Cancer cell lines have been widely used for decades to study biological processes driving cancer development, and to identify biomarkers of response to therapeutic agents. Advances in genomic sequencing have made possible large-scale genomic characterizations of collections of cancer cell lines and primary tumors, such as the Cancer Cell Line Encyclopedia (CCLE) and The Cancer Genome Atlas (TCGA). These studies allow for the first time a comprehensive evaluation of the comparability of cancer cell lines and primary tumors on the genomic and proteomic level.
View Article and Find Full Text PDFBackground: Diffuse midline gliomas with histone H3 K27M (H3K27M) mutations occur in early childhood and are marked by an invasive phenotype and global decrease in H3K27me3, an epigenetic mark that regulates differentiation and development. H3K27M mutation timing and effect on early embryonic brain development are not fully characterized.
Results: We analyzed multiple publicly available RNA sequencing datasets to identify differentially expressed genes between H3K27M and non-K27M pediatric gliomas.
Cold Spring Harb Mol Case Stud
October 2019
Gliomatosis peritonei is a rare pathologic finding that is associated with ovarian teratomas and malignant mixed germ cell tumors. The occurrence of gliomatosis as a mature glial implant can impart an improved prognosis to patients with immature ovarian teratoma, making prompt and accurate diagnosis important. We describe a case of recurrent immature teratoma in a 10-yr-old female patient, in which comparative analysis of the RNA sequencing gene expression data from the patient's tumor was used effectively to aid in the diagnosis of gliomatosis peritonei.
View Article and Find Full Text PDFAlthough increasingly recognized as critical to genomic research, genomic data sharing is hindered by an absence of standards regarding timing, patient privacy, use agreement standards, and data characterization and quality. Only after months of identifying, permissioning for use, committing to terms restricting use and sharing, downloading, and assessing quality, is it possible to know whether or not a dataset can be used. In this paper, we evaluate the barriers to data sharing based on the Treehouse experience and offer recommendations for use agreement standards, data characterization and metadata standardization to enhance data sharing and outcomes for all pediatric cancer patients.
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