The controlled collection and processing of clinical specimens from patients with myeloid leukemia and myelodysplastic syndrome continues to be a critical activity forthe accurate, efficient, and comprehensive acquisition of genomic data required for this program project. Similarly, a repository of quality controlled and standardized gene expression, genomic copy number, genotyping, and epigenetic data corresponding to these specimens will continue to aid in elucidating the genomic basis of AML and MDS. Procedural enhancements and operation within a regulated laboratory environment will accelerate the transition of key genomic findings to application in clinical trials. Accordingly, this Core has two Specific Aims:
Specific Aim 1. We will collect, store, and process tissue specimens from patients and families with AML and MDS seen at this institution. We will include malignant cell populations from bone marrow aspirates, peripheral blood, and extramedullary sites 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/refractory disease) and where appropriate, archival specimens from previous malignancies will be retrieved. Specimens will be processed to cellular RNA (mRN/VncRNA), genomic 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 high standards of quality control will be practiced.
Specific Aim 2 : Using microarray platforms, we will generate whole transcriptome expression (mRNA, miRNA), whole genome copy number and genotyping, and whole epigenome DNA methylation data. Affymetrix Exon 1 .OST and miRNA 2.0 arrays will be used to generate quantitative transcriptional profiles. Affymetrix SNP 6.0 arrays will generate genomic copy number, loss of heterozygosity (LOH), and genotype data, lllumina Infinium HumanMethylation450 arrays will generate epigenome-wide DNA methylation data. While massively parallel sequencing approaches will be performed for primary tumor specimens in Projects 1-4, use of these microarray platforms will be concentrated in experiments with multiple conditions (e.g., chemotherapy sensitivity, xenograft studies) and for susceptibility studies (Project 3) to best allocate grant resources.
Core B will continue to provide several functions critical for the success of this Program Project and, ultimately, for the better understanding of the genetic and epigenetic basis of AML. We will continue to accrue a large inventory of patient material and to generate targeted gene expression, genotyping, and epigenetic microarray data for experiments proposed herein, all tracked and maintained by a state ofthe art database. While this growing catalog of patient biospecimens and associated molecular data will be of tremendous use to participants in this Program Project, the resources generated may be leveraged by other investigators focused on acute myeloid leukemias through other, independent initiatives.
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