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Sydney, Australia

Rush A.,The Kids Research Institute | Battisti R.,The Childrens Hospital Education Research Institute | Barton B.,The Childrens Hospital Education Research Institute | Barton B.,University of Sydney | And 2 more authors.
Journal of Pediatrics | Year: 2015

Objective: To evaluate young adult cancer survivor opinions on whether their biobanked tissue and associated de-identified clinical data obtained during their childhood should require re-consent at the age of majority, when parental consent was originally provided. Study design: Thirty young adults (18-34years old), who were former pediatric oncology patients of The Children's Hospital at Westmead with stored research biospecimens, were recruited. They completed a semistructured interview, which included questions on biobanking re-consent, awareness of biobanked tissue, satisfaction about banked tissue, and independence within the family. Analyses included descriptive and inferential statistics. Results: Sixty percent of participants thought that permission for biobanking should be sought again at adulthood, and the remaining 40% did not think that re-consent was necessary. Seventy percent of participants were unaware of their previously banked tissue, which was dependent upon age at diagnosis. When asked whether they granted permission for their tissue to remain in the biobank, all participants agreed. Conclusions: Although results on whether young adults prefer to re-consent or not for previously biobanked tissue and corresponding clinical data are equivocal, survivors appear to be highly favorable about ongoing biobanking of their childhood specimens for future unspecified research. © 2015 Elsevier Inc. Source


Rush A.,The Kids Research Institute | Battisti R.,The Childrens Hospital Education Research Institute | Barton B.,The Childrens Hospital Education Research Institute | Catchpoole D.,The Childrens Hospital Education Research Institute
The Journal of pediatrics | Year: 2015

OBJECTIVE: To evaluate young adult cancer survivor opinions on whether their biobanked tissue and associated de-identified clinical data obtained during their childhood should require re-consent at the age of majority, when parental consent was originally provided.STUDY DESIGN: Thirty young adults (18-34 years old), who were former pediatric oncology patients of The Children's Hospital at Westmead with stored research biospecimens, were recruited. They completed a semistructured interview, which included questions on biobanking re-consent, awareness of biobanked tissue, satisfaction about banked tissue, and independence within the family. Analyses included descriptive and inferential statistics.RESULTS: Sixty percent of participants thought that permission for biobanking should be sought again at adulthood, and the remaining 40% did not think that re-consent was necessary. Seventy percent of participants were unaware of their previously banked tissue, which was dependent upon age at diagnosis. When asked whether they granted permission for their tissue to remain in the biobank, all participants agreed.CONCLUSIONS: Although results on whether young adults prefer to re-consent or not for previously biobanked tissue and corresponding clinical data are equivocal, survivors appear to be highly favorable about ongoing biobanking of their childhood specimens for future unspecified research. Copyright © 2015 Elsevier Inc. All rights reserved. Source


Chen L.,U.S. National Institutes of Health | Shern J.F.,U.S. National Institutes of Health | Wei J.S.,U.S. National Institutes of Health | Yohe M.E.,U.S. National Institutes of Health | And 8 more authors.
PLoS Genetics | Year: 2015

To infer the subclonality of rhabdomyosarcoma (RMS) and predict the temporal order of genetic events for the tumorigenic process, and to identify novel drivers, we applied a systematic method that takes into account germline and somatic alterations in 44 tumor-normal RMS pairs using deep whole-genome sequencing. Intriguingly, we find that loss of heterozygosity of 11p15.5 and mutations in RAS pathway genes occur early in the evolutionary history of the PAX-fusion-negative-RMS (PFN-RMS) subtype. We discover several early mutations in non-RAS mutated samples and predict them to be drivers in PFN-RMS including recurrent mutation of PKN1. In contrast, we find that PAX-fusion-positive (PFP) subtype tumors have undergone whole-genome duplication in the late stage of cancer evolutionary history and have acquired fewer mutations and subclones than PFN-RMS. Moreover we predict that the PAX3-FOXO1 fusion event occurs earlier than the whole genome duplication. Our findings provide information critical to the understanding of tumorigenesis of RMS. Source


Tafavogh S.,Intelligent Systems Technology, Inc. | Catchpoole D.R.,The Kids Research Institute | Kennedy P.J.,University of Technology, Sydney
BMC Bioinformatics | Year: 2014

Background: Neuroblastoma Tumor (NT) is one of the most aggressive types of infant cancer. Essential to accurate diagnosis and prognosis is cellular quantitative analysis of the tumor. Counting enormous numbers of cells under an optical microscope is error-prone. There is therefore an urgent demand from pathologists for robust and automated cell counting systems. However, the main challenge in developing these systems is the inability of them to distinguish between overlapping cells and single cells, and to split the overlapping cells. We address this challenge in two stages by: 1) distinguishing overlapping cells from single cells using the morphological differences between them such as area, uniformity of diameters and cell concavity; and 2) splitting overlapping cells into single cells. We propose a novel approach by using the dominant concave regions of cells as markers to identify the overlap region. We then find the initial splitting points at the critical points of the concave regions by decomposing the concave regions into their components such as arcs, chords and edges, and the distance between the components is analyzed using the developed seed growing technique. Lastly, a shortest path determination approach is developed to determine the optimum splitting route between two candidate initial splitting points.Results: We compare the cell counting results of our system with those of a pathologist as the ground-truth. We also compare the system with three state-of-the-art methods, and the results of statistical tests show a significant improvement in the performance of our system compared to state-of-the-art methods. The F-measure obtained by our system is 88.70%. To evaluate the generalizability of our algorithm, we apply it to images of follicular lymphoma, which has similar histological regions to NT. Of the algorithms tested, our algorithm obtains the highest F-measure of 92.79%.Conclusion: We develop a novel overlapping cell splitting algorithm to enhance the cellular quantitative analysis of infant neuroblastoma. The performance of the proposed algorithm promises a reliable automated cell counting system for pathology laboratories. Moreover, the high performance obtained by our algorithm for images of follicular lymphoma demonstrates the generalization of the proposed algorithm for cancers with similar histological regions and histological structures. © 2014 Tafavogh et al.; licensee BioMed Central Ltd. Source


Xiong F.,Chongqing Medical University | Garnett S.P.,Institute of Endocrinology and Diabetes | Cowell C.T.,Institute of Endocrinology and Diabetes | Biesheuvel C.,The Kids Research Institute | And 6 more authors.
Public Health Nutrition | Year: 2010

OBJECTIVE: To derive age- and sex-specific reference values for waist circumference (WC) and waist-to-height ratio (WHtR) for Han Chinese children and adolescents and to establish the prevalence of excess central adiposity in our study population. DESIGN: Cross-sectional study of schoolchildren attending randomly selected primary and secondary schools in south-west China in October 2003 and April 2004. Anthropometry was measured using standard procedures. The LMS method was used to construct smoothed WC and WHtR percentile curves. Overweight and obesity were defined by the International Obesity Task Force (IOTF) criteria and the Working Group on Obesity in Children. Excess central adiposity fat was defined by previously published WC cut-points and a WHtR ≥ 0·5. SETTING: Primary and secondary schools in Chongqing, south-west China. SUBJECTS: A total of 7326 (49·2 % boys) Han Chinese students at 5-17 years old. RESULTS: On the basis of the IOTF criteria, 26·4 % of boys were overweight or obese compared with 16·4 % of girls (P < 0·001). WC cut-points identified 31 % of boys and 28 % of girls as having excess central adiposity, whereas using the WHtR criterion, 14·8 % of boys and 5·6 % of girls were identified. Young boys (5-12 years) had a significantly (P < 0·001) higher WHtR than girls. CONCLUSIONS: We have constructed WC and WHtR percentile curves for Han Chinese children and adolescents living in Chongqing. Our measurements were based on a student population with a relatively high rate of overweight and obesity. These data will provide a point of reference for future studies measuring the prevalence of overweight and obesity in China. Source

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