Cancer Research Informatics Shared Resource Facility (CRI SRF)

CRI SRF Overview

The mission of the Cancer Research Informatics (CRI) Shared Resource Facility (SRF) is to develop and sustain biomedical informatics expertise and resources needed to enable and accelerate Markey Cancer Center (MCC) research. In accordance with MCC’s Strategic Plan, CRI efforts are aligned to meet the needs of an aspiring Comprehensive Cancer Center serving Kentucky’s high cancer burden. CRI aims are achieved through exceptional faculty and staff who provide integrated local and statewide cancer data from the Surveillance, Epidemiology and End Results (SEER) Kentucky Cancer Registry (KCR), and develop innovative informatics methods and computational resources widely utilized by all Research Programs and multiple SRFs. CRI provides data and resources to assist the Cancer Prevention and Control Research Program and other partners in cancer prevention and control initiatives throughout the state. 

Specific Aims

  1. Provide the cancer data ecosystem that empowers MCC investigators with integrated datasets from diverse sources ranging from molecular biomarkers to population-based SEER patient data.
  2. Develop artificial intelligence (AI) and high throughput computational methods that elevate MCC Research Program science. 
  3. Provide secure computational resources, biomedical informatics applications and expertise to facilitate interoperability among MCC SRFs and Research Programs. 

The Markey Cancer Center (MCC) Cancer Research Informatics Shared Resource Facility (CRI) facilitates collaborative research among members of the MCC through the optimal application of informatics technologies and methods that maximize the accessibility and usability of data, information, and knowledge. The primary goal of CRI is to provide comprehensive and centralized data acquisition and informatics support that is readily available to cancer center members.

CRI services are broadly categorized into three areas: 

  • Development and use of an integrated data ecosystem
  • Design and implementation of informatics methods
  • Deployment and maintenance of secure computational resources and applications. 

To request services from CRI SRF, please complete the Service Request Form.

Directors and Faculty

Eric durbin

Eric B. Durbin, DrPH, MS
CRI SRF Director

Isaac Hands

Isaac Hands, MPH
CRI SRF Assistant Director

rama kavuluru

Ramakanth Kavuluru, PhD
Associate Professor

Jong Cheol Jeong

Jong Cheol (JC) Jeong, PhD
Assistant Professor

Sally Ellingson

Sally Ellingson, PhD
Assistant Professor

Jenny Gregory

Jenny Gregory, MS
IT Systems Manager

 

 

Staff

Chaney Blue

Chaney Blu
Database Analyst

Justin Levens

Justin Levens
Database Analyst

Lisa Witt

Lisa Witt
Data Management Specialist

Mattingly

F. Scot Mattingly
Data Management Specialist

Max chang

Max Chang
Data Management Specialist

Amir

Amir Elbiheary
Data Management Specialist

Carlee Burton

Carlee Burton
Data Management Specialist

sword

Aaron Sword
Programmer Systems Analyst

Cancer Research Informatics Shared Resource Facility (CRI SRF)
2365 Harrodsburg Road, Suite A230
Lexington KY 40504-3381

The CRI SRF covers operational costs through salary support for personnel from grants and contracts, CCSG funds, as well as state and institutional support from UK. For projects that require significant staff effort, CRI works with investigators to estimate total costs for grant proposals.

What molecular data is available through CRI?

Molecular data at CRI is currently available from 3 different providers:

Providers

Pros

Cons

Foundation Medicine

  • Approved for clinical use (FDA approved)
  • Mutations are detected with higher-depth WES
  • +1,000 cases are linked to KCR 
  • cases are collected from multiple institutes in KY
  • part of data is available via MCC cBioPortal 
  • FM only provides sequencing results for predetermined genes (+300 genes)
  • It doesn’t distinguish germline and somatic mutations 
  • Using hg19/GRCh37 reference genome

ORIEN

  • Providing both germline & somatic mutations
  • Providing total RNAseq and WES
  • +3,000 cases are linked to KCR
  • can request more results from ORIEN network via M2Gen
  • Bioinformatician (e.g., BB SRF) is needed to analyze the data
  • Data has been approved for research only

Caris

  • Approved for clinical use
  • Provide total RNAseq and WES 
  • Provide BAM files
  • Cases have not been linked to KCR data yet (we are working on it)
  • Caris has MCC patient only

 

How do I get access to Molecular Data at CRI?

Molecular data can be accessed in multiple ways depending on the requested study type:

How do I access UK Healthcare data, SEER cancer registry data, or other CRI hosted data sets? 

CRI can help facilitate access to research data sets, please fill out our service request form depending on the source of the data you are requesting:

What data variables are available? 

Please review the data dictionaries at the websites below, depending on the data source:

What computational and data storage resources are available from CRI?

CRI hosts a secure virtual environment, PII secured HPC Cluster, and data storage resources. CRI staff can create servers in the virtual environment and host them for investigators. CRI’s data storage includes over 700TB of storage. CRI hosts a PII secured HPC cluster with five compute nodes including a GPU node.

Please visit the following links for public software and additional information.

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Acknowledge the CRI SRF

Investigators are required to acknowledge the Markey Cancer Center Cancer Research Informatics Shared Resource Facility (CRI SRF) in any publications, research papers and/or grant applications that result from services or CRI member-provided intellectual input or collaborative support received through the CRI SRF. Please use the following statement to acknowledge the CRI SRF. 

“This research was supported by the Cancer Research Informatics Shared Resource Facility of the University of Kentucky Markey Cancer Center (P30CA177558).”

Markey Cancer Center is NCI-designated

The UK Markey Cancer Center was first designated by the National Cancer Institute in 2013 – a distinction that recognizes our extraordinary ability to provide world-class care for our patients. We are the only NCI-designated cancer center in Kentucky and one of only 71 in the nation.

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