Core B - Bioinformatics Research Resource. The objectives of this Research Resource (Core) are as follows: provide bioinformatics capabilities to support the proposed Research Projects, to enable data sharing, and to provide the capacity to link with the BETRNet Coordination Center. This Core will also address timely sharing of data, including data on the availability of biospecimens at the Research Center, and their submission for centralized data collection at the Coordinating Center. The Core B investigators will work closely with the Project 1 investigators to choose a panel of candidate genes that will be studied in larger sets of samples at the protein level using tissue microarrays in Aim 2. A smaller subset of these genes would then be further selected to be part of a screening strategy to guide tissue biopsy collection in patients, and so we seek candidate genes that can be expected to perform well at discriminating high-grade dysplasia in this ultimate task. In addition, the Core B investigators will work closely with the Project 2 investigators to support statistical analyses for the validation of candidate peptides on purified protein targets and cell lines engineered to overexpress these targets, including T-tests or ANOVAs, and to support the study design for the Phase 1 clinical studies of the peptide panel. Moreover, the Core B investigators will work closely with the Core C investigators to validate the panel of peptides on endoscopically resected specimens of esophageal mucosa by comparing the log-transformed intensity measurements between the different histological classifications (squamous, metaplasia, low-grade dysplasia (LGD), high-grade dysplasia (HGD), and adenocarcinoma) using 1-way ANOVAs and painwise comparisons between the two higher-grade categories (HGD, adenocarcinoma).

Agency
National Institute of Health (NIH)
Type
Specialized Center--Cooperative Agreements (U54)
Project #
5U54CA163059-04
Application #
8724436
Study Section
Special Emphasis Panel (ZCA1)
Project Start
Project End
Budget Start
Budget End
Support Year
4
Fiscal Year
2014
Total Cost
Indirect Cost
Name
University of Michigan Ann Arbor
Department
Type
DUNS #
City
Ann Arbor
State
MI
Country
United States
Zip Code
48109
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Joshi, Bishnu P; Wang, Thomas D (2016) Gastrointestinal imaging in 2015: Emerging trends in endoscopic imaging. Nat Rev Gastroenterol Hepatol 13:72-3
Joshi, Bishnu P; Zhou, Juan; Pant, Asha et al. (2016) Design and Synthesis of Near-Infrared Peptide for in Vivo Molecular Imaging of HER2. Bioconjug Chem 27:481-94
Zhou, Quan; Li, Zhao; Zhou, Juan et al. (2016) In vivo photoacoustic tomography of EGFR overexpressed in hepatocellular carcinoma mouse xenograft. Photoacoustics 4:43-54
Zhou, Juan; Joshi, Bishnu P; Duan, Xiyu et al. (2015) EGFR Overexpressed in Colonic Neoplasia Can be Detected on Wide-Field Endoscopic Imaging. Clin Transl Gastroenterol 6:e101
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Jiang, Hui; Salzman, Julia (2015) A penalized likelihood approach for robust estimation of isoform expression. Stat Interface 8:437-445

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