PubMed · 11433177
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B D MacQueen. Imagining the brain.. https://pubmed.ncbi.nlm.nih.gov/11433177/
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Background: DNA methylation profiling is a tool that provides key support for central nervous system (CNS) tumor classification. However, diagnostically ambiguous pediatric cases may result in discordant outputs across classifiers. We developed MAGIBU, a cross-platform, projection-based framework that embeds individual methylomes into a fixed CNS reference landscape, ranking diagnostic entities by local epigenetic proximity to support clinician-led integrative diagnosis. Methods: As a proof-of-concept, we evaluated MAGIBU in eight morphologically challenging pediatric/juvenile CNS tumors with unresolved diagnoses after institutional and central pathology review. To establish a benchmark in the absence of a definitive histopathological ground truth, a consensus epigenetic reference was defined a priori for cases showing concordant results between the Heidelberg CNS Tumor Methylation Classifier and Methylscape Analysis. Comparisons were also performed with Epigenomic Digital Pathology (EpiDiP). To validate MAGIBU beyond this discovery cohort, performance was assessed at the family level across the CNS methylation spectrum (n = 678, 28 methylation families), on non-array platforms (whole-genome bisulfite sequencing and Oxford Nanopore), and in a focused analysis of the low-grade glioma and diffuse midline glioma compartment across four independent cohorts (n = 670). Results: In the discovery cohort, MAGIBU achieved high concordance with the consensus reference (Cohen's κ = 0.855), outperforming EpiDiP (κ = 0.278), which frequently placed low-grade tumors in proximity to higher-grade reference regions. Conclusions: MAGIBU provides a stable, quantitative differential diagnosis framework that mitigates the limitations of rigid categorical assignments. By leveraging a distance-based proximity metric, it offers a transparent decision-support tool that integrates effectively with clinical, radiological, and molecular data. While performance is inherently dependent on reference atlas composition, MAGIBU represents a robust complementary approach for the diagnostic workup of ambiguous CNS tumors.
Low-frequency 1q21.1 distal deletion and duplication copy number variant (CNV) carriers are predisposed to multiple neurodevelopmental disorders, including schizophrenia, autism and intellectual disability. Human carriers display a high prevalence of micro- and macrocephaly in deletion and duplication carriers, respectively. The underlying brain structural diversity remains largely unknown. We systematically called CNVs in 38 cohorts from the large-scale ENIGMA-CNV collaboration and the UK Biobank and identified 28 1q21.1 distal deletion and 22 duplication carriers and 37,088 non-carriers (48% male) derived from 15 distinct magnetic resonance imaging scanner sites. With standardized methods, we compared subcortical and cortical brain measures (all) and cognitive performance (UK Biobank only) between carrier groups also testing for mediation of brain structure on cognition. We identified positive dosage effects of copy number on intracranial volume (ICV) and total cortical surface area, with the largest effects in frontal and cingulate cortices, and negative dosage effects on caudate and hippocampal volumes. The carriers displayed distinct cognitive deficit profiles in cognitive tasks from the UK Biobank with intermediate decreases in duplication carriers and somewhat larger in deletion carriers-the latter potentially mediated by ICV or cortical surface area. These results shed light on pathobiological mechanisms of neurodevelopmental disorders, by demonstrating gene dose effect on specific brain structures and effect on cognitive function.
Changes in regional blood oxygen level dependent (BOLD) signals in response to brief visual stimuli can exhibit a variety of time-courses. To demonstrate the anatomical distribution of BOLD response shapes during a match to sample task, a formal analysis of their time-courses is presented. An event-related design was used to estimate regional BOLD responses evoked by a cue word, which instructed the subject to attend to the motion or color of an upcoming target, and those evoked by a briefly presented moving target consisting of colored dots. Regional BOLD time-courses were adequately represented by the linear combination of three orthogonal waveforms. BOLD response shapes were then classified using a fuzzy clustering scheme. Three classes (sustained, phasic, and negative) best characterized cue responses. Four classes (sustained, sustained-phasic, phasic, and bi-phasic) best characterized target responses. In certain regions, the shape of the BOLD responses was modulated by the instruction to attend to the target's motion or color. A left frontal and a posterior parietal region showed sustained activity when motion was cued and transient activity when color was cued. A right thalamic and a left lateral occipital region showed sustained activity when color was cued and transient activity when motion was cued. Following the target several regions showed more sustained activity during motion than color trials. In summary, the effect of the task variable was focal following the cue and widespread following the target. We conclude that the temporal patterns of neural activity affected the shape of the BOLD signal.