Occupational outcomes after high-grade or low-grade brain tumors in childhood: A Swedish, nationwide, registry-based study.

BACKGROUND: Survivors of pediatric brain tumors are at high risk of late complications that may affect their daily life in both short- and long-term perspectives. METHODS: In this nationwide registry-based study we explored the occupational outcomes, including employment, sickness or activity compensation and parental leave, in 452 individuals in Sweden, born 1988-1996, and diagnosed with a brain tumor before their 15th birthday. Their results were compared with 2188 matched controls. RESULTS: There were significant differences between cases and controls for all assessed variables. The cases had benefitted from sickness or activity compensation 11 times more often than controls (CI 7.90-15.83; p < 0.001) between 2005 and 2016. Controls were almost three times more likely to have an employment (OR 0.36; CI 0.28-0.47; p < 0.001) and nearly twice as likely to have been on parental leave (OR 0.56; CI 0.39-0.80; p = 0.002). Although cases treated for high-grade tumors typically fared worse than those treated for low-grade tumors, significant differences for all assessed variables were also observed for cases treated for a low-grade tumor compared with controls. CONCLUSIONS: Our findings emphasize the need for follow-up programs for all brain tumor diagnoses, not only those known to be at most risk. This is evident, for example, from the high number of cases who received sickness or activity compensation.

A Study Protocol for Validation and Implementation of Whole-Genome and -Transcriptome Sequencing as a Comprehensive Precision Diagnostic Test in Acute Leukemias.

Background: Whole-genome sequencing (WGS) and whole-transcriptome sequencing (WTS), with the ability to provide comprehensive genomic information, have become the focal point of research interest as novel techniques that can support precision diagnostics in routine clinical care of patients with various cancer types, including hematological malignancies. This national multi-center study, led by Genomic Medicine Sweden, aims to evaluate whether combined application of WGS and WTS (WGTS) is technically feasible and can be implemented as an efficient diagnostic tool in patients with acute lymphoblastic leukemia (ALL) and acute myeloid leukemia (AML). In addition to clinical impact assessment, a health-economic evaluation of such strategy will be performed. Methods and Analysis: The study comprises four phases (i.e., retrospective, prospective, real-time validation, and follow-up) including approximately 700 adult and pediatric Swedish AML and ALL patients. Results of WGS for tumor (90×) and normal/germline (30×) samples as well as WTS for tumors only will be compared to current standard of care diagnostics. Primary study endpoints are diagnostic efficiency and improved diagnostic yield. Secondary endpoints are technical and clinical feasibility for routine implementation, clinical utility, and health-economic impact. Discussion: Data from this national multi-center study will be used to evaluate clinical performance of the integrated WGTS diagnostic workflow compared with standard of care. The study will also elucidate clinical and health-economic impacts of a combined WGTS strategy when implemented in routine clinical care. Clinical Trial Registration: [https://doi.org/10.1186/ISRCTN66987142], identifier [ISRCTN66987142].

Post-Compulsory Education in Teenagers and Young Adults Treated for Brain Tumors in Childhood: A Swedish Nationwide Registry-Based Study.

The risk of late complications after a brain tumor in childhood is high. Both the tumor itself and the treatments give rise to sequelae that affect daily life activities. In this registry study, we explored post-compulsory education, i.e., further education following the nine compulsory years in school, in 452 cases born 1988-1996 and diagnosed with a brain tumor before their fifteenth birthday. They were compared with 2188 individual controls who were not treated for cancer. Significantly fewer teenagers and young adults treated for brain tumors in childhood attended high school or university compared with controls, especially individuals treated for embryonal tumors or optic pathway gliomas. A significantly larger proportion of subjects treated for embryonal tumors and craniopharyngiomas attended folk high schools, a type of post-compulsory school with a more accessible learning environment. For both cases and controls, we observed a positive correlation between parental education levels and attendance in high school and university. In our previous studies we have shown that children treated for brain tumors, as a group, tend to perform worse during their last year of compulsory school compared with their peers, and the current study confirms that these differences remain over time.

Mutational patterns and clonal evolution from diagnosis to relapse in pediatric acute lymphoblastic leukemia.

The mechanisms driving clonal heterogeneity and evolution in relapsed pediatric acute lymphoblastic leukemia (ALL) are not fully understood. We performed whole genome sequencing of samples collected at diagnosis, relapse(s) and remission from 29 Nordic patients. Somatic point mutations and large-scale structural variants were called using individually matched remission samples as controls, and allelic expression of the mutations was assessed in ALL cells using RNA-sequencing. We observed an increased burden of somatic mutations at relapse, compared to diagnosis, and at second relapse compared to first relapse. In addition to 29 known ALL driver genes, of which nine genes carried recurrent protein-coding mutations in our sample set, we identified putative non-protein coding mutations in regulatory regions of seven additional genes that have not previously been described in ALL. Cluster analysis of hundreds of somatic mutations per sample revealed three distinct evolutionary trajectories during ALL progression from diagnosis to relapse. The evolutionary trajectories provide insight into the mutational mechanisms leading relapse in ALL and could offer biomarkers for improved risk prediction in individual patients.

A best practice framework for applying physiologically-based pharmacokinetic modeling to pediatric drug development.

Pediatric physiologically-based pharmacokinetic (PBPK) models have broad application in the drug development process and are being used not only to project doses for clinical trials but increasingly to replace clinical studies. However, the approach has yet to become fully integrated in regulatory submissions. Emerging data support an expanded integration of the PBPK model informed approach in regulatory guidance on pediatrics. Best practice standards are presented for further development through interaction among regulators, industry, and model providers.

Can National Tests from the Last Year of Compulsory School Be Used to Obtain More Detailed Information about Academic Performance in Children Treated for Brain Tumours? A Nationwide, Population-Based Study from Sweden.

Children treated for brain tumours often have late-appearing complications that may affect their school performance. Uneven skill profiles may help reveal late complications that can be compensated for but otherwise remain undetected. We investigated Swedish national school tests of oral, reading and writing skills in the first foreign language (English), the mother tongue (Swedish) and mathematics. Data were obtained from The Swedish Childhood Cancer Registry and Statistics Sweden. The results from 475 children diagnosed with a brain tumour before their 15th birthday and 2197 matched controls showed that children treated for brain tumours evinced more difficulties with national tests than controls in almost all subtests, especially in the subject English, and that they may perform better on oral than written tasks. There were larger differences between female cases and controls than between male cases and controls; age at diagnosis played a significant role for some subtests, whereas tumour grade did not. Missing information from national tests proved to be a strong predictor of poor academic performance. Our results show that regular educational follow-ups, as a complement to neuropsychological follow-ups, are important for all children treated for brain tumours, regardless of sex, age at diagnosis or tumour grade.

Artificial Intelligence and Machine Learning Applied at the Point of Care.

INTRODUCTION: The increasing availability of healthcare data and rapid development of big data analytic methods has opened new avenues for use of Artificial Intelligence (AI)- and Machine Learning (ML)-based technology in medical practice. However, applications at the point of care are still scarce. OBJECTIVE: Review and discuss case studies to understand current capabilities for applying AI/ML in the healthcare setting, and regulatory requirements in the US, Europe and China. METHODS: A targeted narrative literature review of AI/ML based digital tools was performed. Scientific publications (identified in PubMed) and grey literature (identified on the websites of regulatory agencies) were reviewed and analyzed. RESULTS: From the regulatory perspective, AI/ML-based solutions can be considered medical devices (i.e., Software as Medical Device, SaMD). A case series of SaMD is presented. First, tools for monitoring and remote management of chronic diseases are presented. Second, imaging applications for diagnostic support are discussed. Finally, clinical decision support tools to facilitate the choice of treatment and precision dosing are reviewed. While tested and validated algorithms for precision dosing exist, their implementation at the point of care is limited, and their regulatory and commercialization pathway is not clear. Regulatory requirements depend on the level of risk associated with the use of the device in medical practice, and can be classified into administrative (manufacturing and quality control), software-related (design, specification, hazard analysis, architecture, traceability, software risk analysis, cybersecurity, etc.), clinical evidence (including patient perspectives in some cases), non-clinical evidence (dosing validation and biocompatibility/toxicology) and other, such as e.g. benefit-to-risk determination, risk assessment and mitigation. There generally is an alignment between the US and Europe. China additionally requires that the clinical evidence is applicable to the Chinese population and recommends that a third-party central laboratory evaluates the clinical trial results. CONCLUSIONS: The number of promising AI/ML-based technologies is increasing, but few have been implemented widely at the point of care. The need for external validation, implementation logistics, and data exchange and privacy remain the main obstacles.

Inhibitors of Organic Anion-Transporting Polypeptides 1B1 and 1B3: Clinical Relevance and Regulatory Perspective.

Organic anion-transporting polypeptides (OATPs) 1B1 and 1B3 are the primary hepatic transporters responsible for uptake of drugs into the liver and, as such, an area of growing research focus. Currently, evaluation of these transporters as potential mediators of drug-drug interactions (DDIs) is recommended by regulatory agencies worldwide during the drug development process. Despite the growing focus on OATP1B1/1B3 as mediators of DDIs, only 2 drugs are recommended as index inhibitors for use in clinical studies, single-dose rifampin and cyclosporine, each with limitations for the utility of the resulting data. In this study a thorough analysis of the available in vitro and clinical data was conducted to identify drugs that are clinically relevant inhibitors of OATP1B1/1B3 and, from those, to select any novel index inhibitors. A total of 13 drugs and 16 combination products were identified as clinical inhibitors of OATP1B1/1B3, showing significant changes in exposure for sensitive substrates of the transporters, with strong supporting in vitro evidence. Although none of the identified inhibitors qualified as index inhibitors, this study confirmed the utility of cyclosporine and single-dose rifampin as index inhibitors to evaluate the effect of broad, multiple-pathway inhibition and more selective OATP1B1/1B3 inhibition, respectively.

Nationwide, population-based study of school grades in practical and aesthetic subjects of children treated for brain tumour.

BACKGROUND: Children treated for brain tumour (hereafter termed paediatric brain tumour survivors (PBTS)) often need extra support in school because of late-appearing side effects after their treatment. We explored how this group of children perform in the five practical and aesthetic (PRAEST) subjects: home and consumer studies, physical education and health, art, crafts and music. METHODS: In this nationwide population-based study of data from the Swedish Childhood Cancer Registry and Statistics Sweden, we included 475 children born between 1988 and 1996, diagnosed with a brain tumour before their 15th birthday. We compared their grades in PRAEST subjects with those of 2197 matched controls. We also investigated if there were any differences between girls and boys, children diagnosed at different ages, and children with high-grade or low-grade tumours. RESULTS: The odds for failing a subject were two to three times higher for girls treated for a brain tumour compared with their controls in all five PRAEST subjects, whereas there were no significant differences between the boys and their controls in any subject. PBTS had lower average grades from year 9 in all PRAEST subjects, and girls differed from their controls in all five subjects, while boys differed in physical education and health and music. PBTS treated for high-grade tumours neither did have significantly different average grades nor did they fail a subject to a significantly higher extent than PBTS treated for low-grade tumours. CONCLUSIONS: Children treated for a brain tumour, especially girls, are at risk of lower average grades or failing PRAEST subjects. All children treated for brain tumour may need extra support as these subjects are important for their well-being and future skills.

A nationwide, population-based study of school grades, delayed graduation, and qualification for school years 10-12, in children with brain tumors in Sweden.

BACKGROUND: As many as 95.7% of children diagnosed with a brain tumor will experience persistent late effects as adults. These include difficulties with general executive functions, lower IQ, and mental fatigue, which may negatively affect school performance. METHODS: Through the Swedish Childhood Cancer Registry, we identified 475 children born between 1988 and 1996, diagnosed with a brain tumor before their 15th birthday. School grades in "Swedish," "mathematics," and "English," if their graduation was delayed, and qualification for school years 10-12 were compared with 2197 matched controls. Furthermore, we checked for interaction effects between sex and age at diagnosis, and possible effects of tumor grade (high or low) as well as parents' education. RESULTS: Children treated for a brain tumor performed worse in the subjects compared to controls and also had delayed graduation to a greater extent. Fewer children treated for a brain tumor than controls qualified for school years 10-12. Children treated at a young age, especially females, and children whose parents have low education seem to be at particular risk. Unexpectedly, there were no differences in outcomes between survivors with high- and low-grade tumors. CONCLUSIONS: It is important that schools provide regular pedagogical assessment and individualized support to meet the different needs of children treated for a brain tumor. Children treated for low-grade tumors do not perform better than children treated for high-grade tumors, despite the lighter treatment, and hence require the same attention and support.

Transcriptome sequencing in pediatric acute lymphoblastic leukemia identifies fusion genes associated with distinct DNA methylation profiles.

BACKGROUND: Structural chromosomal rearrangements that lead to expressed fusion genes are a hallmark of acute lymphoblastic leukemia (ALL). In this study, we performed transcriptome sequencing of 134 primary ALL patient samples to comprehensively detect fusion transcripts. METHODS: We combined fusion gene detection with genome-wide DNA methylation analysis, gene expression profiling, and targeted sequencing to determine molecular signatures of emerging ALL subtypes. RESULTS: We identified 64 unique fusion events distributed among 80 individual patients, of which over 50% have not previously been reported in ALL. Although the majority of the fusion genes were found only in a single patient, we identified several recurrent fusion gene families defined by promiscuous fusion gene partners, such as ETV6, RUNX1, PAX5, and ZNF384, or recurrent fusion genes, such as DUX4-IGH. Our data show that patients harboring these fusion genes displayed characteristic genome-wide DNA methylation and gene expression signatures in addition to distinct patterns in single nucleotide variants and recurrent copy number alterations. CONCLUSION: Our study delineates the fusion gene landscape in pediatric ALL, including both known and novel fusion genes, and highlights fusion gene families with shared molecular etiologies, which may provide additional information for prognosis and therapeutic options in the future.

Affected Aspects Regarding Literacy and Numeracy in Children Treated for Brain Tumors.

The aim of this study was to investigate the test results of reading speed, reading comprehension, word comprehension, spelling, basic arithmetic skills, and number sense (intuitive understanding of numbers) by children treated for brain tumors. This is a retrospective study based on medical records, including standardized academic tests. In the years of 2010 to 2014, all children in the area of Stockholm between 7 and 18 years (IQ <70) who had no major linguistic or motor difficulties after they had undergone treatment for brain tumors were offered a special education assessment one year after treatment, at school start, or the year before a transition from one stage to another. Our results indicate that children treated for a brain tumor are at risk of having difficulties in spelling, reading speed, and arithmetic and that the test performance may decline over years in arithmetic and spelling. Children diagnosed at age 0 to 6 years may need extra tutoring at school start, especially in basic arithmetic skills. In both reading and mathematics, many children perform better on tests focused on understanding than on tests focused on speed. Continuous special needs assessments including different aspects of literacy and numeracy, are important for understanding each child's specific needs.

Deep targeted sequencing in pediatric acute lymphoblastic leukemia unveils distinct mutational patterns between genetic subtypes and novel relapse-associated genes.

To characterize the mutational patterns of acute lymphoblastic leukemia (ALL) we performed deep next generation sequencing of 872 cancer genes in 172 diagnostic and 24 relapse samples from 172 pediatric ALL patients. We found an overall greater mutational burden and more driver mutations in T-cell ALL (T-ALL) patients compared to B-cell precursor ALL (BCP-ALL) patients. In addition, the majority of the mutations in T-ALL had occurred in the original leukemic clone, while most of the mutations in BCP-ALL were subclonal. BCP-ALL patients carrying any of the recurrent translocations ETV6-RUNX1, BCR-ABL or TCF3-PBX1 harbored few mutations in driver genes compared to other BCP-ALL patients. Specifically in BCP-ALL, we identified ATRX as a novel putative driver gene and uncovered an association between somatic mutations in the Notch signaling pathway at ALL diagnosis and increased risk of relapse. Furthermore, we identified EP300, ARID1A and SH2B3 as relapse-associated genes. The genes highlighted in our study were frequently involved in epigenetic regulation, associated with germline susceptibility to ALL, and present in minor subclones at diagnosis that became dominant at relapse. We observed a high degree of clonal heterogeneity and evolution between diagnosis and relapse in both BCP-ALL and T-ALL, which could have implications for the treatment efficiency.

Hormone Replacement Therapy Associated White Blood Cell DNA Methylation and Gene Expression are Associated With Within-Pair Differences of Body Adiposity and Bone Mass.

The loss of estrogen during menopause causes changes in the female body, with wide-ranging effects on health. Estrogen-containing hormone replacement therapy (HRT) leads to a relief of typical menopausal symptoms, benefits bone and muscle health, and is associated with tissue-specific gene expression profiles. As gene expression is controlled by epigenetic factors (including DNA methylation), many of which are environmentally sensitive, it is plausible that at least part of the HRT-associated gene expression is due to changes in DNA methylation profile. We investigated genome-wide DNA methylation and gene expression patterns of white blood cells (WBCs) and their associations with body composition, including muscle and bone measures of monozygotic (MZ) female twin pairs discordant for HRT. We identified 7,855 nominally significant differentially methylated regions (DMRs) associated with 4,044 genes. Of the genes with DMRs, five (ACBA1, CCL5, FASLG, PPP2R2B, and UHRF1) were also differentially expressed. All have been previously associated with HRT or estrogenic regulation, but not with HRT-associated DNA methylation. All five genes were associated with bone mineral content (BMC), and ABCA1, FASLG, and UHRF1 were also associated with body adiposity. Our study is the first to show that HRT associates with genome-wide DNA methylation alterations in WBCs. Moreover, we show that five differentially expressed genes with DMRs associate with clinical measures, including body fat percentage, lean body mass, bone mass, and blood lipids. Our results indicate that at least part of the known beneficial HRT effects on body composition and bone mass may be regulated by DNA methylation associated alterations in gene expression in circulating WBCs.

The mutational landscape in pediatric acute lymphoblastic leukemia deciphered by whole genome sequencing.

Genomic characterization of pediatric acute lymphoblastic leukemia (ALL) has identified distinct patterns of genes and pathways altered in patients with well-defined genetic aberrations. To extend the spectrum of known somatic variants in ALL, we performed whole genome and transcriptome sequencing of three B-cell precursor patients, of which one carried the t(12;21)ETV6-RUNX1 translocation and two lacked a known primary genetic aberration, and one T-ALL patient. We found that each patient had a unique genome, with a combination of well-known and previously undetected genomic aberrations. By targeted sequencing in 168 patients, we identified KMT2D and KIF1B as novel putative driver genes. We also identified a putative regulatory non-coding variant that coincided with overexpression of the growth factor MDK. Our results contribute to an increased understanding of the biological mechanisms that lead to ALL and suggest that regulatory variants may be more important for cancer development than recognized to date. The heterogeneity of the genetic aberrations in ALL renders whole genome sequencing particularly well suited for analysis of somatic variants in both research and diagnostic applications.

Towards quantitation of the effects of renal impairment and probenecid inhibition on kidney uptake and efflux transporters, using physiologically based pharmacokinetic modelling and simulations.

BACKGROUND AND OBJECTIVES: The kidney is a major drug-eliminating organ. Renal impairment or concomitant use of transporter inhibitors may decrease active secretion and increase exposure to a drug that is a substrate of kidney secretory transporters. However, prediction of the effects of patient factors on kidney transporters remains challenging because of the multiplicity of transporters and the lack of understanding of their abundance and specificity. The objective of this study was to use physiologically based pharmacokinetic (PBPK) modelling to evaluate the effects of patient factors on kidney transporters. METHODS: Models for three renally cleared drugs (oseltamivir carboxylate, cidofovir and cefuroxime) were developed using a general PBPK platform, with the contributions of net basolateral uptake transport (T up,b) and apical efflux transport (T eff,a) being specifically defined. RESULTS AND CONCLUSION: We demonstrated the practical use of PBPK models to: (1) define transporter-mediated renal secretion, using plasma and urine data; (2) inform a change in the system-dependent parameter (≥10-fold reduction in the functional 'proximal tubule cells per gram kidney') in severe renal impairment that is responsible for the decreased secretory transport activities of test drugs; (3) derive an in vivo, plasma unbound inhibition constant of T up,b by probenecid (≤1 µM), based on observed drug interaction data; and (4) suggest a plausible mechanism of probenecid preferentially inhibiting T up,b in order to alleviate cidofovir-induced nephrotoxicity.

Accurate detection of subclonal single nucleotide variants in whole genome amplified and pooled cancer samples using HaloPlex target enrichment.

BACKGROUND: Target enrichment and resequencing is a widely used approach for identification of cancer genes and genetic variants associated with diseases. Although cost effective compared to whole genome sequencing, analysis of many samples constitutes a significant cost, which could be reduced by pooling samples before capture. Another limitation to the number of cancer samples that can be analyzed is often the amount of available tumor DNA. We evaluated the performance of whole genome amplified DNA and the power to detect subclonal somatic single nucleotide variants in non-indexed pools of cancer samples using the HaloPlex technology for target enrichment and next generation sequencing. RESULTS: We captured a set of 1528 putative somatic single nucleotide variants and germline SNPs, which were identified by whole genome sequencing, with the HaloPlex technology and sequenced to a depth of 792-1752. We found that the allele fractions of the analyzed variants are well preserved during whole genome amplification and that capture specificity or variant calling is not affected. We detected a large majority of the known single nucleotide variants present uniquely in one sample with allele fractions as low as 0.1 in non-indexed pools of up to ten samples. We also identified and experimentally validated six novel variants in the samples included in the pools. CONCLUSION: Our work demonstrates that whole genome amplified DNA can be used for target enrichment equally well as genomic DNA and that accurate variant detection is possible in non-indexed pools of cancer samples. These findings show that analysis of a large number of samples is feasible at low cost, even when only small amounts of DNA is available, and thereby significantly increases the chances of indentifying recurrent mutations in cancer samples.

Genome-wide signatures of differential DNA methylation in pediatric acute lymphoblastic leukemia.

BACKGROUND: Although aberrant DNA methylation has been observed previously in acute lymphoblastic leukemia (ALL), the patterns of differential methylation have not been comprehensively determined in all subtypes of ALL on a genome-wide scale. The relationship between DNA methylation, cytogenetic background, drug resistance and relapse in ALL is poorly understood. RESULTS: We surveyed the DNA methylation levels of 435,941 CpG sites in samples from 764 children at diagnosis of ALL and from 27 children at relapse. This survey uncovered four characteristic methylation signatures. First, compared with control blood cells, the methylomes of ALL cells shared 9,406 predominantly hypermethylated CpG sites, independent of cytogenetic background. Second, each cytogenetic subtype of ALL displayed a unique set of hyper- and hypomethylated CpG sites. The CpG sites that constituted these two signatures differed in their functional genomic enrichment to regions with marks of active or repressed chromatin. Third, we identified subtype-specific differential methylation in promoter and enhancer regions that were strongly correlated with gene expression. Fourth, a set of 6,612 CpG sites was predominantly hypermethylated in ALL cells at relapse, compared with matched samples at diagnosis. Analysis of relapse-free survival identified CpG sites with subtype-specific differential methylation that divided the patients into different risk groups, depending on their methylation status. CONCLUSIONS: Our results suggest an important biological role for DNA methylation in the differences between ALL subtypes and in their clinical outcome after treatment.