The Glioma Molecular Diagnostic Initiative: Characterizing Brain Tumor Data

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The Neuro-Oncology Branch (NOB) of the National Cancer Institute (NCI) for the past six years has been collecting and characterizing nearly one thousand gliomas of every grade and histopathological class (oligodendrogliomas, astrocytomas, ependymomas) under a multi-institutional study conceived of, written by and chaired by H. Fine (NABTC protocol 01-07). This study is broadly termed the Glioma Molecular Diagnostic Initiative (GMDI), and was designed to obtain a large amount of molecular data on DNA and RNA of freshly collected tumor samples that were collected, processed and analyzed in a standardized fashion to allow for large-scale cross sample analysis. Moreover, the sample collection is accompanied by careful and prospective clinical data acquisition, allowing an unprecedented wealth of matched molecular and clinical data permitting a wide variety of analyses. The effort has been accompanied by a similarly extensive collaborative effort between the NOB and the NCI Center for Bioinformatics to create a data warehouse and user-friendly cross-data platform bioinformatics tool shed for GMDI data analyses known as REMBRANDT. The resultant public database is nearly unprecedented, not only in oncology, but in all of molecular medicine and is a testament to what is possible within the intramural program and how it can impact on the overall national cancer research enterprise.GMDI has accrued a total of 268 fresh frozen tumors in the retrospective phase (all from the Henry Ford Hospital, without germline DNA) and 670 fresh frozen tumors in the prospective phase (from a variety of institutions) for a total of 938 tumors representing all glioma types and grades. Of these, 756 (80.5%) have been processed and hybridized to the Genechip Human Genome U133 Plus 2.0 Expression Arrays, while 729 (77.7%) have been hybridized to the Affymetrix Genechip Human Mapping 100K arrays for genomic characterization. Realizing that a majority of patients who come to us do not have obtainable fresh frozen tissue we spent over a year developing and optimizing a methodology that allows us to extract high quality DNA from FFPE enabling genomic analyses of these patients. To date, one hundred and sixty five such cases have been collected, and of these, 117 (71%) have been genomically characterized using Affymetrix Genechip Human Mapping 250K StyI arrays and our FFPE DNA restoration protocol. *Cell Lines: In addition to characterizing the samples from patients enrolled in GMDI, the microarray group has generated genomic-scale analyses of the many human and canine glioma initiating cells/glioma stem cells (GIC/GSC) lines, as well as many canine and murine normal neural stem cell (NSC) lines produced in laboratory. This characterization is both at the primary cell level (including evolution through passages) as well as evaluation of the impact of different treatments (differentiation, animal passages, drug treatment, etc) on the biological behavior of the cells. In all, 202 expression arrays have been completed (from human, mouse and canine sources) as well as 40 human SNP arrays.The Neuro-Oncology Branch (NOB) of the National Cancer Institute (NCI) for the past six years has been collecting and characterizing nearly one thousand gliomas of every grade and histopathological class (oligodendrogliomas, astrocytomas, ependymomas) under a multi-institutional study conceived of, written by and chaired by H. Fine (NABTC protocol 01-07). This study is broadly termed the Glioma Molecular Diagnostic Initiative (GMDI), and was designed to obtain a large amount of molecular data on DNA and RNA of freshly collected tumor samples that were collected, processed and analyzed in a standardized fashion to allow for large-scale cross sample analysis. Moreover, the sample collection is accompanied by careful and prospective clinical data acquisition, allowing an unprecedented wealth of matched molecular and clinical data permitting a wide variety of analyses. The effort has been accompanied by a similarly extensive collaborative effort between the NOB and the NCI Center for Bioinformatics to create a data warehouse and user-friendly cross-data platform bioinformatics tool shed for GMDI data analyses known as REMBRANDT. The resultant public database is nearly unprecedented, not only in oncology, but in all of molecular medicine and is a testament to what is possible within the intramural program and how it can impact on the overall national cancer research enterprise.GMDI has accrued a total of 268 fresh frozen tumors in the retrospective phase (all from the Henry Ford Hospital, without germline DNA) and 670 fresh frozen tumors in the prospective phase (from a variety of institutions) for a total of 938 tumors representing all glioma types and grades. Of these, 756 (80.5%) have been processed and hybridized to the Genechip Human Genome U133 Plus 2.0 Expression Arrays, while 729 (77.7%) have been hybridized to the Affymetrix Genechip Human Mapping 100K arrays for genomic characterization. Realizing that a majority of patients who come to us do not have obtainable fresh frozen tissue we spent over a year developing and optimizing a methodology that allows us to extract high quality DNA from FFPE enabling genomic analyses of these patients. To date, one hundred and sixty five such cases have been collected, and of these, 117 (71%) have been genomically characterized using Affymetrix Genechip Human Mapping 250K StyI arrays and our FFPE DNA restoration protocol. *Cell Lines: In addition to characterizing the samples from patients enrolled in GMDI, the microarray group has generated genomic-scale analyses of the many human and canine glioma initiating cells/glioma stem cells (GIC/GSC) lines, as well as many canine and murine normal neural stem cell (NSC) lines produced in laboratory. This characterization is both at the primary cell level (including evolution through passages) as well as evaluation of the impact of different treatments (differentiation, animal passages, drug treatment, etc) on the biological behavior of the cells. In all, 202 expression arrays have been completed (from human, mouse and canine sources) as well as 40 human SNP arrays.