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Background:We have recently demonstrated that expression profiling is a more accurate and objective method to classify gliomas than histology. Similar to most expression profiling studies, our experiments were performed using fresh frozen (FF) glioma samples whereas most archival samples are fixed in formalin and embedded in paraffin (FFPE). Identification of the same, expression-based intrinsic subtypes in FFPE-stored samples would enable validation of the prognostic value of these subtypes on these archival samples. In this study, we have therefore determined whether the intrinsic subtypes identified using FF material can be reproduced in FFPE-stored samples.Methods:We have performed expression profiling on 55 paired FF-FFPE glioma samples using HU133 plus 2.0 arrays (FF) and Exon 1.0 ST arrays (FFPE). The median time in paraffin of the FFPE samples was 14.1 years (range 6.6-26.4 years).Results:In general, the correlation between FF and FFPE expression in a single sample was poor. We then selected the most variable probe sets per gene (n=17 583), and of these, the 5000 most variable probe sets on FFPE expression profiles. This unsupervised selection resulted in a better concordance (R2=0.54) between expression of FF and FFPE samples. Importantly, this probe set selection resulted in a correct assignment of 87% of FFPE samples into one of seven intrinsic subtypes identified using FF samples. Assignment to the same molecular cluster as the paired FF tissue was not correlated to time in paraffin.Conclusion:We are the first to examine a large cohort of paired FF and FFPE samples. We show that expression data from FFPE material can be used to assign samples to intrinsic molecular subtypes identified using FF material. This assignment allows the use of archival material, including material derived from large-randomised clinical trials, to determine the predictive and/or prognostic value of 'intrinsic glioma subtypes' on Exon arrays. This would enable clinicians to provide patients with an objective and accurate diagnosis and prognosis, and a personalised treatment strategy. [ABSTRACT FROM AUTHOR]

In this article we analyse diary reports concerning childhood symptoms of illness, these data are part of a larger study with other types of measurements on childhood asthma. The children are followed for three years and the diaries are updated, by the parents, on a daily basis. Here we focus on the methodological implications of analysing such data. We investigate two ways of representing the data and explore which tools are applicable given both representations. The first representation relies on proper alignment and point by point comparison of the signals. The second approach takes into account combinations of symptoms on a day by day basis and boils down to the analysis of counts. In the present case both methods are well applicable. However, more generally, when symptom episodes are occurring more at random locations in time, a point by point comparison becomes less applicable and shape based approaches will fail to come up with satisfactory results. In such cases, pattern based methods will be of much greater use. The pattern based representation focuses on reoccurring patterns and ignores ordering in time. With this representation we stratify the data on the level of years, so that possibly yearly differences can still be detected., Competing Interests: The authors have declared that no competing interests exist.

Background: Surgery for sagittal synostosis aims at correction of skull shape and restoration of growth potential. Small cranial volume is associated with raised intracranial pressure (ICP). Although many techniques have been described, information on postoperative volume related to early and late remodeling is lacking., Methods: Between 2004 and 2008, a total of 95 patients were collected who underwent either early extended strip craniectomy or late total cranial remodeling according to age of presentation. Volume was measured on three-dimensional (3D) photogrammetry. Volume measurements were related to cranial index (CI), head circumference (HCsd), and signs of raised ICP. In a small subset of patients, volume measurements on 3D photogrammetry were assessed for inter- and intrarater reliability and compared to 3D computed tomography (CT)., Results: Volume was increased in all patients before and after surgery compared to normative values. Postoperatively, late total cranial remodeling resulted in a slightly larger volume than early extended strip craniectomy. Volume measurements showed a good correlation with HCsd (0.67) and a poor relationship with CI (0.13). Headache occurred more frequently in patients with a lower cranial volume. Although papilledema and reoperation showed the same trend, the numbers were too small for statistical analysis. Reproducibility of volume measurements on 3D photogrammetry was high, as was the correlation with measurements on CT., Conclusion: Late total cranial remodeling results in a larger postoperative volume, as measured on 3D photogrammetry, than extended strip craniectomy. Clinical signs of raised ICP occur more frequently in patients with a smaller volume. To measure volume, 3D photogrammetry is a good alternative to CT., (Copyright © 2016. Published by Elsevier Ltd.)

Object: Craniosynostosis syndromes are characterized by prematurely fused skull sutures, however, less is known about skull base synchondroses. This study evaluates how foramen magnum (FM) size, and closure of its intra-occipital synchondroses (IOS) differ between patients with different craniosynostosis syndromes and control subjects; and whether this correlates to ventriculomegaly and/or Chiari malformation type I (CMI), intracranial disturbances often described in these patients., Methods: Surface area and anterior-posterior (A-P) diameter were measured in 175 3D-CT scans of 113 craniosynostosis patients, and in 53 controls (0-10 years old). Scans were aligned in a 3D multiplane-platform. The frontal and occipital horn ratio was used as an indicator of ventricular volume, and the occurrence of CMI was recorded. Synchondroses were studied in scans with a slice thickness ≤1.25 mm. A generalized linear mixed model and a repeated measures ordinal logistic regression model were used to study differences., Results: At birth, patients with craniosynostosis syndromes have a smaller FM than controls (p < 0.05). This is not related to the presence of CMI (p = 0.36). In Crouzon-Pfeiffer patients the anterior and posterior IOS fused prematurely (p < 0.01), and in Apert patients only the posterior IOS fused prematurely (p = 0.028)., Conclusion: The FM is smaller in patients with craniosynostosis syndromes than in controls, and is already smaller at birth. In addition to the timing of IOS closure, other factors may influence FM size., (Copyright © 2015 European Association for Cranio-Maxillo-Facial Surgery. Published by Elsevier Ltd. All rights reserved.)

Objective: Patients with craniosynostosis syndromes are at risk of increased intracranial pressure (ICP) and Chiari I malformation (CMI), caused by a combination of restricted skull growth, venous hypertension, obstructive sleep apnea (OSA), and an overproduction or insufficient resorption of cerebrospinal fluid. This study evaluates whether craniosynostosis patients with CMI have an imbalance between cerebellar volume (CV) and posterior fossa volume (PFV), that is, an overcrowded posterior fossa., Methods: Volumes were measured in 3D-SPGR T1-weighted MR scans of 28 'not-operated' craniosynostosis patients (mean age: 4.0 years; range: 0-14), 85 'operated' craniosynostosis patients (mean age: 8.0 years; range: 1-18), and 34 control subjects (mean age: 5.4 years; range: 0-15). Volumes and CV/PFV ratios were compared between the operated and not-operated craniosynostosis patients, between the individual craniosynostosis syndromes and controls, and between craniosynostosis patients with and without CMI. Data were logarithmically transformed and studied with analysis of covariance (ANCOVA)., Results: The CV, PFV, and CV/PFV ratios of not-operated craniosynostosis patients and operated craniosynostosis patients were similar to those of the control subjects. None of the individual syndromes was associated with a restricted PFV. However, craniosynostosis patients with CMI had a significantly higher CV/PFV ratio than the control group (0.77 vs. 0.75; p = 0.008). The range of CV/PFV ratios for craniosynostosis patients with CMI, however, did not exceed the normal range., Conclusion: Volumes and CV/PFV ratio cannot predict which craniosynostosis patients are more prone to developing CMI than others. Treatment should focus on the skull vault and other contributing factors to increased ICP, including OSA and venous hypertension., (Copyright © 2015 European Association for Cranio-Maxillo-Facial Surgery. Published by Elsevier Ltd. All rights reserved.)

Three distinct immature T-cell acute lymphoblastic leukemia entities have been described including cases that express an early T-cell precursor immunophenotype or expression profile, immature MEF2C-dysregulated T-cell acute lymphoblastic leukemia cluster cases based on gene expression analysis (immature cluster) and cases that retain non-rearranged TRG@ loci. Early T-cell precursor acute lymphoblastic leukemia cases exclusively overlap with immature cluster samples based on the expression of early T-cell precursor acute lymphoblastic leukemia signature genes, indicating that both are featuring a single disease entity. Patients lacking TRG@ rearrangements represent only 40% of immature cluster cases, but no further evidence was found to suggest that cases with absence of bi-allelic TRG@ deletions reflect a distinct and even more immature disease entity. Immature cluster/early T-cell precursor acute lymphoblastic leukemia cases are strongly enriched for genes expressed in hematopoietic stem cells as well as genes expressed in normal early thymocyte progenitor or double negative-2A T-cell subsets. Identification of early T-cell precursor acute lymphoblastic leukemia cases solely by defined immunophenotypic criteria strongly underestimates the number of cases that have a corresponding gene signature. However, early T-cell precursor acute lymphoblastic leukemia samples correlate best with a CD1 negative, CD4 and CD8 double negative immunophenotype with expression of CD34 and/or myeloid markers CD13 or CD33. Unlike various other studies, immature cluster/early T-cell precursor acute lymphoblastic leukemia patients treated on the COALL-97 protocol did not have an overall inferior outcome, and demonstrated equal sensitivity levels to most conventional therapeutic drugs compared to other pediatric T-cell acute lymphoblastic leukemia patients.

Purpose: The long-term follow-up results from the EORTC-26951 trial showed that the addition of procarbazine, CCNU, and vincristine (PCV) after radiotherapy increases survival in anaplastic oligodendrogliomas/oligoastrocytomas (AOD/AOA). However, some patients appeared to benefit more from PCV treatment than others., Experimental Design: We conducted genome-wide methylation profiling of 115 samples included in the EORTC-26951 trial and extracted the CpG island hypermethylated phenotype (CIMP) and MGMT promoter methylation (MGMT-STP27) status., Results: We first show that methylation profiling can be conducted on archival tissues with a performance that is similar to snap-frozen tissue samples. We then conducted methylation profiling on EORTC-26951 clinical trial samples. Univariate analysis indicated that CIMP+ or MGMT-STP27 methylated tumors had an improved survival compared with CIMP- and/or MGMT-STP27 unmethylated tumors [median overall survival (OS), 1.05 vs. 6.46 years and 1.06 vs. 3.8 years, both P < 0.0001 for CIMP and MGMT-STP27 status, respectively]. Multivariable analysis indicates that CIMP and MGMT-STP27 are significant prognostic factors for survival in presence of age, sex, performance score, and review diagnosis in the model. CIMP+ and MGMT-STP27 methylated tumors showed a clear benefit from adjuvant PCV chemotherapy: the median OS of CIMP+ samples in the RT and RT-PCV arms was 3.27 and 9.51 years, respectively (P = 0.0033); for MGMT-STP27 methylated samples, it was 1.98 and 8.65 years. There was no such benefit for CIMP- or for MGMT-STP27 unmethylated tumors. MGMT-STP27 status remained significant in an interaction test (P = 0.003). Statistical analysis of microarray (SAM) identified 259 novel CpGs associated with treatment response., Conclusions: MGMT-STP27 may be used to guide treatment decisions in this tumor type., (©2013 AACR.)

The output of many instruments can be modeled as a convolution of an impulse response and a series of sharp spikes. Deconvolution considers the inverse problem: estimate the input spike train from an observed (noisy) output signal. We approach this task as a linear inverse problem, solved using penalized regression. We propose the use of an L(0) penalty and compare it with the more common L(2) and L(1) penalties. In all cases a simple and iterative weighted regression procedure can be used. The model is extended with a smooth component to handle drifting baselines. Application to three different data sets shows excellent results., (Copyright © 2011 Elsevier B.V. All rights reserved.)