scholarly journals An Integrated Analysis of Tumor Purity of Common Central Nervous System Tumors in Children Based on Machine Learning Methods

2021 ◽  
Vol 12 ◽  
Author(s):  
Jian Yang ◽  
Jiajia Wang ◽  
Shuaiwei Tian ◽  
Qinhua Wang ◽  
Yang Zhao ◽  
...  
Keyword(s):  
Machine Learning ◽  
Central Nervous System ◽  
Nervous System ◽  
Random Forest ◽  
Cns Tumors ◽  
Integrated Analysis ◽  
Immune Microenvironment ◽  
Cns Tumor ◽  
Tumor Sample ◽  
Tumor Purity

Background: Tumor purity is defined as the proportion of cancer cells in the tumor tissue, and its effects on molecular genetics, the immune microenvironment, and the prognosis of children’s central nervous system (CNS) tumors are under-researched.Methods: We applied random forest machine learning, the InfiniumPurify algorithm, and the ESTIMATE algorithm to estimate the tumor purity of every child’s CNS tumor sample in several published pediatric CNS tumor sample datasets from Gene Expression Omnibus (GEO), aiming to perform an integrated analysis on the tumor purity of children’s CNS tumors.Results: Only the purity of CNS tumors in children based on the random forest (RF) machine learning method was normally distributed. In addition, the children’s CNS tumor purity was associated with primary clinical pathological and molecular indicators. Enrichment analysis of biological pathways related to the purity of medulloblastoma (MB) revealed some classical signaling pathways associated with MB biology and development-related pathways. According to the correlation analysis between MB purity and the immune microenvironment, three immune-related genes, namely, CD8A, CXCR2, and TNFRSF14, were negatively related to MB purity. In contrast, no significant correlation was detected between immunotherapy-associated markers, such as PD-1, PD-L1, and CTLA4; most infiltrating immune cells; and MB purity. In the tumor purity–related survival analysis of MB, ependymoma (EPN), and children’s high-grade glioma, we discovered a minor effect of tumor purity on the survival of the aforementioned pediatric patients with CNS tumors.Conclusion: Our purity pediatric pan-CNS tumor analysis provides a deeper understanding and helps with the clinical management of pediatric CNS tumors.

scholarly journals Co-Deregulated miRNA Signatures in Childhood Central Nervous System Tumors: In Search for Common Tumor miRNA-Related Mechanics

Cancers ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 3028
Author(s):  
George I. Lambrou ◽  
Apostolos Zaravinos ◽  
Maria Braoudaki
Keyword(s):  
Central Nervous System ◽  
Nervous System ◽  
Cns Tumors ◽  
Normal Brain ◽  
Cns Tumor ◽  
Different Types ◽  
Receiver Operator Curve Analysis ◽  
The Central Nervous System ◽  
Tumor Types ◽  
Operator Curve

Despite extensive experimentation on pediatric tumors of the central nervous system (CNS), related to both prognosis, diagnosis and treatment, the understanding of pathogenesis and etiology of the disease remains scarce. MicroRNAs are known to be involved in CNS tumor oncogenesis. We hypothesized that CNS tumors possess commonly deregulated miRNAs across different CNS tumor types. Aim: The current study aims to reveal the co-deregulated miRNAs across different types of pediatric CNS tumors. Materials: A total of 439 CNS tumor samples were collected from both in-house microarray experiments as well as data available in public databases. Diagnoses included medulloblastoma, astrocytoma, ependydoma, cortical dysplasia, glioblastoma, ATRT, germinoma, teratoma, yoc sac tumors, ocular tumors and retinoblastoma. Results: We found miRNAs that were globally up- or down-regulated in the majority of the CNS tumor samples. MiR-376B and miR-372 were co-upregulated, whereas miR-149, miR-214, miR-574, miR-595 and miR-765 among others, were co-downregulated across all CNS tumors. Receiver-operator curve analysis showed that miR-149, miR-214, miR-574, miR-595 and miR765 could distinguish between CNS tumors and normal brain tissue. Conclusions: Our approach could prove significant in the search for global miRNA targets for tumor diagnosis and therapy. To the best of our knowledge, there are no previous reports concerning the present approach.

scholarly journals Long-term medical imaging use in children with central nervous system tumors

PLoS ONE ◽  
2021 ◽  
Vol 16 (4) ◽  
pp. e0248643
Author(s):  
Erin J. A. Bowles ◽  
Diana L. Miglioretti ◽  
Marilyn L. Kwan ◽  
Ute Bartels ◽  
Adam Furst ◽  
...  
Keyword(s):  
Central Nervous System ◽  
Nervous System ◽  
Medical Imaging ◽  
Tumor Grade ◽  
Tumor Diagnosis ◽  
Cns Tumors ◽  
Cns Tumor ◽  
Longitudinal Imaging ◽  
The U.S

Background Children with central nervous system (CNS) tumors undergo frequent imaging for diagnosis and follow-up, but few studies have characterized longitudinal imaging patterns. We described medical imaging in children before and after malignant CNS tumor diagnosis. Procedure We conducted a retrospective cohort study of children aged 0–20 years diagnosed with CNS tumors between 1996–2016 at six U.S. integrated healthcare systems and Ontario, Canada. We collected computed topography (CT), magnetic resonance imaging (MRI), radiography, ultrasound, nuclear medicine examinations from 12 months before through 10 years after CNS diagnosis censoring six months before death or a subsequent cancer diagnosis, disenrollment from the health system, age 21 years, or December 31, 2016. We calculated imaging rates per child per month stratified by modality, country, diagnosis age, calendar year, time since diagnosis, and tumor grade. Results We observed 1,879 children with median four years follow-up post-diagnosis in the U.S. and seven years in Ontario, Canada. During the diagnosis period (±15 days of diagnosis), children averaged 1.10 CTs (95% confidence interval [CI] 1.09–1.13) and 2.14 MRIs (95%CI 2.12–2.16) in the U.S., and 1.67 CTs (95%CI 1.65–1.68) and 1.86 MRIs (95%CI 1.85–1.88) in Ontario. Within one year after diagnosis, 19% of children had ≥5 CTs and 45% had ≥5 MRIs. By nine years after diagnosis, children averaged one MRI and one radiograph per year with little use of other imaging modalities. Conclusions MRI and CT are commonly used for CNS tumor diagnosis, whereas MRI is the primary modality used during surveillance of children with CNS tumors.

Practical Neuropathology Synoptic Reporting for Central Nervous System Tumors

2011 ◽  
Vol 135 (6) ◽  
pp. 789-792
Author(s):  
Mark W. Becher
Keyword(s):  
Central Nervous System ◽  
Nervous System ◽  
Data Extraction ◽  
Tnm Classification ◽  
Cns Tumors ◽  
Imaging Data ◽  
Cns Tumor ◽  
Narrative Report ◽  
Laboratory Information Systems ◽  
Synoptic Reporting

Abstract Context.—Synoptic reporting for central nervous system (CNS) tumors has never been formally addressed, and neuropathologists lack practical templates that they can adapt to their laboratory information system to be compliant with College of American Pathologists (CAP) standards. Objectives.—To provide practical synoptic report templates designed for CNS tumors that allow for easy data extraction and CAP compliance and improve the reporting of CNS tumors. Data Sources.—Review of literature and synoptic report format experience in our practice. Conclusions.—Synoptic reporting of required elements is a recently introduced standard for CNS tumors. It is difficult to use a universal non-CNS tumor synoptic report template for CNS tumors because they are heavily weighted to include items not important or required for CNS tumors, such as margins and the TNM classification system. In addition, the CAP CNS protocol, published in 2008, is an immense comprehensive document that is not conducive to simple inclusion in a narrative report. We describe our experience using a synoptic template for CNS tumors that includes all required elements, is tailored to the practice of neuropathology, and can easily be adapted to other laboratory information systems. Because of the multidisciplinary nature of CNS tumor diagnoses, neuropathologists typically collect clinical, demographic, and imaging data on all CNS tumor cases. These data can readily be entered into a primary synoptic report that could replace our standard narrative report.

scholarly journals PATH-21. CLINICAL UTILITY OF DNA METHYLATION PROFILING FOR DIAGNOSIS OF CHALLENGING CENTRAL NERVOUS SYSTEM TUMORS: THE TORONTO EXPERIENCE

2019 ◽  
Vol 21 (Supplement_6) ◽  
pp. vi147-vi147
Author(s):  
Shirin Karimi ◽  
Jeffrey Zuccato ◽  
Yasin Mamatjan ◽  
Sheila Mansouri ◽  
Suganth Suppiah ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Central Nervous System ◽  
Nervous System ◽  
Clinical Utility ◽  
Cns Tumors ◽  
Cns Tumor ◽  
Dna Methylation Profiling ◽  
Diffuse Gliomas ◽  
Methylation Profiling

Abstract The update on the WHO classification of central nervous system (CNS) tumors incorporated molecular signatures for a more accurate diagnosis. Recently, DKFZ has demonstrated the utility of DNA methylation profiling(MP) for molecular classification of CNS tumors. We performed a prospective clinical study over the last three years to evaluate the clinical utility ofDNA MP on FFPE samples of 66 challenging CNS tumor cases using online DKFZ classifier. Eleven samples were excluded due to low tumor DNA content or low calibration(predictive) scores(CS)< 0.3.DNA MP confirmed the original pathology diagnoses in 15(27%)cases. The integrated molecular diagnoses were changed in 38/55(70%) including establishment of a new diagnostic entity, change in molecular signature and subtyping. TheWHO grades were changed in 16(27%) of the tumors; about two-thirds resulted in upgrading. We detected non-canonical IDH mutations in 9 diffuse gliomas and the CNV plots revealed false positive FISH results for 1p/19q co-deletion in two diffuse gliomas. The CNV plots contributed to the final diagnosis in 40(72%) patients. The molecular subtypes of medulloblastoma, ependymoma and glioblastoma subclasses were determined in 36(65%) cases. Seventy-five percent of cases with confirmation of initial diagnosis or change in molecular diagnosis had CS > 0.5, among which 51% had a CS >0.9. The median and range CS of cases with new diagnostic entity and confirmed cases were 0.86(0.37–0.99) and 0.98(0.42–0.99), respectably. Furthermore, we detected higher CS in IDH-mutant gliomas in comparison to glioblastoma IDH-wild type(P=0.04). We also observed lower CS in mesenchymal glioblastoma in comparison to other subclasses. The MGMT promoter methylation was determined in 17/20(85%) glioblastoma cases. While the DKFZ group established CS of 0.9 as a cut-off for matching to methylation classes, our findings suggest lower threshold values in challenging CNS tumor cases. Our experience indicates clinical utility of MP of challenging CNS tumors as a reliable ancillary diagnostic tool in routine neuropathology practice.

scholarly journals AURKA gene polymorphisms and central nervous system tumor susceptibility in Chinese children

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Yong-Ping Chen ◽  
Li Yuan ◽  
Hui-Ran Lin ◽  
Xiao-Kai Huang ◽  
Ji-Chen Ruan ◽  
...  
Keyword(s):  
Central Nervous System ◽  
Nervous System ◽  
Chinese Children ◽  
Cns Tumors ◽  
Childhood And Adolescence ◽  
Control Analysis ◽  
Central Nervous System Tumor ◽  
Nucleotide Polymorphisms ◽  
Cns Tumor ◽  
Tumor Susceptibility

Abstract Introduction Central nervous system (CNS) tumors comprise 15–20% of all malignancies occurring in childhood and adolescence. Previous researches have shown that overexpression and amplification of the AURKA gene could induce multiple human malignancies, with which the connection of CNS tumor susceptibility has not been extensively studied. Material and methods In this study, we assessed whether and to what extent AURKA gene single nucleotide polymorphisms (SNPs) (rs1047972 C > T, rs2273535 T > A, rs8173 G > C) were associated with CNS tumor susceptibility, based on a case–control analysis in 191 CNS tumor patients and 248 controls. We determined this correlation using odds ratios (ORs) and 95% confidence intervals (CIs). Results AURKA gene rs8173 G > C exhibited a crucial function to CNS tumor susceptibility fall-off (GC/CC vs. GG: adjusted OR = 0.68, 95% CI = 0.46–0.998, P = 0.049). In addition, the combined effect of lowering the risk of developing CNS tumors was more pronounced in carriers with 3 protective genotypes than others (adjusted OR = 0.55, 95% CI = 0.31–0.98, P = 0.044). Further stratification analysis illustrated that the existence of rs8173 GC/CC and three protective genotypes lowered CNS tumor risk in some subgroups. Conclusions Our research suggested that the AURKA gene rs8173 G > C could significantly reduce CNS tumor susceptibility in Chinese children. More functional experiments are needed to explore the role of the AURKA gene rs8173 G > C.

scholarly journals Raised cardiovascular disease mortality after central nervous system tumor diagnosis: analysis of 171,926 patients from UK and USA

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Kai Jin ◽  
Paul M Brennan ◽  
Michael T C Poon ◽  
Cathie L M Sudlow ◽  
Jonine D Figueroa
Keyword(s):  
Cardiovascular Disease ◽  
Central Nervous System ◽  
Nervous System ◽  
General Population ◽  
Cerebrovascular Disease ◽  
Mortality Risk ◽  
Cns Tumors ◽  
Tumor Patients ◽  
Cns Tumor ◽  
Cvd Mortality

Abstract Background Patients with central nervous system (CNS) tumors may be at risk of dying from cardiovascular disease (CVD). We examined CVD mortality risk in patients with different histological subtypes of CNS tumors. Methods We analyzed UK(Wales)-based Secure Anonymized Information Linkage (SAIL) for 8743 CNS tumors patients diagnosed in 2000–2015, and US-based National Cancer Institute’s Surveillance, Epidemiology, and End Results (SEER) for 163,183 patients in 2005–2015. We calculated age-, sex-, and calendar-year-adjusted standardized mortality ratios (SMRs) for CVD comparing CNS tumor patients to Wales and US residents. We used Cox regression models to examine factors associated with CVD mortality among CNS tumor patients. Results CVD was the second leading cause of death for CNS tumor patients in SAIL (UK) and SEER (US). Patients with CNS tumors had higher CVD mortality than the general population (SAIL SMR = 2.64, 95% CI = 2.39–2.90, SEER SMR = 1.38, 95% CI = 1.35–1.42). Malignant CNS tumor patients had over 2-fold higher mortality risk in US and UK cohorts. SMRs for nonmalignant tumors were almost 2-fold higher in SAIL than in SEER. CVD mortality risk particularly cerebrovascular disease was substantially greater in patients diagnosed at age younger than 50 years, and within the first year after their cancer diagnosis (SAIL SMR = 2.98, 95% CI = 2.39–3.66, SEER SMR = 2.14, 95% CI = 2.03–2.25). Age, sex, race/ethnicity in USA, deprivation in UK and no surgery were associated with CVD mortality. Conclusions Patients with CNS tumors had higher risk for CVD mortality, particularly from cerebrovascular disease compared to the general population, supporting further research to improve mortality outcomes.

scholarly journals Incidence trends in pediatric central nervous system tumors in Canada: a 15 years report from Cancer and Young People in Canada (CYP-C) registry

2020 ◽  
Vol 2 (1) ◽  
Author(s):  
Valérie Larouche ◽  
Annie-Kim Toupin ◽  
Benoît Lalonde ◽  
David Simonyan ◽  
Nada Jabado ◽  
...  
Keyword(s):  
Central Nervous System ◽  
Nervous System ◽  
Young People ◽  
Pediatric Patients ◽  
Incidence Rates ◽  
Cns Tumors ◽  
Benign Tumors ◽  
Low Grade ◽  
Age Group ◽  
Cns Tumor

Abstract Background The aim of this study is to present a national surveillance report on pediatric central nervous system (CNS) tumors in Canada during the period between 2001 and 2015. Methods All pediatric patients with a diagnosis of primary CNS tumors were collected by the Cancer in Young People in Canada (CYP-C) surveillance system that includes every patient less than 15 years of age with a tumor seen in one of the 17 pediatric oncology centres in Canada. This registry included malignant and benign CNS tumors. We calculated the age-adjusted incidence rates (AAIRs) per 100 000 person-years for CNS tumors overall and by age group, major histology subgroups, and geographical distribution over the country. Results Overall, 3306 patients less than 15 years old had been diagnosed with a CNS tumor in Canada in 2001–2015 with a 1.23:1 male to female ratio. The overall AAIR is 3.80. The three most frequent groups of tumors were low-grade gliomas (36.4%), high-grade gliomas (22.3%), and embryonal tumors (18.7%) with incidence rates of 1.41, 0.86, and 0.72 per 100 000 person-years, respectively. The incidence rate of pediatric CNS tumors is stable during the period 2001–2015 in Canada and no significant differences were seen between malignant and benign tumors over the country. Conclusions These data represent all the pediatric patients 0–14 years old with a CNS tumor in the Canadian population. Incidence rates by age group, sex, and subgroups of tumors are similar to those seen in the literature.

scholarly journals CBTRUS Statistical Report: Primary Brain and Other Central Nervous System Tumors Diagnosed in the United States in 2014–2018

2021 ◽  
Vol 23 (Supplement_3) ◽  
pp. iii1-iii105
Author(s):  
Quinn T Ostrom ◽  
Gino Cioffi ◽  
Kristin Waite ◽  
Carol Kruchko ◽  
Jill S Barnholtz-Sloan
Keyword(s):  
United States ◽  
Central Nervous System ◽  
Nervous System ◽  
Malignant Tumors ◽  
Relative Survival ◽  
The United States ◽  
Population Based ◽  
Cns Tumors ◽  
Relative Survival Rate ◽  
Cns Tumor

Abstract The Central Brain Tumor Registry of the United States (CBTRUS), in collaboration with the CDC and NCI, is the largest population-based registry focused exclusively on primary brain and other central nervous system (CNS) tumors in the United States (US) and represents the entire US population. This report contains the most up-to-date population-based data on primary brain tumors available and supersedes all previous reports in terms of completeness and accuracy and is the first CBTRUS Report to provide the distribution of molecular markers for selected brain and CNS tumor histologies. All rates are age-adjusted using the 2000 US standard population and presented per 100,000 population. The average annual age-adjusted incidence rate (AAAIR) of all malignant and non-malignant brain and other CNS tumors was 24.25 (Malignant AAAIR=7.06, Non-malignant AAAIR=17.18). This overall rate was higher in females compared to males (26.95 versus 21.35) and non-Hispanics compared to Hispanics (24.68 versus 22.12). The most commonly occurring malignant brain and other CNS tumor was glioblastoma (14.3% of all tumors and 49.1% of malignant tumors), and the most common non-malignant tumor was meningioma (39% of all tumors and 54.5% of non-malignant tumors). Glioblastoma was more common in males, and meningioma was more common in females. In children and adolescents (age 0–19 years), the incidence rate of all primary brain and other CNS tumors was 6.21. An estimated 88,190 new cases of malignant and non-malignant brain and other CNS tumors are expected to be diagnosed in the US population in 2021 (25,690 malignant and 62,500 non-malignant). There were 83,029 deaths attributed to malignant brain and other CNS tumors between 2014 and 2018. This represents an average annual mortality rate of 4.43 per 100,000 and an average of 16,606 deaths per year. The five-year relative survival rate following diagnosis of a malignant brain and other CNS tumor was 66.9%, for a non-malignant brain and other CNS tumors the five-year relative survival rate was 92.1%.

scholarly journals CBTRUS Statistical Report: Primary Brain and Other Central Nervous System Tumors Diagnosed in the United States in 2013–2017

2020 ◽  
Vol 22 (Supplement_1) ◽  
pp. iv1-iv96 ◽  
Author(s):  
Quinn T Ostrom ◽  
Nirav Patil ◽  
Gino Cioffi ◽  
Kristin Waite ◽  
Carol Kruchko ◽  
...  
Keyword(s):  
United States ◽  
Central Nervous System ◽  
Nervous System ◽  
Incidence Rate ◽  
Relative Survival ◽  
The United States ◽  
Population Based ◽  
Cns Tumors ◽  
Cns Tumor ◽  
Incidence And Mortality

Abstract The Central Brain Tumor Registry of the United States (CBTRUS), in collaboration with the Centers for Disease Control (CDC) and National Cancer Institute (NCI), is the largest population-based registry focused exclusively on primary brain and other central nervous system (CNS) tumors in the United States (US) and represents the entire US population. This report contains the most up-to-date population-based data on primary brain tumors (malignant and non-malignant) and supersedes all previous CBTRUS reports in terms of completeness and accuracy. All rates (incidence and mortality) are age-adjusted using the 2000 US standard population and presented per 100,000 population. The average annual age-adjusted incidence rate (AAAIR) of all malignant and non-malignant brain and other CNS tumors was 23.79 (Malignant AAAIR=7.08, non-Malignant AAAIR=16.71). This rate was higher in females compared to males (26.31 versus 21.09), Blacks compared to Whites (23.88 versus 23.83), and non-Hispanics compared to Hispanics (24.23 versus 21.48). The most commonly occurring malignant brain and other CNS tumor was glioblastoma (14.5% of all tumors), and the most common non-malignant tumor was meningioma (38.3% of all tumors). Glioblastoma was more common in males, and meningioma was more common in females. In children and adolescents (age 0-19 years), the incidence rate of all primary brain and other CNS tumors was 6.14. An estimated 83,830 new cases of malignant and non-malignant brain and other CNS tumors are expected to be diagnosed in the US in 2020 (24,970 malignant and 58,860 non-malignant). There were 81,246 deaths attributed to malignant brain and other CNS tumors between 2013 and 2017. This represents an average annual mortality rate of 4.42. The 5-year relative survival rate following diagnosis of a malignant brain and other CNS tumor was 36.0% and for a non-malignant brain and other CNS tumor was 91.7%.

Sign in / Sign up

Export Citation Format

Share Document