? CORE B The Cell and Molecular Core (Core B) laboratories, physically located at St. Jude Children?s Research Hospital (SJCRH), includes the central Sample Accessioning laboratory and the Molecular Analysis laboratory for the 3 research projects. Samples (ALL samples, normal blood or bone marrow samples, RNA or DNA) will come to the Sample Accessioning laboratory from multiple sources: the Children?s Oncology Group (COG), Alliance for Clinical Trials in Oncology, Eastern Cooperative Oncology Group (ECOG/ACRIN), MD Anderson, Erasmus University, and SJCRH. Samples are accessioned, labelled, and tracked electronically. ALL cell samples are provided to Project 2 for in vitro drug sensitivity. DNA and RNA samples are sent to the Molecular Analysis laboratory for molecular profiling in support of the Aims of each project, to include single nucleotide polymorphism (SNP) arrays to analyze DNA copy number and SNP genotypes in both germline and ALL cells, whole exome sequencing (WES) of both germline and ALL cells, transcriptome sequencing (RNA-seq) of ALL cells, CpG methylation arrays to analyze ALL cells, and exome SNP arrays to analyze rare coding variants in germline samples. Core B facilitates sample tracking and cross-project data sharing by curation of sample meta-data to a centralized data warehouse, GDBALL (Genomic DataBase for ALL), tracking what assays have been done for all samples, by whom, and where the raw data are. Core B provides retrievals on the status of molecular assays for samples to assess success in meeting milestones for all three projects, set by Core A, and to provide feedback to Project investigators and to the participating cell banks of COG, ECOG, Alliance, MD Anderson, and Erasmus on status of their samples. Core B is responsible for making and tracking data deposits in public databases. By centralizing each of these functions, Core B provides an efficient resource for basic quality control of the genome-wide data for this Center. Core B will ensure that each project generates high quality data for secondary and tertiary data analyses that will be performed by the Bioinformatics and Biostatistics Core (Core C).
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