing Method to Detect RB1 Mutations Improves Care for Retinoblastoma Patients and Their Families

Retinoblastoma is a childhood eye malignancy that can lead to the loss of vision, eye(s), and sometimes life. The tumors are initiated by inactivating mutations in both alleles of the tumor-suppressor gene, RB1, or, rarely, by MYCN amplification. Timely identification of a germline RB1 mutation in blood samples or either somatic RB1 mutation or MYCN amplification in tumors is important for effective care and management of retinoblastoma patients and their families. However, current procedures to thoroughly test RB1 mutations are complicated and lengthy. Herein, we report a next-generation sequencing-based method capable of detecting point mutations, small indels, and large deletions or duplications across the entire RB1 gene and amplification of MYCN gene on a single platform. From DNA extraction to clinical interpretation requires only 3 days, enabling early molecular diagnosis of retinoblastoma and optimal treatment outcomes. This method can also detect low-level mosaic mutations in blood samples that can be missed by routine Sanger sequencing. In addition, it can differentiate between RB1 mutation- and MYCN amplification-driven retinoblastomas. This rapid, comprehensive, and sensitive method for detecting RB1 mutations and MYCN amplification can readily identify RB1 mutation carriers and thus improve the management and genetic counseling for retinoblastoma patients and their families.

Assessing multiple dimensions of urgency sensation: The University of South Australia Urinary Sensation Assessment (USA2 )

AIMS

To develop and assess structure, test-retest reliability, and discriminative validity of a self-report questionnaire (University of South Australia Urinary Sensation Assessment: USA² ) to assess multiple dimensions of urgency sensation.

METHODS

The USA² was designed and tested over two prospective, observational studies (2013-2014). Participants were English speaking Australians aged 50 or more with and without overactive bladder (OAB; determined by OAB awareness tool), recruited via health and recreation centers. In Study 1, exploratory factor analysis determined USA² structure and subscales. In Study 2, confirmatory factor analysis reassessed structure; Mann-Whitney U-tests determined discriminative validity (OAB vs. non-OAB for subscale and total scores) with Cohen's d effect sizes. Thirty-three individuals completed the USA² twice; intraclass correlation coefficients (ICCs) and Wilcoxon signed rank tests assessed test-retest reliability.

RESULTS

Questionnaires were returned by 189 eligible participants in Study 1 and 211 in Study 2. Exploratory factor analysis revealed three subscales: "urgency," "affective," "fullness." Confirmatory factor analysis supported these subscales. Subscale and total scores were significantly different between groups with and without OAB (P < 0.001). Cohen's d effect sizes (95%CI) were total score 1.8 (0.5-3.1), "urgency" subscale 1.8 (1.3-2.3), "affective" 1.7 (0.95-2.4), and "fullness" 0.75 (0.42-1.09). Total and subscales scores demonstrated test-retest reliability; ICCs (95%CIs) of 0.95 (0.9-0.98), 0.96 (0.92-0.98), 0.94 (0.88-0.97), and 0.78 (0.56-0.89).

CONCLUSIONS

The USA² assesses multiple dimensions of urgency sensation, is reliable over a 2-week period, and discriminates between older adults with and without OAB. Further validation is required in conditions other than overactive bladder. Neurourol. Urodynam. 36:667-672, 2017. © 2016 Wiley Periodicals, Inc.

Interaction of erythrocyte eicosapentaenoic acid and physical activity predicts reduced risk of mild cognitive impairment

OBJECTIVES

To evaluate relationships between self-reported physical activity, proportions of long-chain omega-3 polyunsaturated fatty acids (LCn3) in erythrocyte content (percentage of total fatty acids) and risk of mild cognitive impairment (MCI) in older adults.

METHOD

A cross-sectional study was conducted. Community-dwelling male and female (n = 84) participants over the age of 65 years with and without MCI were tested for erythrocyte proportions of the LCn3s eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA). Physical activity was measured using a validated questionnaire.

RESULTS

The interaction between erythrocyte EPA, but not DHA, and increased physical activity was associated with increased odds of a non-MCI classification.

CONCLUSION

An interaction between physical activity and erythrocyte EPA content (percentage of fatty acids) significantly predicted MCI status in older adults. Randomised control trials are needed to examine the potential for supplementation with EPA in combination with increased physical activity to mitigate the risk of MCI in ageing adults.

A combined vascular surgical and clinical genetics approach to diffuse aneurysmal disease

We report two patients who presented with extensive aneurysmal disease, in association with minimal external physical signs. Patient 1 remained genetically undiagnosed despite multiple structural, biochemical and genetic investigations. He made a good recovery following surgery for popliteal and left axillary artery aneurysms. Patient 2 was diagnosed with vascular type Ehlers-Danlos syndrome, associated with a high degree of tissue and blood vessel fragility, and is being managed conservatively. Early multidisciplinary assessment of such patients facilitates accurate diagnosis and management.

Acute effects of a dietary non-starch polysaccharide supplement on cognitive performance in healthy middle-aged adults

OBJECTIVE

Certain plant polysaccharides may provide psychological health benefits. The aim of this study was to evaluate whether they can acutely improve mood and cognitive function.

METHOD

In a randomized, double-blind, placebo-controlled, between subjects design trial, 73 middle-aged adults consumed 4 g of a proprietary mixture of non-starch polysaccharides (NSPs) (Ambrotose® complex), a rice flour placebo, or a sucrose control. Participants completed testing at baseline and 30 minutes post-consumption. Acute effects of consumption on mood, cognition, and blood glucose were evaluated during mental tests designed to induce mental fatigue.

RESULTS

Significant improvement in recognition and working memory performance was observed in the group that consumed NSP compared with placebo or sucrose. Improvements in memory performance following NSP intake were independent of changes in blood glucose.

DISCUSSION

This is the first report of acute behavioural improvement following plant polysaccharide intake in healthy middle-aged adults under conditions of mental fatigue. The findings suggest that certain NSP may enhance memory performance through mechanisms other than elevated blood glucose.

Retrograde intramedullary nails with distal screws locked to the nail have higher fatigue strength than locking plates in the treatment of supracondylar femoral fractures

We investigated a new intramedullary locking nail that allows the distal interlocking screws to be locked to the nail. We compared fixation using this new implant with fixation using either a conventional nail or a locking plate in a laboratory simulation of an osteoporotic fracture of the distal femur. A total of 15 human cadaver femora were used to simulate an AO 33-A3 fracture pattern. Paired specimens compared fixation using either a locking or non-locking retrograde nail, and using either a locking retrograde nail or a locking plate. The constructs underwent cyclical loading to simulate single-leg stance up to 125 000 cycles. Axial and torsional stiffness and displacement, cycles to failure and modes of failure were recorded for each specimen. When compared with locking plate constructs, locking nail constructs had significantly longer mean fatigue life (75 800 cycles (sd 33 900) vs 12 800 cycles (sd 6100); p = 0.007) and mean axial stiffness (220 N/mm (sd 80) vs 70 N/mm (sd 18); p = 0.005), but lower mean torsional stiffness (2.5 Nm/° (sd 0.9) vs 5.1 Nm/° (sd 1.5); p = 0.008). In addition, in the nail group the mode of failure was either cut-out of the distal screws or breakage of nails, and in the locking plate group breakage of the plate was always the mode of failure. Locking nail constructs had significantly longer mean fatigue life than non-locking nail constructs (78 900 cycles (sd 25 600) vs 52 400 cycles (sd 22 500); p = 0.04).

The new locking retrograde femoral nail showed better stiffness and fatigue life than locking plates, and superior fatigue life to non-locking nails, which may be advantageous in elderly patients.

Cite this article: Bone Joint J 2014;96-B:114–21.

Dimensions of sensation assessed in urinary urgency: a systematic review

PURPOSE

Urinary urgency is an adverse sensory experience. Confirmation of the multidimensional nature of other adverse sensory experiences such as pain and dyspnea has improved the understanding of neurophysiological and perceptual mechanisms leading to innovations in assessment and treatment. It has been suggested that the sensation of urgency may include multiple dimensions such as intensity, suddenness and unpleasantness. In this systematic review we determine which dimensions of sensation have been assessed by instruments used to measure urinary urgency.

MATERIALS AND METHODS

A systematic search was undertaken of MEDLINE, Embase, AMED, CINAHL, Ageline, Web of Science, InformIT Health and Scopus databases to identify studies that included assessments of urinary urge or urgency. Articles were included in the analysis if they were primary studies that described the method used to measure urge/urgency in adults and published in English in peer reviewed publications since January 1, 2000. Articles were excluded from study if urgency was measured only in conjunction with other symptoms (eg frequency or incontinence) or if there was no English version of the instrument. Secondary analyses and systematic reviews were retained to hand search references for additional primary studies. Data were extracted for the instruments used to measure urge/urgency. For each instrument the items specific to urinary urgency were reviewed using a prospectively developed categorization process for the sensory dimension and the measurement metric. Items used to assess urinary urgency were collated in a matrix (sensory dimensions vs assessment metric). The most frequently used dimensions, metrics and combinations were descriptively analyzed.

RESULTS

After removal of duplicate articles 1,048 full text articles were screened and 411 were excluded, leaving 637 eligible articles from which data were extracted. A total of 216 instruments were identified which were 1 of 6 types, namely 1) wider symptom questionnaires, 2) urgency specific questionnaires, 3) ordinal scales, 4) visual analog scales, 5) event records or 6) body maps. These 216 instruments contained a total of 309 urgency specific items. Of the instruments 51% did not define a dimension of sensation and 26% did not define the metric used. From the remaining instruments 8 dimensions of sensation and 5 types of metrics were identified. From most common to least common, the sensory dimensions assessed were behavioral response, intensity, suddenness, bother, affective response, unpleasantness, quality (descriptors) and problems associated with sensation. Metrics were magnitude, frequency, presence, time frame or location. The most common sensory dimension/metric combinations were frequency of a behavioral response (14% of items) and magnitude of bother caused by the sensation (8% of items).

CONCLUSIONS

The hypothesis that urinary urgency is multidimensional is supported by the range of dimensions assessed with available instruments. To clarify the nature of urinary urgency compared with the normal desire to void, prospective studies are required to determine whether sensory dimensions are distinct, and which may delineate between normal and pathological sensation.