bluuebunny/crossref_metadata_2025_split huggingface dataset:
OTHR-07. A new framework for missing value tolerant data integration
Authors: Voß Hannah , Schlumbohm Simon , Wurlitzer Marcus , Dottermusch Matthias , Neumann Philipp , Barwikowski Philip , Schlüter Hartmut , Krisp Christoph , Neumann Julia 
Published: June 2022

Abstract
Dataset integration is common practice to overcome limitations, e.g., in statistically underpowered omics datasets. This is of particular importance when analyzing rare tumor entities. However, combining datasets leads to the introduction of biases, so called 'batch effects', which are due to differences in quantification techniques, laboratory equipment or used tissue type. A common problem is the missing quantification for features like gene transcripts or proteins within a dataset. These missing values can appear at random in a given dataset and also get introduced by combination of multiple datasets. Currently, strategies beyond common normalization for batch effect reduction are either missing entirely or are unable to handle absence of data points and therefore rely on error-prone data imputation. We introduce a framework that enables batch effect adjustments for combined datasets while avoiding data loss by appropriately handling missing values without imputation. The underlying idea is based on a matrix dissection approach, adjusting common information from the integrated dataset under guarantee of sufficient data presence. The strategy is implemented within the R environment and linked with popular software stacks that are built on top of R. Successful data adjustment is exemplarily shown for proteomic data generated by different quantification approaches and LC-MS/MS instrumentation setups.
OTHR-15. Papillary tumor of the pineal region: case series of this rare pediatric entity
Authors: Shatara Margaret , Cantor Evan , Meyer Ashley , Ogle Andrea , Green Tammy , Beck Mary , McHugh Michele , Brossier Nicole , Cluster Andrew , Rubin Joshua , Mian Ali , Dahiya Sonika , Perkins Stephanie , Abdelbaki Mohamed S , Strahle Jennifer , Limbrick David , McEvoy Sean D 
Published: June 2022

Abstract
BACKGROUND: The optimal management of pediatric papillary tumors of the pineal region (PTPR) is not yet established. We report three cases, as an addition to the existing literature. PATIENT 1: A 22-month-old female presented with progressive ataxia and incoordination, found to have an enhancing solid and cystic mass centered within the pineal region, with associated obstructive hydrocephalus. Tumor biopsy revealed PTPR, prompting a subsequent subtotal resection. No adjuvant therapy was recommended. Patient has remained without evidence of disease progression for 92 months, since resection. PATIENT 2: An 8-year-old female presented with progressive headaches and new-onset generalized seizures, found to have a heterogeneously enhancing pineal lesion, with associated obstructive hydrocephalus. Following a biopsy demonstrating PTPR, patient underwent subtotal resection of the tumor. A second resection was completed 6 months later followed by focal irradiation. Targeted next-generation sequencing (NGS) demonstrated two non-targetable genomic alterations (CREBBP and MLL2). The patient remains without tumor recurrence, now 37 months, since irradiation. PATIENT 3: A 7-year-old male with Autism spectrum disorder presented with new-onset focal complex seizures. A brain MRI showed a heterogeneously enhancing lesion in the region of the pineal gland, with associated obstructive hydrocephalus. A tumor biopsy revealed PTPR, prompting a subsequent gross total resection (GTR). NGS demonstrated no reportable genomic alterations. Methylome profiling classified the tumor as PTPR, group B. Post-operative imaging with no residual tumor and he has remained without tumor progression, now eight months, since resection. CONCLUSION: PTPR are extremely rare in the pediatric setting, and were initially introduced in the WHO 2007 classification as grade II-III pineal gland tumors with distinct morphologic and immunohistochemical features. GTR is the mainstay of treatment but post-surgical management remains controversial. The clinical course is characterized by frequent local recurrence, hence, adjuvant chemotherapy and/or irradiation may be necessary upon disease progression.
OTHR-23. Development of a cerebrospinal fluid liquid biopsy platform in pediatric patients with central nervous system tumors
Authors: O’Halloran Katrina , Ostrow Dejerianne , Christodoulou Eirini , Bootwalla Moiz , Yellapantula Venkata , Chapman Nicholas , Chiarelli Peter , Chu Jason , Krieger Mark , Gai Xiaowu , Biegel Jaclyn 
Published: June 2022

Abstract
Pediatric central nervous system (CNS) tumors carry high morbidity and mortality. The advent of targeted agents is aiming to change that through individualized, less invasive, and real-time molecular profiling. We successfully developed a cerebrospinal fluid (CSF) liquid biopsy (LB) platform combining low-pass whole genome sequencing (WGS) and targeted mutation and gene fusion analysis of cell-free (cf) DNA. WGS libraries were constructed with the xGen Prism DNA Library Prep Kit using 5ng of input cfDNA and paired-end sequenced (Illumina NextSeq 500) for an average 0.5x coverage across the genome. Copy number (CN) profiles were analyzed using the ichorCNA R package and compared with CN abnormalities of the primary tumors detected with CytoScanHD or Oncoscan arrays. Selected cases were analyzed for mutations or gene fusions using a custom glioma hybrid capture-based panel (Twist Bioscience) sequenced to 500-1000x across targeted regions. Mutations identified in LBs were compared with primary tumor OncoKids NGS panel results. CSF LBs from 44 tumor cases and 15 non-tumor controls were analyzed. Sixteen primary tumors had copy number changes, 10 had cfDNA detected in the LB across various primary tumor diagnoses (AT/RT, diffuse midline glioma, ependymoma, high-grade glioma, medulloblastoma, pilocytic astrocytoma). Four primary tumors had sequence alterations from the custom panel, two with detectable cfDNA (diffuse midline glioma H3K27M variant allele frequency (VAF) 49% and low-grade glioma BRAFV600E VAF 1.7%). Three patients had TP53 variants detected, all ultimately germline. Controls were negative across WGS and hybrid gene capture. Tumor DNA is detectable by both WGS and hybrid gene capture. Various histologic subtypes are detectable including embryonal and glioneuronal. CSF seems more enriched for cfDNA in high grade versus low grade tumors. These data suggest that NGS-based LB assays may be used to monitor pediatric patients with a variety of CNS tumors, from diagnosis through treatment and recurrence.
OTHR-31. The molecular profile of secondary meningiomas in survivors of childhood non-central nervous system (CNS) cancers
Authors: Corriveau-Bourque Catherine , Wong Derek , van Landeghem Frank , Snuderl Matija , Spavor Maria , Yip Stephen , Eisenstat David 
Published: June 2022

Abstract
INTRODUCTION: Secondary meningiomas are a late effect in children who received cranial irradiation, frequently with a long latency. The molecular genetic profile of primary meningiomas is well studied; however, few studies describe the genomic landscape of radiation-induced meningiomas (RIM). METHODS: Patients followed at the Stollery Children’s Hospital (Edmonton, Canada) with a history of non-CNS malignancies who received cranial irradiation and then developed meningiomas between 1971 and 2013 were identified. Whole exome sequencing (WES), RNA sequencing as well as DNA methylation profiling were performed for patients with available tumor tissue and germline DNA. RESULTS: Of 96 patients who received cranial irradiation for non-CNS tumors, 16 (16.7%) developed symptomatic meningiomas. This patient cohort is unique; all 16 patients identified received 2000-2400 cGy of cranial irradiation, suggesting a threshold dose. 9/16 (56%) had WHO Grade 2 meningiomas or greater and 7/16 (44%) of meningiomas infiltrated other tissues. Post-surgical recurrences occurred in 43%. Patients experienced considerable morbidities directly attributable to the meningiomas or their treatment. 14 patients had samples suitable for further analysis. NF2 mutations were identified in 50% (8; 4 DNA,4 fusion). Other meningioma related genes with mutations identified in other cohorts were not identified. Copy number alternations were noted in all 16 patients in chromosomes 1p and 22q. 850k methylation analysis with PCA as well as UMAP and tSNE did not demonstrate clustering. Ongoing additional studies include examining tumor mutation burden and the radiation mutational profile. CONCLUSIONS: This study examined the RIM in a cohort of patients having received similar doses of radiation for their childhood cancer. There is increased risk of radiation-induced meningioma in survivors of non-CNS cancers given ≥ 2000 cGy during childhood. To date, our findings are consistent with previously described primary and RIM mutations. Enhanced knowledge in secondary meningiomas is crucial for accurate patient counselling, prognostication, and treatment.
OTHR-33. INTRODUCTION OF A MULTIDICIPLINARY NEURO ONCOLOGY LONG TERM FOLLOW UP CLINIC
Authors: Dahl Christine , Farrell Nicola , Blount Nicola , Mould ryan , Simcox Angela , Malcolm Charlotte , Freeman Anita , King Vicky , Bell Daniel , Michalski Antony , Gan Hoong-Wei 
Published: June 2022

Abstract
INTRODUCTION: The number of children and young people (CYP) surviving brain tumours is increasing annually with a doubling of 5-year survival over the last 40 years. More than two-thirds of these survivors suffer multiple long-term co-morbidities (“late effects”) from their tumour and/ or treatment(s) necessitating lifelong multiprofessional follow-up. This results in multiple appointments and increases the burden of care on patients. Method/Project description To establish a collaborative multidisciplinary “one stop shop” long-term follow-up clinic for CYP &gt;5 years from the end of neuro-oncological treatment to the reduce the need for multiple hospital appointments and to provide holistic assessment and care.The first clinic began in January 2020 as a collaboration between the departments of neuro-oncology, endocrinology, neuropsychology, psychology, physiotherapy and occupational therapy. RESULTS: We have audited the last 60 patients seen in clinic in 2 years and the services they required both in and out of clinic are noted below: Endocrinology – 58 patients Educational help and formal neuropsychology (44 and 39 respectively) There are significant emotional problems in the group and 32 saw clinical psychology and 13 were referred to CAMHS. Physical function issues – 31 saw both physiotherapy and occupational therapy. 10 required referral to orthopaedics Neurology and neurosurgery (13 and 11 respectively) Visual impairment – 33 saw ophthalmology Hearing problems – 17 saw audiology Other organ dysfunction – 4 saw cardiology and 3 urology. We have some feedback data on patient and parent satisfaction with the clinic which shows 92% (13 of 14) families preferred to be seen in the MDT setting rather than by separate clinicians. DISCUSSION: Few models of similar multidisciplinary neuro-oncology long-term follow-up clinics exist in the UK with a lack of streamlined funding, despite recognition from families and professionals about their utility.
OTHR-34. Identifying mechanisms of microglia-tumor cell interactions in retinoblastoma
Authors: Pohlmann Anike , Gerling Teresa , Walter Carolin , Melcher Viktoria , de Faria Flavia W , Disch Alina , Kanber Deniz , Wöstefeld Julia , Steenpass Laura , Lohmann Dietmar , Ryl Tatsiana , Riedel Nicole , Ketteler Petra , Schönberger Stefan , Ting Saskia , Bedzhov Ivan , Kiefer Tobias , Lever Mael , Schlüter Sabrina , Biewald Eva , Bechrakis Nikolaos , Albert Thomas K , Kerl Kornelius 
Published: June 2022

Abstract
BACKGROUND: Treatment-related long-term sequelae and chemotherapy resistance diminish the success of retinoblastoma (RB) treatment. To unravel the mechanisms leading to tumor progression and resistance we examined the intratumoral cellular heterogeneity of RB and its interactions with cells of the tumor microenvironment (TME). METHODS: We used single-cell RNA (scRNA-seq) and ATAC sequencing (scATAC-seq) as well as spatial transcriptomics to analyze and compare RB samples from patients with or without previous chemotherapy (chemo-treated vs. naïve). In addition, we developed a 3D model by injection of RB and TME cells into retinal organoids, which mimics the heterogeneous surrounding of the tumor in a spatially and functionally organized manner. RESULTS: ScRNA-seq revealed a high intratumoral heterogeneity of tumor cells representing distinct developmental stages from progenitors to more differentiated photoreceptor cells. The predominant cell type in the TME was M2-activated microglia (MG). M2-MG exerted multiple receptor-ligand interactions with RB tumor cells which were not found in non-diseased retinas. These tumor-specific cellular interactions regulate multiple signaling pathways (e. g. VEGF-, WNT-, BMP-, PGF- signaling) known to be involved in RB progression. By comparing chemo-treated and chemo-naïve RB samples we were able to identify treatment-resistant and -sensitive subpopulations of tumor cells. Finally, data from our RB-retina in vitro model highlighted the impact of RB cells on gene expression programs of normal retinal cells. CONCLUSION: In summary, we deciphered the intratumoral heterogeneity of RB, uncovered an intricate network of microglia-tumor cell interactions that connects numerous important signaling pathways, and further identified chemotherapy-resistant/sensitive tumor cell populations. The latter observation could prove to be very helpful in the development of novel therapeutic approaches in the treatment of RB.
OTHR-37. Pediatrics Cutaneous Reactions in Patient Treated with the Mitogen-Activated Protein Kinase Extracellular Signal-Regulated Kinase Inhibitor Trametinib
Authors: Gluck Mirit , Ben-amitai Dan , Friedland Rivka , Toledano Helen 
Published: June 2022

Abstract
OBJECTIVE: To describe the cutaneous adverse effects (AE) to MAPK Extracellular Signal-Regulated Kinase (MEK) Inhibitor Trametinib in the pediatric population. METHODS: This was a retrospective single-center study. Included were all pediatric patients, treated with trametinib, for an oncologic indication. All patients were evaluated by a pediatric dermatologist, prior to, and during treatment, with documentation of cutaneous findings. RESULT: Twenty patients were enrolled in the study. All patients received treatment with trametinib, of which 6 received a combination of trametinib and dabrafenib (BRAF inhibitor). Out of twenty patients, 18 patients (90%) presented with at least one cutaneous AE. Xerosis and pruritic eczematous changes were the most common (15 patients, 75%), which, in most cases, were tolerable and responded well to the use of emollients and topical corticosteroids. Eleven patients (55%) presented with paronychia which was treated with topical combined corticosteroids antifungals and antibiotics, all with good response. Six patients (30%) presented with acneiform eruption, treated with topical antibiotic, benzoyl peroxide and tretinoin, mostly with good response. Six patients (30%) presented with irreversible hair heterochromia. Reaction grades were reported for cutaneous reactions, most of them were Grade I or II. Only 2 patients reported to have grade III and IV cutaneous reactions: exfoliative dermatitis and erythema multiforme, respectively. Out of 6 patients that received combined treatment of trametinib and dabrafenib one patient had no cutaneous adverse reaction, and one had panniculitis (which was related to dabrafenib). The rest presented relatively mild AE. DISCUSSION: Cutaneous AEs are very common in children and adolescents treated with trametinib, and in most cases are classified as mild. Nevertheless, as this treatment is usually chronic, it is important to inform the patients and their guardians of the potential cutaneous toxicities prior to treatment initiation, and to refer them to a dermatologist for proper management.
OTHR-38. The development of patient-derived models of pediatric brain tumors
Authors: Messiaen Julie , Derweduwe Marleen , Claeys Annelies , Solie Lien , Sciot Raf , Bempt Isabelle Vanden , Devleeschouwer Steven , Van Calenbergh Frank , De Vloo Philippe , Depreitere Bart , Jacobs Sandra , De Smet Frederik 
Published: June 2022

Abstract
Brain tumors are still a major cause of morbidity and mortality in children, despite extensive research. An individualized therapy is warranted to combat the heterogeneity present in these tumors. Therefore, this study aims at developing patient-derived models from both low- and high-grade tumors. As such, the heterogeneity in these tumors can be further characterized and treatment sensitivities can be studied. All pediatric patients diagnosed with a brain tumor at the University Hospitals Leuven and receiving surgical intervention were included after informed consent. If sufficient tumoral material was available, a fresh tumor sample was collected during surgery. The sample was processed into dissociated cells, which were grown in culture in order to develop a patient-derived cell line (PDCL). Biomarker expression using a qPCR array was performed if growth beyond passage 3 was achieved. Established PDCLs were subsequently subjected to genomic and transcriptional profiling and cytotoxicity assays were performed to determine therapeutic sensitivities. Patient-derived xenografts (PDX) are developped in selected cases. 70 patients were included prospectively up until January 2022 and tumoral material was available for 50 of them. In total, 10 PDCLs could be generated (3 high-grade, 7 low-grade tumors), while 9 early cultures (3 high-grade, 6 low-grade) are still being expanded. qPCR and sequencing analysis confirm preservation of driving mutations. The high level of growth failures of the PDCLs can be explained by the high proportion of lower grade tumors included. One PDX model was generated. In conclusion, novel patient-derived models from pediatric brain tumors have been generated, which recapitulate the characteristics of the original tumor. The models are a valuable tool to study these tumors and the responses to different treatments. Further on, we will continue with the development of these models and the study of their therapeutic sensitivities. This will help further improving the understanding of these tumors.
PATH-06. Molecular subgrouping of medulloblastoma via low-depth whole genome bisulfite sequencing
Authors: Thompson Dean , Castle Jemma , Hicks Debbie , Schwalbe Ed , Clifford Steve 
Published: June 2022

Abstract
INTRODUCTION: International consensus recognises four molecular subgroups of medulloblastoma, each with distinct molecular features and clinical outcomes. Assigning molecular subgroup is typically achieved via the Illumina DNA methylation microarray. Given the rapidly-expanding WGS capacity in healthcare institutions, there is an unmet need to develop platform-independent, sequence-based subgrouping assays. Whole genome bisulfite sequencing (WGBS) enables the assessment of genome-wide methylation status at single-base resolution. To date, its routine application for subgroup assignment has been limited, due to high economic cost and sample input requirements. Currently, no optimised pipeline exists that is tailored to handle samples sequenced at low-pass (i.e., &lt;10x depth). METHODOLOGY: Two datasets were utilised; 36 newly sequenced low-depth (10x) and 42 publicly available high-depth (30x) WGBS medulloblastoma samples (n=34), alongside cerebellar control samples (n=8), all with matched DNA methylation microarray data. We applied imputation to low-pass WGBS data, assessed inter-platform correlation and identified molecular subgroups by directly integrating WGBS sample data with pre-existing array-trained models. We developed machine learning WGBS-based classifiers and compared performance against microarray. We optimised reference-free aneuploidy detection with low-pass WGBS and assessed concordance with microarray-derived aneuploidy calls. RESULTS: We optimised a pipeline for processing, QC, and analysis of low-pass WGBS data, suitable for routine molecular subgrouping and reference-free aneuploidy assessment that achieves 96% sensitivity compared to microarray approaches. A pilot study of the suitability of FFPE was promising, and we demonstrate that WGBS data can be integrated into existing array-trained models with high assignment probabilities. Also, WGBS-derived classifier performance measures exceeded microarray-derived classifiers. CONCLUSION: We describe a platform-independent WGBS assay for molecular subgrouping of medulloblastoma. It performs equivalently to array-based methods at increasingly comparable cost ($400 vs $580) and provides a proof-of-concept for routine clinical adoption using standard WGS technology. Finally, the full methylome enabled elucidation of additional biological heterogeneity that has hitherto been inaccessible.
PATH-09. Liquid biopsy of cerebrospinal fluid enables detecting and monitoring ofMYC/MYCN amplification in pediatric CNS malignancies
Authors: Stepien Natalia , Haberler Christine , Furtner-Srajer Julia , Dorfer Christian , Czech Thomas , Lötsch-Gojo Daniela , Mayr Lisa , Baumgartner Alicia , Azizi Amedeo A , Peyrl Andreas , Slavc Irene , Müllauer Leonhard , Madlener Sibylle , Gojo Johannes 
Published: June 2022

Abstract
In the era of precision oncology, rapid molecular profiling as well as continuous monitoring of response to treatment or relapse are of increasing importance. We investigated digital droplet (dd)PCR for cerebrospinal fluid (CSF) derived cell-free (cf)DNA detection as a new method for rapid diagnosing of MYC/MYCN amplification in CNS malignancies - a patient collective with a dismal prognosis. Wet lab validated ddPCR probes for MYC were first investigated in D425 cells, a human medulloblastoma cell line with confirmed MYC amplification. Results of the methylation array of patients with stored CSF/serum samples (-80°C) were screened for patients with MYC/MYCN amplification. Five patients with medulloblastoma (group 3/4) and MYC-amplification and one patient with a diffuse glioma and MYCN-amplification were included in this study. ddPCR was performed on cfDNA isolated from CSF or serum. MYC amplification was detected by ddPCR in 28/33 (85%) CSF samples, with 4/5 negative samples being from one patient, and only one sample showing an unsuccessful analysis. MYC amplification was detectable in all longitudinal samples in 4/5 patients. 1/1 sample from the patient with MYCN amplific ation was positive in ddPCR. We were not able to detect MYC amplification in serum samples. Importantly, a turn-around time of only six hours from sample thawing/acquisition to result generation was easily achievable. Concluding, detection of MYC/MYCN-amplification in CSF by ddPCR is feasible in the clinical setting and allows for a rapid molecular diagnosis. MYC-amplification was constantly detectable in 4/5 patients with longitudinal CSF samples, which is in-line with the tumor burden our patients suffered from. Interestingly, the detectability in the patient’s serum was low, presumably due to the lower percentage of cell-free tumor (ct)DNA in serum when compared to CSF. Our results render ddPCR as a promising tool for bed-side molecular diagnosis and disease monitoring.