Specimen Acquistition and Expression Profiling

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The controlled collection and processing of clinical specimens from patients with myeloid leukemia and myelodysplastic syndrome continues to be a critical activity for the accurate, efficient, and comprehensive acquisition of genomic data required for this program project. Similarly, a repository of quality controlled and standardized tumor gene expression, gene copy number, and genotyping data corresponding to these specimens will continue to aid in elucidating the genomic basis of AMI. Procedural enhancements and operation of microarray analytical platforms in a regulated laboratory environment will further prepare this technology for use in the context of molecular-based clinical trials for leukemia patients. Accordingly, this Core has two Specific Aims: Specific Aim 1: We will collect, store, and process tissue specimens from all patients with a diagnosis of AML and MDS seen at this institution. We will include malignant cell populations from bone marrow aspirates and peripheral blood as well as skin punch biopsy and buccal lavage specimens representing non-malignant cell populations. Serum and plasma will be collected for future proteomic biomarker studies. Specimens will be collected throughout each patient's disease course (initial presentation, remission, relapse) and where appropriate, archival specimens from previous malignancies will be retrieved. Specimens will be processed to cellular RNA, genomic DMA, whole genome amplified DNA, and protein extracts as required for each study. Cellular populations will also be viably frozen for future xenograft studies. Particular attention to specimen procurement (e.g. rapid processing of leukemia cells to preserve transcript profiles) and quality control will be practiced. Specific Aim 2: Using the Affymetrix GeneChip¿ platform, we will generate whole genome expression, copy number, and allelic loss data from all AML specimens collected during this study, under nationally accredited laboratory guidelines. Affymetrix whole genome (U133Plus2) and exonspecific expression arrays will be used to generate quantitative and qualitative transcriptional profiles while whole genome genotyping (500K and 1M SNP) arrays will be used to simultaneously generate germline genotype data, somatic copy number change data, and allelic loss (LOH) data from tumor and non-malignant sample pairs. Emphasis will be place on developing new methods for rapid turnaround.