Cancer is the second leading cause of death in the United States after heart disease [1] and anticipated to cause 570,000 deaths in 2012 alone. This revised proposal (revisions/progress are italicized) is focused on the clinical sequencing of patients with rare cancers, which are defined as cancers with fewer than 15 per 100,000 individuals per year[2]. Of these diverse rare cancer types, sarcomas make up a significant fraction, including over 50 different subtypes that arise from cells of mesenchymal origin. This is in contrast to the much more common carcinomas, such as cancers of the lung, breast and colon, which arise from epithelial cells. Over the past five years, rapidly evolving technology in nucleic acid sequencing has enabled large scale sequencing projects of cancer genomes and transcriptomes have poised the research community to implement strategies for personalized oncology(3-5). Supporting this approach, in late 2011, the National Academy of Sciences (NAS) released a publication supporting a need to build and utilize a "New Taxonomy of human disease" to facilitate precision medicine(6). "Precision medicine" as defined in this report refers to tailoring of medical treatment to the individual characteristics of each patient. While the NAS projected this to play out over the next decade(s), we believe our proposal is directly aligned with this vision. The Human Genome Project established a high quality reference genome that provided a foundation for subsequent investigations of cancer genomics [3,4]. Over the past five years, rapidly evolving technology in nucleic acid sequencing enabled large scale sequencing projects of cancer genomes and transcriptomes with exhaustive identification of copy number changes, point mutations, rearrangements, insertions/deletions, and gene expression changes [5,6]. However, the clinical application of sequencing for individual patients presents unique challenges and has not yet been fully realized [7]. Project 2 provides the framework for processing tumor and normal biospecimens from sarcoma and other rare cancer patients enrolled on this protocol (See Project 1), sequencing components of their genome (including their "expressed genome"), and nominating "actionable" or otherwise informative gene mutations and germline alterations. We plan to do this with the latest sequencing technology available to us, with high quality standards, in an expedited time frame, and under an efficient cost structure. Fig. 1 provides a general timeline of specimen processing, sequencing and analysis that will be the focus of Project 2. ?Since submission of the first version of this grant, we have established a robust pipeline for processing, tracking, and sequencing samples from advanced cancer patients. In fact, as outlined in Project 1, we have already enrolled and sequenced over 70 patients in our IRB approved clinical sequencing program (MI-ONCOSEQ) based on expansion of our pilot feasibility study published in the November 2011 issue of Science Translational Medicine[8]. Of the over 70 cancer patients enrolled, 10 had sarcoma while 19 had other rare cancers. In the revised application, as recommended, we decreased the scope of the project and rather than taking on advanced cancer of all types, we have focused the application on rare cancer types. Thus, as we are actively engaged in clinical sequencing, we are among the few centers in the country uniquely positioned to "spread this technology", a decisive example being the commitment to develop parallel systems at Ohio State University under the leadership of Dr. Sameek Roychowdhury (formally a Lecturer and trainee in the previous proposal). We propose an "integrative sequencing approach" utilizing whole exome and transcriptome sequencing to provide a relatively comprehensive landscape of the genetic alterations in individual tumor specimens. This approach will enable the detection of point mutations, insertions/deletions, gene fusions and rearrangements, amplifications/deletions, and outlier expressed genes. Furthermore, we will identify certain germline alterations that may also be relevant. The Sequencing Tumor Board (STB) will deliberate on actionable or informative findings and, when appropriate, disclosed to patients.

National Institute of Health (NIH)
National Human Genome Research Institute (NHGRI)
Research Project with Complex Structure Cooperative Agreement (UM1)
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Special Emphasis Panel (ZHG1-HGR-N (J2))
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University of Michigan Ann Arbor
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Udager, Aaron M; Shi, Yang; Tomlins, Scott A et al. (2014) Frequent discordance between ERG gene rearrangement and ERG protein expression in a rapid autopsy cohort of patients with lethal, metastatic, castration-resistant prostate cancer. Prostate 74:1199-208
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McDaniel, Andrew S; Zhai, Yali; Cho, Kathleen R et al. (2014) HRAS mutations are frequent in inverted urothelial neoplasms. Hum Pathol 45:1957-65
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