Louisiana Cancer Research Consortium (LCRC) Translational Genomics Core (TGC)
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The Louisiana Cancer Research Consortium (LCRC) Translational Genomics Core (TGC) was initially created as a standard sequencing facility to support the basic research infrastructure of the school of Medicine. With the support of Phases I and II of this COBRE, the LSU School of Medicine and the Stanley S. Scott Cancer Center, the TGC has developed into a state-of-the-art facility capable of developing next generation sequencing (NGS) protocols including whole transcriptome, RNASeq, whole exome sequencing and SNP analysis, and transcriptional profiling. The TGC has served multiple projects through the establishment of service contracts, MTAs and collaborations at the institutional, local and international level. In Phase III, we plan to keep our services up to date and offer a new platform for ChIP-Seq optimization, single-cell sequencing, and single-molecule sequencing. These services will allow us to increase the number of researchers and institutions using our facilities. Additionally, we plan to enter the field of clinical genomics through a partnership with the Translational Genomics Research Institute (TGen), a major national and international player in this field. The construction of a new 424 bed state-of-the-art teaching University Medical Center and a new VA center in New Orleans, just across the street from the LCRC Building (which hosts the TGC), and the renewal of the NCI funded Minority-Based NCORP clinical trials state-wide network, present a unique opportunity for genomics medicine and clinical research in our area. To take advantage of this opportunity we have agreed to develop a CLIA-certified clinical genomics lab in collaboration with TGen. The TGC’s long-term goal is to become the regional genomics reference center serving basic, translational and clinical researchers with state-of-the-art technology, training, and service.
FACILITIES AND OTHER RESOURCES
Contribution to Success: With the support of Phase I and II, the School of Medicine and the Stanley S. Scott Cancer Center the TGC was established in 2008 and since then has served the LSU-HSC scientific community studying the molecular mechanisms and genomic signatures underlying inflammatory and infectious diseases. The TGC has become the site to generate genomic information for researcher from neighboring universities including LSUHSC, Tulane, Xavier and Dillard. In addition, the Core has been instrumental for the establishment of national and international collaborations that would benefit not only our external partners but also our researchers in New Orleans. In addition to the support for the facilities, the COBRE, the LSU Cancer Center, and the School of Medicine have also supported the TGC personnel, including Dr. Zabaleta and Li Li, MD, Core’s Manager. This support has facilitated the creation of genomic research lines all based on human studies and confirmed by in vitro and in vivo approaches. With the support of this COBRE Dr. Zabaleta has helped in the generation of data for major grants including P20MD004817 and 1U54MD008176-01 NIMHD, and has secure local funding through the Louisiana Clinical and Translational Science Center (LACaTS). In addition, this support has enabled the development of infrastructure necessary to provide services from standard to cutting-edge methodologies in inflammation research.
The Dean of the School of Medicine, Steve Nelson, MD, has agreed to continue providing the partial financial support for the TGC facilities now and after the COBRE Phase III ends. Moreover, Dr. Nelson will facilitate the integration of the TGC and other COBRE cores into the research structure of LSUHSC (See letter of Support from Dr. Nelson).
Institutional Commitment to Success: The School of Medicine and the Cancer Center at Louisiana State University Health Sciences Center are committed to the success of TGC as a laboratory that will facilitate the development of translational research in the field of Genomics. The LSU-Cancer Center and the School of Medicine have provided extensive support to obtain and to maintain equipment. After completion of this Phase II of the COBRE, we expect that the TGC will be funded by the user fees (approximately 30%), LSU Cancer Center funds (40%) and School of Medicine funds (30%).
The TGC currently provide services three different services: 1) microarray analysis with the Illumina’s BeadArry Reader which allows the whole genome gene expression analysis of mouse and human RNA. In addition, specific focused arrays (i.e. GoldeGate Genotyping Cancer Panel) are also offered. We are planning to upgrade our BeadArray Reader with the iScan from Illumina which would allow us to do whole genome methylation analysis, GWAS studies, among other techniques requiring highly dense chips; 2) standard DNA sequencing with two ABI 3130xl Genetic Analyzers from Life Technologies. This technology also allows the analysis of DNA fragments, validation of SNPs and mutations and confirmation of CpG methylation status; 3) high throughput sequencing with the Genome Analyzer IIx from Illumina wich allow the deep sequencing of DNA, RNA miRNA, ChIP, and methylated fragments. In addition we offer quality assessment of nucleic acids with the NanoDop (Thermo Scientific) and the Agilent BioAnalyzer 2100 (Agilent). The TGC has also two real- time PCR machines, ABI 7900HT and QuantStudio 12K Flex from Life Technologies, used to confirm any data obtained from the analysis in the sequencing and microarray platforms. The Core has multiple 9700 Thermal Cyclers for 96- and 384-well plates, nucleic acid concentrators, hybridization ovens, Sorval and Eppendorf centrifuges and micro-centrifuges, freezers (-80°C and -20°C) and refrigerators (4°C).
Laboratory: The TGC is located in the 9th floor of the Louisiana Cancer Research Center building at 1700 Tulane Ave. R-934, New Orleans, LA. 70112. Phone (504) 210-2044. It consists of three laboratories, totaling 600 square feet in laboratory numbers 928, 929 and 930. Drs. Zabaleta’s and Miele’s laboratories and offices, are located on the same floor. The laboratories are equipped with benches and full sets of pipettes.
Computers: Each major equipment in the TGC is equipped with Dell Optiplex (755 and GX620) or Precision Computers (690). The laboratory is fully connected to the Internet and the LSUHSC mainframe computers.
The TGC offers services to investigators with approved protocols from the LSUHSC Institutional Biosafety Committee (IBC). External users are required to provide approval from their respective Biosafety committee which is reviewed by LSUHSC’ IBC for approval. LSUHSC has a control plan that provides policies and guidance to protect workers with occupational exposure to blood and other potentially infectious materials. All personnel working in this proposal adhere to these policies, and all have received the Occupational Exposure to bloodborne pathogens Training and completed the Biosafety and Radioactivity Courses. Research-related incidents will be reported immediately to the IBC at LSUHSC. Such incidents include research-related accidents and illnesses, as well as inadvertent release or improper disposal of bio-hazardous materials.
The biohazard substances used in this study require biosafety level one or two (BL1 or 2). These include exposure to nucleic acids from tumor cell lines, bacteria and recombinant DNA, among others. All personnel have taken the LSUHSC on-line Training for Shipping Biological Materials. All personnel are required to use the proper personal protective equipment (PPE) to avoid exposure. The proper handling, transport, and disposal of these biological and chemical materials will be implemented by following the policies, guidelines, and programs established by the IBC at LSUHSC to guarantee the biological safety of the community and the environment.
Biohazard signs are prominently placed to be easily read by all entering the laboratories. Additional biohazard signs are placed on refrigerators, biosafety hoods, and cabinets containing the reagents. Sharps materials, including needles and scalpels, will be discarded immediately into approved sharps disposal containers for biohazard disposal. All non-sharp laboratory materials utilized in experiments with biological will be treated with 1% sodium hypochlorite prior to disposal and placed in boxes containing the international biohazard label.
The Translational Genomics Core (TGC) provides services, infrastructure, experimental design, and data analysis support for genomics and epigenomic studies for researchers in New Orleans and throughout Louisiana. Established in 2008 and expanded in 2010, this Core supports sequencing, SNP analysis, methylation studies, and next-generation sequencing (NGS). The TGC’s long-term goal is to become the regional genomics reference center serving basic, translational and clinical researchers with state-of-the-art technology, training and service. Located at the LSU Cancer Center in the new Louisiana Cancer Research Center Building where researchers from LSUHSC, Tulane Medical Center, Ochsner Medical Center and Xavier University converge to develop cancer-related research, we are uniquely positioned to expand our catchment area for basic and clinical research. Our basic science capabilities have become essential for investigators in our region. TGC also serves as the genomics core for the LSU Cancer Center NCI-funded Gulf South Minority- Based NCI Cooperative Oncology Research Program, an NCI-supported clinical trials network that includes Louisiana and Southern Mississippi. During Phases I and II of this COBRE, the TGC served basic and pre- clinical researchers, working in concert with the Cellular Immunology and Immune Metabolism Core (CIMC) and the Molecular Histopathology and Analytic Microscopy Core (MHAM) to offer COBRE-supported and LSU Cancer Center investigators a complete array of genomics and epigenomics technologies. We established techniques to support a wide range of projects including inflammation and cancer, obesity and inflammatory diseases, SIV infection in macaques, and genetics of neuroendocrine tumors. Another major research focus has been the study of genetic and epigenetic factors that contribute to health disparities among the minority populations of Louisiana. We have active contracts and/or collaborations with the National Cancer Institute – NIH, Stanford University, the Instituto Nacional de Cancerologia in Colombia, the Instituto Nacional de Salud Pública in Mexico and the Universidad Católica del Norte in Chile. During Phase III, we build on the successes of Phases I and II, and expand our services to include advanced research tools such as chromatin structure/function studies (ChIP-Seq) and single-cell NGS. In addition, we plan to develop a CLIA-certified clinical genomics laboratory in partnership with Translational Genomics Research Institute (TGen, Phoenix, AZ), a recognized scientific leader in the clinical application of genomics.
To achieve our goal, we propose the following Specific Aims:
Specific Aim 1. To provide high quality service for our users. TGC personnel constantly strive to improve the quality of our services by staying abreast of the latest technological developments, seeking feedback and input from Core users, implementing new techniques, streamlining existing protocols and SOPs, performing regular preventive maintenance on our equipment, planning for equipment upgrades/updates and exploring ways to improve cost-effectiveness.
Specific Aim 2. To provide continuing education and expert training to interested researchers. We successfully established regular training seminars for our scientific community with vendors representatives and on-site training, and offer the opportunity to acquire hands-on experience in the Core laboratories.
Specific Aim 3. To create a clinical genomics laboratory. The integration of human biospecimens and genomic/epigenomic biomarkers in clinical and translational research projects is becoming increasingly critical to maintain competitiveness. “Genomic Tumor Boards” are becoming standard at major Cancer Centers, and investigational therapeutics is often paired with companion diagnostic biomarkers. To serve these growing needs, we have partnered with TGen, one of the most experienced organizations in human genomics. We will create a dedicated, CLIA-certified human genomics laboratory, and in collaboration with TGen scientists, we plan to develop in-house clinical genomics capabilities, coupled with TGen bioinformatics resources to provide cutting edge resources to our translational and clinical investigators.
LSU’s TGC and TGen will obtain CLIA certification for the NGS laboratory. This will provide a new and expedited path for patient-focused research at TGen-LSUCC (Figure 4). The creation of an internal CLIA laboratory will establish an efficient process to provide patients and their treating physicians with a report generated from study results consistent with appropriate CLIA quality control guidelines. This will remove the time delay and the logistical concerns imposed an external CLIA laboratory. Samples will be shipped to the CLIA laboratory from the clinical collection sites in Louisiana (within the NCORP network) for immediate nucleic acid extraction under CLIA-certified conditions. NGS analysis would be summarized in a report without any need for further validation.
TGC and TGen will meet several milestones to obtain CLIA certification. These include, in order: hiring a laboratory manager, implementing a laboratory management system, complete the laboratory SOP manual, pass audit by a consultant firm, pass site inspection by an accreditation agency, obtain CLIA certification and run tests samples by the already established CLIA laboratory. The equipment necessary for the CLIA lab as planned by the partners is listed under “Budget Justification”. Dr. Zabaleta, TGC Director, will directly supervise the laboratory manager and assure adherence to the planned milestones. Dr. Miele will assist and advice Dr.
Zabaleta in the selection of the laboratory manager, participate directly in the interaction with TGen and connect the TGC with the MB- NCORP leadership team (which he is a part of), to identify clinical trial opportunities that would benefit from the LSU-TGen translational genomics partnership. We estimate that this process will take between 1 and 2 years to complete. The timing for the creation of this CLIA-certified laboratory could not be more favorable. In 2015, the new University Medical Center (UMC), located directly across the street from both the Interim LSU Hospital and the LCRC Building, hosting the TGC, will open. UMC is a 424-bed modern teaching hospital that will provide inpatient services, trauma care, and a cancer program including radiation therapy and a chemotherapy clinic; outpatient surgery; outpatient imaging; and rehabilitation services. Treatment areas are being designed to maximize collaboration with the adjacent Veterans Affairs Medical Center, which will also be open by 2015. UMC will serve as an important referral center for patients from community hospitals, clinics, and organizations throughout the region. As an example of the institutional commitment the LSUHSC Cancer Center is one of 5 sites selected to participate in a genomics-driven clinical trial under the SWOG1400 protocol (Phase II/III Biomarker-Driven Master Protocol for Second Line Therapy Squamous Cell Lung Cancer). In this SWOG protocol, in which biomarker profiles will dictate patient stratification to separate sub-studies with targeted agents. Participation in this trial is a milestone for the LSU Cancer Center and its clinicians. The TGen-LSUCC CLIA-certified laboratory will allow us to design and implement local and regional biomarker-driven discovery studies led by investigators from our region.