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.

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Research Project with Complex Structure Cooperative Agreement (UM1)
Project #
5UM1HG006508-03
Application #
8857145
Study Section
Special Emphasis Panel (ZHG1-HGR-N)
Project Start
Project End
2016-05-31
Budget Start
2015-06-01
Budget End
2016-05-31
Support Year
3
Fiscal Year
2015
Total Cost
$1,242,163
Indirect Cost
$402,237
Name
University of Michigan Ann Arbor
Department
Type
DUNS #
073133571
City
Ann Arbor
State
MI
Country
United States
Zip Code
48109
Roberts, J Scott; Robinson, Jill O; Diamond, Pamela M et al. (2018) Patient understanding of, satisfaction with, and perceived utility of whole-genome sequencing: findings from the MedSeq Project. Genet Med 20:1069-1076
Mankuzhy, Nikhil P; Walling, Emily; Anderson, Bailey et al. (2018) Cryptic ETV6-ABL1 Fusion and MLL2 Truncation Revealed by Integrative Clinical Sequencing in Multiply Relapsed Acute Lymphoblastic Leukemia. J Pediatr Hematol Oncol :
Christensen, Kurt D; Bernhardt, Barbara A; Jarvik, Gail P et al. (2018) Anticipated responses of early adopter genetic specialists and nongenetic specialists to unsolicited genomic secondary findings. Genet Med 20:1186-1195
Prasad, Rahul M; Mody, Rajen J; Myers, George et al. (2018) A genome-wide analysis of colorectal cancer in a child with Noonan syndrome. Pediatr Blood Cancer 65:e27362
Weipert, Caroline M; Ryan, Kerry A; Everett, Jessica N et al. (2018) Physician Experiences and Understanding of Genomic Sequencing in Oncology. J Genet Couns 27:187-196
Wu, Yi-Mi; Cie?lik, Marcin; Lonigro, Robert J et al. (2018) Inactivation of CDK12 Delineates a Distinct Immunogenic Class of Advanced Prostate Cancer. Cell 173:1770-1782.e14
Spector-Bagdady, Kayte; Prince, Anya E R; Yu, Joon-Ho et al. (2018) Analysis of state laws on informed consent for clinical genetic testing in the era of genomic sequencing. Am J Med Genet C Semin Med Genet 178:81-88
Tran, Dustin; Camelo-Piragua, Sandra; Gupta, Avneesh et al. (2017) Loss of CDKN1C in a Recurrent Atypical Teratoid/Rhabdoid Tumor. J Pediatr Hematol Oncol 39:e466-e469
Ryan, Kerry A; De Vries, Raymond G; Uhlmann, Wendy R et al. (2017) Public's Views toward Return of Secondary Results in Genomic Sequencing: It's (Almost) All about the Choice. J Genet Couns 26:1197-1212
Koschmann, Carl; Farooqui, Zishaan; Kasaian, Katayoon et al. (2017) Multi-focal sequencing of a diffuse intrinsic pontine glioma establishes PTEN loss as an early event. NPJ Precis Oncol 1:32

Showing the most recent 10 out of 52 publications