Transcatheter Aortic Valve Replacement With the Navitor System: Real-World United Kingdom Experience

The Navitor transcatheter heart valve (THV) is the latest iteration of the Portico self-expanding valve system. Early prospective studies have shown promising outcomes, however, there is a lack of complementary 'real-world' data. This study aimed to assess early safety and efficacy outcomes of the Navitor THV using registry data from 6 high-volume United Kingdom transcatheter aortic valve replacement (TAVR) centers. Demographic, procedural, and in-hospital outcome data were retrieved from 6 United Kingdom centers. The primary safety end point was 30-day mortality. Primary efficacy end points were procedural success, mean aortic gradient, and ≥moderate paravalvular leak. Secondary end points included rates of new permanent pacemaker implantation, stroke, and vascular injury. A total of 574 patients (mean age 83.4 years; 54.5% female) underwent Navitor TAVR between January 2020 and May 2023. The 30-day mortality in this patient cohort was 1.6%. Procedural success was 98.1%, mean echo-derived gradient post-TAVR was 7.7 ± 4.8 mm Hg (95% confidence interval [CI] 7.2 to 8.3, p <0.001) and 5.1% of patients had ≥moderate paravalvular leak (sample proportion estimate [p̂] = 0.051, 95% CI [0.035, 0.073], p <0.001). New permanent pacemaker implantation to discharge was required in 11% (p̂ = 0.119, 95% CI 0.088 to 0.158, p <0.001), stroke occurred in 1.2% of patients (p̂ = 0.017, 95% CI 0.006 to 0.036, p <0.001) and significant vascular injury in 1.6% (p̂ = 0.014, 95% CI 0.005 to 0.032, p <0.001). In conclusion, early procedural outcomes with Navitor TAVR compare favorably to new-generation THVs. Procedural success was high with a low incidence of complications.

Balloon aortic valvuloplasty with or without percutaneous coronary intervention in the TAVR era

Introduction The role of balloon aortic valvuloplasty (BAV) amid the era of transcatheter aortic valve replacement (TAVR) remains a topic of debate. We sought to study the safety and feasibility of combined balloon aortic valvuloplasty and percutaneous coronary intervention (BAV-PCI). Methods Between November 2009 and July 2020, all patients undergoing BAV were identified and divided into three groups: combined BAV-PCI (group A), BAV with significant unrevascularised CAD (group B) and BAV without significant CAD (group C). Procedural outcomes, 30-day and one-year mortality were compared. Results A total of 264 patients were studied (n = 84, 93 and 87 patients in group A, B and C, respectively). The STS score was 10.2 ±8, 13.3 ±19 and 8.1 ±7, p = 0.026, in group A, B and C, respectively. VARC-3 adjudicated complications were similar among groups (11%, 13% and 5%, respectively, p = 0.168, respectively). Thirty-day and one-year mortality were 9.8% (n =26) and 32% (n = 86) of the entire cohort. The differences among groups did not reach statistical significance. Using univariate Cox regression analysis, group B were at higher risk of dying compared to group A patients (HR 1.58, 95% CI 1.11 - 2.25, p = 0.010). With multivariate Cox regression analysis, the predictors of mortality were STS score, cardiogenic shock, and mode of presentation and lack of subsequent definitive valve intervention. Conclusion In high-risk patients with aortic valve stenosis, combined BAV-PCI is safe and feasible with comparable outcomes to BAV with and without significant CAD.

Anthelmintic resistance and homeostatic plasticity (Brugia malayi)

Homeostatic plasticity refers to the capacity of excitable cells to regulate their activity to make compensatory adjustments to long-lasting stimulation. It is found across the spectrum of vertebrate and invertebrate species and is driven by changes in cytosolic calcium; it has not been explored in parasitic nematodes when treated with therapeutic drugs. Here we have studied the adaptation of Brugia malayi to exposure to the anthelmintic, levamisole that activates muscle AChR ion-channels. We found three phases of the Brugia malayi motility responses as they adapted to levamisole: an initial spastic paralysis; a flaccid paralysis that follows; and finally, a recovery of motility with loss of sensitivity to levamisole at 4 h. Motility, calcium-imaging, patch-clamp and molecular experiments showed the muscle AChRs are dynamic with mechanisms that adjust their subtype composition and sensitivity to levamisole. This homeostatic plasticity allows the parasite to adapt resisting the anthelmintic.

Abstract 3118: Next generation sequencing assay for detection of gene fusions and exon deletion events in tissue and liquid biopsy samples at very low frequency

Introduction: Gene fusions caused by chromosomal rearrangements and the exon deletion events caused by aberrant RNA splicing events play a key role in oncogenesis and the progression of cancer. Next generation sequencing using molecular tagged AmpliSeq HD chemistry enables highly sensitive variant detection down to &lt;=0.1% mutant allele fractions. Here we present the Oncomine Precision RNA Assay developed using the Ion AmpliSeq HD Technology for use on both tissue and liquid biopsy samples to detect fusion and exon deletions with very high sensitivity. The assay also includes capabilities for novel fusion detection in driver genes via exon level expression measurements.

Methods: The Oncomine Precision RNA assay can detect &gt;900 known fusion isoforms including those of ALK, ROS1, RET, NTRK1,2,3, FGFR1,2,3, and BRAF and exon deletion events in MET and EGFR genes. The assay also includes amplicons in 8 key driver genes like NTRK1,2,3 to detect novel gene fusions in a partner agnostic manner based on the expression imbalance. The amplicons to detect targeted isoforms are designed strategically around the known break-points of the targeted fusions and exon skipping events. These amplicons generate reads when the target variant is present in the sample and provide complete information of the fusion event including the precise break-point with annotations such as cosmic ID. The unique molecular tags attached on both ends of the reads are used for error correction and this enables us to detect fusions at a very low frequency with high accuracy which is critical in liquid biopsy samples . The assay also includes amplicons to measure the wild-type expression of MET and EGFR genes and the exon deletion events are detected by comparing the expression of the exon-deletion transcript to that of the wild-type transcript.

Results: To test the panel, we used the GenexusTM sequencer to sequence ALK, ROS1, RET,FGFR3 and NTRK1 fusion positive cell lines and correctly identified all the targeted fusions and concordant results with expression imbalance. We sequenced cell-free total nucleic acid(cfTNA) control samples and identified the expected fusions in ALK, RET and ROS1 genes and the MET Exon 14 skipping event. We sequenced 16 FFPE samples with known truth and correctly identified all the 11 ALK and 5 ROS1 fusion isoforms and observed highly concordant results with the expression imbalance in the samples positive for ALK fusion. We sequenced the ALK, RET, NTRK1 and FGFR3 cell lines diluted to 2%, 2%, 5% and 20% respectively with the background of wild-type RNA and detected the expected fusions and observed concordant results with the expression imbalance.

Conclusions: This targeted sequencing assay enables researchers to detect gene fusions and exon deletions in both FFPE and blood samples with &gt;99% sensitivity and high specificity.

For research use only. Not for use in diagnostic procedures.

Citation Format: Rajesh K. Gottimukkala, Fiona C. Hyland, Amir Marcovitz, Jeoffrey Schageman, Varun Bagai, Ru Cao, Paul D. Williams, Scott P. Myrand, Jian Gu, Seth Sadis, Kelli S. Bramlett. Next generation sequencing assay for detection of gene fusions and exon deletion events in tissue and liquid biopsy samples at very low frequency [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 3118.

Abstract 177: RNA sequencing based gene fusion detection with oncomine comprehensive assay plus

Introduction

Detection of oncogenic fusions has been of great importance for understanding tumorigenesis and for precision oncology in enhancing diagnosis and selection of targeted therapies. Herein, we describe an extended Oncomine targeted RNA sequencing assay for detection of fusion transcripts and intragenic rearrangements (exon deletion/skipping). For multiple key driver genes we also supplemented the panel with a complementary transcript-based expression imbalance assay designed to identify gene fusions in a partner agnostic manner.

Methods

Based on evidence from Oncomine™ Knowledgebase and collaboration with leading oncology researchers, we designed an Ion AmpliSeq™ panel to target &gt; 1,200 fusion breakpoints in &gt; 50 driver genes, &gt; 40 intragenic rearrangements (e.g., MET exon 14 skipping, ARv7, EGFRvIII) in 7 genes, and 5 RNA expression controls. In addition, the panel supports detection and reporting of non-targeted fusions (i.e., novel combinations of drivers and partners). We supplemented the panel with exon tiling expression imbalance assays, using amplicons tiling the exon junctions of ALK, RET, NTRK1, NTRK2 and NTRK3 to measure 3'/5' expression imbalance signatures. We developed a bioinformatic tool to call fusions from a normalized and corrected expression imbalance profile per gene (using a baseline from normal formaldehyde fixed paraffin embedded [FFPE samples]). We optimized the gene fusion algorithms and integrated them as workflows into the Ion ReporterTM Software to facilitate the summary of the results with relevant annotations, rich data visualizations and easily interpretable reports.

Results

We sequenced hundreds of positive and negative fusion samples including commercial reference standards, cell lines and FFPE clinical research samples on the Ion GeneStudioTM S5 sequencer. To assess the feasibility of the combined panel, we sequenced the Seraseq® FFPE tumor fusion RNA reference, 7 fusion positive cell lines with ALK, RET, ROS1, NTRK1, FGFR1, FGFR2 and FGFR3 rearrangements, and cohorts of FFPE samples using 20ng RNA as input and successfully detected the expected fusion isoforms or other RNA rearrangements in each sample. We applied the exon tiling fusion detection method for ALK, RET and NTRK1 and observed perfect concordance between the true isoform in the positive samples and the predicted breakpoint position and magnitude of 3'/5' expression imbalance indicated by the exon tiling method.

Conclusions

We developed an extended, multiplexed RNA panel for fusions and intragenic rearrangements that retains the simple workflow and fast turn-around time of previous Oncomine fusion panels and significantly expands the scope of fusion isoform detection including methods to detect gene fusions in a partner agnostic manner.

For research use only. Not for use in diagnostic procedures.

Citation Format: Amir Marcovitz, Rajesh K. Gottimukkala, Gary G. Bee, Jennifer M. Kilzer, Vinay K. Mital, Elain Wong-Ho, Chenchen Yang, Yu-Ting Tseng, Scott P. Myrand, Paul D. Williams, Seth Sadis, Fiona C. Hyland. RNA sequencing based gene fusion detection with oncomine comprehensive assay plus [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 177.

Increased shear in the North Atlantic upper-level jet stream over the past four decades

Earth's equator-to-pole temperature gradient drives westerly mid-latitude jet streams through thermal wind balance¹. In the upper atmosphere, anthropogenic climate change is strengthening this meridional temperature gradient by cooling the polar lower stratosphere^2,3 and warming the tropical upper troposphere^4-6, acting to strengthen the upper-level jet stream⁷. In contrast, in the lower atmosphere, Arctic amplification of global warming is weakening the meridional temperature gradient^8-10, acting to weaken the upper-level jet stream. Therefore, trends in the speed of the upper-level jet stream^11-13 represent a closely balanced tug-of-war between two competing effects at different altitudes¹⁴. It is possible to isolate one of the competing effects by analysing the vertical shear-the change in wind speed with height-instead of the wind speed, but this approach has not previously been taken. Here we show that, although the zonal wind speed in the North Atlantic polar jet stream at 250 hectopascals has not changed since the start of the observational satellite era in 1979, the vertical shear has increased by 15 per cent (with a range of 11-17 per cent) according to three different reanalysis datasets^15-17. We further show that this trend is attributable to the thermal wind response to the enhanced upper-level meridional temperature gradient. Our results indicate that climate change may be having a larger impact on the North Atlantic jet stream than previously thought. The increased vertical shear is consistent with the intensification of shear-driven clear-air turbulence expected from climate change^18-20, which will affect aviation in the busy transatlantic flight corridor by creating a more turbulent flying environment for aircraft. We conclude that the effects of climate change and variability on the upper-level jet stream are being partly obscured by the traditional focus on wind speed rather than wind shear.

Rapid Aspirin Desensitization is Safe and Feasible in Patients With Stable and Unstable Coronary Artery Disease: A Single-Center Experience

AIMS

There are limited data on aspirin (ASA) desensitization for patients with coronary disease. We present our experience with a rapid nurse-led oral desensitization regimen in patients with aspirin sensitivity undergoing coronary angiography.

METHODS

This single-center retrospective observational study includes patients with a history of ASA sensitivity undergoing coronary angiography with intent to perform percutaneous coronary intervention (PCI).

RESULTS

Between January 2012 and January 2017, 24 patients undergoing coronary angiography for stable coronary disease (7 cases) or acute coronary syndromes (non-ST-segment myocardial infarction [NSTEMI; 8 cases], STEMI [9 cases]) underwent aspirin desensitization having reported previous reactions to aspirin. At initial presentation, previous sensitivity reactions were reported as: mucocutaneous reactions in 17 patients (urticaria in 3 [13%], nonurticarial rash in 6 [25%], angio-oedema in 8 [33%]), respiratory sensitivity in 4 (17%), and systemic anaphylactoid reactions in 3 (13%). Seventeen (71%) patients underwent PCI. Desensitization was acutely successful in 22 (92%) patients and unsuccessful in 2 (8%) patients who both had a single short-lived episode of acute bronchospasm treated successfully with nebulized salbutamol. Fifteen successfully desensitized patients completed 12 months of aspirin; no patient had recurrent hypersensitivity reaction. Aspirin was stopped prior to 12 months in 7 patients (replaced by warfarin [1 case], no antiplatelet or single antiplatelet clinically indicated and clopidogrel chosen [4 cases], patient choice without evidence of recurrent hypersensitivity [1 case], and death due to cardiogenic shock following STEMI [1 case]).

CONCLUSION

A rapid aspirin desensitization protocol is safe and effective across a broad spectrum of hypersensitivity reactions and clinical presentations.

Optical Coherence Tomography Evaluation of Coronary Dissection and Intramural Hematoma

Image series shows an extensive intramural hematoma causing luminal compression corresponding to the angiographic stenosis. Although intramural hematomas are identifiable on intravascular ultrasound, OCT offers superior characterization and exclusion of alternate diagnoses, such as plaque erosion.

Abstract 3863: Analytical performance of a novel next generation sequencing assay for myeloid cancers

Title: Analytical performance of a novel next generation sequencing assay for myeloid cancers

Nick Khazanov, Wally Zhang, Dinesh Cyanam, Scott P. Myrand, Denis Kaznadzey, Paul Williams, Vinay Mittal, Dan Mazur, Sihong Chen, Jason Wustman, Efren Ballesteros-Villagrana, Goutam Nistala, Jon Sherlock, Michael Hogan, Jim Veitch, John Bishop, Seth Sadis

Introduction: Myeloid malignancies contain a diverse and heterogeneous set of genomic alterations that include recurrent somatic mutations in key driver genes as well as frequent and diagnostic chromosomal rearrangements that generate a wide array of gene fusion products. To support clinical and translational research into precision oncology strategies for myeloid cancers, a next-generation sequencing (NGS) assay was generated to detect common and relevant somatic alterations.

Methods: To define gene targets that were recurrently altered in myeloid cancers and relevant for clinical and translational research, an extensive survey of investigators at hematology oncology research labs was performed. The gene targets identified by researchers were complemented by a comprehensive survey of literature and genomic databases. Clinical guidelines for myeloid diseases in the US and in Europe were reviewed to ensure representation of relevant alterations. A targeted Ion AmpliSeq panel was generated to support the detection of recurrent single-nucleotide variants, insertions/deletions, and gene fusions from blood or bone marrow samples. The panel was developed for manual or automated library preparation and sequencing on the Ion Torrent PGM or Ion S5 instruments.

Results: The Oncomine™ Myeloid Research Assay gene panel included 58 genes and generated an average read depth of &gt;2,000 reads per targeted amplicon with an average uniformity of &gt;95%. Important GC-rich targets such as CEBPA generated sufficient balanced read depth to support variant detection. A cohort of samples positive for FLT3 alterations was analyzed and successful detection of FLT3-internal tandem repeat variants was demonstrated. Several gene fusion transcripts common to myeloid cancers were detected. Comparable results were observed on Ion Torrent PGM and Ion S5 instruments.

Conclusions: A novel myeloid specific NGS assay capable of detecting relevant DNA and RNA alterations from the same sample was developed. The assay is useful for characterizing relevant alterations in a range of myeloid diseases including acute myeloid leukemia, myelodysplastic syndrome, myeloproliferative neoplasms, chronic myelogenous leukemia, chronic myelomonocytic leukemia, and juvenile myelomonocytic leukemia. A review of the analytical studies will be presented.

Citation Format: Nickolay Khazanov, Wally Zhang, Dinesh Cyanam, Scott P. Myrand, Denis Kaznadzey, Paul D. Williams, Vinay Mittal, Daniel J. Mazur, Sihong Chen, Jason Wustman, Efren Ballesteros-Villagrana, Goutam Nistala, Santhoshi Bandla, Jim Veitch, Jon Sherlock, John Bishop, Seth Sadis. Analytical performance of a novel next generation sequencing assay for myeloid cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3863.

On-farm storage of livestock vaccines may be a risk to vaccine efficacy: a study of the performance of on-farm refrigerators to maintain the correct storage temperature

BACKGROUND

Livestock vaccines (LV) are often stored on-farm, in a refrigerator (fridge), prior to use and little is documented about the storage conditions during this period. As the quality of a vaccine can be impaired by storage at an incorrect temperature, the present study aimed to evaluate the on-farm performance of farm fridges to maintain the correct storage temperature. From January to August 2014, temperature data loggers were placed on selected farms fridges used to store LV (n = 20) in South-West England.

RESULTS

Temperature recording data was available from 17 of the 20 farms. Fifty-nine percent of farm fridges had at least one temperature recording above 8 °C, 53% had at least one recording below 2 °C and 41% at or below 0 °C. Internal fridge temperatures attained 24 °C and dropped to - 12 °C as an absolute maximum and minimum respectively. Fridges tested spent an average of 16% of the total time recorded above 8 °C. Time of the year significantly influenced the percentage of time above 8 °C. External and internal temperatures were found to be positively correlated (p < 0.001). Statistical significant differences in internal and external temperatures were found between March and August.

CONCLUSIONS

The majority of fridges in this study would have failed to keep any stored LV within the recommended storage temperature range. If LV are going to be stored on-farm prior to use, then urgent improvements in this part of the cold-chain are required in order to insure vaccine efficacy is not compromised.

Transradial Secondary Access to Guide Valve Implantation and Manage Peripheral Vascular Complications During Transcatheter Aortic Valve Implantation

BACKGROUND

Vascular complications from transfemoral (TF) secondary access during transcatheter aortic valve implantation (TAVI) are common. We compare our experience of transradial (TR) versus transfemoral secondary access during TAVI and describe techniques for performing iliofemoral arterial intervention from the transradial approach.

METHODS

All TAVI procedures with a single secondary access were included. Demographics, procedural details and 30-day outcomes were recorded. VARC-2 criteria were used for procedural complications. Procedures with TF primary access were stratified by the site of secondary arterial access.

RESULTS

Single secondary access was used in 199 cases, of which 20 were performed via non-TF access. Of the 179 TF primary access cases, 115 (64%) used TR secondary access and 64 (36%) used TF secondary access. In the TR cohort percutaneous vascular intervention was performed from the transradial approach in 19 cases (17%). Emergent TF secondary access was not required in any case. There were no differences in procedural time, radiation dose, contrast use, bleeding complications, stroke or mortality between the groups. There was one secondary access complication in the TF cohort and none in the TR cohort.

CONCLUSIONS

Transradial (TR) secondary access during TAVI is safe and feasible and may reduce the secondary access site vascular complication rate. With appropriate equipment, most peripheral vascular complications can be managed entirely via TR access avoiding unplanned femoral arterial access. TR secondary access should be considered the default approach for non-TF TAVI cases and can be considered for all TF cases as long as dedicated equipment is available.

Incomplete host immunity favors the evolution of virulence in an emergent pathogen

Immune memory evolved to protect hosts from reinfection, but incomplete responses that allow future reinfection may inadvertently select for more-harmful pathogens. We present empirical and modeling evidence that incomplete immunity promotes the evolution of higher virulence in a natural host-pathogen system. We performed sequential infections of house finches with Mycoplasma gallisepticum strains of various levels of virulence. Virulent bacterial strains generated stronger host protection against reinfection than less virulent strains and thus excluded less virulent strains from infecting previously exposed hosts. In a two-strain model, the resulting fitness advantage selected for an almost twofold increase in pathogen virulence. Thus, the same immune systems that protect hosts from infection can concomitantly drive the evolution of more-harmful pathogens in nature.

Note: A self-calibrating wide range electrometer for in-cloud measurements

Charge is observed in clouds of all forms, which may influence their development and properties. In-cloud charge measurements require a wide dynamic range, extending from charge in aerosols and dusts to that present in thunderstorms. Unexpectedly large charge densities (>200 pC m^-3) have recently been detected in layer clouds using balloon-carried linear electrometers. These, however, lead to instrument saturation if sufficient sensitivity for aerosol and droplet charge is maintained. Logarithmic electrometers provide an alternative but suffer strong non-linear thermal effects. This is a limitation for balloon-carried instruments that encounter temperature changes up to ∼100 °C, as full thermal compensation requires complexity inappropriate for disposable devices. Here, a novel hybrid system is described, combining linear and logarithmic electrometers to provide extended dynamic range (±50 pA), employing the negligible (±4%) total temperature drift of the linear device to provide in situ calibration of the logarithmic device. This combination opens up new measurement opportunities for charge in clouds, dusts, and aerosols.

Functionality and the Evolution of Marginal Stability in Proteins: Inferences from Lattice Simulations

It has been known for some time that many proteins are marginally stable. This has inspired several explanations. Having noted that the functionality of many enzymes is correlated with subunit motion, flexibility, or general disorder, some have suggested that marginally stable proteins should have an evolutionary advantage over proteins of differing stability. Others have suggested that stability and functionality are contradictory qualities, and that selection for both criteria results in marginally stable proteins, optimised to satisfy the competing design pressures. While these explanations are plausible, recent research simulating the evolution of model proteins has shown that selection for stability, ignoring any aspects of functionality, can result in marginally stable proteins because of the underlying makeup of protein sequence-space. We extend this research by simulating the evolution of proteins, using a computational protein model that equates functionality with binding and catalysis. In the model, marginal stability is not required for ligand-binding functionality and we observe no competing design pressures. The resulting proteins are marginally stable, again demonstrating that neutral evolution is sufficient for explaining marginal stability in observed proteins.

Note: A miniature oscillating microbalance for sampling ice and volcanic ash from a small airborne platform

A lightweight and low power oscillating microbalance for in situ sampling of atmospheric ice and volcanic ash is described for airborne platforms. Using a freely exposed collecting wire fixed at only one end to a piezo transducer, the instrument collects airborne materials. Accumulated mass is determined from the change in natural frequency of the wire. The piezo transducer is used in a dual mode to both drive and detect the oscillation. Three independent frequency measurement techniques are implemented with an on-board microcontroller: a frequency sweep, a Fourier spectral method, and a phase-locked loop. These showed agreement to ±0.3 Hz for a 0.5 mm diameter collecting wire of 120 mm long, flown to 19 km altitude on a weather balloon. The instrument is well suited to disposable use with meteorological radiosondes, to provide high resolution vertical profiles of mass concentration.

Somatic mutation burden in cancer samples determined by targeted next generation sequencing

15

Background: High somatic mutation burden in tumor tissues is associated with the presentation of neoantigens that promote immune responses particularly in the context of immune checkpoint therapies. Herein, we characterize the ability of targeted cancer research panels to generate estimates of somatic mutation burden. Methods: Somatic mutation data from > 8000 cancer samples obtained from The Cancer Genome Atlas (TCGA) was curated and standardized, and the number of single nucleotide variants (SNVs) in exonic regions of each sample determined. Next, the number of SNVs associated with target regions of two Ion AmpliSeq cancer panels (Oncomine Comprehensive Assay [OCA, 146 genes, 0.35 MB]; Comprehensive Cancer Panel [CCP, 409 genes, 1.7 MB]) was likewise determined and the frequency of mutation counts in the exome and the panel target regions was compared. Mutation counts of samples containing truncating mutations in mismatch repair (MMR) and other DNA repair genes were characterized. A facile workflow with less than 60 minutes of hands-on time was developed to estimate mutation counts for a batch of 8 samples using the Ion Chef for automated library preparation and templating followed by sequencing on the Ion S5. Results: The sensitivity of targeted panels in estimating somatic mutation burden was positively correlated with panel size. The area under the Receiver Operating Characteristic (ROC) curve showed that CCP had > 90% sensitivity and > 95% specificity to differentiate high and low mutation burden based on informatics analysis of TCGA data. As expected, truncating mutations in MMR genes were associated with higher somatic mutation counts in colorectal tumor tissue. Using data generated from OCA and CCP, we characterized a set of filters that provided a good estimate of somatic mutation counts when applied to a tumor-only workflow. Conclusions: A simple workflow was developed on the Ion Torrent sequencing platform to estimate somatic mutation burden in cancer samples. The methods described herein will help advance research in immuo-oncology.

On the detection and attribution of gravity waves generated by the 20 March 2015 solar eclipse

Internal gravity waves are generated as adjustment radiation whenever a sudden change in forcing causes the atmosphere to depart from its large-scale balanced state. Such a forcing anomaly occurs during a solar eclipse, when the Moon's shadow cools part of the Earth's surface. The resulting atmospheric gravity waves are associated with pressure and temperature perturbations, which in principle are detectable both at the surface and aloft. In this study, surface pressure and temperature data from two UK sites at Reading and Lerwick are examined for eclipse-driven gravity wave perturbations during the 20 March 2015 solar eclipse over northwest Europe. Radiosonde wind data from the same two sites are also analysed using a moving parcel analysis method, to determine the periodicities of the waves aloft. On this occasion, the perturbations both at the surface and aloft are found not to be confidently attributable to eclipse-driven gravity waves. We conclude that the complex synoptic weather conditions over the UK at the time of this particular eclipse helped to mask any eclipse-driven gravity waves.This article is part of the themed issue 'Atmospheric effects of solar eclipses stimulated by the 2015 UK eclipse'.

Coordinated weather balloon solar radiation measurements during a solar eclipse

Solar eclipses provide a rapidly changing solar radiation environment. These changes can be studied using simple photodiode sensors, if the radiation reaching the sensors is unaffected by cloud. Transporting the sensors aloft using standard meteorological instrument packages modified to carry extra sensors, provides one promising but hitherto unexploited possibility for making solar eclipse radiation measurements. For the 20 March 2015 solar eclipse, a coordinated campaign of balloon-carried solar radiation measurements was undertaken from Reading (51.44°N, 0.94°W), Lerwick (60.15°N, 1.13°W) and Reykjavik (64.13°N, 21.90°W), straddling the path of the eclipse. The balloons reached sufficient altitude at the eclipse time for eclipse-induced variations in solar radiation and solar limb darkening to be measured above cloud. Because the sensor platforms were free to swing, techniques have been evaluated to correct the measurements for their changing orientation. In the swing-averaged technique, the mean value across a set of swings was used to approximate the radiation falling on a horizontal surface; in the swing-maximum technique, the direct beam was estimated by assuming that the maximum solar radiation during a swing occurs when the photodiode sensing surface becomes normal to the direction of the solar beam. Both approaches, essentially independent, give values that agree with theoretical expectations for the eclipse-induced radiation changes.This article is part of the themed issue 'Atmospheric effects of solar eclipses stimulated by the 2015 UK eclipse'.

Genomic Profiling of Penile Squamous Cell Carcinoma Reveals New Opportunities for Targeted Therapy

Penile squamous cell carcinoma (PeSCCA) is a rare malignancy for which there are limited treatment options due to a poor understanding of the molecular alterations underlying disease development and progression. Therefore, we performed comprehensive, targeted next-generation sequencing to identify relevant somatic genomic alterations in a retrospective cohort of 60 fixed tumor samples from 43 PeSCCA cases (including 14 matched primary/metastasis pairs). We identified a median of two relevant somatic mutations and one high-level copy-number alteration per sample (range, 0-5 and 0-6, respectively). Expression of HPV and p16 was detectable in 12% and 28% of patients, respectively. Furthermore, advanced clinical stage, lack of p16 expression, and MYC and CCND1 amplifications were significantly associated with shorter time to progression or PeSCCA-specific survival. Notably, four cases harbored EGFR amplifications and one demonstrated CDK4 amplification, genes for which approved and investigational targeted therapies are available. Importantly, although paired primary tumors and lymph node metastases were largely homogeneous for relevant somatic mutations, we identified heterogeneous EGFR amplification in primary tumor/lymph node metastases in 4 of 14 cases, despite uniform EGFR protein overexpression. Likewise, activating HRAS mutations occurred in 8 of 43 cases. Taken together, we provide the first comprehensive molecular PeSCCA analysis, which offers new insight into potential precision medicine approaches for this disease, including strategies targeting EGFR.

Development and validation of a scalable next-generation sequencing system for assessing relevant somatic variants in solid tumors

Next-generation sequencing (NGS) has enabled genome-wide personalized oncology efforts at centers and companies with the specialty expertise and infrastructure required to identify and prioritize actionable variants. Such approaches are not scalable, preventing widespread adoption. Likewise, most targeted NGS approaches fail to assess key relevant genomic alteration classes. To address these challenges, we predefined the catalog of relevant solid tumor somatic genome variants (gain-of-function or loss-of-function mutations, high-level copy number alterations, and gene fusions) through comprehensive bioinformatics analysis of >700,000 samples. To detect these variants, we developed the Oncomine Comprehensive Panel (OCP), an integrative NGS-based assay [compatible with < 20 ng of DNA/RNA from formalin-fixed paraffin-embedded (FFPE) tissues], coupled with an informatics pipeline to specifically identify relevant predefined variants and created a knowledge base of related potential treatments, current practice guidelines, and open clinical trials. We validated OCP using molecular standards and more than 300 FFPE tumor samples, achieving >95% accuracy for KRAS, epidermal growth factor receptor, and BRAF mutation detection as well as for ALK and TMPRSS2:ERG gene fusions. Associating positive variants with potential targeted treatments demonstrated that 6% to 42% of profiled samples (depending on cancer type) harbored alterations beyond routine molecular testing that were associated with approved or guideline-referenced therapies. As a translational research tool, OCP identified adaptive CTNNB1 amplifications/mutations in treated prostate cancers. Through predefining somatic variants in solid tumors and compiling associated potential treatment strategies, OCP represents a simplified, broadly applicable targeted NGS system with the potential to advance precision oncology efforts.

Abstract A1-43: Targeted amplicon-based next-generation sequencing of routine solid tumor specimens to detect clinically relevant somatic alterations

Background: Although precision medicine approaches have revolutionized oncology, widespread adoption requires robust, inexpensive approaches enabling the targeted assessment of all relevant alteration classes from routine tissue samples.

Methods: Here we interrogated &gt;7,000 cancer exomes and transcriptomes, along with &gt;30,000 array based cancer genomes to identify recurrent somatic alterations (mutations, copy number alterations [CNAs] and gene fusions) across solid tumors. From this analysis, we developed and validated an integrated multiplexed PCR based Ion Torrent next generation sequencing panel (Oncomine Cancer Research Panel [OCP]) targeting the actionable somatic cancer genome optimized for 20ng of formalin-fixed, paraffin-embedded (FFPE) tissue isolated DNA/RNA.

Results: We validated the OCP using FFPE cell line mixtures, as well as a prospective cohort of 104 FFPE tumor specimens sent for concurrent clinical molecular testing, with &gt;97% sensitivity and specificity for the presence/absence of KRAS, EGFR, BRAF and ALK point mutations, indels or gene fusions in this molecular testing cohort. We also applied the OCP to 100 lung cancers, identifying known and novel alterations, including ALK and ROS1 gene fusions. Lastly, applying the OCP to 116 prostate cancers, including 50 previously treated samples, we recapitulated known molecular subtypes, observed distinct profiles according to previous treatment and obtained 100% concordance for isoform specific TMPRSS2:ERG gene fusion detection compared to qPCR. Additionally, OCP profiling supports a novel molecular subtype of prostate cancer defined by IDH1 R132 hotspot mutations and informed on resistance mechanisms in a pre- and post-treatment sample pair. Importantly, 44%, 35% and 9% of patients in the molecular testing, lung and prostate cancer cohorts, respectively, harbored additional alterations (beyond routine molecular testing) associated with FDA approved or NCCN guideline referenced therapies.

Conclusions: Through analysis of both DNA and RNA to assess the actionable somatic cancer genome, the validated OCP panel may have utility in both clinical and research settings.

Citation Format: Daniel H. Hovelson, Andrew S. McDaniel, Bryan Johnson, Andi K. Cani, Kate Rhodes, Paul D. Williams, Chia-Jen Liu, Santhoshi Bandla, Catherine S. Grasso, Michael J. Quist, Seth Sadis, Daniel R. Rhodes, Scott A. Tomlins. Targeted amplicon-based next-generation sequencing of routine solid tumor specimens to detect clinically relevant somatic alterations. [abstract]. In: Proceedings of the AACR Special Conference on Translation of the Cancer Genome; Feb 7-9, 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 1):Abstract nr A1-43.

Next-Gen Sequencing Exposes Frequent MED12 Mutations and Actionable Therapeutic Targets in Phyllodes Tumors

Phyllodes tumors are rare fibroepithelial tumors with variable clinical behavior accounting for a small subset of all breast neoplasms, yet little is known about the genetic alterations that drive tumor initiation and/or progression. Here, targeted next-generation sequencing (NGS) was used to identify somatic alterations in formalin-fixed paraffin-embedded (FFPE) patient specimens from malignant, borderline, and benign cases. NGS revealed mutations in mediator complex subunit 12 (MED12) affecting the G44 hotspot residue in the majority (67%) of cases spanning all three histologic grades. In addition, loss-of-function mutations in p53 (TP53) as well as deleterious mutations in the tumor suppressors retinoblastoma (RB1) and neurofibromin 1 (NF1) were identified exclusively in malignant tumors. High-level copy-number alterations (CNA) were nearly exclusively confined to malignant tumors, including potentially clinically actionable gene amplifications in IGF1R and EGFR. Taken together, this study defines the genomic landscape underlying phyllodes tumor development, suggests potential molecular correlates to histologic grade, expands the spectrum of human tumors with frequent recurrent MED12 mutations, and identifies IGF1R and EGFR as potential therapeutic targets in malignant cases.

IMPLICATIONS

Integrated genomic sequencing and mutational profiling provides insight into the molecular origin of phyllodes tumors and indicates potential druggable targets in malignant disease. Visual Overview: http://mcr.aacrjournals.org/content/early/2015/04/02/1541-7786.MCR-14-0578/F1.large.jpg.

Note: A balloon-borne accelerometer technique for measuring atmospheric turbulence

A weather balloon and its suspended instrument package behave like a pendulum with a moving pivot. This dynamical system is exploited here for the detection of atmospheric turbulence. By adding an accelerometer to the instrument package, the size of the swings induced by atmospheric turbulence can be measured. In test flights, strong turbulence has induced accelerations greater than 5g, where g = 9.81 m s(-2). Calibration of the accelerometer data with a vertically orientated lidar has allowed eddy dissipation rate values of between 10(-3) and 10(-2) m(2) s(-3) to be derived from the accelerometer data. The novel use of a whole weather balloon and its adapted instrument package can be used as a new instrument to make standardized in situ measurements of turbulence.

Right and left heart catheterization via an antecubital fossa vein and the radial artery--a prospective study

Right heart catheterization has been described via the arm but previous reports have been retrospective, performed for limited indications, and may not give an accurate assessment of the success rate or safety of this technique. We sought to prospectively examine the feasibility and safety of left and right heart catheterization entirely via the arm using the radial artery and an antecubital fossa vein for a broad range of indications. Fifty-eight consecutive procedures were included. Transradial arterial access was successful in 57 patients (98%), right heart catheterization via the antecubital fossa vein was successful in 54 patients (93%) and bilateral catheterization from the arm was achieved in 53 patients (91%). Standard diagnostic catheterization was the most frequent procedure (59%), although thermodilution (6.9%), percutaneous coronary intervention (33%), and coronary sinus sampling (16%) were also performed in selected cases. Compared to a historical cohort of patients undergoing right and left heart catheterization via femoral access, mean procedural time (38 vs 47 minutes; P=.03) and screening time (8.1 vs 11.2 minutes; P<.001) were significantly reduced. There was 1 venous forearm hematoma that was managed conservatively. Right and left heart catheterization can be performed routinely via the arm in a broad range of patients and is associated with reduced procedural and fluoroscopy time as compared to femoral access. This approach can be considered for all patients in whom right and left heart catheterization is planned.

Does diabetic status in the ICU predict haemofiltration requirement? The haemofiltration in the ICU and diabetic status (HIDS) study

Diabetes is already a major health burden and prevalence is expected to double by 2025. The impact of diabetes and clinical outcomes in the intensive care unit is an evolving area of research. This study seeks to identify whether diabetic status is an independent risk factor for haemofiltration. This is a retrospective cohort study. All unique patients from a seven-year period from 2004 to 2010 at a major intensive care unit in Melbourne, Australia were analysed using multivariate regression to look for an association between diabetic status and haemofiltration. After exclusion criteria there were 7262 patients, 1674 with a history of diabetes (median age of 69, 66.72% male) and 5588 without a history of diabetes (median age 64, 64.13% male). Diabetic status was an independent risk factor (odds ratio 1.401, 95% confidence interval 1.079 to 1.820, P=0.011) for haemofiltration. Further research may identify intensive care unit-based renoprotective measures specifically for patients with diabetes.

Evidence of trade-offs shaping virulence evolution in an emerging wildlife pathogen

In the mid-1990s, the common poultry pathogen Mycoplasma gallisepticum (MG) made a successful species jump to the eastern North American house finch Haemorhous mexicanus (HM). Subsequent strain diversification allows us to directly quantify, in an experimental setting, the transmission dynamics of three sequentially emergent geographic isolates of MG, which differ in the levels of pathogen load they induce. We find significant among-strain variation in rates of transmission as well as recovery. Pathogen strains also differ in their induction of host morbidity, measured as the severity of eye lesions due to infection. Relationships between pathogen traits are also investigated, with transmission and recovery rates being significantly negatively correlated, whereas transmission and virulence, measured as average eye lesion score over the course of infection, are positively correlated. By quantifying these disease-relevant parameters and their relationships, we provide the first analysis of the trade-offs that shape the evolution of this important emerging pathogen.

Periluminal expression of a secreted transforming growth factor-β type II receptor inhibits in-stent neointima formation following adenovirus-mediated stent-based intracoronary gene transfer

Transforming growth factor-β1 (TGF-β1) has been shown unequivocally to enhance neointima formation in carotid and ileo-femoral arteries. In our previous studies, however, TGF-β1 expression in coronary arteries actually reduced neointima formation without affecting luminal loss postangioplasty, while expression of a TGF-β1 antagonist (RIIs) in balloon-injured coronary arteries reduced luminal loss without affecting neointima formation. These observed effects may be a consequence of the mode of coronary artery gene transfer employed, but they may also represent differences in the modes of healing of coronary, carotid, and ileo-femoral arteries after endoluminal injury. To help clarify whether a gene therapy strategy to antagonize TGF-β might have application within the coronary vasculature, we have investigated the effect of high-level periluminal expression of RIIs using stent-based adenovirus-mediated intracoronary gene transfer. Porcine coronary arteries were randomized to receive a custom-made CoverStent preloaded with saline only, or with 1×10(9) infectious units of adenovirus expressing RIIs or β-galactosidase (lacZ). Vessels were analyzed 28 days poststenting, at which time angiographic in-stent diameter was significantly greater in RIIs-treated arteries, and in-stent luminal loss significantly reduced. Computerized morphometric minimum in-stent lumen area was ~300% greater in RIIs-exposed vessels than in lacZ or saline-only groups. This was because of significantly reduced neointima formation in the RIIs group. RIIs had no demonstrable effect on cellular proliferation or apoptosis, but greater normalized neointimal/medial collagen content was observed in RIIs-exposed arteries. These data highlight the qualitatively similar effect of TGF-β antagonism on neointima formation in injured coronary and noncoronary arteries, and suggest that since cellular proliferation is unaffected, TGF-β1 antagonism might prevent in-stent restenosis without the delayed healing that is associated with drug-eluting stents in current clinical use.

Transradial intervention via large-bore guide catheters: a study of coronary bifurcation disease treatment using the crush technique

Transradial access for coronary intervention significantly reduces vascular complications and may be associated with a reduced risk of major adverse cardiovascular events. However, the small caliber of the radial artery has been considered a limitation to performing complex coronary intervention. Fifty-three patients with true bifurcation disease, in whom a two-stent strategy was felt to be indicated, were scheduled to undergo crush stenting via the transradial approach. Procedural outcome was recorded and 6- and 18-month clinical follow-up was performed. Successful crush stenting via the radial artery was performed in 51/55 lesions (93%). Crush stenting was performed in 53 lesions overall and successful final kissing inflation was achieved in 51/53 (96%). There were no in-hospital or procedural complications. The overall rate of death, myocardial infarction, or target vessel revascularization was 9.8% at 18-month follow-up. Complex percutaneous coronary intervention requiring large-bore catheters can be performed successfully in a high proportion of patients via the transradial approach. Crush stenting, with a very high rate of final kissing inflation, was associated in this series with excellent procedural and medium-term outcomes.

Renal sympathetic nerve denervation for the treatment of resistant hypertension

Improvements in BP control with pharmacotherapy undoubtedly translate into significant individual and population health benefits. RDN results in impressive reductions in BP, which are likely to be associated with further improvements in clinical outcomes. With more clinical trials and concurrent development of new devices, we hope that RDN holds up to its current accolades.

Mathematics applied to the climate system: outstanding challenges and recent progress

The societal need for reliable climate predictions and a proper assessment of their uncertainties is pressing. Uncertainties arise not only from initial conditions and forcing scenarios, but also from model formulation. Here, we identify and document three broad classes of problems, each representing what we regard to be an outstanding challenge in the area of mathematics applied to the climate system. First, there is the problem of the development and evaluation of simple physically based models of the global climate. Second, there is the problem of the development and evaluation of the components of complex models such as general circulation models. Third, there is the problem of the development and evaluation of appropriate statistical frameworks. We discuss these problems in turn, emphasizing the recent progress made by the papers presented in this Theme Issue. Many pressing challenges in climate science require closer collaboration between climate scientists, mathematicians and statisticians. We hope the papers contained in this Theme Issue will act as inspiration for such collaborations and for setting future research directions.

Renal sympathetic denervation: hypertension therapy and beyond

Hypertension is one of the most important treatable causes of mortality and morbidity in the world, but despite the wide availability of pharamacological therapy, blood pressure is poorly controlled in many patients. Renal sympathetic denervation (RSD) is a novel therapeutic option whereby the renal sympathetic nerves, which lie within and around the wall of the renal arteries, are ablated using a catheter placed within the arterial lumen. The Symplicity HTN-2 trial has shown that RSD reduces blood pressure to a clinically relevant degree; this finding has resulted in an explosion in interest in the procedure and RSD has the potential to become a standard therapy for many hypertensive patients. Many new devices are in development that will simplify the procedure, and several novel indications for RSD are currently being investigated in clinical trials.

Abstract 3173: High-throughput, systematic analysis of paired-end next-generation sequencing data to characterize the gene fusion landscape in cancer

Gene fusions encode oncogenic drivers in hematological and solid tumors and are often associated with dramatic clinical responses with the appropriate targeted agents. In principle, massively parallel paired-end sequencing can identify structural rearrangements in tumor genomes and transcriptomes. However, computational methods to identify gene fusions are varied, still evolving and largely trained on cell line data. We sought to develop systematic methods to characterize known oncogenic gene fusions and to discover novel gene fusions in cancer. RNASeq data for approximately 3,400 clinical cases from 16 cancer types was obtained from the Cancer Genomics Hub (CGHub) of The Cancer Genome Atlas (TCGA). We surveyed the performance of several gene fusion callers and chose two (deFuse and TopHat) for further method development. An analysis pipeline was developed and executed in parallel on a high-performance computing cluster. Filtering and annotation was conducted on the aggregated data as a post-processing step, to enable exploratory analyses of various filters. We optimized filtering approaches on datasets that included known standards (e.g., TMPRSS2-ERG in prostate adenocarcinoma, PML-RARA in acute myeloid leukemia, etc.) to enrich for these and other gene fusions with correct 5’-3’ orientation while excluding cases with ambiguous breakpoints and spanning reads, alignment errors, and read-through transcripts from adjacent genes. Predicted fusions were summarized based on the occurrence of unique genes participating in fusions with multiple partners and of unique gene pairs, each within specific diseases. Elevated expression was observed after the predicted breakpoint of the 3’ gene in cases positive for predicted fusions, and added important confirmatory evidence. Thus, we characterized the incidence and distribution of several known oncogenic gene fusions including EML4-ALK and CCDC6-RET while expanding the number of gene partners identified in combination with oncogenes such as ROS1. In addition to characterizing the incidence and distribution of 31 known gene fusions, we nominated over 100 novel gene fusion pairs. One example of a novel gene fusion susceptible to available targeted therapy was FGFR3-TACC3 in 4% of bladder cancer, 2% of squamous cell lung carcinoma, and 1% each of glioblastoma and head and neck squamous cell carcinoma. Computational methods are now poised to complement biochemical approaches in the definition of the gene fusion landscape in cancer.

Citation Format: Seth E. Sadis, Nickolay A. Khazanov, Armand R. Bankhead, Dinesh Cyanam, Paul D. Williams, Sean F. Eddy, Peter J. Wyngaard, Daniel R. Rhodes. High-throughput, systematic analysis of paired-end next-generation sequencing data to characterize the gene fusion landscape in cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3173. doi:10.1158/1538-7445.AM2013-3173