Evaluation of cerebrospinal fluid alpha-synuclein seed amplification assay in PSP and CBS

Background

Seed amplification assay (SAA) testing has become an important biomarker in the diagnosis of alpha-synuclein related neurodegenerative disorders.

Objectives

To assess the rate of alpha-synuclein SAA positivity in progressive supranuclear palsy (PSP) and corticobasal syndrome (CBS), and analyse the clinical and pathological features of SAA positive and negative cases.

Methods

106 CSF samples from clinically diagnosed PSP (n=59), CBS (n=37) and indeterminate parkinsonism cases (n=10) were analysed using alpha-synuclein SAA.

Results

Three cases (1 PSP, 2 CBS) were Multiple System Atrophy (MSA)-type SAA positive. 5/59 (8.5%) PSP cases were Parkinson's disease (PD)-type SAA positive, and these cases were older and had a shorter disease duration compared with SAA negative cases. In contrast, 9/35 (25.7%) CBS cases were PD-type SAA positive.

Conclusions

Our results suggest that PD-type seeds can be detected in PSP and CBS using a CSF alpha-synuclein SAA, and in PSP this may impact on clinical course.

Abstract 1192: The Clinical Genome Resource (ClinGen) somatic cancer clinical domain working group

Interpretation of the clinical significance of somatic gene variants in cancer remains a major challenge in cancer diagnosis, prognosis and treatment response prediction. We will report on progress and plans of the Clinical Genome Resource (ClinGen) Somatic Cancer Clinical Domain Working Group (CDWG). The CDWG membership consists of over 150 multi-disciplinary experts in cancer biology, oncology, pathology, genetics, genomics and informatics. The mission of the ClinGen Somatic Cancer CDWG is to facilitate the development of data curation guidelines and standards to determine the clinical significance of somatic alterations in cancer, thereby enhancing the usability, dissemination and implementation of cancer somatic changes in the ClinGen resource and other knowledgebases including CIViC, ClinVar, and the Variant Interpretation for Cancer Consortium (VICC) MetaKB. Our goal is to create high-quality assertions of the clinical significance of specific somatic variants in cancer by leveraging the CIViC curation interface, adapting the germline procedures of ClinGen to somatic variant interpretation, and implementing the interoperability standards of the Global Alliance for Genomics and Health (GA4GH). The ClinGen Somatic effort is overseen by the Somatic CDWG and reports progress to the overall ClinGen consortium. There are Somatic Cancer subdomains focused on particular clinically important domains of cancer variant interpretation including three Task Forces (covering Pediatric Cancer, Hematologic Cancer, and Solid Tumors) and a growing number of Somatic Cancer Variant Curation Expert Panels (SC-VCEPs). To improve quality and consistency of clinical interpretations, each candidate somatic cancer VCEP must complete a four step approval process adapted from ClinGen’s work in Germline disease domains. The Somatic CDWG works to ensure that each group is aware of available training materials and detailed standard operating procedures. Each SC-VCEP also coordinates with the ClinGen Cancer Variant Interpretation Committee (CVI) whose goal is to support development of granular specifications for the AMP/ASCO/CAP guidelines for somatic variant interpretation. New SC-VCEPs are anticipated to focus on specific clinically relevant genes, pathways, disease entities, variant classes or treatment modalities. Currently, three SC-VCEPs have begun to work through the four step process (focused on FGFR mutations, NTRK fusions, and FLT3 mutations respectively), and two more SC-VCEPs are in the planning stage (Histone H3 and Ph-like ALL). To date, ClinGen Somatic groups have contributed 619 evidence lines into CIViC from 353 published papers and 21 assertions of clinical significance. Input from the AACR community is critical for the establishment of new SC-VCEPs that address areas of variant interpretation with the greatest need.

Citation Format: Jason Saliba, Gordana Raca, Angshumoy Roy, Ian King, Shamini Selvarajah, Xinjie Xu, Rashmi Kanagal-Shamanna, Laveniya Satgunaseelan, David Meredith, Mark Evans, Alanna Church, Panieh Terraf, Yassmine Akkari, Heather E. Williams, Wan-Hsin Lin, Chimene Kesserwan, Deborah I. Ritter, Kilannin Krysiak, Arpad Danos, Alex Wagner, Marilyn M. Li, Dmitriy Sonkin, Jonathan S. Berg, Sharon E. Plon, Heidi L. Rehm, Shashikant Kulkarni, Ramaswamy Govindan, Obi L. Griffith, Malachi Griffith, on behalf of the ClinGen Somatic CDWG. The Clinical Genome Resource (ClinGen) somatic cancer clinical domain working group [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1192.

Abstract 1193: Enhancing pediatric cancer variant curation and representation through standardized classification and automation

Childhood cancers present unique challenges for variant interpretation in a clinical context due to their rarity, low mutation burden, diversity of molecular alterations, and heterogeneity among patients. Consequently, genes and variants associated with childhood tumors are under-represented in public cancer databases and knowledgebases. A focused effort is needed for the structured curation of genetic variant-level data to document diagnostic, prognostic, and therapeutic biomarkers for childhood cancers. The Pediatric Cancer Curation Advancement Subcommittee (PCCAS), a collaboration between the Clinical Interpretations of Variants in Cancer knowledgebase (CIViC; civicdb.org), the ClinGen Somatic Pediatric Cancer Taskforce, Disease Ontology (DO; disease-ontology.org) and CIViCmine (bionlp.bcgsc.ca/civicmine/), is addressing this challenge through enhanced curation, tagging, and automation.

PCCAS created a pediatric specific curation standard operating procedure (SOP) to harmonize pediatric evidence entered in CIViC. Our SOP provides general guidance and considerations to define and classify childhood cancers and to represent childhood cancer evidence on a spectrum of age-related incidence and presentation. For instance, pediatric evidence in CIViC is now tagged using Human Phenotype Ontology (HPO) age of onset terms, allowing pediatric evidence to be easily searched, tracked, and sorted. We also initiated the addition of new age of onset terms to enhance the granularity of these tags.

WHO ICD-O nomenclature has been chosen for pediatric disease classification in CIViC. ICD-O provides updated terminology including specific genetic subtypes, which are important in pediatric cancers where their underlying molecular profiles often define the disease. To aid curator selection of disease, we verified pediatric relevant ICD-O terms inclusion in DO and restructured DO disease hierarchies to ensure proper mapping.

CIViC highlights our pediatric cancer initiative in multiple areas including a homepage feature linking directly to a dedicated pediatric advanced search that returns all evidence tagged with pediatric or young adult age of onset. Most importantly, our childhood specific SOP and initiatives are included in all ClinGen Somatic Cancer and CIViC training sessions for consistent implementation.

CIViCmine supports CIViC by using natural language processing to identify important cancer biomarkers in the literature. To better identify pediatric biomarkers, we are adapting and refining CIViCmine to use MeSH terms and other approaches to enhance accuracy in the identification of childhood evidence in both the literature and CIViC. In conclusion, implementation of these procedures, features, and automation are pushing to make childhood cancer variant evidence more accessible and interpretable.

Citation Format: Jason Saliba, Jake Lever, Kilannin Krysiak, Arpad Danos, Alex Wagner, Heather E. Williams, Laveniya Satgunaseelan, David Meredith, Cameron J. Grisdale, Chimene Kesserwan, Jianling Ji, Shruti Rao, Catherine Cottrell, Alanna Church, Mark Evans, Yasmina Jaufeerally-Fakim, Lynn M. Schriml, Angshumoy Roy, Gordana Raca, Malachi Griffith, Obi L. Griffith. Enhancing pediatric cancer variant curation and representation through standardized classification and automation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1193.

Apparatus for simultaneous dynamic light scattering-small angle neutron scattering investigations of dynamics and structure in soft matter

Dynamic Light Scattering (DLS) and Small-Angle Neutron Scattering (SANS) are two key tools to probe the dynamic and static structure factors, respectively, in soft matter. Usually, DLS and SANS measurements are performed separately, in different laboratories, on different samples, and at different times. However, this methodology has particular disadvantages for a large variety of soft materials, which exhibit a high sensitivity to small changes in fundamental parameters, such as waiting times, concentration, pH, and ionic strength. Here, we report on a new portable DLS-SANS apparatus that allows one to simultaneously measure both the microscopic dynamics (through DLS) and the static structure (through SANS) on the same sample. The apparatus has been constructed as a collaboration between two laboratories, each an expert in one of the scattering methods, and was commissioned on the LOQ and ZOOM SANS instruments at the ISIS Pulsed Neutron and Muon Source, U.K.

Laboratory biomarkers associated with COVID-19 severity and management

The heterogeneous disease course of COVID-19 is unpredictable, ranging from mild self-limiting symptoms to cytokine storms, acute respiratory distress syndrome (ARDS), multi-organ failure and death. Identification of high-risk cases will enable appropriate intervention and escalation. This study investigates the routine laboratory tests and cytokines implicated in COVID-19 for their potential application as biomarkers of disease severity, respiratory failure and need of higher-level care.

From analysis of 203 samples, CRP, IL-6, IL-10 and LDH were most strongly correlated with the WHO ordinal scale of illness severity, the fraction of inspired oxygen delivery, radiological evidence of ARDS and level of respiratory support (p ≤ 0.001). IL-6 levels of ≥3.27 pg/ml provide a sensitivity of 0.87 and specificity of 0.64 for a requirement of ventilation, and a CRP of ≥37 mg/l of 0.91 and 0.66.

Reliable stratification of high-risk cases has significant implications on patient triage, resource management and potentially the initiation of novel therapies in severe patients.

Abstract A67: Improving tissue allocation for research in pediatric solid tumors

Introduction: In pediatric cancer, there is an urgent need for research that can identify and validate new therapeutic modalities for pediatric cancers. Diagnostic biopsy samples remain the ideal tissue samples for research and must be collected from surplus biopsy material, which is often extremely limited. Here we describe our efforts to optimize tissue allocation for clinical care and research as a joint effort between Department of Pathology at Boston Children’s Hospital and the Pediatric Solid Tumor Program at the Dana-Farber/Boston Children’s Cancer and Blood Disorders Center.

Methods: Oncologists, pathologists, surgeons, interventional radiologists, pathology technical staff, and clinical research coordinators participated in the workflow design. The group agreed to develop a formalized procedure to address these five steps: 1) patient identification and consent, 2) prioritization of research objectives, 3) advance communication of tissue requests to the pathology staff, 4) tissue preparation, and 5) tissue distribution. It was unanimously agreed that all tissue must flow through the pathology department. On or before the day of surgery, clinical research teams sent the pathologist a patient-specific electronic communication indicating research consent and detailing the prioritized disease-specific research requests, including the procedure planned, all tissue types and tissue volumes requested, and details of any special preparation needed, such as avoiding decalcification in bone tumors. The communication was optimized to be clear but brief, with the goal of minimizing the impact to the pathologist’s work load. Pathologists were surveyed about the change in process.

Results: Over a five-year period (2013-2018), 662 pediatric DFCI/BCH solid tumor patients have consented to one or more trials that request FFPE, frozen, or fresh tissue. Tumor types represent a spectrum of cases, with many rare and singular diagnoses. Of 1,768 research tissue requests, 1,121 (63%) were fulfilled. Clinical study requests from resection specimens were the most likely to be fulfilled (95% of 390 requests fulfilled), while basic research requests from core biopsies were the least likely to be fulfilled (26% of 255 requests fulfilled). In an anonymous survey, 7 of 7 pathologists report that the process had improved since the introduction of the electronic communication.

Conclusions: A collaborative and informed model for tissue allocation is successful in distributing tissue for clinical studies and basic research projects. Our workflows and policies have gained pathologist approval and streamlined our processes. As clinical and research programs evolve, a thoughtful tissue allocation process will facilitate ongoing research.

Citation Format: R. Seth Pinches, Catherine Clinton, Abigail Ward, Stephanie C Meyer, Alyaa Al-Ibraheemi, Suzanne Forrest, Gianna R. Strand, Hillary Detert, Anne Piche-Schulman, Kristen Gil, Tamara Restrepo, Rosemarie Tavares-Proulx, Jeffrey Goldsmith, Raja Shaikh, Christopher Weldon, Sanda Alexandrescu, Allison F. O’Neill, Monica Hollowell, Marian H. Harris, Katherine A. Janeway, Brian D. Crompton, Alanna Church. Improving tissue allocation for research in pediatric solid tumors [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr A67.

Abstract A16: Genomic and immunologic characterization of a cohort of INI1-deficient pediatric cancers

Several aggressive cancers impacting children are characterized by alterations in the SWI/SNF complex, including rhabdoid tumors, epithelioid sarcoma, and chordoma. With recent early-phase trials showing responses to EZH2 inhibitors, it is important to understand the optimal approach to identifying INI1-deficient cancers. As tumor profiling is becoming a more routine part of clinical care, this study was designed to determine the relationship between SMARCB1 genetic variants identified by a sequencing panel test and INI1 protein expression. Beyond EZH2 inhibitors, therapeutic approaches for INI1-deficient tumors are limited. Thus, we also sought to investigate PD-L1 expression in a cohort of INI1-deficient pediatric brain and solid malignancies. Patients were identified by two methods: 1) search of our institutional pathology database from 2000-2015 for INI1-deficient tumors and 2) presence of SMARCB1 genomic alteration in a database of 280 cases with somatic panel sequencing results. Patients were included in the study if sufficient archival tumor tissue was available for repeat, confirmatory sequencing and immunohistochemistry (IHC). Somatic next-generation sequencing (NGS) was performed via a panel assay, OncoPanel, which surveys exonic DNA sequences of 447 cancer genes and 191 regions across 60 genes for rearrangement detection. IHC stains for INI1 and PD-L1 were performed according to standardized procedure on Leica Bond automated platforms and expression was assessed by two investigators (AA, JP) who were blinded to sequencing results. The study included 43 patients. IHC was performed on at least one specimen for all patients and repeat, confirmatory NGS was successful in 91% (39/43). Single-copy deletion of SMARCB1 on NGS panel was not predictive of loss of INI1 expression by IHC with only 1/10 (10%) SMARCB1 single-copy deletion cases having INI1 loss. In the 26 cases with INI1 loss by IHC and successful tumor sequencing, 23 (89%) had a genomic alteration in SMARCB1 detected. Five cases (22%) had 1-copy deletion, 12 (52%) had 2-copy deletion, 2 (9%) had nonsense mutations, and 4 (17%) had two inactivating alterations. 40% (12/30) of the patients with INI1-deficient tumors had at least one tumor specimen that was PD-L1 positive (≥1%). PD-L1 status was not associated with timing of tumor sampling or prior treatment. TMB ranged from 0.76 to 9.13 mut/Mb of DNA. We have observed 2 patients with INI1-deficient cancers with evidence of efficacy of immune checkpoint inhibitors. SMARCB1 2-copy deletions and inactivating mutations are associated with loss of INI1 protein expression, but 1-copy deletion of INI1 in histologies other than those already known to be INI1-deficient is not predictive of loss of protein expression. These results, along with two case reports of successful disease control with immune checkpoint inhibitors, suggest that clinical trials of PD-1 or PD-L1 inhibitors, either as single agents or in combination with an EZH2 inhibitor, are warranted in malignancies with INI1 loss.

Citation Format: Suzanne J. Forrest, Alyaa Al-Ibraheemi, Abigail Ward, Duong Doan, Catherine Clinton, Juan Putra, R. Seth Pinches, Cigall Kadoch, Susan Chi, Steve G. Dubois, Patrick Leavy, Natalie Collins, Alanna Church, Katherine A. Janeway. Genomic and immunologic characterization of a cohort of INI1-deficient pediatric cancers [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr A16.

Recurrent RET gene fusions in paediatric spindle mesenchymal neoplasms

AIMS

The classification of paediatric spindle mesenchymal tumours is evolving, and the spectrum of so-called 'infantile fibrosarcoma' has expanded to include tumours with NTRK, BRAF and MET gene fusions. RET-rearranged paediatric spindle cell neoplasms are an emerging group; there is sparse literature on their clinical, pathological and genetic features, and their nosological place in the canon of soft tissue tumours is uncertain. In this study, we report five RET-rearranged paediatric spindle cell tumours with fusion partners MYH10, KIAA1217 and CLIP2.

METHODS AND RESULTS

The tumours occurred in the pelvic region, paraspinal region, kidney and subcutaneous tissue of hand and abdomen. The patients' ages ranged from 6 months to 13 years (median 1 year). The tumours were composed of monomorphic spindle cells arranged in a fascicular pattern. Lesional cells had minimally atypical ovoid or tapered nuclei and pale cytoplasm with indistinct borders. Necrosis was not identified. Mitoses numbered three to 12 per 10 high-power field. Cases showed inconsistent and variable expression of S100, CD34 and SMA. Clinical behaviour ranged from small lesions potentially cured by simple resection to large lesions exhibiting metastasis, but responsive to kinase inhibitor therapy.

CONCLUSIONS

Our findings help to define RET-rearranged spindle cell tumours. Although it is likely that these tumours comprise part of the morphological and clinical spectrum of infantile fibrosarcoma (IFS), identification of RET gene alteration is important for its unique therapeutic implications.

A Novel ALK Fusion in Pediatric Medullary Thyroid Carcinoma

Medullary thyroid carcinoma (MTC) is most commonly associated with RET gene mutations. ALK fusions have rarely been described, although not previously in pediatrics and not previously partnered with CCDC6 in MTC or any other cancer. A 10-year-old boy with progressive stridor was found to have metastatic MTC, including lung, lymph node, and adrenal metastases. Baseline calcitonin was 6703 pg/mL. While molecular testing was pending, he was treated empirically with the investigational selective RET inhibitor, LOXO-292, without improvement. Molecular testing revealed a novel CCDC6-ALK fusion. His therapy was changed to crizotinib and then to alectinib for improved tolerability. Calcitonin decreased to 663 pg/mL after 6 days of ALK inhibition. He remains on alectinib with ongoing response. A novel CCDC6-ALK fusion has now been implicated in a pediatric case of metastatic MTC. This fusion has profound clinical sensitivity to ALK inhibitors. This report expands the spectrum of ALK fusions seen in MTC, including the first pediatric case of ALK translocated MTC. This novel fusion with CCDC6 has not previously been reported in other human cancers. Given the dramatic response to ALK inhibition in this case, identifying patients with ALK fusion MTC has important therapeutic implications.

Abstract CT112: A Phase I multicenter trial of the dual MDM2/MDMX inhibitor ALRN-6924 in children and young adults with relapsed/refractory pediatric cancers

BACKGROUND: TP53 mutations are rare across pediatric cancers. Recent work using CRISPR-Cas9 screens has demonstrated that MDM2 and MDMX are strong dependencies in a range of TP53-wildtype pediatric malignancies. Increased expression of MDM2 and MDMX is a common mechanism for suppressing p53 in pediatric malignancies and can occur by copy number gain or amplification, as has been reported in retinoblastoma and hepatoblastoma. In pediatric high-grade gliomas, activating PPM1D mutations drive p53 suppression, likely through MDM2 stabilization.

ALRN-6924 is a novel, first-in-class, cell-permeating stapled peptide that disrupts the inhibitory interactions between MDM2/MDMX(MDM4) and p53. ALRN-6924 has been evaluated in two adult Phase I trials, with good tolerability and evidence of clinical activity across a range of cancer subtypes. Given the oncogenic roles of MDM2 and MDMX in pediatric malignancies, we developed a Phase I clinical trial designed to evaluate the tolerability, pharmacokinetics, and pharmacodynamic and antitumor activity of ALRN-6924.

METHODS: This is a Phase I, open-label, investigator-initiated multicenter study of ALRN-6924 in children 1-21 years of age with relapsed/refractory cancer (NCT03654716). The primary objectives are to determine the recommended phase 2 dose, and to describe toxicities and pharmacokinetic parameters of ALRN-6924 in this population. The monotherapy arm consists of two cohorts: Cohort A for patients with TP53-wildtype solid tumors and lymphomas; and Cohort B for patients with retinoblastoma, or TP53-wildtype tumors that meet any of the following criteria: hepatoblastoma, malignant rhabdoid tumor, MDM2 or MDMX amplification, TET2 loss, or PPM1D activating mutations. Patients with CNS primary tumors are only eligible for Cohort B. In Cohorts A and B, patients receive ALRN-6924 intravenously on Days 1, 4, 8 and 11 of a 21-day cycle starting at a dose of 2.2 mg/kg. An expansion cohort for patients eligible for Cohort B will open following completion of monotherapy dose escalation. Patients with relapsed/refractory leukemias enroll to Cohort C and receive ALRN-6924 in combination with low-dose cytarabine on days 1, 8 and 15 of a 28-day cycle starting at a dose of 2.7 mg/kg. Pharmacokinetic sampling and pharmacodynamic testing (serum MIC-1 modulation) is required for all patients. Correlative biology studies will include evaluation of circulating tumor DNA for TP53 mutations in patients with solid tumors and serial assessment of leukemic blasts in patients with relapsed leukemia. Enrollment began in October 2018. Up to 69 patients will be enrolled.

Citation Format: David S. Shulman, Kieuhoa T. Vo, Elizabeth Fox, Jodi A. Muscal, Loren D. Walensky, Yana Pikman, Kimberly Stegmaier, Alanna Church, Brian D. Crompton, Andrew E. Place, Susan N. Chi, Allison F. O'Neill, Junne Kamihara, Suzanne Ezrre, Cecilia Carlowicz, Dawn Pinchasik, Hasan Al-Sayegh, Clement Ma, Wendy B. London, Steven G. DuBois. A Phase I multicenter trial of the dual MDM2/MDMX inhibitor ALRN-6924 in children and young adults with relapsed/refractory pediatric cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr CT112.

Development and content validation of measures assessing adherence barriers and behaviors for use in clinical care

BACKGROUND

Providers are often unaware of poor adherence to prescribed medications for their patients with chronic diseases.

OBJECTIVE

To develop brief, computer-administered patient-reported measures in English and Spanish assessing adherence behaviors and barriers. Design, Participants, and Main Measures: Item pools were constructed from existing measures of medication adherence behaviors and barriers, which informed development of a patient concept elicitation interview guide to identify medication adherence behavior and barrier-related concepts. Two hundred six patients either living with HIV (PLWH) or without were interviewed. Interviews were coded, concepts matched to item pool content, and new items were developed for novel concepts. A provider/investigator team highlighted clinically relevant items. Cognitive interviews were conducted with patients on final candidate items (n = 37). The instruments were administered to 2081 PLWH.

KEY RESULTS

Behavioral themes from concept elicitation interviews included routines incorporating time of day, placement, visual cues, and intentionality to miss or skip doses. Barrier themes included health-related (e.g. depressed mood, feeling ill), attitudes/beliefs (e.g., need for medication), access (e.g., cost/insurance problems), and circumstantial barriers (e.g., lack of privacy, disruption of daily routine). The final instruments included 6 behavior items, and 1 barrier item with up to 23 response options. PLWH endorsed a mean (SD) of 3.5 (1.1) behaviors. The 201 PLWH who missed ≥2 doses in the previous week endorsed a mean (SD) of 3.1 (2.5) barriers. The intraclass correlation coefficient (ICC) for the numbers of behaviors endorsed in 61 PLWH after 4-16 days was 0.54 and for the number of barriers for the 20 PLWH with ≥2 missed doses the ICC was 0.89, representing fair and excellent test-retest reliability.

CONCLUSION

Measures of medication adherence behaviors and barriers were developed for use with patients living with chronic diseases focusing on clinical relevance, brevity, and content validity for use in clinical care.

Abstract 4872: Gene fusion detection in pediatric tumor samples utilizing multi-caller fusion detection approach and integrative data analysis

Gene fusions are an important mechanism of oncogenesis in pediatric cancers. Fusion detection from RNA sequencing data is challenging for several reasons including a high false positive rate by individual fusion callers. We developed a new pipeline for gene fusion detection utilizing a multi-caller fusion detection approach and focusing on improved specificity, annotation and visual presentation.

Multiple fusion detection algorithms, integrative data analysis and known fusions and cancer genes annotation databases are integral parts of our new pipeline. The following fusion callers were included in the pipeline: Chimerascan, TopHat Fusion and STAR-Fusion. Fusions called by at least two fusion callers were included in the final results and annotated by utilizing the TARGET database (Tumor Alterations Relevant for Genomics-driven Therapy) and TICdb (Translocation breakpoints In Cancer database). A Venn diagram was produced for visual presentation of candidate fusions detected by multiple fusion callers. IGV (Integrative Genomics Viewer) was used to visualize the alignment of reads at fusion break points.

The fusion detection pipeline was tested with RNA sequencing data from 11 pediatric tumor samples either suspected to harbor fusions based on diagnosis (n=7; renal cell carcinoma, osteosarcoma, synovial sarcoma, glomus tumor, undifferentiated sarcoma) or known to have fusions based on standard methods (n=4; Ewing-like sarcoma, EWSR1 FISH+ sarcoma, clear cell sarcoma). In most cases, fusions previously known to be present were identified with our pipeline. For the difficult to detect fusion CIC-DUX4, optimization by adding another fusion caller (FusionCatcher) and adjusting the filtering and annotation parameters was required to increase sensitivity. Novel fusions were identified in cases suspected to harbor fusions and in some cases these novel fusions have been validated to be present with other methods. In one case (synovial sarcoma) the expected fusion, which was not detected with standard testing (FISH), was identified with our pipeline. The pipeline was also successfully utilized to analyze prostate cancer samples (PMID: 27167109).

Our new multi-caller fusion detection pipeline has been successful in increasing specificity and decreasing the false positive rate for gene fusion calling in transcriptomic data, while being sensitive enough to detect the more challenging gene fusions. Additional updates to the pipeline are anticipated like the realignment against a modified reference sequence including the gene rearrangement for improved sensitivity.

Citation Format: Alma Imamovic, Marian Harris, Alanna Church, Brian Crompton, Eliezer Van Allen, Katherine Janeway. Gene fusion detection in pediatric tumor samples utilizing multi-caller fusion detection approach and integrative data analysis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4872. doi:10.1158/1538-7445.AM2017-4872

Medication understanding among patients living with multiple chronic conditions: Implications for patient-reported measures of adherence

BACKGROUND

Low health literacy is associated with poor medication adherence and poor health outcomes. Limited understanding of prescribed medications may decrease validity of patient-reported adherence measures.

OBJECTIVES

To assess knowledge of names and purposes of prescribed medications among patients with multiple chronic conditions.

METHODS

Individual interviews were conducted with a convenience sample of patients from six U.S. primary care clinics. Participants (n = 57) were English and/or Spanish-speaking patients prescribed 3+ medications for chronic conditions, for which non-adherence may lead to disability or death. In individual interviews, patients were asked to name their medications, explain the purpose of each, and to explain how they distinguish them from one another. Interviews were audio recorded, transcribed, and coded; coded content was quantified by 1) whether or not the patient could name medications; 2) method of categorizing medications; 3) whether or not the purpose of the medication was understood. Descriptive statistics were compiled using Fisher's exact test to determine the relationship between patient knowledge and medication characteristics.

RESULTS

Thirty percent of patients could not name at least one of their medications; 19% did not know their purpose; 30% held misconceptions about the purpose of one or more medications. There was no significant difference in ability to name medications or state their medication's purpose between patients using medi-sets, pre-packaged rolls, or blister packs, and patients who stored pills in their original containers (p = 0.56 and p = 0.73, respectively), or across demographic groups (p = 0.085 to 0.767).

CONCLUSIONS

Many patients demonstrated difficulty identifying the name and purpose of prescribed medications; this did not differ by demographic group or medication storage type. Patients may benefit from routine review of medications with their provider in order to improve health literacy, outcomes, and patient-reported adherence measurement.

Institutional implementation of clinical tumor profiling on an unselected cancer population

BACKGROUND. Comprehensive genomic profiling of a patient's cancer can be used to diagnose, monitor, and recommend treatment. Clinical implementation of tumor profiling in an enterprise-wide, unselected cancer patient population has yet to be reported. METHODS. We deployed a hybrid-capture and massively parallel sequencing assay (OncoPanel) for all adult and pediatric patients at our combined cancer centers. Results were categorized by pathologists based on actionability. We report the results for the first 3,727 patients tested. RESULTS. Our cohort consists of cancer patients unrestricted by disease site or stage. Across all consented patients, half had sufficient and available (>20% tumor) material for profiling; once specimens were received in the laboratory for pathology review, 73% were scored as adequate for genomic testing. When sufficient DNA was obtained, OncoPanel yielded a result in 96% of cases. 73% of patients harbored an actionable or informative alteration; only 19% of these represented a current standard of care for therapeutic stratification. The findings recapitulate those of previous studies of common cancers but also identify alterations, including in AXL and EGFR, associated with response to targeted therapies. In rare cancers, potentially actionable alterations suggest the utility of a "cancer-agnostic" approach in genomic profiling. Retrospective analyses uncovered contextual genomic features that may inform therapeutic response and examples where diagnoses revised by genomic profiling markedly changed clinical management. CONCLUSIONS. Broad sequencing-based testing deployed across an unselected cancer cohort is feasible. Genomic results may alter management in diverse scenarios; however, additional barriers must be overcome to enable precision cancer medicine on a large scale. FUNDING. This work was supported by DFCI, BWH, and the National Cancer Institute (5R33CA155554 and 5K23CA157631).

Multicenter Feasibility Study of Tumor Molecular Profiling to Inform Therapeutic Decisions in Advanced Pediatric Solid Tumors: The Individualized Cancer Therapy (iCat) Study

Importance

Pediatric cancers represent a unique case with respect to cancer genomics and precision medicine, as the mutation frequency is low, and targeted therapies are less available. Consequently, it is unknown whether clinical sequencing can be of benefit.

Objective

To assess the feasibility of identifying actionable alterations and making individualized cancer therapy (iCat) recommendations in pediatric patients with extracranial solid tumors.

Design, Setting, and Participants

Clinical sequencing study at 4 academic medical centers enrolling patients between September 5, 2012, and November 19, 2013, with 1 year of clinical follow-up. Participants were 30 years or younger with high-risk, recurrent, or refractory extracranial solid tumors. The data analysis was performed October 28, 2014.

Interventions

Tumor profiling performed on archived clinically acquired specimens consisted of mutation detection by a Sequenom assay or targeted next-generation sequencing and copy number assessment by array comparative genomic hybridization. Results were reviewed by a multidisciplinary expert panel, and iCat recommendations were made if an actionable alteration was present, and an appropriate drug was available.

Main Outcomes and Measures

Feasibility was assessed using a 2-stage design based on the proportion of patients with recommendations.

Results

Of 100 participants (60 male; median [range] age, 13.4 [0.8-29.8] years), profiling was technically successful in 89 (89% [95% CI, 83%-95%]). Median (range) follow-up was 6.8 (2.0-23.6) months. Overall, 31 (31% [95% CI, 23%-41%]) patients received an iCat recommendation and 3 received matched therapy. The most common actionable alterations leading to an iCat recommendation were cancer-associated signaling pathway gene mutations (n = 10) and copy number alterations in MYC/MYCN (n = 6) and cell cycle genes (n = 11). Additional alterations with implications for clinical care but not resulting in iCat recommendations were identified, including mutations indicating the possible presence of a cancer predisposition syndrome and translocations suggesting a change in diagnosis. In total, 43 (43% [95% CI, 33%-53%]) participants had results with potential clinical significance.

Conclusions and Relevance

A multi-institution clinical genomics study in pediatric oncology is feasible and a substantial proportion of relapsed or refractory pediatric solid tumors have actionable alterations.

Trial Registration

clinicaltrials.gov Identifier: NCT01853345.

Abstract B38: Developing a functional genomics platform to interrogate rare pediatric cancers

Of pediatric solid tumors, as many as 10% of tumors are categorized as rare. Many of these rare tumors lack standard effective known therapy. The ability to identify vulnerabilities for many rare tumors has been significantly limited by the lack of in vitro and in vivo models. Furthermore, current approaches to study such vulnerabilities are usually limited to a specific compound or target. Our objectives were 1) to develop a platform to collect tumor samples and generate in vitro models and 2) to develop systematic and orthogonal approaches focused on currently known druggable cancer targets to identify vulnerabilities in these difficult to treat cancers. We have developed a proof of concept cell line from a patient who succumbed to progressive undifferentiated sarcoma treated on an aggressive multi-therapy regimen. This cell line, in its early passages, has novel gene fusions that match that of the primary tumor. Furthermore, even at early passages, this cell line was amenable to high throughput functional screens. Using a targeted pooled shRNA screen (employing matched seed controls) and an analogous CRISPR screen we identified dependencies to XPO1 and CDK4. In parallel, compounds against these targets were identified in a small molecule compound screen. These targetable dependencies were further validated in vivo with a micro-dosing device. These observations identify new targets in this rare malignancy. Furthermore, this suggests that the interrogation of patient derived cell lines facilitates the identification of testable therapeutic approaches.

Citation Format: Andrew L. Hong, Glenn S. Cowley, Yuen-Yi Tseng, Jaime H. Cheah, Oliver Jonas, Mihir B. Doshi, Bryan D. Kynnap, Coyin Oh, Stephanie Meyer, Paul Clemons, Michael Burger, Francisca Vazquez, Barbara Weir, Gregory V. Kryukov, Alanna Church, Alma Imamovic, Aviad Tsherniak, Craig Bielski, Brian Crompton, Elizabeth Mullen, Charles Roberts, Carlos Rodriguez-Galindo, Katherine A. Janeway, Kimberly Stegmaier, Paul van Hummelen, Robert Langer, Levi A. Garraway, Stuart L. Schreiber, David E. Root, Jesse S. Boehm, William C. Hahn. Developing a functional genomics platform to interrogate rare pediatric cancers. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Pediatric Cancer Research: From Mechanisms and Models to Treatment and Survivorship; 2015 Nov 9-12; Fort Lauderdale, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(5 Suppl):Abstract nr B38.

Developing principles of sustainability and stakeholder engagement for "gentle" remediation approaches: the European context

Gentle Remediation Options (GRO) are risk management strategies or techniques for contaminated sites that result in no gross reduction in soil functionality (or a net gain) as well as risk management. Intelligently applied GROs can provide: (a) rapid risk management via pathway control, through containment and stabilisation, coupled with a longer term removal or immobilisation/isolation of the contaminant source term; and (b) a range of additional economic (e.g. biomass generation), social (e.g. leisure and recreation) and environmental (e.g. CO2 sequestration) benefits. In order for these benefits to be optimised or indeed realised, effective stakeholder engagement is required. This paper reviews current sector practice in stakeholder engagement and its importance when implementing GRO and other remediation options. From this, knowledge gaps are identified, and strategies to promote more effective stakeholder engagement during GRO application are outlined. Further work is required on integrating stakeholder engagement strategies into decision support systems and tools for GRO (to raise the profile of the benefits of effective stakeholder engagement and participation, particularly with sector professionals), and developing criteria for the identification of different stakeholder profiles/categories. Demonstrator sites can make a significant contribution to stakeholder engagement via providing evidence on the effectiveness of GRO under varying site contexts and conditions. Effective and sustained engagement strategies however will be required to ensure that site risk is effectively managed over the longer-term, and that full potential benefits of GRO (e.g. CO2 sequestration, economic returns from biomass generation and "leverage" of marginal land, amenity and educational value, ecosystem services) are realised and communicated to stakeholders.

Efficacy and safety of once-daily umeclidinium/vilanterol 62.5/25 mcg in COPD

STUDY OBJECTIVE

To examine the efficacy and safety of the once-daily, inhaled, long-acting muscarinic antagonist/β2-agonist combination umeclidinium/vilanterol (UMEC/VI) compared with UMEC and VI monotherapies in patients with chronic obstructive pulmonary disease (COPD).

METHODS

In this 24-week, double-blind, placebo-controlled, parallel-group study (ClinicalTrials.gov: NCT01313650) eligible patients were randomised 3:3:3:2 to treatment with UMEC/VI 62.5/25 mcg, UMEC 62.5 mcg, VI 25 mcg or placebo administered once daily via dry powder inhaler (N = 1532; intent-to-treat population). Primary endpoint was trough forced expiratory volume in one second (FEV1) on Day 169 (23-24 h post-dose). Additional lung-function, symptomatic, and health-related quality-of-life endpoints were assessed, including 0-6 h weighted-mean FEV1, rescue salbutamol use, Transition Dyspnoea Index (TDI), Shortness Of Breath With Daily Activity (SOBDA) and St. George's Respiratory Questionnaire (SGRQ) scores. Safety evaluations included adverse events (AEs), vital signs, 12-lead/24-h Holter electrocardiography parameters and clinical laboratory/haematology measurements.

RESULTS

All active treatments produced statistically significant improvements in trough FEV1 compared with placebo on Day 169 (0.072-0.167 L, all p < 0.001); increases with UMEC/VI 62.5/25 mcg were significantly greater than monotherapies (0.052-0.095 L, p ≤ 0.004). Improvements were observed for UMEC/VI 62.5/25 mcg vs placebo for weighted-mean FEV1 on Day 168 (0.242 L, p < 0.001), rescue salbutamol use during Weeks 1-24 (-0.8 puffs/day, p = 0.001), TDI (1.2 units, p < 0.001), SOBDA (-0.17 units, p < 0.001) and SGRQ (-5.51 units, p < 0.001) scores. No clinically-significant changes in vital signs, electrocardiography, or laboratory parameters were observed.

CONCLUSION

Once-daily UMEC/VI 62.5/25 mcg was well tolerated and provided clinically-significant improvements in lung function and symptoms in patients with COPD.

Foot care education in patients with diabetes at low risk of complications: a consensus statement

AIMS

To define and agree a practical educational framework for delivery by all healthcare professionals managing patients with diabetes, particularly those at low risk of developing foot complications.

METHODS

A consensus meeting of a multidisciplinary expert panel. Prior to the meeting, relevant clinical papers were disseminated to the panel for review. The consensus was largely based upon the experts' clinical experience and judgement.

RESULTS

Four main health behaviours were identified for those at low risk of developing foot complications, namely: control of blood glucose levels; attendance at annual foot screening examination; reporting of any changes in foot health immediately; and the engagement in a simple daily foot care routine.

CONCLUSION

There is currently little evidence-based literature to support specific foot care practices. Patients with diabetes at low risk of developing complications should be encouraged to undertake a basic foot care regimen to reduce their likelihood of developing complications.

Scintigraphy can be used to compare delivery of sore throat formulations

AIMS

Sore throat (pharyngitis) is commonly treated with over-the-counter lozenges, tablets, sprays and gargles. While the efficacy of the active ingredients has been examined, less is known about the comparative efficacy of the different delivery formats.

METHODS

A pilot study was initially performed, followed by an open-label, four-way crossover study in healthy volunteers to quantitatively assess the delivery efficacy of a lozenge, tablet, spray and gargle, using technetium-99m and scintigraphy as a marker of deposition and clearance of the active ingredients.

RESULTS

Initial deposition in the mouth and throat combined was significantly greater for the solid dose forms (lozenge and tablet) than for the spray or gargle. Rates of clearance were initially similar for the tablet and lozenge with low levels of radioactivity present at up to 2 h. At 10 and 20 min, significantly more of the dose remained for the lozenge than for the tablet. The mouth appeared to act as a reservoir for continued clearance to the throat.

DISCUSSION AND CONCLUSION

Scintigraphy is an effective means of quantifying the delivery efficiency, and hence availability, of sore throat medications. The results presented here suggest that both lozenges and tablets offer considerable advantages over sprays or gargles, both in terms of proportion of the dose delivered to the mouth and throat, combined, and clearance from these regions. These delivery formats provide fast, effective and prolonged delivery of active ingredients, highlighting their potential benefits for sore throat medication.

Anti-basal ganglia antibodies and Tourette's syndrome: a voxel-based morphometry and diffusion tensor imaging study in an adult population

Anti-basal ganglia antibodies (ABGAs) have been suggested to be a hallmark of autoimmunity in Gilles de la Tourette's syndrome (GTS), possibly related to prior exposure to streptococcal infection. In order to detect whether the presence of ABGAs was associated with subtle structural changes in GTS, whole-brain analysis using independent sets of T(1) and diffusion tensor imaging MRI-based methods were performed on 22 adults with GTS with (n = 9) and without (n = 13) detectable ABGAs in the serum. Voxel-based morphometry analysis failed to detect any significant difference in grey matter density between ABGA-positive and ABGA-negative groups in caudate nuclei, putamina, thalami and frontal lobes. These results suggest that ABGA synthesis is not related to structural changes in grey and white matter (detectable with these methods) within frontostriatal circuits.

Late recurrences of Sydenham's chorea are not associated with anti-basal ganglia antibodies

Anti-basal ganglia antibodies (ABGA) have been associated with 100% of acute cases and 69% of persistent cases of Sydenham's chorea. We describe two cases of late recurrences of Sydenham's chorea with absence of ABGA. Both patients had several childhood episodes of Sydenham's chorea. MRI imaging of the basal ganglia and exhaustive investigations for other causes of chorea were normal or negative. The absence of ABGA may be evidence against an autoimmune pathology in late and some persistent recurrences. We suggest the likely pathophysiology to be dopamine hypersensitivity of chronically damaged basal ganglia neurones possibly following induction of an autoimmune antibody response in childhood.

Oral contraceptive induced chorea: another condition associated with anti-basal ganglia antibodies

Use of oral contraceptives is a recognised but infrequent cause of chorea. This type of chorea has usually been considered a reactivation of Sydenham's chorea by an unknown mechanism. A patient developed a chorea triggered by the use of oral contraceptives with no definite evidence of previous Sydenham's chorea or recent streptoccocal infections. However, the patient had positive anti-basal ganglia antibodies, which supports an immunological basis for the pathophysiology of this chorea.

Herlitz junctional epidermolysis bullosa presenting at birth with anonychia: a case report and review of H-JEB

A 15-day-old Yemeni boy presented with anonychia and granulomatous nail beds and white patches in the mouth. Biopsy specimens from the nail beds were nondiagnostic. Shortly thereafter the child developed multiple tense bullae, a hoarse voice, and poor appetite. Hematoxylin and eosin staining along with monoclonal antibody studies of a skin biopsy specimen revealed subepidermal bullae through the lamina lucida and a marked decrease in laminin 5. A diagnosis of junctional epidermolysis bullosa Herlitz variant was made. His course was complicated by multiple nonhealing wounds, oral pharyngeal involvement, sepsis, anemia, and poor nutrition, leading to his eventual death. This report emphasizes the unusual presentation of Herlitz junctional epidermolysis bullosa with anonychia as the initial finding and a relatively prolonged period before cutaneous blister formation, resulting in delay of diagnosis.

DNA typing of the human MN and Ss blood group antigens in amniotic fluid and following massive transfusion

Although red blood cell (RBC) antigen typing by agglutination is generally useful, several situations exist where this approach is difficult or impossible. For example, following a massive transfusion, a patient's residual RBCs are mixed with transfused normal donor RBCs. In this case, typing by hemagglutination primarily detects the antigens on the heterogeneous population of transfused RBCs. Agglutination testing is also of limited use for determining the phenotype of a fetus at risk for hemolytic disease of the newborn because fetal RBCs must be obtained by periumbilical blood sampling. Determining the genotype of an individual by analyzing genomic DNA isolated from peripheral blood nucleated cells or amniocytes is an alternative approach for determining the RBC antigen type. In this report, the allele specific polymerase chain reaction (AS-PCR) was used to identify the alleles at the MN and Ss loci that encode the corresponding antigens on glycophorin A (GPA) and glycophorin B (GPB), respectively. This method was used to type these alleles in peripheral blood samples obtained from normal individuals and from patients following massive transfusion. Of 23 peripheral blood specimens analyzed, all were correctly typed by this method. The allele specific polymerase chain reaction was also used to determine these alleles using amniotic fluid samples. Of 11 amniotic fluid specimens analyzed, 8 were correctly typed at both loci. Mistyping of three amniotic fluid specimens was explained by possible maternal blood contamination.

Urban Regeneration in London Docklands: A Five-Year Policy Review

An urban development corporation was established in London Docklands in 1981. Recently, central government has announced its intention to set up similar organisations elsewhere in Britain, and, therefore, a review of the impact of the London Docklands' initiative is appropriate. In this paper I outline the impact of the urban development corporation, in terms of economic regeneration and of the effect on local unemployment. It is argued that demand-led economic regeneration, based on the redevelopment of derelict land, has changed the nature of the local economy, although as yet it has not had any significant effect on the numbers of jobs in the local economy, because of continued decline in existing industries and because of pressures on firms to relocate. Local unemployment has gone on increasing, and evidence is presented to show that labour-market adjustment mechanisms and recruitment patterns severely limit the impact of economic regeneration on unemployment in Docklands. Even major developments, such as the proposed office complex on Canary Wharf, will have only a relatively small effect on local unemployment. Local labour-market intervention has been slow to occur, limited in its aims, and uncoordinated. Urban development corporations are useful policy devices for the encouragement of large-scale land redevelopment, but in their present form they do not represent a complete solution to the economic and employment problems of depressed urban areas.