Genome-matched treatments and patient outcomes in the Maine Cancer Genomics Initiative (MCGI)

Genomic tumor testing (GTT) is an emerging technology aimed at identifying variants in tumors that can be targeted with genomically matched drugs. Due to limited resources, rural patients receiving care in community oncology settings may be less likely to benefit from GTT. We analyzed GTT results and observational clinical outcomes data from patients enrolled in the Maine Cancer Genomics Initiative (MCGI), which provided access to GTTs; clinician educational resources; and genomic tumor boards in community practices in a predominantly rural state. 1603 adult cancer patients completed enrollment; 1258 had at least one potentially actionable variant identified. 206 (16.4%) patients received a total of 240 genome matched treatments, of those treatments, 64% were FDA-approved in the tumor type, 27% FDA-approved in a different tumor type and 9% were given on a clinical trial. Using Inverse Probability of Treatment Weighting to adjust for baseline characteristics, a Cox proportional hazards model demonstrated that patients who received genome matched treatment were 31% less likely to die within 1 year compared to those who did not receive genome matched treatment (HR: 0.69; 95% CI: 0.52-0.90; p-value: 0.006). Overall, GTT through this initiative resulted in levels of genome matched treatment that were similar to other initiatives, however, clinical trials represented a smaller share of treatments than previously reported, and "off-label" treatments represented a greater share. Although this was an observational study, we found evidence for a potential 1-year survival benefit for patients who received genome matched treatments. These findings suggest that when disseminated and implemented with a supportive infrastructure, GTT may benefit cancer patients in rural community oncology settings, with further work remaining on providing genome-matched clinical trials.

Towards optimal use of antithrombotic therapy of people with cancer at the end of life: A research protocol for the development and implementation of the SERENITY shared decision support tool

BACKGROUND

Even though antithrombotic therapy has probably little or even negative effects on the well-being of people with cancer during their last year of life, deprescribing antithrombotic therapy at the end of life is rare in practice. It is often continued until death, possibly resulting in excess bleeding, an increased disease burden and higher healthcare costs.

METHODS

The SERENITY consortium comprises researchers and clinicians from eight European countries with specialties in different clinical fields, epidemiology and psychology. SERENITY will use a comprehensive approach combining a realist review, flash mob research, epidemiological studies, and qualitative interviews. The results of these studies will be used in a Delphi process to reach a consensus on the optimal design of the shared decision support tool. Next, the shared decision support tool will be tested in a randomised controlled trial. A targeted implementation and dissemination plan will be developed to enable the use of the SERENITY tool across Europe, as well as its incorporation in clinical guidelines and policies. The entire project is funded by Horizon Europe.

RESULTS

SERENITY will develop an information-driven shared decision support tool that will facilitate treatment decisions regarding the appropriate use of antithrombotic therapy in people with cancer at the end of life.

CONCLUSIONS

We aim to develop an intervention that guides the appropriate use of antithrombotic therapy, prevents bleeding complications, and saves healthcare costs. Hopefully, usage of the tool leads to enhanced empowerment and improved quality of life and treatment satisfaction of people with advanced cancer and their care givers.

The Maine Cancer Genomics Initiative: Implementing a Community Cancer Genomics Program Across an Entire Rural State

PURPOSE

The Maine Cancer Genomics Initiative (MCGI) aimed to overcome patient- and provider-level barriers to using genomic tumor testing (GTT) in rural practices by providing genomic tumor boards (GTBs), clinician education, and access to comprehensive large-panel next-generation sequencing to all patients with cancer in Maine. This paper describes the successful implementation of the initiative and three key services made operative between 2016 and 2020.

METHODS

A community-inclusive, hub-and-spoke approach was taken to implement the three program components: (1) a centralized GTB program; (2) a modular online education program, designed using an iterative approach with broad clinical stakeholders; and (3) GTT free of charge to clinicians and patients. Implementation timelines, participation metrics, and survey data were used to describe the rollout.

RESULTS

The MCGI was launched over an 18-month period at all 19 oncology practices in the State. Seventy-nine physicians (66 medical oncologists, 5 gynecologic oncologists, 1 neuro-oncologist, and 7 pediatric oncologists) enrolled on the study, representing 100% of all practicing oncologists in Maine. Between July 2017 and September 2020, 1610 patients were enrolled. A total of 515 cases were discussed by 47 (73%) clinicians in 196 GTBs. Clinicians who participated in the GTBs enrolled significantly more patients on the study, stayed in Maine, and reported less time spent in clinical patient care.

CONCLUSION

The MCGI was able to engage geographically and culturally disparate cancer care practices in a precision oncology program using a hub-and-spoke model. By facilitating access to GTT, structured education, and GTBs, we narrowed the gap in the implementation of precision oncology in one of the most rural states in the country.

Sport concussion assessment in New Zealand high school rugby players: a collaborative approach to the challenges faced in primary care

PRIMARY OBJECTIVE

To describe the collaborative development of a New Zealand Rugby Concussion Assessment (NZRCA) for primary care and to provide normative baseline data from a representative group of high school rugby players.

METHODS

This study, conducted over the 2018 and 2019 community rugby season where players were baseline tested during the pre- or start of season period.

RESULTS

Data were collected from 1428 players (males n = 1121, females n = 307) with a mean age of 15.9 ± 1.4 years. The mean ± SD symptom severity score was 11.3 ± 8.6, the mean number of endorsed symptoms was 8.5 ± 5.3 and the percentage feeling "normal" was 80.2 ± 15.3%. Only 5.3% of players reported no symptoms at baseline. The most common reported were: 'distracted easily' (72.5%), 'forgetful' (68.5%), and 'often tired' (62.6%). None of the participants achieved a perfect score for the SAC50. The majority of participants (89.7%) passed the tandem gait test with a time of 12.2 ± 1.7 seconds. Age, gender, and ethnicity were associated with NZRCA performance; albeit weakly.

CONCLUSION

This study provides normative reference values for high-school rugby players. These data will aid healthcare providers in their identification of suspected concussion in the absence of individualized baselines.

Baseline concussion assessment performance of community-based senior rugby players: a cross-sectional study

OBJECTIVE

To report pre-season baseline concussion assessment performance among senior rugby players and explore associations between assessment performance and player demographics.

DESIGN

A cross-sectional study using the New Zealand Rugby Concussion Assessments (NZRCA), comprising symptom, cognitive and dynamic coordination assessments was conducted in the 2018-2019 season.

METHODS

Players' baseline assessments were characterised using descriptive statistics; effect sizes (ES) and t-tests were used to explore associations between player demographic characteristics and NZRCA performance.

RESULTS

A total of 733 players (11.4% female) aged between 16 and 52 years completed the NZRCA. The median (range) value for symptom severity, endorsed symptoms and "percentage normal" was respectively, 5 (0-40), 5 (0-21) and 90% (30-100%). A perfect standardised assessment of concussion score was achieved by one participant; seven achieved ≥27/30 for immediate recall, and 22 achieved a perfect delayed recall score. Most participants (n = 674, 92%) passed the tandem gait test. Associations between NZRCA performance and gender, concussion history, and Pasifika ethnicity were observed with effect sizes ranging from small (0.18) to large (0.70). Six hundred and twenty-three (85%) participants reported at least one symptom.

CONCLUSIONS

The results from this study could help support decision-making by clinicians, improving the management of concussions in the community setting.

Predicting the severity of the grass pollen season and the effect of climate change in Northwest Europe

Allergic rhinitis is an inflammation in the nose caused by overreaction of the immune system to allergens in the air. Managing allergic rhinitis symptoms is challenging and requires timely intervention. The following are major questions often posed by those with allergic rhinitis: How should I prepare for the forthcoming season? How will the season's severity develop over the years? No country yet provides clear guidance addressing these questions. We propose two previously unexplored approaches for forecasting the severity of the grass pollen season on the basis of statistical and mechanistic models. The results suggest annual severity is largely governed by preseasonal meteorological conditions. The mechanistic model suggests climate change will increase the season severity by up to 60%, in line with experimental chamber studies. These models can be used as forecasting tools for advising individuals with hay fever and health care professionals how to prepare for the grass pollen season.

Optimizing the response, precision, and cost of a DNA double-strand break dosimeter

We developed a dosimeter that measures biological damage following delivery of therapeutic beams in the form of double-strand breaks (DSBs) to DNA. The dosimeter contains DNA strands that are labeled on one end with biotin and on the other with fluorescein and attached to magnetic microbeads. Following irradiation, a magnet is used to separate broken from unbroken DNA strands. Then, fluorescence is utilized to measure the relative amount of broken DNA and determine the probability for DSB. The long-term goal for this research is to evaluate whether this type of biologically based dosimeter holds any advantages over the conventional techniques. The purpose of this work was to optimize the dosimeter fabrication and usage to enable higher precision for the long-term research goal. More specifically, the goal was to optimize the DNA dosimeter using three metrics: the response, precision, and cost per dosimeter. Six aspects of the dosimeter fabrication and usage were varied and evaluated for their effect on the metrics: (1) the type of magnetic microbeads, (2) the microbead to DNA mass ratio at attachment, (3) the type of suspension buffer used during irradiation, (4) the concentration of the DNA dosimeter during irradiation, (5) the time waited between fabrication and irradiation of the dosimeter, and (6) the time waited between irradiation and read out of the response. In brief, the best results were achieved with the dosimeter when attaching 4.2 µg of DNA with 1 mg of MyOne T1 microbeads and by suspending the microbead-connected DNA strands with 200 µl of phosphate-buffered saline for irradiation. Also, better results were achieved when waiting a day after fabrication before irradiating the dosimeter and also waiting an hour after irradiation to measure the response. This manuscript is meant to serve as guide for others who would like to replicate this DNA dose measurement technique.

Oak pollen seasonality and severity across Europe and modelling the season start using a generalized phenological model

Oak pollen seasons are relatively unexplored in large parts of Europe despite producing allergens and being a common tree in both continental and northern parts. Many studies are concentrated only on the Iberian Peninsula. In this study, the seasonal pattern of oak pollen in Europe was analysed using 10 observation sites, ranging from Spain to Sweden. The magnitude of peaks and annual pollen integral together with season-length were studied and substantially higher pollen levels and longer seasons were found in Spain. Two northern sites in Denmark and Sweden showed high oak pollen peaks together with two sites in Spain and United Kingdom. The study also tested four common definitions of season start and applied a generalized phenological model for computing the start of the pollen season. The most accurate definition for a European-wide description of the observed oak pollen start was when the cumulative daily average pollen count reached 50 grains per cubic meter. For the modelling of the start a thermal time method based on Growing Degree Day (GDD) was implemented, utilizing daily temperatures and a generalized approach to identify model parameters applicable to all included sites. GDD values varied between sites and generally followed a decreasing gradient from south to north, with some exceptions. Modelled onsets with base temperatures below 7 °C matched well with observed onsets and 76% of the predictions differed ≤4 days compared to observed onsets when using a base temperature of 2 °C. Base temperatures above 7 °C frequently predicted onsets differing >1 week from the observed. This general approach can be extended to a larger area where pollen observations are non-existent. The presented work will increase the understanding of oak pollen variation in Europe and provide knowledge of its phenology, which is a critical aspect both for modelling purposes on large-scale and assessing the human exposure to oak allergens.

Association of patient navigation with care coordination in an Lynch syndrome screening program

Lynch syndrome (LS) identification leads to improved health outcomes. Universal tumor screening (UTS) facilitates LS identification among colorectal cancer (CRC) and uterine cancer (UC) cases; institutional management affects screening program implementation and outcomes. There has been limited study of institutional UTS program care coordination needs, including patient navigation of genetic counseling referrals. We examined the influence of patient navigators on access to cancer genetic services among LS UTS screen-positive cases within a single institution. Electronic health record review of screen-positive CRC and UC cases for a 12-month period assessed the relationship between patient navigation and follow-through to genetic services. Among 451 newly diagnosed CRC (n = 175) and UC (n = 276) cases, 96 (21%; 28 CRC/68 UC cases) had abnormal UTS results. Among these, 66 (69%) showed MLH1 promoter hypermethylation (i.e., screen-negative). Of 30 screen-positive cases, 16 (53%) received navigation services. Among these, 14/16 (88%) and 13/14 (81%) underwent genetic counseling and testing, respectively; 7/13 (54%) had pathogenic or likely pathogenic variants detected. Among non-navigated screen-positive patients, 2/14 (14%) were excluded due to incomplete UTS results. Five of the remaining 12 cases (42%) sought genetic counseling, 4/12 (33%) underwent genetic testing; 1/4 (25%) tested positive for a pathogenic variant. The difference in navigated (88%) versus non-navigated cases (42%) undergoing genetic counseling was statistically significant (p = .02). Patient navigation was associated with follow-through to genetic counseling and testing services among LS screen-positive cases. This model deserves additional prospective investigation to confirm these findings and to assess their generalizability.

Influence of a Concentrated Ethylester Compound of n-3 Fatty Acids on Lipids, Platelets and Coagulation in Patients Undergoing Coronary Bypass Surgery

Twenty patients accepted for coronary bypass surgery were randomized to receive either a concentrated ethylester compound of n-3 fatty acids, with a daily dose of 3.15 g of eicosapentaenoic acid (EPA) and 1.89 g of docosahexaenoic acid (DHA), or corn oil (controls) in a double blind study, to evaluate the effect on lipids, platelets and coagulation during the pre- and postoperative phase.

Only patients with fasting triglyceride (TG) levels ≥1.6 mmol/1 at recruitment were eligible. The study was continued for 5 to 6 months. Surgery was usually performed at mid-intervention. Blood samples were collected during morning hours in fasting subjects, just prior to intervention, preoperatively and at final postoperative follow-up. Moreover, blood loss was accurately accounted for postoperatively.

A threefold increase (p = 0.0001) of EPA was noted at pre-and postoperative follow-up. TG-levels were reduced 20 and 39%, respectively, in patients on n-3 fatty acids, reaching statistical significance at end of intervention (p = 0.034). TG-levels in controls remained largely unchanged. In patients on n-3 fatty acids, there was a statistically significant increase in serum total cholesterol preoperatively, but this change was no longer present at completion of the study.

No significant changes were noted in platelet function, as judged by bleeding time, collagen induced platelet aggregation and release of TxB2 during aggregation. Parameters of extrinsic coagulation, including phospholipase C-sensitive factor VII (PLC-VII) and extrinsic pathway inhibitor (EPI), also remained essentially unchanged in both groups of patients. However, fibrinogen was significantly reduced in controls (p <0.05) at end of intervention. Moreover, a strong positive correlation was noted between PLC-VII and TG (r = 0.77, p = 0.0001).

No significant difference in postoperative bleeding was noted between the two groups of patients.

Lipopolysaccharide Induced Monocyte Thromboplastin Synthesis and Coagulation Responses in Patients Undergoing Coronary Bypass Surgery after Preoperative Supplementation with n-3 Fatty Acids

Twenty patients with coronary heart disease (CHD) and elevated serum lipids were randomized into 2 groups of 10 to receive encapsulated preparations of either a concentrated ethylester form of eicosapentaenoic acid (EPA) and docosa-hexaenoic acid (DHA) or corn oil in doses of 6 g per day, given double blindly for approximately two months prior to coronary bypass surgery. Lipopolysaccharide (LPS) induced monocyte thromboplastin synthesis was studied during the preoperative period and one week following surgery. The ability of n-3 fatty acids to modify tissue factor pathway inhibitor (TFPI) and tissue plasminogen activator inhibitor (PAI-1) was also evaluated along with fibrinogen and thrombin-antithrombin III (TAT) complexes.

No significant changes were noted preoperatively. Monocyte reactivity, PAI-1, fibrinogen and TAT increased significantly after surgery. These changes were not modified by preoperative loading with n-3 fatty acids.

Climate-change-induced range shifts of three allergenic ragweeds (Ambrosia L.) in Europe and their potential impact on human health

Invasive allergenic plant species may have severe health-related impacts. In this study we aim to predict the effects of climate change on the distribution of three allergenic ragweed species (Ambrosia spp.) in Europe and discuss the potential associated health impact. We built species distribution models based on presence-only data for three ragweed species, using MAXENT software. Future climatic habitat suitability was modeled under two IPCC climate change scenarios (RCP 6.0 and RCP 8.5). We quantify the extent of the increase in 'high allergy risk' (HAR) areas, i.e., parts of Europe with climatic conditions corresponding to the highest quartile (25%) of present day habitat suitability for each of the three species. We estimate that by year 2100, the distribution range of all three ragweed species increases towards Northern and Eastern Europe under all climate scenarios. HAR areas will expand in Europe by 27-100%, depending on species and climate scenario. Novel HAR areas will occur mostly in Denmark, France, Germany, Russia and the Baltic countries, and overlap with densely populated cities such as Paris and St. Petersburg. We conclude that areas in Europe affected by severe ragweed associated allergy problems are likely to increase substantially by year 2100, affecting millions of people. To avoid this, management strategies must be developed that restrict ragweed dispersal and establishment of new populations. Precautionary efforts should limit the spread of ragweed seeds and reduce existing populations. Only by applying cross-countries management plans can managers mitigate future health risks and economical consequences of a ragweed expansion in Europe.

Comparative Effects of LY3020371, a Potent and Selective Metabotropic Glutamate (mGlu) 2/3 Receptor Antagonist, and Ketamine, a Noncompetitive N-Methyl-d-Aspartate Receptor Antagonist in Rodents: Evidence Supporting the Use of mGlu2/3 Antagonists, for the Treatment of Depression

The ability of the N-methyl-d-aspartate receptor antagonist ketamine to alleviate symptoms in patients suffering from treatment-resistant depression (TRD) is well documented. In this paper, we directly compare in vivo biologic responses in rodents elicited by a recently discovered metabotropic glutamate (mGlu) 2/3 receptor antagonist 2-amino-3-[(3,4-difluorophenyl)sulfanylmethyl]-4-hydroxy-bicyclo[3.1.0]hexane-2,6-dicarboxylic acid (LY3020371) with those produced by ketamine. Both LY3020371 and ketamine increased the number of spontaneously active dopamine cells in the ventral tegmental area of anesthetized rats, increased O₂ in the anterior cingulate cortex, promoted wakefulness, enhanced the efflux of biogenic amines in the prefrontal cortex, and produced antidepressant-related behavioral effects in rodent models. The ability of LY3020371 to produce antidepressant-like effects in the forced-swim assay in rats was associated with cerebrospinal fluid (CSF) drug levels that matched concentrations required for functional antagonist activity in native rat brain tissue preparations. Metabolomic pathway analyses from analytes recovered from rat CSF and hippocampus demonstrated that both LY3020371 and ketamine activated common pathways involving GRIA2 and ADORA1. A diester analog of LY3020371 [bis(((isopropoxycarbonyl)oxy)-methyl) (1S,2R,3S,4S,5R,6R)-2-amino-3-(((3,4-difluorophenyl)thio)methyl)-4-hydroxy-bicyclo[3.1.0]hexane-2,6-dicarboxylate (LY3027788)] was an effective oral prodrug; when given orally, it recapitulated effects of intravenous doses of LY3020371 in the forced-swim and wake-promotion assays, and augmented the antidepressant-like effects of fluoxetine or citalopram without altering plasma or brain levels of these compounds. The broad overlap of biologic responses produced by LY3020371 and ketamine supports the hypothesis that mGlu2/3 receptor blockade might be a novel therapeutic approach for the treatment of TRD patients. LY3020371 and LY3027788 represent molecules that are ready for clinical tests of this hypothesis.

Spatial and temporal variations in airborne Ambrosia pollen in Europe

The European Commission Cooperation in Science and Technology (COST) Action FA1203 "SMARTER" aims to make recommendations for the sustainable management of Ambrosia across Europe and for monitoring its efficiency and cost-effectiveness. The goal of the present study is to provide a baseline for spatial and temporal variations in airborne Ambrosia pollen in Europe that can be used for the management and evaluation of this noxious plant. The study covers the full range of Ambrosia artemisiifolia L. distribution over Europe (39°N-60°N; 2°W-45°E). Airborne Ambrosia pollen data for the principal flowering period of Ambrosia (August-September) recorded during a 10-year period (2004-2013) were obtained from 242 monitoring sites. The mean sum of daily average airborne Ambrosia pollen and the number of days that Ambrosia pollen was recorded in the air were analysed. The mean and standard deviation (SD) were calculated regardless of the number of years included in the study period, while trends are based on those time series with 8 or more years of data. Trends were considered significant at p < 0.05. There were few significant trends in the magnitude and frequency of atmospheric Ambrosia pollen (only 8% for the mean sum of daily average Ambrosia pollen concentrations and 14% for the mean number of days Ambrosia pollen were recorded in the air). The direction of any trends varied locally and reflected changes in sources of the pollen, either in size or in distance from the monitoring station. Pollen monitoring is important for providing an early warning of the expansion of this invasive and noxious plant.

Monitoring of Pancreatic Graft Perfusion by First Passage Radionuclide Angiography

The perfusion of two pancreatic transplants were examined three times a week for the first five postoperative weeks by intravenous angiography using 99Tcm-pertechnetate. Worsening of the perfusion always preceded or was associated with deterioration of the pancreatic function. Accordingly, radionuclide angiography may have an important place in the systematic monitoring of pancreatic transplants in the critical postoperative period.

Predictive Value of Parathyroid Scintigraphy in the Preoperative Evaluation of Patients with Primary Hyperparathyroidism

Background and Aims:

The surgical gold standard in primary hyperparathyroidism was until recently exploration of all four parathyroid glands. Today more patients undergo minimal invasive procedures demanding more accurate preoperative localization studies. The aim of the study was to determine the positive predictive value (PPV) of parathyroid scintigraphy (PS) and to some extent ultrasonography (US), defined as the probability of finding one single adenoma on the affected side at surgery when the scans had shown one single focus.

Material and Methods:

Eighty-eight surgically treated patients (76 women and 12 men, 8 with multiglandular disease) were included. The PS consisted of 99mTc-sestamibi scan with dual-phase technique, both planar and SPECT imaging, followed by 99mTc-pertechnetate scan. A positive scan was defined as a single focus accumulating sestamibi. Focal lesions on US were defined as hypoechoic nodules.

Results:

PS was positive in 80 patients. Seventy-nine had only one focus, of which 64 were correctly localized adenomas (PPV 81%). Forty-seven of 77 US examinations were positive. In 44 there was only one focus of which 38 were correctly localized (PPV 86%). PPV was 97% when both examinations were positive.

Conclusions:

Both PS and US have acceptably high PPVs defined as the ability to predict whether or not one single focus represents a parathyroid adenoma. Concordant positive results were accompanied by a PPV close to 100%.

The Rapidly Acting Antidepressant Ketamine and the mGlu2/3 Receptor Antagonist LY341495 Rapidly Engage Dopaminergic Mood Circuits

Ketamine is a rapidly acting antidepressant in patients with treatment-resistant depression (TRD). Although the mechanisms underlying these effects are not fully established, inquiry to date has focused on the triggering of synaptogenesis transduction pathways via glutamatergic mechanisms. Preclinical data suggest that blockade of metabotropic glutamate (mGlu2/3) receptors shares many overlapping features and mechanisms with ketamine and may also provide rapid efficacy for TRD patients. Central dopamine circuitry is recognized as an end target for mood regulation and hedonic valuation and yet has been largely neglected in mechanistic studies of antidepressant-relevant effects of ketamine. Herein, we evaluated the changes in dopaminergic neurotransmission after acute administration of ketamine and the mGlu2/3 receptor antagonist LY341495 [(2S)-2-amino-2-[(1S,2S)-2-carboxycycloprop-1-yl]-3-(xanth-9-yl) propanoic acid ] in preclinical models using electrophysiologic, neurochemical, and behavioral endpoints. When given acutely, both ketamine and LY341495, but not the selective serotonin reuptake inhibitor (SSRI) citalopram, increased the number of spontaneously active dopamine neurons in the ventral tegmental area (VTA), increased extracellular levels of dopamine in the nucleus accumbens and prefrontal cortex, and enhanced the locomotor stimulatory effects of the dopamine D2/3 receptor agonist quinpirole. Further, both ketamine and LY341495 reduced immobility time in the tail-suspension assay in CD1 mice, which are relatively resistant to SSRI antidepressants. Both the VTA neuronal activation and the antidepressant phenotype induced by ketamine and LY341495 were attenuated by the α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor antagonist 1,2,3,4-tetrahydro-6-nitro-2,3-dioxo- (9CI)-benzo[f]quinoxaline-7-sulfonamide, indicating AMPA-dependent effects. These findings provide another overlapping mechanism of action of ketamine and mGlu2/3 receptor antagonism that differentiates them from conventional antidepressants and thus support the potential rapidly acting antidepressant actions of mGlu2/3 receptor antagonism in patients.

N-Acetyl-l-cysteine effects on multi-species oral biofilm formation and bacterial ecology

Future therapies for the treatment of dental decay have to consider the importance of preserving bacterial ecology while reducing biofilm adherence to teeth. A multi-species plaque-derived (MSPD) biofilm model was used to assess how concentrations of N-acetyl-l-cysteine (NAC) (0, 0·1, 1, 10%) affected the growth of complex oral biofilms. Biofilms were grown (n = 96) for 24 h on hydroxyapatite discs in BMM media with 0·5% sucrose. Bacterial viability and biomass formation was examined on each disc using a microtitre plate reader. In addition, fluorescence microscopy and Scanning Electron Microscopy was used to qualitatively examine the effect of NAC on bacterial biofilm aggregation, extracellular components and bacterial morphology. The total biomass was significantly decreased after exposure of both 1% (from 0·48, with a 95% confidence interval of (0·44, 0·57) to 0·35, with confidence interval (0·31, 0·38)) and 10% NAC (0·14 with confidence interval (0·11, 0·17)). 16S rRNA amplicon sequencing analysis indicated that 1% NAC reduced biofilm adherence while preserving biofilm ecology.

SIGNIFICANCE AND IMPACT OF THE STUDY

As a compound with a wide safety margin, N-acetyl-l-cysteine (NAC) has the potential to be used as a long term anti-plaque bacteriostatic agent for managing chronic dental decay without substantially altering biofilm's bacterial ecology. The potential anti-caries benefit of NAC is directly related to reducing the biofilm coverage which reduces the degree of acid generation and the amount of time that the surface is exposed to a lower pH.

Abstract 4816: Design, validation, and interpretation of an NGS assay for actionable variants in solid tumors

The Jackson Laboratory Cancer Treatment Profile™ (JAX-CTP™) is a next generation sequencing (NGS)-based molecular diagnostic assay that detects actionable gene variants in solid tumors to inform the selection of targeted therapeutics for cancer treatment. We will describe the design of the 358- gene panel, analytical validation, and the curation and clinical reporting of actionable variants. Selection of the gene panel was based on known drug targets, casual implications in cancer, and a thorough pathway analysis. DNA is extracted from FFPE tumor samples and using hybrid capture, the genes of interest are enriched and sequenced on Illumina HiSeq 2500 or MiSeq sequencers. FASTQ files generated from Illumina's CASAVA software are submitted to the JAX Clinical Genome Analytics (CGA) data analysis pipeline to perform automated read quality assessment, alignment, and variant calling. Identified variants are then submitted for clinical curation using a combination of the in-house JAX Clinical Knowledgebase (CKB) and the external Genetic Variant Annotation (GVA) from CollabRx. Once clinically annotated, the variants are graded relative to their clinical utility for the specific tumor type and compiled into a clinical report to inform patient treatment. Extensive analytical validation, following CAP guidelines, was conducted to assess limit of detection, accuracy, precision, sensitivity, and specificity of the assay. The summarized optimized sensitivity of the assay is a minimum coverage of samples at 300X, a limit of detection of 10% for SNP’s/indels and ≥6 copies for CNV’s, and an average of 3-4 actionable variants per sample. The challenges of interpreting gene variants for clinical actionability and for establishing an analytically valid bioinformatic pipeline will be discussed in-depth.

Citation Format: Susan M. Mockus, Guruprasad Ananda, Micaela Lundquist, Vanessa Spotlow, Al Simons, Talia Mitchell, Grace A. Stafford, Christopher S. Potter, Vivek Philip, Timothy Stearns, Anuj Srivastava, Mary Barter, Lucy Rowe, Joan Malcolm, Carol Bult, Radha Krishna Murthy Katuturi, Karen Rasmussen, Douglas Hinerfeld. Design, validation, and interpretation of an NGS assay for actionable variants in solid tumors. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4816. doi:10.1158/1538-7445.AM2015-4816

Development and validation of the JAX Cancer Treatment Profile™ for detection of clinically actionable mutations in solid tumors

BACKGROUND

The continued development of targeted therapeutics for cancer treatment has required the concomitant development of more expansive methods for the molecular profiling of the patient's tumor. We describe the validation of the JAX Cancer Treatment Profile™ (JAX-CTP™), a next generation sequencing (NGS)-based molecular diagnostic assay that detects actionable mutations in solid tumors to inform the selection of targeted therapeutics for cancer treatment.

METHODS

NGS libraries are generated from DNA extracted from formalin fixed paraffin embedded tumors. Using hybrid capture, the genes of interest are enriched and sequenced on the Illumina HiSeq 2500 or MiSeq sequencers followed by variant detection and functional and clinical annotation for the generation of a clinical report.

RESULTS

The JAX-CTP™ detects actionable variants, in the form of single nucleotide variations and small insertions and deletions (≤50 bp) in 190 genes in specimens with a neoplastic cell content of ≥10%. The JAX-CTP™ is also validated for the detection of clinically actionable gene amplifications.

CONCLUSIONS

There is a lack of consensus in the molecular diagnostics field on the best method for the validation of NGS-based assays in oncology, thus the importance of communicating methods, as contained in this report. The growing number of targeted therapeutics and the complexity of the tumor genome necessitate continued development and refinement of advanced assays for tumor profiling to enable precision cancer treatment.

Investigation of solvent dynamic effects on the electron self-exchange in two thianthrene couples with large inner reorganization energies

The electron self-exchange of thianthrenes, which show large structural changes during the reaction, is strongly affected by a solvent dynamic effect controlled by the longitudinal relaxation time.

Growth factor and proteinase profile of Vivostat® platelet-rich fibrin linked to tissue repair

BACKGROUND AND OBJECTIVES

Autologous platelet-rich fibrin (PRF(®)) is prepared by the automatic Vivostat(®) system. Conflicting results with Vivostat PRF in acute wound healing prompted us to examine its cellular and biomolecular composition. Specifically, platelets, selected growth factors and matrix metalloproteinase (MMP)-9 were quantified using novel analytical methods.

MATERIALS AND METHODS

Ten healthy non-thrombocytopenic volunteers donated blood for generation of intermediate fibrin-I and final PRF. Anticoagulated whole blood and serum procured in parallel served as baseline controls. Leucocyte, erythrocyte and platelet counts in whole blood and fibrin-I were determined by automated haematology analyser. Platelet concentration in PRF was quantified manually by stereologic analysis of Giemsa-stained tissue sections, and the total content of five growth factors and MMP-9 by enzyme-linked immunosorbent assays.

RESULTS

The number of leucocytes and erythrocytes was reduced (P < 0·001), whereas platelets increased (P < 0·001) in fibrin-I versus whole blood. PRF contained 982 ± 206 × 10(9) platelets/l representing 3·9-fold (P < 0·001) enrichment relative to whole blood. Growth factor abundance in Vivostat PRF and serum was in descending order: transforming growth factor-β1 [5·1-fold higher in PRF than serum, P < 0·001] > platelet-derived growth factor (PDGF)-AB [2·5-fold, P < 0·01] > PDGF-BB [1·6-fold, P < 0·05] > vascular endothelial growth factor > basic fibroblast growth factor [75-fold, P < 0·001]. MMP-9 was reduced 139-fold (P < 0·001) compared with serum, reflecting leucocyte depletion in PRF.

CONCLUSION

The gained knowledge on platelet enrichment and biomolecular constituents may guide clinicians in their optimal use of Vivostat PRF for tissue regenerative applications.