Clinical and Genomic Predictors of Adverse Events in Newly Diagnosed Glioblastoma

PURPOSE

Adverse clinical events cause significant morbidity in patients with GBM (GBM). We examined whether genomic alterations were associated with AE (AE) in patients with GBM.

EXPERIMENTAL DESIGN

We identified adults with histologically confirmed IDH-wild-type GBM with targeted next-generation sequencing (OncoPanel) at Dana Farber Cancer Institute from 2013 to 2019. Seizure at presentation, lymphopenia, thromboembolic events, pseudoprogression, and early progression (within 6 months of diagnosis) were identified as AE. The biologic function of genetic variants was categorized as loss-of-function (LoF), no change in function, or gain-of-function (GoF) using a somatic tumor mutation knowledge base (OncoKB) and consensus protein function predictions. Associations between functional genomic alterations and AE were examined using univariate logistic regressions and multivariable regressions adjusted for additional clinical predictors.

RESULTS

Our study included 470 patients diagnosed with GBM who met the study criteria. We focused on 105 genes that had sequencing data available for ≥ 90% of the patients and were altered in ≥10% of the cohort. Following false-discovery rate (FDR) correction and multivariable adjustment, the TP53, RB1, IGF1R, and DIS3 LoF alterations were associated with lower odds of seizures, while EGFR, SMARCA4, GNA11, BRD4, and TCF3 GoF and SETD2 LoF alterations were associated with higher odds of seizures. For all other AE of interest, no significant associations were found with genomic alterations following FDR correction.

CONCLUSIONS

Genomic biomarkers based on functional variant analysis of a routine clinical panel may help identify AE in GBM, particularly seizures. Identifying these risk factors could improve the management of patients through better supportive care and consideration of prophylactic therapies.

A discrete choice experiment to elicit preferences for a chronic disease screening programme in Queensland, Australia

OBJECTIVE

Patient-centred care, increasingly highlighted in healthcare strategies, necessitates understanding public preferences for healthcare service attributes. We aimed to understand the preferences of the Australian population regarding the attributes of chronic disease screening programmes.

STUDY DESIGN

The preferences were elicited using the discrete choice experiment (DCE) methodology.

METHODS

A DCE was administered to a sample of the Australian general population. Respondents were asked to make choices, each offering two hypothetical screening scenarios defined by screening conduct, quality and accuracy of the test results, cost to the patient, wait time and source of information. Data were analysed using a panel mixed multinomial logit model.

RESULTS

A strong preference for highly accurate screening tests and nurse-led screenings at local health clinics was evident. They expressed disutility for waiting time and out-of-pocket costs but were indifferent about the source of information. Their preference for a nurse-led programme was highlighted by the fact that they were willing to pay $81 and $88 to get a nurse-led programme when they were offered a general practitioner-led and a specialist-led programme, respectively. Furthermore, they were willing to pay $32 to reduce a week of waiting time and $205 for a 95% accurate test compared to a 75% accurate test. Preferences remained consistent irrespective of the respondent's place of residence.

CONCLUSIONS

Our findings highlight the importance of diagnostic test accuracy and nurse-led service delivery in chronic disease screening programmes. These insights could guide the development of patient-centric services by enhancing test accuracy, reducing waiting times and promoting nurse-led care models.

Evaluation of Storage Conditions and the Effect on DNA from Forensic Evidence Objects Retrieved from Lake Water

DNA analysis of traces from commonly found objects like knives, smartphones, tapes and garbage bags related to crime in aquatic environments is challenging for forensic DNA laboratories. The amount of recovered DNA may be affected by the water environment, time in the water, method for recovery, transport and storage routines of the objects before the objects arrive in the laboratory. The present study evaluated the effect of four storage conditions on the DNA retrieved from bloodstains, touch DNA, fingerprints and hairs, initially deposited on knives, smartphones, packing tapes, duct tapes and garbage bags, and submerged in lake water for three time periods. After retrieval, the objects were stored either through air-drying at room temperature, freezing at -30 °C, in nitrogen gas or in lake water. The results showed that the submersion time strongly influenced the amount and degradation of DNA, especially after the longest submersion time (21 days). A significant variation was observed in success for STR profiling, while mtDNA profiling was less affected by the submersion time interval and storage conditions. This study illustrates that retrieval from water as soon as possible and immediate storage through air-drying or freezing before DNA analysis is beneficial for the outcome of DNA profiling in crime scene investigations.

Complete Mitochondrial DNA Genome Variation in the Swedish Population

The development of complete mitochondrial genome (mitogenome) reference data for inclusion in publicly available population databases is currently underway, and the generation of more high-quality mitogenomes will only enhance the statistical power of this forensically useful locus. To characterize mitogenome variation in Sweden, the mitochondrial DNA (mtDNA) reads from the SweGen whole genome sequencing (WGS) dataset were analyzed. To overcome the interference from low-frequency nuclear mtDNA segments (NUMTs), a 10% variant frequency threshold was applied for the analysis. In total, 934 forensic-quality mitogenome haplotypes were characterized. Almost 45% of the SweGen haplotypes belonged to haplogroup H. Nearly all mitogenome haplotypes (99.1%) were assigned to European haplogroups, which was expected based on previous mtDNA studies of the Swedish population. There were signature northern Swedish and Finnish haplogroups observed in the dataset (e.g., U5b1, W1a), consistent with the nuclear DNA analyses of the SweGen data. The complete mitogenome analysis resulted in high haplotype diversity (0.9996) with a random match probability of 0.15%. Overall, the SweGen mitogenomes provide a large mtDNA reference dataset for the Swedish population and also contribute to the effort to estimate global mitogenome haplotype frequencies.

Energetic Electron Precipitation Driven by Electromagnetic Ion Cyclotron Waves from ELFIN's Low Altitude Perspective

We review comprehensive observations of electromagnetic ion cyclotron (EMIC) wave-driven energetic electron precipitation using data collected by the energetic electron detector on the Electron Losses and Fields InvestigatioN (ELFIN) mission, two polar-orbiting low-altitude spinning CubeSats, measuring 50-5000 keV electrons with good pitch-angle and energy resolution. EMIC wave-driven precipitation exhibits a distinct signature in energy-spectrograms of the precipitating-to-trapped flux ratio: peaks at >0.5 MeV which are abrupt (bursty) (lasting ∼17 s, or Δ L ∼ 0.56 ) with significant substructure (occasionally down to sub-second timescale). We attribute the bursty nature of the precipitation to the spatial extent and structuredness of the wave field at the equator. Multiple ELFIN passes over the same MLT sector allow us to study the spatial and temporal evolution of the EMIC wave - electron interaction region. Case studies employing conjugate ground-based or equatorial observations of the EMIC waves reveal that the energy of moderate and strong precipitation at ELFIN approximately agrees with theoretical expectations for cyclotron resonant interactions in a cold plasma. Using multiple years of ELFIN data uniformly distributed in local time, we assemble a statistical database of ∼50 events of strong EMIC wave-driven precipitation. Most reside at L ∼ 5 - 7 at dusk, while a smaller subset exists at L ∼ 8 - 12 at post-midnight. The energies of the peak-precipitation ratio and of the half-peak precipitation ratio (our proxy for the minimum resonance energy) exhibit an L -shell dependence in good agreement with theoretical estimates based on prior statistical observations of EMIC wave power spectra. The precipitation ratio's spectral shape for the most intense events has an exponential falloff away from the peak (i.e., on either side of ∼ 1.45 MeV). It too agrees well with quasi-linear diffusion theory based on prior statistics of wave spectra. It should be noted though that this diffusive treatment likely includes effects from nonlinear resonant interactions (especially at high energies) and nonresonant effects from sharp wave packet edges (at low energies). Sub-MeV electron precipitation observed concurrently with strong EMIC wave-driven >1 MeV precipitation has a spectral shape that is consistent with efficient pitch-angle scattering down to ∼ 200-300 keV by much less intense higher frequency EMIC waves at dusk (where such waves are most frequent). At ∼100 keV, whistler-mode chorus may be implicated in concurrent precipitation. These results confirm the critical role of EMIC waves in driving relativistic electron losses. Nonlinear effects may abound and require further investigation.

Forensic prediction of sex, age, height, body mass index, hip-to-waist ratio, smoking status and lipid lowering drugs using epigenetic markers and plasma proteins

The prediction of human characteristics from blood using molecular markers would be very helpful in forensic science. Such information can be particularly important in providing investigative leads in police casework from, for example, blood found at crime scenes in cases without a suspect. Here, we investigated the possibilities and limitations of predicting seven phenotypic traits (sex, age, height, body mass index [BMI], hip-to-waist [WTH] ratio, smoking status and lipid-lowering drug use) using either DNA methylation or plasma proteins separately or in combination. We developed a prediction pipeline starting with the prediction of sex followed by sex-specific, stepwise, individual age, sex-specific anthropometric traits and, finally, lifestyle-related traits. Our data revealed that age, sex and smoking status can be accurately predicted from DNA methylation alone, while the use of plasma proteins was highly accurate for prediction of the WTH ratio, and a combined analysis of the best predictions for BMI and lipid-lowering drug use. In unseen individuals, age was predicted with a standard error of 3.3 years for women and 6.5 years for men, while the accuracy in smoking prediction across both men and women was 0.86. In conclusion, we have developed a stepwise approach for the de-novo prediction of individual characteristics from plasma proteins and DNA methylation markers. These models are accurate and may provide valuable information and investigative leads in future forensic casework.

Diagnostic radiography students' perspectives on cultural competence and safety

INTRODUCTION

Cultural competency and safety are essential components to consider in the provision of person-centred equitable healthcare. Therefore, student radiographers' learning should include the necessary knowledge, skill sets and competence to recognise the patient's unique characteristics to enable culturally competent and safe medical imaging services. Therefore, this study explored undergraduate and postgraduate diagnostic radiography students' perspectives on cultural competency and safety.

METHODS

A qualitative phenomenological design with a hermeneutic phenomenological approach was followed to explore student perspectives. Student radiographers (second and third-year undergraduate and first and second-year postgraduate) from the study site were purposively and conveniently recruited to participate in focus group interviews. Fifteen focus group interviews were conducted, recorded and transcribed verbatim before undergoing thematic analysis.

RESULTS

Thematic analysis identified two themes. Theme one centred around the cultural competence and safety learnt by student radiographers at university and the second theme cultural competence and safety learnt in workplace learning.

CONCLUSION

This study demonstrated the importance of cultural competence and safe practice in examining patients of different cultures. It highlights the importance of creating awareness among students of their own abilities and capabilities of cultural sensitivity and safe practice as part of their learning. Future health professionals should be empowered to address and respond to patients' unique needs in a competent, safe and professional manner to reduce health disparities.

IMPLICATIONS FOR PRACTICE

Cultural competence and safety are integral to person-centred care. Including these concepts in radiography education is therefore vital to ensure optimal patient outcomes.

BIOM-47. PREDICTORS OF SEIZURE AT ONSET USING A FUNCTIONAL VARIANT ANALYSIS OF TARGETED NEXT GENERATION SEQUENCING IN GBM

BACKGROUND

Adverse events (AE) including seizures cause significant morbidity in patients with GBM. We propose a novel method for assessing genomic predictors of AEs using results from a clinical targeted sequencing platform with variant function analysis.

METHODS

We identified 1,011 consecutive adult patients with newly diagnosed, histologically confirmed IDH-wildtype GBM with targeted exome NGS (Oncopanel) at Dana-Farber Cancer Institute from 2013-2019. Seizure at presentation was retrospectively identified as an AE. Biologic function (high loss, low loss, neutral, low gain and high gain) was assigned to variants using a three-tiered approach leveraging a genetic variant database (OncoKB), followed by analysis using protein prediction tools (Sift, Polyphen2 and Provean). Univariate logistic regression was performed for each relevant altered gene against the outcome of interest with false-discovery rate correction. Genes associated with seizure at presentation were included iteratively in a multivariate logistic model including other predictors of the outcome.

RESULTS

Our analysis included 470 GBM patients with 107 genes and 12 whole chromosome or arm level candidate variants covered by all versions of Oncopanel and with >10% alteration. Seizure at presentation occurred in 143/463 patients (31%) and was associated with EGFR amplification (high gain) (OR: 2.76, 95% CI: 1.4-5.3, p = 0.04). In a multivariate analysis (including age, sex, and preoperative tumor volume), EGFR amplification remained statistically significant (OR: 1.5, 95% CI: 1.0-2.2, p = 0.03).

CONCLUSION

Genomic biomarkers based on functional variant analysis of a routine clinical panel may predict adverse events in GBM. Seizure at presentation was independently associated with EGFR amplification. Our ongoing analysis will look at predictors of myelosuppression, thromboembolism, pseudoprogression and early progression using a similar approach. Identifying molecular risk factors could improve the management of patients through supportive care and consideration of prophylactic therapies.

Clinical utility of targeted next-generation sequencing assay in IDH-wildtype glioblastoma for therapy decision-making

BACKGROUND

Targeted gene NGS testing is available through many academic institutions and commercial entities and is increasingly incorporated in practice guidelines for glioblastoma (GBM). This single-center retrospective study aimed to evaluate the clinical utility of incorporating NGS results in the management of GBM patients at a clinical trials-focused academic center.

METHODS

We identified 1011 consecutive adult patients with pathologically confirmed GBM (IDHwt or IDHmut) who had somatic tumor sequencing (Oncopanel, ~500 cancer gene panel) at DFCI from 2013-2019. Clinical records of all IDHwt GBM patients were reviewed to capture clinical trial enrollment and off-label targeted therapy use based on NGS results.

RESULTS

Of the 557 IDHwt GBM patients with sequencing, 182 entered clinical trials at diagnosis (32.7%) and 213 (38.2%) entered after recurrence. Sequencing results for 130 patients (23.3%) were utilized for clinical trial enrollment for either targeted therapy indications (6.9 % upfront and 27.7% at recurrent clinical trials and 3.1% for off-label targeted therapy) or exploratory studies (55.4% upfront and 6.9% recurrent clinical trials). Median overall survival was 20.1 months with no survival difference seen between patients enrolled in clinical trials compared to those who were not, in a posthoc analysis.

CONCLUSIONS

While NGS testing has become essential for improved molecular diagnostics, our study illustrates that targeted gene panels remain underutilized for selecting therapy in GBM-IDHwt. Targeted therapy and clinical trial design remain to be improved to help leverage the potential of NGS in clinical care.

Cambridge hybrid closed-loop algorithm in children and adolescents with type 1 diabetes: a multicentre 6-month randomised controlled trial

BACKGROUND

Closed-loop insulin delivery systems have the potential to address suboptimal glucose control in children and adolescents with type 1 diabetes. We compared safety and efficacy of the Cambridge hybrid closed-loop algorithm with usual care over 6 months in this population.

METHODS

In a multicentre, multinational, parallel randomised controlled trial, participants aged 6-18 years using insulin pump therapy were recruited at seven UK and five US paediatric diabetes centres. Key inclusion criteria were diagnosis of type 1 diabetes for at least 12 months, insulin pump therapy for at least 3 months, and screening HbA1c levels between 53 and 86 mmol/mol (7·0-10·0%). Using block randomisation and central randomisation software, we randomly assigned participants to either closed-loop insulin delivery (closed-loop group) or to usual care with insulin pump therapy (control group) for 6 months. Randomisation was stratified at each centre by local baseline HbA1c. The Cambridge closed-loop algorithm running on a smartphone was used with either (1) a modified Medtronic 640G pump, Medtronic Guardian 3 sensor, and Medtronic prototype phone enclosure (FlorenceM configuration), or (2) a Sooil Dana RS pump and Dexcom G6 sensor (CamAPS FX configuration). The primary endpoint was change in HbA1c at 6 months combining data from both configurations. The primary analysis was done in all randomised patients (intention to treat). Trial registration ClinicalTrials.gov, NCT02925299.

FINDINGS

Of 147 people initially screened, 133 participants (mean age 13·0 years [SD 2·8]; 57% female, 43% male) were randomly assigned to either the closed-loop group (n=65) or the control group (n=68). Mean baseline HbA1c was 8·2% (SD 0·7) in the closed-loop group and 8·3% (0·7) in the control group. At 6 months, HbA1c was lower in the closed-loop group than in the control group (between-group difference -3·5 mmol/mol (95% CI -6·5 to -0·5 [-0·32 percentage points, -0·59 to -0·04]; p=0·023). Closed-loop usage was low with FlorenceM due to failing phone enclosures (median 40% [IQR 26-53]), but consistently high with CamAPS FX (93% [88-96]), impacting efficacy. A total of 155 adverse events occurred after randomisation (67 in the closed-loop group, 88 in the control group), including seven severe hypoglycaemia events (four in the closed-loop group, three in the control group), two diabetic ketoacidosis events (both in the closed-loop group), and two non-treatment-related serious adverse events. There were 23 reportable hyperglycaemia events (11 in the closed-loop group, 12 in the control group), which did not meet criteria for diabetic ketoacidosis.

INTERPRETATION

The Cambridge hybrid closed-loop algorithm had an acceptable safety profile, and improved glycaemic control in children and adolescents with type 1 diabetes. To ensure optimal efficacy of the closed-loop system, usage needs to be consistently high, as demonstrated with CamAPS FX.

FUNDING

National Institute of Diabetes and Digestive and Kidney Diseases.

A cross sectional survey on the effect of COVID-19 related restrictions on undergraduate and postgraduate medical education in Qatar

BACKGROUND

COVID-19 pandemic has affected all dimensions of day to day life across the world and medical education was no exception. With this study, we aimed to understand the effect of nationwide restrictions on medical education in Qatar, the models of education adopted during this period and perceptions of participants to the same.

METHODS

We conducted a cross-sectional study utilizing an online questionnaire distributed via convenience sampling between April-October 2020. Study participants were faculty and trainees in governmental undergraduate and postgraduate medical education institutes. Two sets of questionnaires were designed for each group. They were asked a series of questions to assess pre- and post-COVID pandemic educational practices, their preferred teaching methods, and their familiarity with electronic teaching platforms. Faculty respondents were asked about their perceived barriers to delivery of medical education during the pandemic and their agreement on a 5-point Likert scale on specific elements. Trainees were asked a series of multiple-choice questions to characterize their pre- and post-COVID pandemic educational experiences. Both groups were asked open-ended questions to provide qualitative insights into their answers. Data were analysed using STATA software version 12.0.

RESULTS

Majority of trainees (58.5%) responded that the pandemic has adversely affected medical education at both the undergraduate and postgraduate levels. Trainees (58.5%) and faculty (35.7%) reported an increased reliance on e-learning. Trainees preferred face-to-face education, while faculty preferred a combination of models of education delivery (33.5% versus 37.1%, p = 0.38). Although 52.5% of the faculty had no previous experience of delivering education through e-learning modalities, 58.9% however felt confident in using e-learning software.

CONCLUSIONS

Faculty and trainees agree that the COVID-19 pandemic has had a significant impact on the provision of medical education and training in Qatar, with an increased dependence on e-learning. As trainee's prefer face-to-face models of education, we may have to consider restructuring of medical curricula in order to ensure that optimum learning is achieved via e-learning, while at the same time enhancing our use, knowledge and understanding of the e -learning methods. Further research is warranted to assess if these changes have influenced objective educational outcomes like graduation rates or board scores.

The Value of Whole-Genome Sequencing for Mitochondrial DNA Population Studies: Strategies and Criteria for Extracting High-Quality Mitogenome Haplotypes

Whole-genome sequencing (WGS) data present a readily available resource for mitochondrial genome (mitogenome) haplotypes that can be utilized for genetics research including population studies. However, the reconstruction of the mitogenome is complicated by nuclear mitochondrial DNA (mtDNA) segments (NUMTs) that co-align with the mtDNA sequences and mimic authentic heteroplasmy. Two minimum variant detection thresholds, 5% and 10%, were assessed for the ability to produce authentic mitogenome haplotypes from a previously generated WGS dataset. Variants associated with NUMTs were detected in the mtDNA alignments for 91 of 917 (~8%) Swedish samples when the 5% frequency threshold was applied. The 413 observed NUMT variants were predominantly detected in two regions (nps 12,612–13,105 and 16,390–16,527), which were consistent with previously documented NUMTs. The number of NUMT variants was reduced by ~97% (400) using a 10% frequency threshold. Furthermore, the 5% frequency data were inconsistent with a platinum-quality mitogenome dataset with respect to observed heteroplasmy. These analyses illustrate that a 10% variant detection threshold may be necessary to ensure the generation of reliable mitogenome haplotypes from WGS data resources.

Evaluation of Different Cleaning Strategies for Removal of Contaminating DNA Molecules

Decontamination strategies and their efficiencies are crucial when performing routine forensic analysis, and many factors influence the choice of agent to use. In this study, the effects of ten different cleaning strategies were evaluated to compare their ability to remove contaminating DNA molecules. Cell-free DNA or blood was deposited on three surfaces (plastic, metal, and wood) and decontaminated with various treatments. The quantities of recovered DNA, obtained by swabbing the surfaces after cleaning using the different strategies, was analyzed by real-time PCR. Large differences in the DNA removal efficiencies were observed between different cleaning strategies, as well as between different surfaces. The most efficient cleaning strategies for cell-free DNA were the different sodium hypochlorite solutions and Trigene^®, for which a maximum of 0.3% DNA was recovered on all three surfaces. For blood, a maximum of 0.8% of the deposited DNA was recovered after using Virkon^® for decontamination. The recoveries after using these cleaning strategies correspond to DNA from only a few cells, out of 60 ng of cell-free DNA or thousands of deposited blood cells.

INNV-40. REAL WORLD INTEGRATION OF THE NEUROLOGIC ASSESSMENT IN NEURO-ONCOLOGY (NANO) SCALE IN CLINICAL PRACTICE IN PATIENTS WITH IDH-WT GBM

BACKGROUND

The neurologic assessment in neuro-oncology (NANO) scale was developed as a standardized metric to objectively measure neurologic function in patients with brain tumors and complement radiographic assessment in defining overall outcome. The scale has been incorporated in clinical trials. Early data is suggestive of feasibility and that NANO contributes to overall outcome assessment. However, real-world use of the NANO scale to drive clinical-decision making and the predictive value of the NANO scale to determine overall survival remains unclear in IDH-wt GBM.

METHODS

We report on an ongoing study using the NANO scale to evaluate neurologic function in patients with IDH-wt GBM, seen at Dana-Farber Cancer Institute (DFCI). Patient demographics, tumor histology and molecular status, treatment history and progression dates are being captured. NANO score, as collected by a built-in scale in our institutional electronic medical record (EMR), functional status (Karnofsky performance status) and corticosteroid dose are collected at prespecified time points (prior to start of therapy, and during each subsequent MRI visit). Changes in the NANO score will be correlated to overall survival. Statistical analyses including descriptive data analysis and generalized linear models will be performed using R (version 3.4.3).

RESULTS

Since June 2020, 50 patients have been enrolled in this study, including 42 (84%) with ≥2 follow up visits. Study accrual was initially impacted by the COVID-19 pandemic, but adaptation to a virtual platform for NANO allowed for improved recruitment and follow up of patients. Study results will be available for discussion at the 2021 SNO conference.

CONCLUSIONS

Evaluation of neurologic function by NANO is feasible in a virtual framework in a prospective study in patients with GBM, aided by integration of the scale in our institutional EMR. NANO is able to objectively track neurologic function throughout disease course in IDH-wt GBM.

PATH-16. EVALUATION OF SEX-BASED DIFFERENCES IN CLINICAL OUTCOMES AND TUMOR GENOMICS IN PATIENTS WITH NEWLY DIAGNOSED IDH-WILDTYPE GLIOBLASTOMA RECEIVING CHEMORADIATION

BACKGROUND

We evaluated sex-based differences in clinical outcomes and tumor genomics in patients with newly-diagnosed GBM.

METHODS

We reviewed 665 IDH-wild type GBM patients with Karnofsky Performance Status (KPS) ≥60 treated at our institution from 2010-2019 including; 585 patients with targeted exome sequencing of 447 cancer associated genes (OncoPanel). Deleterious mutations were defined as homozygous deletions or loss of function mutations of known tumor suppressors (as reported in TCGA, ≥ 3 times in the COSMIC database, or predicted as “damaging” in SIFT and/or “probably damaging” in Polyphen 2) or known oncogenic mutations in proto-oncogenes (reported in TCGA or ≥ 3 times in COSMIC).

RESULTS

There were 384 (57.7%) males and 281 (42.3%) females. Median OS was 22.5 months for females and 19.3 months for males (hazard ratio [HR] 0.81, 95% CI 1.03-1.48, p = 0.02). On multivariable analysis adjusted for age, KPS ≥90, extent of resection, and MGMT methylation status, female sex (adjusted hazard ratio 0.78, 95% CI [0.64-0.95], p = 0.015) was associated with improved OS. Superior OS in females was observed in MGMT-unmethylated patients (HR 0.69, 95% CI [0.54-0.90], p = 0.005) but not MGMT-methylated patients. Thirteen genes were deleteriously altered in ≥5% of our cohort: CDK4 (12.1% male vs. 7.8% female), CDKN2A (46.5% vs. 45.7%), CDKN2B (41.8% vs. 43.3%), EGFR (34.7% vs. 40.0%, MTAP (18.2% vs. 18.8%), NF1 (11.5% vs. 9.4%), PTEN (28.2% vs. 29.8%), TP53 (28.2% vs. 30.2%), RB1 (5.6% vs. 6.5%), MDM4 (6.2% vs. 5.7%), ATM (5.9% vs. 3.7%), MDM2 (7.4% vs. 4.1%), PIK3R1 (6.2% vs. 4.1%). There were no differences in frequency of mutations in these individual genes between males and females (χ 2 [1, N=585] = 0.05-2.86, p = 0.09-0.86).

CONCLUSIONS

Female sex is associated with improved survival. We did not identify sex-based differences in deleterious genomic alterations amongst commonly altered genes in GBM.

Investigation into clinicopathological and pathological findings, prognosis, and aetiology of lorikeet paralysis syndrome in rainbow lorikeets (Trichoglossus haematodus)

Objective

To report the temporal and spatial distribution of rainbow lorikeets presenting with lorikeet paralysis syndrome (LPS) and their clinicopathologic and pathologic findings, exposure to toxins, and response to treatment.

Methods

Records of lorikeets admitted in 2017 and 2018 to facilities in south‐east Queensland (QLD) were reviewed and LPS and non‐LPS cases were mapped and their distribution compared. Plasma biochemistries and complete blood counts were done on 20 representative lorikeets from south‐east QLD and Grafton, New South Wales (NSW). Tissues from 28 lorikeets were examined histologically. Samples were tested for pesticides (n = 19), toxic elements (n = 23), botulism (n = 15) and alcohol (n = 5).

Results

LPS occurred in warmer months. Affected lorikeets were found across south‐east QLD. Hotspots were identified in Brisbane and the Sunshine Coast. Lorikeets had a heterophilic leucocytosis, elevated muscle enzymes, uric acid and sodium and chloride. Specific lesions were not found. Exposure to cadmium was common in LPS and non‐LPS lorikeets. Treated lorikeets had a 60–93% See Table 2 depending on severity of signs.

Clinical significance

The primary differential diagnosis for lorikeets presenting with lower motor neuron signs during spring, summer and autumn in northern NSW and south‐east Queensland should be LPS. With supportive care, prognosis is fair to good.

PATH-03. CLINICAL UTILITY OF NEXT GENERATION SEQUENCING IN IDH-WILDTYPE GLIOBLASTOMA: THE DANA-FARBER CANCER INSTITUTE EXPERIENCE

BACKGROUND

Comprehensive next generation sequencing (NGS) is available through many academic institutions and commercial entities, and is incorporated in practice guidelines for glioblastoma (GBM). We retrospective evaluated the practice patterns and utility of incorporating NGS data into routine care of GBM patients at a clinical trials-focused academic center.

METHODS

We identified 1,011 consecutive adult patients with histologically confirmed GBM with OncoPanel testing, a targeted exome NGS platform of 447 cancer-associated genes at Dana Farber Cancer Institute (DFCI), from 2013-2019. We selected and retrospectively reviewed clinical records of all IDH-wildtype GBM patients treated at DFCI.

RESULTS

We identified 557 GBM IDH-wildtype patients, of which 227 were male (40.7%). OncoPanel testing revealed 833 single nucleotide variants and indels in 44 therapeutically relevant genes (Tier 1 or 2 mutations) including PIK3CA (n=51), BRAF (n=9), FGFR1 (n=8), MSH2 (n=4), MSH6 (n=2) and MLH1 (n=1). Copy number analysis revealed 509 alterations in 18 therapeutically relevant genes including EGFR amplification (n= 186), PDGFRA amplification (N=39) and CDKN2A/2B homozygous loss (N=223). Median overall survival was 17.5 months for the whole cohort. Seventy-four therapeutic clinical trials accrued 144 patients in the upfront setting (25.9%) and 203 patients (36.4%) at recurrence. Altogether, NGS data for 107 patients (19.2%) were utilized for clinical trial enrollment or targeted therapy indications. High mutational burden (>17mutations/Mb) was identified in 11/464 samples (2.4%); of whom 3/11 received immune checkpoint blockade. Four patients received compassionate use therapy targeting EGFRvIII (rindopepimut, n=2), CKD4/6 (abemaciclib, n=1) and BRAFV600E (dabrafenib/trametinib, n=1).

CONCLUSION

While NGS has greatly improved diagnosis and molecular classification, we highlight that NGS remains underutilized in selecting therapy in GBM, even in a setting where clinical trials and off-label therapies are relatively accessible. Continued efforts to develop better targeted therapies and efficient clinical trial design are required to maximize the potential benefits of genomically-stratified data.

BIOM-44. GENOMIC PREDICTORS OF ADVERSE EVENTS IN NEWLY DIAGNOSED IDH-WILDTYPE GLIOBLASTOMA

BACKGROUND

Adverse outcomes including lymphopenia, thromboembolism (VTE), pseudoprogression and seizures cause significant morbidity in glioblastoma (GBM) patients. The association between genomic biomarkers and adverse outcomes in IDH-wildtype (IDH-wt) GBM needs to be further validated.

METHODS

We identified 1,011 consecutive adult patients with histologically confirmed GBM with OncoPanel testing (capture-based next-generation sequencing of 447 cancer-associated genes) at Dana-Farber Cancer Institute from 2013–2019. IDH-mutant patients and those without consistent follow-up at DFCI were excluded. Seizure at presentation, lymphopenia (absolute lymphocyte count < 1.0x109/L) at the beginning and end of chemoradiation, VTE, radiographic pseudoprogression (< 6 months of RT end) and early progression (< 6 months since completing RT) were identified retrospectively as adverse events. Single nucleotide variants and indels of relevant genes (Tier 1 or 2 mutations) and copy number analysis were derived. Variables were compared using Wilcoxon rank-sum test or Fisher’s Exact test with p< 0.05 indicating statistical significance.

RESULTS

Among 557 patients included, 198/508 (39%) had MGMT-methylated GBMs. Seizure at presentation occurred in 176/542 (32%) and was more common in TP53- or RB1-mutant GBM. Pre-RT 83/338 (25%), but not post-RT lymphopenia (249/367, 68%), was associated with PIK3CA mutation. VTE was detected in 74/509 (15%) during follow-up and was associated with mutations in PIK3CA and POLE. Pseudoprogression was noted in 43/457 (9%) of patients and was not associated with MGMT status or genomic alterations. Early progressive disease occurred in 33% of patients and was associated with unmethylated MGMT, PIK3CA, STAG2 and PTPN11 mutations. Median overall survival for the entire cohort was 17.5 months.

CONCLUSION

PIK3CA mutations were associated with baseline lymphopenia, risk of VTE and early progression in this cohort. Genomic biomarkers may help identify patients at higher risk of select adverse events in IDH-wt GBM. This could benefit patients through tailoring of supportive care and prophylactic therapies.

Experimental exploration of the amphoteric defect model by cryogenic ion irradiation of a range of wide band gap oxide materials

The evolution of electrical resistance as function of defect concentration is examined for the unipolarn-conducting oxides CdO,β-Ga₂O₃, In₂O₃, SnO₂and ZnO in order to explore the predictions of the amphoteric defect model. Intrinsic defects are introduced by ion irradiation at cryogenic temperatures, and the resistance is measured in-situ by current-voltage sweeps as a function of irradiation dose. Temperature dependent Hall effect measurements are performed to determine the carrier concentration and mobility of the samples before and after irradiation. After the ultimate irradiation step, the Ga₂O₃and SnO₂samples have both turned highly resistive. In contrast, the In₂O₃and ZnO samples are ultimately found to be less resistive than prior to irradiation, however, they both show an increased resistance at intermediate doses. Based on thermodynamic defect charge state transitions computed by hybrid density functional theory, a model expanding on the current amphoteric defect model is proposed.

Population genomics of the Viking world

The maritime expansion of Scandinavian populations during the Viking Age (about AD 750-1050) was a far-flung transformation in world history^1,2. Here we sequenced the genomes of 442 humans from archaeological sites across Europe and Greenland (to a median depth of about 1×) to understand the global influence of this expansion. We find the Viking period involved gene flow into Scandinavia from the south and east. We observe genetic structure within Scandinavia, with diversity hotspots in the south and restricted gene flow within Scandinavia. We find evidence for a major influx of Danish ancestry into England; a Swedish influx into the Baltic; and Norwegian influx into Ireland, Iceland and Greenland. Additionally, we see substantial ancestry from elsewhere in Europe entering Scandinavia during the Viking Age. Our ancient DNA analysis also revealed that a Viking expedition included close family members. By comparing with modern populations, we find that pigmentation-associated loci have undergone strong population differentiation during the past millennium, and trace positively selected loci-including the lactase-persistence allele of LCT and alleles of ANKA that are associated with the immune response-in detail. We conclude that the Viking diaspora was characterized by substantial transregional engagement: distinct populations influenced the genomic makeup of different regions of Europe, and Scandinavia experienced increased contact with the rest of the continent.

Population genomics of the Viking world

The maritime expansion of Scandinavian populations during the Viking Age (about AD 750-1050) was a far-flung transformation in world history^1,2. Here we sequenced the genomes of 442 humans from archaeological sites across Europe and Greenland (to a median depth of about 1×) to understand the global influence of this expansion. We find the Viking period involved gene flow into Scandinavia from the south and east. We observe genetic structure within Scandinavia, with diversity hotspots in the south and restricted gene flow within Scandinavia. We find evidence for a major influx of Danish ancestry into England; a Swedish influx into the Baltic; and Norwegian influx into Ireland, Iceland and Greenland. Additionally, we see substantial ancestry from elsewhere in Europe entering Scandinavia during the Viking Age. Our ancient DNA analysis also revealed that a Viking expedition included close family members. By comparing with modern populations, we find that pigmentation-associated loci have undergone strong population differentiation during the past millennium, and trace positively selected loci-including the lactase-persistence allele of LCT and alleles of ANKA that are associated with the immune response-in detail. We conclude that the Viking diaspora was characterized by substantial transregional engagement: distinct populations influenced the genomic makeup of different regions of Europe, and Scandinavia experienced increased contact with the rest of the continent.

The ELFIN Mission

The Electron Loss and Fields Investigation with a Spatio-Temporal Ambiguity-Resolving option (ELFIN-STAR, or heretoforth simply: ELFIN) mission comprises two identical 3-Unit (3U) CubeSats on a polar (∼93^∘ inclination), nearly circular, low-Earth (∼450 km altitude) orbit. Launched on September 15, 2018, ELFIN is expected to have a >2.5 year lifetime. Its primary science objective is to resolve the mechanism of storm-time relativistic electron precipitation, for which electromagnetic ion cyclotron (EMIC) waves are a prime candidate. From its ionospheric vantage point, ELFIN uses its unique pitch-angle-resolving capability to determine whether measured relativistic electron pitch-angle and energy spectra within the loss cone bear the characteristic signatures of scattering by EMIC waves or whether such scattering may be due to other processes. Pairing identical ELFIN satellites with slowly-variable along-track separation allows disambiguation of spatial and temporal evolution of the precipitation over minutes-to-tens-of-minutes timescales, faster than the orbit period of a single low-altitude satellite (T_orbit ∼ 90 min). Each satellite carries an energetic particle detector for electrons (EPDE) that measures 50 keV to 5 MeV electrons with Δ E/E < 40% and a fluxgate magnetometer (FGM) on a ∼72 cm boom that measures magnetic field waves (e.g., EMIC waves) in the range from DC to 5 Hz Nyquist (nominally) with <0.3 nT/sqrt(Hz) noise at 1 Hz. The spinning satellites (T_spin ∼ 3 s) are equipped with magnetorquers (air coils) that permit spin-up or -down and reorientation maneuvers. Using those, the spin axis is placed normal to the orbit plane (nominally), allowing full pitch-angle resolution twice per spin. An energetic particle detector for ions (EPDI) measures 250 keV - 5 MeV ions, addressing secondary science. Funded initially by CalSpace and the University Nanosat Program, ELFIN was selected for flight with joint support from NSF and NASA between 2014 and 2018 and launched by the ELaNa XVIII program on a Delta II rocket (with IceSatII as the primary). Mission operations are currently funded by NASA. Working under experienced UCLA mentors, with advice from The Aerospace Corporation and NASA personnel, more than 250 undergraduates have matured the ELFIN implementation strategy; developed the instruments, satellite, and ground systems and operate the two satellites. ELFIN's already high potential for cutting-edge science return is compounded by concurrent equatorial Heliophysics missions (THEMIS, Arase, Van Allen Probes, MMS) and ground stations. ELFIN's integrated data analysis approach, rapid dissemination strategies via the SPace Environment Data Analysis System (SPEDAS), and data coordination with the Heliophysics/Geospace System Observatory (H/GSO) optimize science yield, enabling the widest community benefits. Several storm-time events have already been captured and are presented herein to demonstrate ELFIN's data analysis methods and potential. These form the basis of on-going studies to resolve the primary mission science objective. Broad energy precipitation events, precipitation bands, and microbursts, clearly seen both at dawn and dusk, extend from tens of keV to >1 MeV. This broad energy range of precipitation indicates that multiple waves are providing scattering concurrently. Many observed events show significant backscattered fluxes, which in the past were hard to resolve by equatorial spacecraft or non-pitch-angle-resolving ionospheric missions. These observations suggest that the ionosphere plays a significant role in modifying magnetospheric electron fluxes and wave-particle interactions. Routine data captures starting in February 2020 and lasting for at least another year, approximately the remainder of the mission lifetime, are expected to provide a very rich dataset to address questions even beyond the primary mission science objective.

Comparison of routine field epidemiology and whole genome sequencing to identify tuberculosis transmission in a remote setting

Yukon Territory (YT) is a remote region in northern Canada with ongoing spread of tuberculosis (TB). To explore the utility of whole genome sequencing (WGS) for TB surveillance and monitoring in a setting with detailed contact tracing and interview data, we used a mixed-methods approach. Our analysis included all culture-confirmed cases in YT (2005-2014) and incorporated data from 24-locus Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats (MIRU-VNTR) genotyping, WGS and contact tracing. We compared field-based (contact investigation (CI) data + MIRU-VNTR) and genomic-based (WGS + MIRU-VNTR + basic case data) investigations to identify the most likely source of each person's TB and assessed the knowledge, attitudes and practices of programme personnel around genotyping and genomics using online, multiple-choice surveys (n = 4) and an in-person group interview (n = 5). Field- and genomics-based approaches agreed for 26 of 32 (81%) cases on likely location of TB acquisition. There was less agreement in the identification of specific source cases (13/22 or 59% of cases). Single-locus MIRU-VNTR variants and limited genetic diversity complicated the analysis. Qualitative data indicated that participants viewed genomic epidemiology as a useful tool to streamline investigations, particularly in differentiating latent TB reactivation from the recent transmission. Based on this, genomic data could be used to enhance CIs, focus resources, target interventions and aid in TB programme evaluation.

AccuMeter noninstrumented quantitative assay of high-density lipoprotein in whole blood

A novel noninstrumented technology (ChemTrak AccuMeter) for the quantitative measurement of analytes in biological fluids was reported at the 1990 Oak Ridge Conference (Clin Chem 1990;36:1591-7). This instrument-free technology has been adapted for the quantitative measurement of high-density lipoprotein (HDL). An in situ lipoprotein separation method has been developed and incorporated into the test for HDL determination. The sensitivity of the assay system has been adjusted so that HDL is measured over a clinically significant range of 250 to 1000 mg/L. This compares to a range of 1000 to 4000 mg/L for the total cholesterol in the earlier reported assay. Like the AccuMeter total cholesterol test, the Accumeter HDL test system is self-contained and consolidates blood separation, lipoprotein separation, and specimen measurement into a single step. The test procedure is simple, and the results are accurate.

3M™ Petrifilm™ Staph Express Count Plate Method for the Enumeration of Staphylococcus aureus in Selected Types of Meat, Seafood, and Poultry: Collaborative Study

The 3M™ Petrifilm™ Staph Express Count plate method was compared with AOAC Official Method 975.55 for the enumeration of Staphylococcus aureus in selected foods. Four foods—cooked, diced chicken; cured ham; smoked salmon; and pepperoni—were analyzed for S. aureus by 12 collaborating laboratories. For each food tested, the collaborators received 8 blind test samples consisting of a control sample, a low inoculation level, a medium inoculation level, and a medium inoculation level with background flora, each in duplicate. The mean log10 counts for the methods were comparable for all 4 foods. The repeatability and reproducibility variances of the 24 h Petrifilm Staph Express Count plate method were similar to those of the 72 h standard method.

VIDAS® Enzyme-Linked Immunofluorescent Assay for Detection of Listeria in Foods: Collaborative Study

The VIDAS LIS method and the traditional culture methods for detection of Listeria species in food were evaluated in a multilaboratory comparative study. The 6 foods tested were either naturally contaminated or inoculated with 3 different concentrations of Listeria. Results for each food and each contamination level with the VIDAS LIS method were as good as or better than those obtained with the traditional culture method. Of 1558 samples tested, 935 were positive: 839 by the VIDAS method and 809 by standard culture methods. Overall false negative rates were 10.3 and 13.5% for the VIDAS LIS and culture methods, respectively. The false positive rate for the VIDAS LIS assay was 1.4% based on 9 VIDAS LIS positive assays that did not confirm positive by isolation of Listeria. The agreement between the VIDAS LIS and culture methods for all samples tested was 86%.

Abstract P1-15-08: Pathologic complete response rates following neoadjuvant systemic therapy in 794 patients with early breast cancer: The Royal Marsden experience

Background

The presence and extent of residual invasive cancer after neoadjuvant treatment (NACT) is a strong prognostic factor for risk of recurrence, especially in triple-negative (TN) and human epidermal growth factor receptor 2-positive (HER2+) breast cancer (BC). Recent advances in the standard-of-care NACT improved pathological complete response (pCR) rates in published clinical trials.

We evaluated the pCR rates, defined as ypT0-is ypN0, in our real-world BC population and in estrogen receptor-positive [ER+] HER2-, HER2+ and TN subgroups and their association with tumour, patients' characteristics and disease-free survival (DFS).

Methods

We retrospectively identified early BC patients receiving NACT between January 2013 and December 2017. Demographics, patient and disease characteristics, pathological responses, toxicities, dose delays and reductions were recorded. Simple statistics, Fisher's exact test, chi-squared method and Cox regression were used as appropriate.

Results

794 patients identified had median age of 50 years (range 24-87) and 93.9% (745 patients) ECOG performance status (PS) 0. 3.0% (24) had clinical stage I disease, 68.0% (540) stage II and 29.0% (230) stage III. 71.0% (564) had grade 3 disease and 91.8% (729) ductal histology. 33.7% (257) had ER+/HER2-, 25.8% (205) had TN and 38.0% (301) HER2+ disease. Overall, 6.8% (54) patients received platinum. 36.6% (291) patients had dose reductions and 24.3% (193) dose delays. Along with NACT, 51.6% (147) of the HER2+ patients received Trastuzumab and Pertuzumab and 48.4% (138) Trastuzumab alone.

pCR rate was 33.1% in the overall population and significantly different in ER+/HER2-, HER2+ and TN subgroups (12.84% versus 52.0% versus 28.43% respectively, p&lt;0.001). pCR was influenced by grade (1: 0%; 2: 24.3%; 3: 36.1%, p 0.005) and histology (ductal: 34.2%; lobular: 10.0%; mixed 25.0%; p 0.01). In the HER2+ subgroup, there was a trend for improved pCR rates for patients receiving Pertuzumab and Trastuzumab (57.0%) versus Trastuzumab alone (51.0%). No statistically significant differences were seen based on patients' characteristics including age and PS or in case of treatment dose reductions and delays. Early discontinuation of NACT was associated with lower pCR rates (20.5% vs 36.29%, p &lt;0.001).

Of interest, pCR rates remained consistent across the period 2013-2017 in the overall population. We observed a trend for improved pCR in the HER2+ (2013: 47.5%; 2014: 44.4%; 2015: 66.7%; 2016: 51.0%; 2017: 51.4%) and TN cohorts (2013: 23.5%; 2014: 25.0%; 2015: 25.0%; 2016: 33.3%; 2017: 34.1%) but not in the ER+/HER2- group.

Median DFS was 83.8 months (95% CI 62.0-NR) in the overall population. Although not reached in the TN cohort, median DFS was different according to disease subgroups (HER2+: 83.78 months; TN: NR; ER+/HER2-: 62.0 months, p &lt;0.0001).

Conclusions

In our analysis pCR rates are consistent with data published in literature and higher in HER2+ and TN disease. The impact of new agents had a relatively low impact on pCR rates in our overall population over the last 5 years, although they produced gradual improvements in the HER2+ and TN subgroups.

Citation Format: Battisti NML, True V, Chaabouni N, Chopra N, Lee K, Shepherd S, Shapira-Rotenberg T, Joshi R, Mohammed K, Allen M, Ring A. Pathologic complete response rates following neoadjuvant systemic therapy in 794 patients with early breast cancer: The Royal Marsden experience [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P1-15-08.

Abstract P5-18-08: Defining molecular signatures to personalise management of patients with early breast cancer

Background

A review of breast screening highlighted the need to reduce overdiagnosis. Ductal Carcinoma In-Situ (DCIS) contributes significantly to this overdiagnosis. Epithelial cells in DCIS are as genetically advanced as those in invasive disease, focusing attention on the tumour microenvironment (ME). A key components of the ME in DCIS is the myoepithelial cell(MEC). These cells lie at the interface of the epithelial and stromal compartments, regulating cell function. We previously have identified changes in the MEC that contribute to tumour progression. Here we investigate the functional and clinical significance of a novel change in MEC phenotype: loss of Galectin-7 (Gal-7) expression. Gal-7 is proposed to play a role in apoptosis. We hypothesise that changes in MEC phenotype in DCIS alter the ME towards a pro-invasive phenotype, and hypothesise that loss of Gal-7 modifies the ME, destabilizes the MEC interface and ultimately may lead to loss of the MEC population through apoptosis.

Methods

Gal-7 expression and function was investigated in clinical samples and in-vitro model systems, respectively.

Gal-7 expression was assessed in a series of pure DCIS samples (low risk model) and DCIS with co-existant invasion (high risk model). Tissue sections were stained for Gal-7 and MEC expression scored on a duct-by-duct basis as positive, heterogeneous or negative.

An in-vitro model of normal primary myoepithelial cells isolated from reduction mammoplasty was used to investigate the functional impact of loss of Gal-7. These cells have high endogenous levels of Gal-7. Gal-7 was knocked down using siRNA and apoptosis assessed using cleaved caspase-3. The effect of Gal-7 on MEC layer integrity was assessed using immunofluorescence and adhesion assays.

The global impact of loss of Gal-7 was investigated using RNA sequencing.

Results

In the tissue analysis 1926 DCIS ducts were scored for MEC expression of Gal-7. Significantly more ducts showed loss of Gal-7 in DCIS with co-existant invasion, with pure DCIS showing 388 ducts positive and DCIS with invasion 144 DCIS ducts positive (p=0.0014). Pure DCIS and DCIS with invasion had 99 and 646 negative DCIS ducts respectively (p=0.0002).

In model systems of primary MEC, knockdown of Gal-7 resulted in increased expression of cleaved caspase-3, suggesting lower levels of Gal-7 increases apoptosis. In functional assays silencing Gal-7 reduces adhesion to both fibronectin and laminin extracellular matrices (p-value 0.005 and 0.001 respectively)

RNA sequencing indicates silencing Gal-7 increases LOX expression - a key regulator of the collagen matrix of the microenvironment.

Conclusion

Normal MEC strongly express Gal-7. Expression is lost in DCIS, with significantly more frequent loss in DCIS with co-existant invasion, suggesting that loss is associated with a more advanced phenotype. Functional assays indicate that loss of MEC Gal-7 enhances MEC apoptosis, which may be one mechanism by which this interface is lost during progression. Gal-7 negative MEC also show impaired adhesion to matrix proteins and lead to up-regulation of LOX, an enzyme key in promoting tumourigenesis. The incorporation of Gal-7 expression into a risk stratification algorithm has functional evidence and is currently being investigated.

Citation Format: Allen N, Allen M, Ahmed K, Gomm J, Nelan R, Nagano A, Chelala C, Gadaleta E, Thorat M, Cuzick J, Jones LJ. Defining molecular signatures to personalise management of patients with early breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P5-18-08.

Whole genome sequencing for improved understanding of Mycobacterium tuberculosis transmission in a remote circumpolar region

Few studies have used genomic epidemiology to understand tuberculosis (TB) transmission in rural and remote settings - regions often unique in history, geography and demographics. To improve our understanding of TB transmission dynamics in Yukon Territory (YT), a circumpolar Canadian territory, we conducted a retrospective analysis in which we combined epidemiological data collected through routine contact investigations with clinical and laboratory results. Mycobacterium tuberculosis isolates from all culture-confirmed TB cases in YT (2005-2014) were genotyped using 24-locus Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats (MIRU-VNTR) and compared to each other and to those from the neighbouring province of British Columbia (BC). Whole genome sequencing (WGS) of genotypically clustered isolates revealed three sustained transmission networks within YT, two of which also involved BC isolates. While each network had distinct characteristics, all had at least one individual acting as the probable source of three or more culture-positive cases. Overall, WGS revealed that TB transmission dynamics in YT are distinct from patterns of spread in other, more remote Northern Canadian regions, and that the combination of WGS and epidemiological data can provide actionable information to local public health teams.

Tag retention and mortality of adult Atlantic salmon Salmo salar gastrically tagged with different sized telemetry transmitters

A batch of 1 sea winter pre-spawning adult Salmo salar from the Bush river in Northern Ireland, U.K., were gastrically tagged with large (13 mm diameter) and small (9 mm diameter) dummy acoustic telemetry tags alongside untagged control fish. Survival differed between control and tagged fish and the estimated probability of survival by the end of the study for control fish with no tag was 0·94, small tags was 0·90 and large tags was 0·72. Tag loss through regurgitation was slightly higher for fish tagged with larger tags than for fish tagged with smaller tags and the estimated probability of tag loss for fish with a small tag was 0·10 and for large tags was 0·14.

Implications of possible interpretations of 'greenhouse gas balance' in the Paris Agreement

The main goal of the Paris Agreement as stated in Article 2 is 'holding the increase in the global average temperature to well below 2°C above pre-industrial levels and pursuing efforts to limit the temperature increase to 1.5°C'. Article 4 points to this long-term goal and the need to achieve 'balance between anthropogenic emissions by sources and removals by sinks of greenhouse gases'. This statement on 'greenhouse gas balance' is subject to interpretation, and clarifications are needed to make it operational for national and international climate policies. We study possible interpretations from a scientific perspective and analyse their climatic implications. We clarify how the implications for individual gases depend on the metrics used to relate them. We show that the way in which balance is interpreted, achieved and maintained influences temperature outcomes. Achieving and maintaining net-zero CO2-equivalent emissions conventionally calculated using GWP100 (100-year global warming potential) and including substantial positive contributions from short-lived climate-forcing agents such as methane would result in a sustained decline in global temperature. A modified approach to the use of GWP100 (that equates constant emissions of short-lived climate forcers with zero sustained emission of CO2) results in global temperatures remaining approximately constant once net-zero CO2-equivalent emissions are achieved and maintained. Our paper provides policymakers with an overview of issues and choices that are important to determine which approach is most appropriate in the context of the Paris Agreement.This article is part of the theme issue 'The Paris Agreement: understanding the physical and social challenges for a warming world of 1.5°C above pre-industrial levels'.

Origin of the U87MG glioma cell line: Good news and bad news

Human tumor-derived cell lines are indispensable tools for basic and translational oncology. They have an infinite life span and are easy to handle and scalable, and results can be obtained with high reproducibility. However, a tumor-derived cell line may not be authentic to the tumor of origin. Two major questions emerge: Have the identity of the donor and the actual tumor origin of the cell line been accurately determined? To what extent does the cell line reflect the phenotype of the tumor type of origin? The importance of these questions is greatest in translational research. We have examined these questions using genetic profiling and transcriptome analysis in human glioma cell lines. We find that the DNA profile of the widely used glioma cell line U87MG is different from that of the original cells and that it is likely to be a bona fide human glioblastoma cell line of unknown origin.