Integrating EM and Patch-seq data: Synaptic connectivity and target specificity of predicted Sst transcriptomic types

Neural circuit function is shaped both by the cell types that comprise the circuit and the connections between those cell types ¹ . Neural cell types have previously been defined by morphology ^{2, 3} , electrophysiology ^{4, 5} , transcriptomic expression ^6-8 , connectivity ^9-13 , or even a combination of such modalities ^14-16 . More recently, the Patch-seq technique has enabled the characterization of morphology (M), electrophysiology (E), and transcriptomic (T) properties from individual cells ^17-20 . Using this technique, these properties were integrated to define 28, inhibitory multimodal, MET-types in mouse primary visual cortex ²¹ . It is unknown how these MET-types connect within the broader cortical circuitry however. Here we show that we can predict the MET-type identity of inhibitory cells within a large-scale electron microscopy (EM) dataset and these MET-types have distinct ultrastructural features and synapse connectivity patterns. We found that EM Martinotti cells, a well defined morphological cell type ^{22, 23} known to be Somatostatin positive (Sst+) ^{24, 25} , were successfully predicted to belong to Sst+ MET-types. Each identified MET-type had distinct axon myelination patterns and synapsed onto specific excitatory targets. Our results demonstrate that morphological features can be used to link cell type identities across imaging modalities, which enables further comparison of connectivity in relation to transcriptomic or electrophysiological properties. Furthermore, our results show that MET-types have distinct connectivity patterns, supporting the use of MET-types and connectivity to meaningfully define cell types.

LB0006 SARILUMAB IN PATIENTS WITH RELAPSING POLYMYALGIA RHEUMATICA: A PHASE 3, MULTICENTER, RANDOMIZED, DOUBLE BLIND, PLACEBO CONTROLLED TRIAL (SAPHYR)

Background

Interleukin-6 (IL-6) is elevated in patients with active polymyalgia rheumatica (PMR) and is associated with disease activity, relapse and severity. Clinical trials with IL-6 receptor (IL-6R) inhibitors in PMR showed higher remission rates and reduced glucocorticoid (GC) use vs GC alone.1-4

Objectives

The SAPHYR study (NCT03600818) assessed the efficacy and safety of sarilumab (SAR), a fully human anti IL-6Rα monoclonal antibody, with a 14 week (wk) GC taper in patients with steroid resistant active PMR who flared on ≥7.5 mg/day prednisone or equivalent.

Methods

Patients were randomized (1:1) to 52 wks of treatment with SAR 200 mg every 2 wks (Q2W) + 14 wk GC tapered regimen (SAR arm) OR placebo Q2W + 52 wk GC tapered regimen (comparator arm). The primary endpoint was the proportion of patients achieving sustained remission at wk 52, defined as disease remission by wk 12, absence of disease flare, CRP normalization from wks 12 to 52 and adherence to the per protocol GC taper from wks 12 to 52.

Results

The study was terminated early due to protracted recruitment timelines during the COVID-19 pandemic, resulting in 118 of the intended 280 patients recruited between Oct 2018 and Jul 2020, and 117 were treated (SAR n=59, comparator n=58). The demographics were balanced; patients were primarily female, Caucasian, and a median age of ~70 years (Table 1). Overall, 78 patients completed the treatment (SAR n=42; comparator n=36). Primary reasons for treatment discontinuation were adverse events (AEs; SAR n=7, comparator n=4) and lack of efficacy (SAR n=4, comparator n=9). Sustained remission rate was significantly higher in the SAR arm vs the comparator arm (28.3% vs 10.3%; P=0.0193). Results of a sensitivity analysis excluding CRP from the sustained remission definition was consistent with the primary analysis (31.7% vs 13.8%; P=0.0280). All sustained remission components favored SAR (Figure 1). Patients in the SAR arm were 44% less likely to have a flare after achieving clinical remission vs the comparator arm (16.7% vs 29.3%; HR 0.56; 95% CI 0.35–0.90; P=0.0158). The comparator arm required more additional GCs vs the SAR arm, mainly due to PMR flare (median difference in actual and expected cumulative dose 199.5 mg vs 0.0 mg; P=0.0189). The cumulative GC toxicity index scores numerically favored SAR but the difference was not statistically significant. PMR activity scores improved in the SAR arm vs the comparator arm (LS mean -15.57 vs -10.27, nominal P=0.0002). Patient reported outcomes (eg, physical and mental health component scores, disability index, etc) favored SAR (Figure 1). Incidence of treatment-emergent AEs (TEAEs) was numerically higher in the SAR arm vs the comparator arm (94.9% vs 84.5%) and included neutropenia (15.3%) and arthralgia (15.3%) in the SAR arm, and insomnia (15.5%) in the comparator arm. Conversely, the frequency of serious AEs was higher in the comparator arm vs the SAR arm (20.7% vs 13.6%). No deaths were reported.

Table 1.

Demographics and baseline characteristics

ParameterSAR + 14 wk GC taperPlacebo + 52 wk GC taper(n=60)(n=58)Age, median years (range)69 (51–88)70 (52–88)Sex (female), n (%)45 (75.0)37 (63.8)Race, n (%) Caucasian50 (83.3)48 (82.8) Asian1 (1.7)2 (3.4) Not reported9 (15.0)8 (13.8)PMR duration (diagnosis date to baseline),* median days (range)292 (78–3992)310 (66–2784)Any prior disease modifying anti rheumatic drugs, n (%) Methotrexate5 (8.3)10 (17.2) Leflunomide2 (3.3)1 (1.7) Azathioprine01 (1.7) Hydroxychloroquine1 (1.7)1 (1.7) Adalimumab1 (1.7)0 Tocilizumab01 (1.7)CRP (mg/L), median (range)6.8 (0.5–38.2)5.7 (0.1–62.3)Erythrocyte sedimentation rate (mm/h), median (range)25.0 (2.0–115.0)22.0 (5.0–85.0)

*SAR n = 54; comparator n= 50.

Conclusion

SAR + 14 wk GC taper demonstrated significant efficacy vs the comparator arm in steroid refractory PMR patients, including clinically meaningful improvement in quality of life. Safety was consistent with the known safety profile of SAR.

References

[1]Mori 2016;

[2]Akiyama 2020;

[3]Lally 2016,

[4]Devauchelle Pensec 2015

Acknowledgements

Medical writing support was provided by Vijay Kadasi of Sanofi and funded by Sanofi.

Disclosure of Interests

Bhaskar Dasgupta Consultant of: Sanofi, Roche Chugai, Speakers bureau: Roche Chugai, Cipla, Grant/research support from: Sanofi, Roche, Abbvie, Sebastian Unizony Consultant of: Sanofi, Kiniksa, Janssen, Grant/research support from: Genentech, Kenneth J Warrington Paid instructor for: Chemocentryx, Grant/research support from: Eli Lilly, Kiniksa, GSK, Jennifer Sloane Lazar Employee of: Sanofi, Angeliki Giannelou Shareholder of: Regeneron, Employee of: Regeneron, Chad Nivens Shareholder of: Regeneron, Employee of: Regeneron, Bolanle Akinlade Shareholder of: Regeneron, Employee of: Regeneron, Wanling Wong Employee of: Sanofi, Yong Lin Employee of: Sanofi, Frank Buttgereit Consultant of: Sanofi, Horizon Pharma, Roche, Galapagos, Abbvie, Novartis, Grant/research support from: Sanofi, Horizon Pharma, Roche, Galapagos, Abbvie, Novartis, Valerie Devauchelle-Pensec: None declared, Andrea Rubbert-Roth Consultant of: Sanofi, Speakers bureau: Sanofi, Roche, Robert Spiera Consultant of: Sanofi, GSK, Novartis, Chemocentryx, Roche-Genetech, Abbvie, Vera, Grant/research support from: GSK, Chemocentryx, Corbus, Inflarx, Boehringer Ingelheim

Modeling radiative and non-radiative pathways at both the Franck-Condon and Herzberg-Teller approximation level

Here, we present a concise model that can predict the photoluminescent properties of a given compound from first principles, both within and beyond the Franck-Condon approximation. The formalism required to compute fluorescence, Internal Conversion (IC), and Inter-System Crossing (ISC) is discussed. The IC mechanism, in particular, is a difficult pathway to compute due to difficulties associated with the computation of required bosonic configurations and non-adiabatic coupling elements. Here, we offer a discussion and breakdown on how to model these pathways at the Density Functional Theory (DFT) level with respect to its computational implementation, strengths, and current limitations. The model is then used to compute the photoluminescent quantum yield (PLQY) of a number of small but important compounds: anthracene, tetracene, pentacene, diketo-pyrrolo-pyrrole (DPP), and Perylene Diimide (PDI) within a polarizable continuum model. Rate constants for fluorescence, IC, and ISC compare well for the most part with respect to experiment, despite triplet energies being overestimated to a degree. The resulting PLQYs are promising with respect to the level of theory being DFT. While we obtained a positive result for PDI within the Franck-Condon limit, the other systems require a second order correction. Recomputing quantum yields with Herzberg-Teller terms yields PLQYs of 0.19, 0.08, 0.04, 0.70, and 0.99 for anthracene, tetracene, pentacene, DPP, and PDI, respectively. Based on these results, we are confident that the presented methodology is sound with respect to the level of quantum chemistry and presents an important stepping stone in the search for a tool to predict the properties of larger coupled systems.

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1-3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10-18.

Long-term loss to follow-up in the TREAT Asia HIV Observational Database (TAHOD)

OBJECTIVES

With earlier antiretroviral therapy (ART) initiation, time spent in HIV care is expected to increase. We aimed to investigate loss to follow-up (LTFU) in Asian patients who remained in care 5 years after ART initiation.

METHODS

Long-term LTFU was defined as LTFU occurring after 5 years on ART. LTFU was defined as (1) patients not seen in the previous 12 months; and (2) patients not seen in the previous 6 months. Factors associated with LTFU were analysed using competing risk regression.

RESULTS

Under the 12-month definition, the LTFU rate was 2.0 per 100 person-years (PY) [95% confidence interval (CI) 1.8-2.2 among 4889 patients included in the study. LTFU was associated with age > 50 years [sub-hazard ratio (SHR) 1.64; 95% CI 1.17-2.31] compared with 31-40 years, viral load ≥ 1000 copies/mL (SHR 1.86; 95% CI 1.16-2.97) compared with viral load < 1000 copies/mL, and hepatitis C coinfection (SHR 1.48; 95% CI 1.06-2.05). LTFU was less likely to occur in females, in individuals with higher CD4 counts, in those with self-reported adherence ≥ 95%, and in those living in high-income countries. The 6-month LTFU definition produced an incidence rate of 3.2 per 100 PY (95% CI 2.9-3.4 and had similar associations but with greater risks of LTFU for ART initiation in later years (2006-2009: SHR 2.38; 95% CI 1.93-2.94; and 2010-2011: SHR 4.26; 95% CI 3.17-5.73) compared with 2003-2005.

CONCLUSIONS

The long-term LTFU rate in our cohort was low, with older age being associated with LTFU. The increased risk of LTFU with later years of ART initiation in the 6-month analysis, but not the 12-month analysis, implies that there was a possible move towards longer HIV clinic scheduling in Asia.

Modeling of Acute Rectal Toxicity to Compare Two Patient Positioning Methods for Prostate Cancer Radiotherapy: Can Toxicity Modeling be Used for Quality Assurance?

Purpose:

Intensity Modulated Radiation Therapy (IMRT) allows for significant dose reductions to organs at risk in prostate cancer patients. However, the accurate delivery of IMRT plans can be compromised by patient positioning errors. The purpose of this study was to determine if the modeling of grade ≥ 2 acute rectal toxicity could be used to monitor the quality of IMRT protocols.

Materials and Methods:

79 patients treated with Image and Fiducial Markers Guided IMRT (FMIGRT) and 302 patients treated with trans-abdominal ultrasound guided IMRT (USGRT) was selected for this study. Treatment plans were available for the FMIGRT group, and hand recorded dosimetric indices were available for both groups. We modeled toxicity in the FMIGRT group using the Lyman Kutcher Burman (LKB) and Univariate Logistic Regression (ULR) models, and we modeled toxicity in USGRT group using the ULR model. We performed Receiver Operating Characteristics (ROC) analysis on all of the models and compared the Area under the ROC curve (AUC) for the FMIGRT and the USGRT groups.

Results:

The observed Incidence of grade ≥ 2 rectal toxicity was 20% in FMIGRT patients and 54% in USGRT patients. LKB model parameters in the FMIGRT group were TD₅₀=56.8 Gy, slope m=0.093, and exponent n=0.131. The most predictive indices in the ULR model for the FMIGRT group were D_25% and V_{50 Gy}. AUC for both models in the FMIGRT group was similar (AUC=0.67). The FMIGRT URL model predicted less than a 37% incidence of grade ≥ 2 acute rectal toxicity in the USGRT group. A fit of the ULR model to USGRT data did not yield a predictive model (AUC=0.5).

Conclusion:

Modeling of acute rectal toxicity provided a quantitative measure of the correlation between planning dosimetry and this clinical endpoint. Our study suggests that an unusually weak correlation may indicate a persistent patient positioning error.

Mortality and morbidity of extremely low birth weight infants in Hong Kong, 2010-2017: a single-centre review

BACKGROUND

Extremely low birth weight (ELBW) infants exhibit high rates of mortality and morbidity. We retrospectively assessed factors associated with mortality and morbidity among ELBW infants.

METHODS

Perinatal demographic data were reviewed for all ELBW infants born between 2010 and 2017 at a tertiary neonatal unit.

RESULTS

For non-survivors (21% of ELBW infants) and survivors, the median gestational ages were 24.1 and 26.2 weeks, respectively, and median birth weights were 650 g and 780 g, respectively (all P<0.001). Regression analyses showed that non-survival was positively associated with lower gestational age (adjusted odds ratio [aOR]=6.71 for every 1-week decrease; 95% confidence interval [CI]=1.73-26.00; P=0.006) and grade 3 or 4 intraventricular haemorrhage (aOR=29.23; 95% CI=1.39-613.84; P=0.030); non-survival was negatively associated with the presence of bronchopulmonary dysplasia (aOR=0.01; 95% CI= <0.001-0.23; P=0.005); length of neonatal intensive care unit stay for survivors was positively associated with the presence of necrotising enterocolitis (B-coefficient=89.60; 95% CI=43.86-135.34; P<0.001); and length of hospital stay for survivors was positively associated with the presence of necrotising enterocolitis (B-coefficient=2.08; 95% CI=0.43-3.73; P=0.015) and a low Apgar score at 1 minute (B-coefficient=-0.63; 95% CI=-1.04 to -0.22; P=0.003).

CONCLUSION

Extremely low birth weight infants exhibited significant mortality and morbidity; there was no survival prior to 23.6 weeks' gestation or below 550 g birth weight. The presence of grade 3 or 4 intraventricular haemorrhage was independently associated with non-survival. Survivors were significantly more likely to exhibit bronchopulmonary dysplasia; survivors with necrotising enterocolitis were more likely to require longer stays in the neonatal intensive care unit and in hospital.

Abstract P2-03-03: A multicenter clinical study of Xpert® breast cancer STRAT4 demonstrates high concordance with central lab ER, PgR, HER2, and Ki67 IHC and HER2 FISH tests in FFPE breast tumor tissues

The Xpert® Breast Cancer STRAT4 (STRAT4) is a CE-IVD marked, semi-quantitative, cartridge-based RT-qPCR assay for the detection of ESR1, PGR, ERBB2 (HER2), and MKi67 mRNAs from formalin fixed, paraffin embedded (FFPE) breast tumors. The assay is fast (&lt; 2 hrs), reproducible, robust, and easy to perform.

The aim of this multicenter clinical study was to assess the performance characteristics of the STRAT4 assay relative to central lab immunohistochemistry (IHC) for ER, PgR, HER2, and Ki67 and to fluorescence in situ hybridization (FISH) for HER2 gene amplification.

Methods: A total of 200 archived primary invasive breast cancer FFPE blocks were sourced from Indivumed for this study. From each block, twelve (12) adjacent tissue sections (4-µm thickness) on slides were prepared for pathological H&E confirmation to define tumor area, and for testing by STRAT4, IHC (ER, PgR, HER2,Ki67), and HER2 FISH. Standard STRAT4 lysate preparation using a single unstained slide per specimen and testing on N=84, N=68, and N=48 samples was performed at 3 independent sites, respectively (2 US and 1 EU). A single slide from each specimen was also processed using the recommended concentrated lysate procedure for STRAT4 testing at Cepheid. All IHC and FISH testing was performed by a central academic reference laboratory in the US. For a given sample, STRAT4 data generated using the standard lysate procedure was included for concordance analysis when all target gene test results were valid. In cases where the standard lysate preparation yielded indeterminate test results for any target, data from the concentrated lysate preparation was used for the data analysis. Receiver Operating Characteristic (ROC) analysis, overall percent agreement (OPA), positive percent agreement (PPA), and negative percent agreement (NPA) between STRAT4 and IHC (IHC/FISH for HER2) were determined for ESR1,PGR, ERBB2, and MKi67.

Results: Of the 200 samples tested by STRAT4, all samples generated valid results for ESR1 and ERBB2, 199 of 200 samples were valid for PGR, and 198 of 200 samples were valid for MKi67 using the standard or concentrated lysate preparation protocol. One sample failed to generate results for both ER and PgR IHC. Twelve samples failed to yield HER2 FISH results.

The STRAT4 success rate and results concordance with IHC were comparable across study sites. OPA between STRAT4 and IHC was 97% for ESR1, 88.9% for PGR, 93.3% for HER2 (92.4% for IHC and FISH), and 90.7% for MKi67 (excluding IHC 10-20% staining). Areas under the ROC curves were 0.9922 for ESR1, 0.9509 for PGR, 0.9958 for ERBB2, and 0.9395 for MKi67.

Conclusion: STRAT4 measurements for ESR1, PGR, ERBB2 and MKi67 mRNA expression are robust and highly concordant with IHC (IHC/FISH for HER2). The technical portion of the assay is easily performed in &lt; 2 hrs including hands-on time using standard FFPE tissue sections. Xpert STRAT4 offers local pathology labs an alternative to centralized, subjective IHC/FISH tests that require a higher level of expertise. Further investigations correlating STRAT4 markers directly with clinical outcomes in independent cohorts are in progress.

Citation Format: Wu NC, Wong E, Acca B, Birkmeier J, Tran L, Zhao S, Wong W, Chu VC, Ho K, Malek M, Lu C, Ge G, David K, Quigley NB, Beqaj SS, Davenport S, Weidler J, Bates M, Press M. A multicenter clinical study of Xpert® breast cancer STRAT4 demonstrates high concordance with central lab ER, PgR, HER2, and Ki67 IHC and HER2 FISH tests in FFPE breast tumor tissues [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P2-03-03.

Abstract P2-03-02: Macrodissection prior to closed system RT-qPCR is not necessary for estrogen receptor and HER2 concordance with IHC/FISH in breast cancer

Background: An on-demand, closed system RT-qPCR (the GeneXpert system, Cepheid, Sunnyvale, CA) has the potential to provide biomarker information in low resourced settings. The system consists of an inexpensive, single-use, disposable, macrofluidic cartridge and an instrument that automates RT-qPCR. Here we use it with a research use only cartridge (STRAT4) that measures the mRNA expression levels of ESR1, PGR, ERBB2, and MKi67 using a single 5uM thick FFPE tissue section from an excisional or core biopsy specimen containing invasive carcinoma of the breast. The assay, results are expressed as a delta cycle threshold (dCt) value, defined as the Ct of a control gene (CYFIP1) minus the Ct of the target gene (ESR1, PGR, ERBB2, or MKi67). We determine whether the dCt result for each marker is equivalent using the entire non-macrodissected section (non m-d) to the dCt results obtained following tumor macro-dissection (m-d) to eliminate non-tumor elements from the assay.

Methods: We evaluated the impact of m-d versus non m-d using STRAT4 on a cohort of 62 formalin-fixed paraffin-embedded (FFPE) tumor core needle biopsy specimens with a range of HER2 expression determined by clinical immunohistochemistry and fluorescence in situ hybridization (IHC/FISH). Concordance (sensitivity and specificity) of the STRAT4 ESR1 and HER2 mRNA versus ER and HER2 IHC/FISH measurements were also assessed.

Results: We observed excellent agreement of the resulting dCt between the paired samples, m-d versus non m-d, for ESR1 (R2=0.92), PGR (R2=0.90), ERBB2 (R2=0.94) and MKi67 (R2=0.90). No significant difference (P value &gt; 0.99) was observed when we compared the dCt between the paired samples m-d versus non m-d. In addition, using the predefined STRAT4 dCt cutoff for ESR and ERBB2 positivity, we found a significant concordance between RT-qPCR and IHC/FISH for ESR-positivity for the paired samples, m-d (P value &lt; 0.001; sensitivity = 0.98; specificity = 1; PPV = 1; NPV = 0.95) versus non m-d (P value &lt; 0.001; sensitivity = 0.98; specificity = 1; PPV = 1; NPV = 0.95) and HER2-positivity for the paired samples, m-d (P value &lt; 0.001; sensitivity = 0.85; specificity = 0.98; PPV = 0.92; NPV = 0.96) versus non m-d (P value &lt; 0.001; sensitivity = 0.71; specificity = 0.98; PPV = 0.90; NPV = 0.92), respectively.

Conclusion: These data suggest that mRNA for ESR and ERBB2 is sufficiently low in surrounding tissues that m-d of whole sections is not required for accurate assessment of key breast cancer mRNA markers in a closed system RT-qPCR assay. The simplicity of the assay workflow may be particularly valuable in low resourced settings where routine access to pathology expertise and to high quality IHC/FISH is challenging.

Citation Format: Gupta S, Carvajal-Hausdorf DE, Wasserman BE, Ho K, Weidler J, Wong W, Rhees B, Bates M, Rimm DL. Macrodissection prior to closed system RT-qPCR is not necessary for estrogen receptor and HER2 concordance with IHC/FISH in breast cancer [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P2-03-02.

The cost-effectiveness of alectinib in anaplastic lymphoma kinase-positive (ALK+) advanced NSCLC previously treated with crizotinib

Introduction Anaplastic lymphoma kinase (ALK) targeting drugs provide an important option for advanced non-small cell lung cancer patients with this distinct tumor type; however, there is considerable uncertainty as to which drug provides the optimal value after crizotinib treatment. This study estimated the cost-utility of alectinib vs ceritinib from a US payer perspective. Methods A cost-utility model was developed using partition survival methods and three health states: progression-free (PF), post-progression (PP), and death. Survival data were derived from the key clinical trials (alectinib: NP28761 & NP28673, ceritinib: ASCEND I and II). Costs included drugs, adverse events, and supportive care. Utilities were based on trial data and the literature. One-way and probabilistic sensitivity analyses (PSA) were performed to assess parameter uncertainty. Results Treatment with alectinib vs ceritinib resulted in increases of 2.55 months in the PF state, 0.44 quality adjusted life-years (QALYs), and $13,868, yielding a mean cost/QALY of $31,180. In the PSA, alectinib had a 96% probability of being cost-effective at a willingness-to-pay of $100,000/QALY. Drivers of model results were drug costs and utilities in the PF health state. The ICER ranged from $10,600-$65,000 per QALY in scenario analyses, including a sub-group analysis limited to patients with prior chemotherapy and crizotinib treatment. Conclusions Treatment with alectinib in ALK + crizotinib-treated patients increased time progression-free and QALYs vs ceritinib. The marginal cost increase was driven by longer treatment durations with alectinib. This model demonstrates that alectinib may be considered a cost-effective treatment after progression on crizotinib.

Perceptions of Residents and Non-residents in Psychiatry on Training Needs and Care of Patients with Intellectual Disability and Mental Health Problems: A Study from Singapore

Background and Objective

Psychiatric assessment and care of people with Intellectual Disability (ID) is complex due to their cognitive and communication impairments. Demand for further training in this area by trainees in psychiatry has been well documented. The main of aims of this study were to explore the attitudes and perceptions of psychiatry residents and non-residents (non-trainees) with regards to care of patients with ID as well as their knowledge and training in this area.

Method

The study was conducted as an anonymous survey at the Institute of Mental Health, Singapore. A survey questionnaire developed by the study team was sent to residents and non-residents in psychiatry.

Results

Forty-eight out of the 76 questionnaires were returned with a response rate of 63.16%. Twenty-eight participants described themselves as non-residents and the rest were residents. All participants responded that postgraduate training was required in the area of ID and mental health and majority reported that available training was inadequate. Ninety percent of respondents believed that people with ID were vulnerable to exploitation by other patients in the inpatient unit and 94% of respondents believed that people with ID should be managed by a specialist team.

Conclusion

Currently residents and non-residents in psychiatry see that training in ID and mental health as well as services for people with ID as inadequate. Efforts should be made to include specialist training in psychiatry of ID in the Singapore psychiatry curriculum to enhance the confidence and expertise of psychiatrists in this field.

Abstract P1-03-03: High concordance of ER, PR, HER2 and Ki67 by central IHC and FISH with mRNA measurements by GeneXpert® breast cancer stratifier assay

Current methods for the assessment of ER, PR, Her2, and Ki67 using FFPE tissues are hard to standardize and difficult to perform in Low and Middle Income Countries (LMIC). The GeneXpert® breast cancer stratifier assay (RUO) (BC Strat) is a cartridge-based, RT-qPCR assay of ESR1, PGR, ERBB2, and MKi67 mRNAs using FFPE specimens. The assay is fast (&lt;2 hours, including &lt;10 minutes of hands-on time) and easy to perform.

The aims of this study were: 1) to evaluate the concordance of BC Strat using different IHC antibodies and scoring methods in a preliminary dataset (Part I); and 2) to assess concordance between BC Strat and high quality standard methods in an expanded dataset (Part II).

Methods

Part I: IHC Antibody Variability

To assess BC Strat concordance with various IHC antibodies, 155 invasive ductal carcinoma blocks were sourced from 3 sites. Twenty-four adjacent slide sections from each block were prepared and shipped to different labs for BC Strat analysis(Cepheid) or IHC and FISH testing. Table 1 summarizes the IHC antibodies and scoring methods used in each reference lab.

Table 1:IHC antibodies and scoring methods used in reference labs Antibody for IHClabIHC scoringERSP1MPLNAutomated (Aperio)ER6F11Path IncAutomated (Aperio)ER6F11USCManualPRIE2MPLNAutomated (Aperio)PR16Path IncAutomated (Aperio)PRPGR636USCManualHer2*4B5MPLNAutomated (Aperio)Her2*HercepTestUSCManualKi6730-9MPLNAutomated (Aperio)Ki67MIB1Path IncAutomated (Aperio)Ki67MIB1USCManual*HER2 FISH (all with PathVysion kit) was performed at USC

Part II: Concordance Study

522 invasive ductal carcinoma FFPE samples were sourced from 5 sites. All BC Strat analysis was performed at Cepheid and all IHC and FISH was performed in the Press laboratory at USC. Overall percent agreement (OPA), positive percent agreement (PPA), and negative percent agreement (NPA) between BC Strat and IHC were determined.

Results

Part I: IHC Antibody Variability

Table 2 summarizes the OPA for BC Strat analysis and IHC performed with different IHC antibodies and scoring methods. Slightly better concordance for ER and PR was observed between the BC Strat and the IHC methods performed at USC. Discordant IHC results were also observed among the reference labs' standard methodologies.

Table 2: Overall Percent Agreement between IHC and BC Strat Reference LabOPA with BC StratERMPLN92%ERPath Inc96%ERUSC98%PRMPLN84%PRPath Inc83%PRUSC87%Her2*MPLN*93%Her2*USC*91%Ki67MPLN75%Ki67Path Inc67%Ki67USC81%*for IHC 2+(equivocal), FISH HER2/CEP17 ratio was examined

Part II: Concordance Study

Of the 522 samples tested, 499 (96%) yielded valid results for both BC Strat and IHC (IHC and FISH for Her2). OPA between BC Strat and IHC was 98% for ESR1, 91% for PGR, 93% for ERBB2 (IHC and FISH, 97% for Her2 IHC excluding IHC2+), and 81% for MKi67.

Conclusion

BC Strat assay measurements for ESR1, PGR, ERBB2 and MKi67 mRNA expression in FFPE breast tumor tissues are highly concordant with IHC and FISH performed by high quality reference labs. Further investigations using clinical outcomes from independent studies including prospective-retrospective clinical trials are in progress.

Citation Format: Wu NC, Wong W, Ho KE, Chu VC, Rizo A, Davonport S, Kelly D, Makar R, Jassem J, Duchnowska R, Biernat W, Radecka B, Fujita T, Klein JL, Stonecypher M, Ohta S, Juhl H, Weidler JM, Bates M, Press MF. High concordance of ER, PR, HER2 and Ki67 by central IHC and FISH with mRNA measurements by GeneXpert® breast cancer stratifier assay [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-03-03.

Abstract P1-03-11: Analytical validation for the RT-qPCR based multiplex mRNA measurements of ER, PgR, HER2, and Ki67 from FFPE tumor tissue using the GeneXpert breast cancer stratifier assay

BACKGROUND: Accurate assessment of ER, PgR, HER2 and Ki67 status is crucial for breast cancer therapy and patient management. Immunohistochemistry (IHC) assays have been standard diagnostic tools but they are complex and time-consuming to perform and may not be readily available in decentralized laboratories, particularly in low-to-middle income countries. Molecular diagnostics can be a sensitive and accurate alternative to the traditional IHC, and the GeneXpert Breast Cancer Stratifier assay RUO (BC Strat), a single use cartridge-based assay performed on the broadly distributed GeneXpert® Instrument (GX) platform, streamlines a technically demanding RT-qPCR process to provide easy, robust, and reproducible ESR1, PGR, ERBB2, and MKi67 mRNA measurements from a 4 µm thick, formalin-fixed paraffin embedded (FFPE) breast tumor section in less than 2 hours.

METHODS: Analytical validation of the BC Strat assay included studies of Linearity/Dynamic Range, Analytical Sensitivity (Minimum Assay Input), Specificity (Potential Interfering Substances), Carryover Contaminations, and Kit and Specimen Slide Stabilities. Both in-vitro RNA transcript (IVT) and/or clinical breast cancer tissues were used as sample input materials. Assay results for each analyte were generated from cycle threshold (Ct) values, and final positive/negative test results for each target were also reported as delta Ct values, where dCt = Ct [CYFIP1 Reference] – Ct [Target], using dCt cutoffs previously derived from a clinical sample cohort.

RESULTS: The BC Strat assay demonstrated ≥3 log Linear Dynamic Range covering 5-7 logs sample input for all 4 Target dCts with R2≥0.95 independently. The assay currently requires minimal sample input equivalent to CYFIP1 Ct≤35 (Ct=33.5 ±1.5Ct SD) from 20 replicates of 5-level serial sample dilutions using two independent assay lot materials. It is acceptably robust against non-tumor tissues, DCIS, necrotic and/or hemorrhagic cells, lymphocytes, and genomic DNA contaminants. No carryover contamination from the same GeneXpert module was observed over 20 repeat tests during 9 consecutive days. Current real-time data supports assay stability at 5, 30, 37, 45 and 50°C for at least 3 months with minimal performance impact. Sectioned FFPE breast tumor tissues generated consistent dCt results when stored at 4°C and 30°C for up to 1 month before BC Strat assay testing.

CONCLUSIONS: The analytical validations of the BC Strat assay demonstrate an easy and robust mRNA detection with high sensitivity, specificity, reproducibility, and stability in order to aid medical pathologists and clinicians to more rapidly and objectively determine ESR1, PGR, ERBB2, and MKi67 mRNA status in breast cancer. Although stability studies out to 37 months are ongoing, current data suggest the assay is stable for at least 3 months over a wide range of temperatures. The GeneXpert Breast Cancer Stratifier assay potentially offers a rapid, standardized, and cost-effective solution to streamlining complex molecular diagnostics available for use in local pathology laboratories worldwide.

Citation Format: Chu VC, Wu N, Ho KE, Rizo A, Malek M, Weidler JM, Bates M, Wong W. Analytical validation for the RT-qPCR based multiplex mRNA measurements of ER, PgR, HER2, and Ki67 from FFPE tumor tissue using the GeneXpert breast cancer stratifier assay [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-03-11.

Abstract P1-03-09: Highly reproducible decentralized gene expression analysis of ESR1, PGR, ERBB2 and MKi67 on an automated, standardized molecular diagnostics platform, GeneXpert

Background: Accurate assessment of ER, PgR, HER2, and Ki67 status using FFPE samples from patients with breast cancer is critical for appropriate patient management, yet immunohistochemistry (IHC), the most common method of assessing these markers, suffers from inherent variability due to pre-analytical/analytical factors and subjective interpretation by pathologists. Here we describe the GeneXpert (GX) Breast Cancer Stratifier RUO Assay (BC Strat), a real time quantitative PCR assay (RT-qPCR) kit which exhibits robust, highly reproducible mRNA measures of ESR1, PGR, ERBB2 (HER2) and MKi67.

The aims of this study were: 1) To assess the impact of variability contributed by pathologist-to-pathologist differences in the selection of the tumor area to be assayed, inter-laboratory assay performance, and macrodissection (MAC) vs. no macrodissection (nonMAC) on decentralized BC Strat results; and 2) to assess preliminary concordance of BC Strat with central IHC and FISH results.

Materials & Methods: The GX BC Strat is a cartridge-based RT-qPCR assay performed on the GeneXpert® Instrument (Cepheid) that automates RNA purification, RT-qPCR amplification and detection of mRNA of target genes (ESR1, PGR, ERBB2, and MKi67) and a control gene (CYFIP1) after sample preparation. Results are reported as delta cycle threshold (dCt) measurements (CYFIP1 Ct - target gene Ct) in less than 2 hrs.

Thirty-two invasive ductal carcinoma FFPE blocks were sourced based on varying levels of ER, PgR, HER2, and Ki67 expression and % tumor cell content/tumor area. Adjacent sections from each block were prepared as slides and sent to 3 external GX testing sites and a reference lab. Each site used its own pathologists/technicians to determine the % tumor cell content/tumor area, perform MAC or nonMAC, prepare lysates, and perform GX testing. Reference IHC/FISH was performed by Geneuity/MPLN (Maryville, TN, USA). Site-to-site concordance in GX results for MAC or nonMAC samples using pre-defined assay cutoffs per marker were analyzed, as were % tumor cell content/tumor area assessments between pathologists.

Results: BC Strat testing of 32 FFPE breast cancer samples with MAC demonstrated excellent GX site-to-site concordance in positive/negative status calls for ESR1 (100%), PGR (100%), ERBB2 (97%), and MKi67 (97%). In most cases, MAC vs. nonMAC had minimal impact on final positive/negative calls for GX, resulting in high overall concordance for MAC vs. nonMAC for ESR1 (91%), PGR (99%), ERBB2 (99%), and MKi67 (95%). The assay also demonstrated a strong overall concordance with IHC for ESR1 (97%), PGR (81%), ERBB2 (98%, IHC/FISH), and MKi67 (89%).

Conclusion: Decentralized performance of the GX BC Strat Assay is feasible and minimally affected by differences in tumor area selection and MAC techniques across tumors with a range of sizes, invasive tumor cell contents, and expression levels of ER, PgR, HER2, and Ki67. GX BC Strat dCt results across sites are highly reproducible and show good concordance of results with central lab IHC and HER2 FISH results. These results suggest standardized, decentralized testing of ESR1, PGR, ERBB2 and MKi67 by the GX BC Strat in local pathology labs is feasible.

Citation Format: Wong W, Ho KE, Wu N, Chu VC, Lalli P, Longshore JW, Klein J, Stonecypher M, Lykke C, Sherwood T, Davenport S, Weidler J, Bates M, Press MF. Highly reproducible decentralized gene expression analysis of ESR1, PGR, ERBB2 and MKi67 on an automated, standardized molecular diagnostics platform, GeneXpert [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-03-09.

Abstract P1-03-07: High concordance of a closed system, near point of care, RT-qPCR breast cancer assay for HER2 (ERBB2) mRNA compared to both IHC/FISH and quantitative immunofluorescence

Background

Reliable assessment of HER2 receptor status in breast cancer by either IHC or FISH does not unequivocally define receptor expression, due to their semi-quantitative nature, and as many as 10-15% of cases fall into the ASCO/CAP “equivocal” category. Historically, RNA measurements by PCR, including using several commercially available platforms, have been tested, but have not gained broad acceptance for assessment of HER2. However, RNA measurement, as a continuous value, has potential for use for adjudication of the equivocal category. In the current study, we used a real-time quantitative reverse transcription polymerase chain reaction (RT-qPCR) assay (GeneXpert® Breast Cancer Stratifier RUO Assay, Cepheid, Sunnyvale, CA, USA) for ERBB2 (HER2) mRNA on the GeneXpert® (GX) platform (Cepheid), which utilizes a closed-system, single-use cartridge, automated system. The RT-qPCR results from GX were then compared with results from clinical HER2 IHC/FISH assays following ASCO/CAP 2013 HER2 testing guidelines (Wolff et al JCO 2013) and quantitative immunofluorescence (QIF).

Methods

Multiple cores (1mm in diameter) were retrospectively collected from 80 formalin-fixed paraffin-embedded (FFPE) tissue blocks with invasive breast cancer seen by Yale Pathology Labs between 1998 and 2011. Tissue cores were processed as lysates for testing at Yale in the automated GX assay. Briefly, gene-specific reverse transcription was performed, followed by RT-qPCR (TaqMan) and ERBB2 mRNA results were expressed as the difference in cycle threshold values (delta Ct) between the endogenous control transcript (CYFIP1) and the ERBB2 mRNA transcript. Results from IHC and FISH were extracted from the pathology reports for the Yale CLIA lab and QIF for each case was measured as previously described (Carvajal et al, JNCI 2015).

Results

Quality control testing showed that the GX platform shows no case to case cross contamination on material from routine histology practices. Concordance between RT-qPCR and IHC/FISH was 91.25% (sensitivity = 0.87; specificity = 0.94; PPV = 0.89; NPV = 0.92) using a pre-defined delta Ct cut-off (dCt ≥ -1) for HER2 (+) based on prior concordance studies with HER2 IHC/FISH. Concordance between RT-qPCR and QIF was 99% (sensitivity = 0.97; specificity = 1.0; PPV = 1.0; NPV = 0.98) using dCt ≥ -1 and the pre-defined cut-point for positivity by QIF.

Conclusions

The GX closed system RT-qPCR assay shows greater than 90% concordance with the ASCO/CAP 2013 HER2 IHC/FISH scoring. Additionally, the GX RT-qPCR assay is highly concordant (99%) with the continuous variable HER2 QIF assay, and may better reflect the true continuum of HER2 receptor status in invasive breast cancer. These initial results suggest that rapid, closed system molecular assays may have future value for the adjudication of the ASCO/CAP HER2 equivocal category. This pilot study did not include ASCO/CAP 2013 “equivocal” cases, but that effort is underway.

Citation Format: Wasserman B, Carvajal-Hausdorf D, Ho K, Wong W, Wu N, Chu VC, Lai EW, Weidler JM, Bates M, Neumenister V, Rimm DL. High concordance of a closed system, near point of care, RT-qPCR breast cancer assay for HER2 (ERBB2) mRNA compared to both IHC/FISH and quantitative immunofluorescence [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-03-07.

The current status of prophylactic femoral intramedullary nailing for metastatic cancer

The most common site for cancer to spread is bone. At post-mortem, bony metastases have been found in 70% of patients dying from breast and prostate cancer. Due to the prevalence of cancer, bone metastasis and the associated management represents a huge burden on NHS resources. In patients with metastasis, around 56% of these involve the lower limb long bones. Due to the huge forces placed upon long bones during weight bearing, there is a high risk of fracture through areas of metastasis. It is reported that 23% of pathological fractures occur in the femoral subtrochanteric region. This area is subjected to forces up to four times the body weight, resulting in poor union rate for these fractures, and significant morbidity associated with difficulty in mobilising, and in patient nursing. As cancer treatments improve, the life expectancy in this subgroup of patients is likely to increase. Therefore medium-to-long-term management of these fractures, beyond the palliative, will become essential. We aim to evaluate the current management for metastatic malignant femoral disease, with particular focus on the prophylactic augmentation of diseased femorii using intramedullary nails.

Adapting Situational Awareness Measures for Hydropower Display Evaluations

This study used Situation Awareness (SA) as a measure to evaluate two new functional displays supplementing existing monitor displays in a large hydropower system control room. Because it was impractical to use traditional SA measures this paper proposes a novel SA measurement framework, in which controllers' SA levels are derived from their in-the-loop utterance and viewing patterns, their context-specific reports of the situations, and their overall SA reflections. Results indicate that the SA measures not only support and complement one another, but also are consistent with performance results. This study offers a novel approach of using convergent lines of evidence to assess SA in the situations that involve a whole control room or command centre or in situations constrained by time and resources.