Shared Resource Newsletter
Issue 2 - February 2014
The mission of the Markey shared resource facilities is to provide dedicated, high-quality, and state-of-the-art technology and services to enhance the conduct of scientific research at Markey. We continue to strive to be integrated in accomplishing the scientific goals of the Markey Research Programs through service-oriented and discipline-oriented approaches to ensure value-added and impact on Markey science.
Shared resource facilities updates
Free radical biology in cancer
Highlights and announcements: The FRBC hosted Dr. Jay Dunn of the Seahorse Corporation, who conducted a "how-to" workshop on Seahorse technology. Dr. Dunn provided tips and procedures for cell culture preparation and other aspects to maximize the utility of Seahorse results on oxygen consumption rate (mitochondrial function) and extracellular acidification rate (glycolysis). As a result of this workshop, user-friendly software is being assembled to help Seahorse users process their findings in an efficient, informative manner.
Impact and usage: In 2013, the FRBC supported 12 papers, 23 ongoing/funded grants, three investigator-initiated trials, and assistance for nine pilot funding applications. Most notably, MCC investigators heavily used FRBC's Seahorse analysis capability and proteomics facility. From 2012 to 2013, the FRBC saw a 10 percent usage increase among MCC PIs.
Highlights and announcements: Use of the BSTP continues to increase, shown by the following output metrics comparing calendar year 2012 to calendar year 2013:
- Number of patients approached for consent - 533 in 2012; 569 in 2013
- Number of specimens procured - 6,464 in 2012; 8,901 in 2013
- Number of biospecimens dispensed - 1,738 in 2012; 2,701 in 2013
- Number of immunohistochemistry slides stained - 1,354 in 2012; 1,553 in 2013
- Number of digital images analyzed - 446 in 2012; 1,458 in 2013
- Number of specimen records annotated - 6,291 in 2012; 8,770 in 2013
- Number of honest broker projects/services/patients - 14 in 2012; 31 in 2013
- Number of researchers provided protocol support - 24 in 2012; 76 in 2013
Construction of breast and lung tissue microarrays is ongoing. An announcement will be made when they are ready for general use.
The BSTP now has the capacity to perform more advanced services including DNA/RNA extraction, pyrosequencing, laser capture microdissection, and in situ hybridization.
The universal consenting process is being implemented along with modifications to the BSTP banking infrastructure and tissue procurement.
Impact and usage: During 2013, BSTP supported 25 papers and 36 ongoing/funded grants from MCC investigators in research programs.
Highlights and announcements: Faculty informaticians have successfully obtained funding from the Kentucky Lung Cancer Research Program to develop informatics methods to mine electronic data sources for patient eligibility criteria. These efforts should lead to increased enrollments into Markey clinical trials. The project is titled "Automated Identification of Lung Cancer Patients Eligible for Clinical Trial Recruitment" and the investigators are Susanne Arnold, Jeff Talbert, Bin Huang, Tamas Gal and Rama Kavuluru.
The UK Center for Computational Science has agreed to provide funding to assist in recruitment of an additional CRI faculty member to lead development of computational support for bioinformatics studies on UK's high-performance computing cluster.
The CRI continues to enhance LabKey Server as its generalized platform to support secure data collection and data sharing for collaborative studies.
Impact and usage: During 2013, CRI supported 17 papers and 10 investigator-initiated trials from MCC investigators. CRI's data warehousing capabilities continue to be heavily used by MCC investigators.
Highlights and announcements: Faculty biostatisticians have successfully obtained funding from the UK CCTS and the Appalachian Translational Research Network (ATRN) to implement and develop relative survival, genomics and bioinformatics methods on studies in the Appalachian population of Kentucky. The projects are titled "Relative Survival in Appalachian Kentucky" (investigators Bin Huang and Tom Tucker) and "Genomics in Cancer for the Appalachian Population of Kentucky" (investigators Chi Wang, Susanne Arnold, Jinze Liu, Heidi Weiss). Results of relative survival estimates and the genomic database will be available to MCC investigators via the web.
Dr. Li Chen has just implemented her statistical methodological work on attributable fraction function for survival data as an R package, called "paf." This package calculates time-dependent attributable fractions of risk factors for survival outcomes under the Cox proportional hazard model. The availability of the "paf" package will improve the assessment of population impact of risk factors on cancer survival outcomes to facilitate decisions on the priority of community-level cancer prevention and control policies. Contact Dr. Chen if you are interested in applying the "paf" to specific studies.
Drs. Heidi Weiss, Emily Van Meter and Brent Shelton participated in the development of three investigator-initiated trials from the Markey Clinical Trials Boot Camp. These IITs are either in the process of protocol review and approval or are gearing up for trial initiation.
Impact and usage: In 2013, BSRF faculty and staff were listed as co-authors on 27 collaborative publications with MCC members. The BSRF also supported more than 50 external and pilot grant applications and the development or implementation of more than 30 investigator-initiated trials.
Download the previous issue of the SRF newsletter (PDF, 39 KB).
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