Translational Research Center

At our Translational Research Center, Bench (basic) research is conducted in the laboratory at a benchtop. Translational studies move bench findings from the laboratory to the bedside. Translational studies can be based on patient populations or patient specimens, and they may or may not be linked to clinical trials. There are many types of translational study designs, but all translational research has the same goal, to bridge the gap between science and medicine.

About Our Translational Research Center

Our lab-based translational studies are designed so that results can be quickly applied to improve treatments and tests for cancer. Clinical specimens obtained under approved protocols are examined in benchtop studies, the results of which may guide the design of preclinical (animal) or early clinical trials. We also run multicenter clinical trials that include translational correlative studies to identify molecular or immunologic markers of clinical outcome. Thus our research moves back and forth from bench to bedside and back again.

This dynamic, interactive approach has allowed our scientists to lay the foundation for therapeutic discoveries that receive worldwide attention.For example, JWCI’s Translational Molecular Medicine Department, led by Dr. Dave Hoon, has been a driving force behind the recent developments in targeted (personalized) therapies for melanoma. His group has developed a specialized blood test to detect the BRAF mutation that is found in many melanomas. This mutation is now the basis for an effective targeted therapy called vermurafenib (Zelboraf) that recently received FDA approval for treatment of advanced melanoma. Dr. Hoon’s group is currently developing another biomarker that may become the basis for additional therapy to complement vermurafenib. Some of the recent results of these studies are now published and are available as a resource for other physicians around the world.

Meanwhile, our Translational Immunology Department, is studying populations of patients with enhanced immunity to melanocytes (the autoimmune disease vitiligo) and examining archived specimens of tumor tissue. Using these translational tools to identify key pathways of the immune response to melanoma may provide insights to fighting cancer in general.

Translational Molecular Medicine

The key focus of the Department of Translational Molecular Medicine is the development and translational application of transcriptomic/ genomic/ epigenomic biomarkers as diagnostic, prognostic and predictive tools in patients with solid tumors, particularly melanoma, breast cancer, prostate cancer, and gastrointestinal tract cancers. For the past 20 years, our emphasis has been on occult tumor cell detection in lymph nodes (Sentinel Lymph Node) and blood circulating tumor cells (CTC). This highly productive group has published more than 330 peer-reviewed studies and reviews. Over the last 25 years, the Department has trained many clinical and laboratory postdoctoral scientists for successful careers in translational molecular medicine at academic institutions in the United States, Japan, the Netherlands, Argentina and China.

The Department has developed novel tests to detect biomarkers of tumor-related gene expression (mRNA), genomic aberrations and epigenomic changes (gene promoter methylation, noncoding repeat sequences, microRNA). Combinations of these biomarkers represent signatures for the presence and progression of cancer. Molecular RNA/DNA biomarkers are used to detect occult metastatic tumor cells in tumor-draining lymph nodes (sentinel lymph nodes) and body fluids (blood) of cancer patients; results are applied to improve staging of disease and to develop prognostic indicators of cancer outcome.

The Department has pioneered novel assays to detect microRNA and DNA biomarkers of cell-free circulating nucleic-acid biomarkers detected in blood from patients with various solid tumors. These biomarkers, which reflect changes in microsatellite instability (loss of heterozygosity), methylation, mutation, microRNA and/or DNA integrity, are being used to determine prognosis and predict response to treatment. These studies have involved assessment of serial bleed specimens obtained in international Phase II/III multicenter clinical trials, a logistical feat made possible by the Department’s rigorously controlled specimen-collection and assay protocols.

The Department also is assessing aberrant cancer and immune molecular pathways to identify potential molecular targets for development of cancer therapeutics. Mechanisms of epigenomic and SNP (single nucleotide polymorphism)-related regulatory events in abnormal gene expression are being studied in various solid tumor types.

The Department has strong collaborative programs in translational studies developed with global and industry partners. We have received awards from the National Institutes of Health/National Cancer Institute (R01, P01, R33), the Dr. Miriam and Sheldon G. Adelson Medical Research Foundation (AMRF), Department of Defense, USA, California Breast Cancer Research Program, the Associates of Breast and Prostate Cancer Studies (ABCs), the Avon Foundation, Melanoma Research Alliance, the Leslie and Susan Gonda (Goldschmied) Foundation, Ruth Weil Family Fund and Susan G. Komen Breast Cancer for the Cure.

The Department’s national and international reach is also shown by active collaborations with Broad Institute MGH (Boston), Genome Institute Singapore (Singapore), National University (Singapore), Fudan University Shanghai Medical College, Huashan Hospital’s Neurosurgery Center (Shanghai), Tel Aviv University’s Cancer Biology Research Center (Israel), the Technion, Haifa (Israel), Keio University, Department of Surgery (Tokyo), Leiden University Medical Center (Netherlands), MD Anderson (Houston), City of Hope Department of Immunoregulation (Duarte, CA).

We are highly focused on developing quantitative translational oncology tools to improve management of solid tumor cancer patients. Discoveries made in molecular studies are rapidly translated for application at the bedside. We have partnered with biotech and pharmaceutical companies in developing treatment protocols and new molecular oncology approaches, the results of which may increase overall survival and eventually expedite development of a cure for patients with solid tumor cancers.

Postdoctoral Lab-Based Translational Molecular Medicine Fellowship

As pioneers in translational studies on “liquid biopsies” involving circulating tumor cells in multiple types of solid tumors, the fellowship program also consists of studying epigenetic mechanisms regulating solid tumor as well as pharmacogenomics and immunogenomic based prediction of response to therapy.

Learn more about this fellowship
DNA strand

Sequencing Center

The John Wayne Cancer Institute Sequencing Center is an Illumina Propel-Certified Service Provider, one of a few select laboratories in a collaborative service partnership with Illumina that have demonstrated proficiency in next generation sequencing at the highest industry standard. We provide sequencing services to both internal and external researchers and welcome opportunities to discuss with you how we can meet your specific research needs.

 

 

 

 

 

 

 

From library preparation to producing high quality sequencing data, we offer a variety of sequencing services to meet today’s fast-paced research environment.

Human Whole Genome
Whole genome sequencing service includes sample QC, library preparation, and deep coverage sequencing that can be scaled according to the needs of the project.

Human and Mouse Exome
Exome enrichment focuses on the coding regions of the genome and is a cost-effective alternative to whole genome sequencing. Exome sequencing captures 50 Mbp of coding exonic regions with high specificity and coverage.  

RNA-seq
Analyzing the transcriptome with mRNA-focused sequencing provides researchers with information to characterize gene expression, gene fusions, alternative splicing, and novel transcripts. Standard coverage ranges from ~20-50 million reads and can be scaled to meet specific project objectives.

Targeted Resequencing and Custom Enrichment
Isolating genomic regions of interest with targeted gene enrichment panels allows for cost-effective, focused detection of germline and somatic mutations. Pre-defined cancer panels cover over 300 cancer-related genes with high specificity and deep coverage. Custom gene panels can also be designed to meet specific project objectives.

OMNI-ATAC-Seq
OMNI-ATAC-Seq is a new and improved assay designed to decrease background noise generated by mitochondrial DNA by ~20% from the original ATAC-Seq method.  Explore chromatin accessibility and identify open/closed regions of DNA with only 50k cells. Standard coverage from ~50 million reads and can be scaled to meet project objectives.

miRNA-seq
Extraction-free direct assay of 2,083 miRNA from plasma, serum, FFPE, and cell lines.  Low-input requirements make this assay ideal for precious specimens. Standard coverage is ~1 million reads per sample.  

ChIP-seq
Analyze interactions between protein and DNA to identify binding-sites for transcription factors and other proteins. Standard coverage from ~20-50 million reads per cell line and can be scaled to meet project objectives.

EPIC 850k Methylation array
Quantitatively interrogate DNA methylation level for >850K CpG sites from a variety of specimen sources, including FFPE.

We can also sequence your pre-made Illumina-compatible libraries. The NextSeq 550 and MiSeq are priced on a per run basis.

Illumina NextSeq 550
High output mode can generate up to 400 million reads per run with single read sequencing and up to 800 million reads per run with paired-end sequencing and offers rapid turnaround time.  Mid output mode can generate up to 130 million reads per run with single read sequencing and up to 260 million reads per run with paired-end sequencing.

Illumina MiSeq
Ideal for small scale projects with rapid turnaround time. In a single run the MiSeq can generate 12-15 million reads with single read sequencing or 24-30 million reads with paired-end sequencing.

Our Sequencing Center is an Illumina Propel-Certified Service Provider, one of a few select laboratories in a collaborative service partnership with Illumina that have demonstrated proficiency in next generation sequencing at the highest industry standard.

The John Wayne Cancer Institute Sequencing Center is equipped with an Illumina NextSeq 550 with two run modes allowing for flexibility and scalability to support a broad range of project sizes and designs. Ideal for whole genome or exome with larger sample sizes, the High Output Mode on the NextSeq 550 can process up 120 Gb of high quality sequence. For smaller scale projects or targeted sequencing applications, the Mid Output Mode on the NextSeq 550 can produce up to 39 Gb of high quality sequencing in as little as 26 hours.

The Sequencing Center is also equipped with an Illumina MiSeq to offer flexibility and fast turnaround time for sequencing small projects, small genomes, or targeted sequencing panels. The MiSeq also offers longer reads lengths (300 bp) and is fully compatible with all libraries that can be sequenced on the Illumina NextSeq.

Pricing for next generation sequencing will depend on the number of samples to be processed, read depth, read length, and the run mode desired. To learn more about our sequencing services or schedule a consultation to discuss your research project and sequencing needs please email us at hoonD@jwci.org.

Quality of starting material is a key factor in producing optimal sequencing data and results. The following are general sample requirement guidelines for our library preparation and sequencing services.

General Guidelines
DNA and/or RNA specimens should be suspended in water, low TE, or Qiagen elution buffer and stored in low binding 1.5 ml tubes. The top and side of each tube should be clearly labeled with the sample name, date, institution and/or PI’s initials. The sample submission form along with the appropriate quality analysis results as detailed below are required for sample submission.

DNA Sample Requirements
Please provide sample analysis results measured by Qubit, Agilent 2100 Bioanalyzer, or Agilent 2200 TapeStation in one or multiple forms. NanoDrop quantification alone is not recommended. For genomic DNA please submit a photograph of the sample separated by agarose gel electrophoresis (1-2%) to confirm the integrity and quality of the sample. Quality genomic DNA should appear as a dark, tight, high molecular weight band with no smearing below 20 kb.

Whole Genome Sequencing
Purity: OD260/280 = 1.8-2.0 without degradation and RNA contamination
Concentration: ≥30ng/µl
DNA amount for each library: ≥2.5µg high quality genomic DNA

Whole Exome Sequencing
Purity: OD260/280 = 1.8-2.0 without degradation and RNA contamination
Concentration: ≥30ng/µl
DNA amount for each library: ≥400 ng high quality genomic DNA or ≥2.5 µg FFPE DNA

RNA Sample Requirements
Please provide analysis results of the RNA sample using at least two of the following methods: Qubit, NanoDrop, Agilent 2100 Bioanalyzer, and Agilent 2200 TapeStation. Please purify samples, avoiding contamination by polycarbonate, protein and exonuclease.

mRNA Sequencing
Purity: OD260/280 = 1.8-2.0; OD260/230 >1.8; RIN ≥ 8 for high quality total RNA or %DV200 ≥ 30% for FFPE total RNA
Concentration: ≥20ng/µl
Total RNA amount for each library: ≥500 ng of high quality total RNA or ≥300 ng of FFPE total RNA

All samples must pass our quality control requirements before they can be processed for sequencing. Please contact us for more detailed sample submission requirements specific to your project.

Specimen Repository

We maintain a unique bank of frozen or paraffin-embedded melanoma specimens collected since 1971. This specimen repository is linked to our historical database, an information system that was begun in 1971 by Dr. Donald Morton and Dr. Robert Elashoff, and now contains records for more than 14,600 melanoma patients.

The specimen repository includes sera, lymphocytes and tumor cells, tumor tissues and normal tissues, and cell lines.

There are more than a million vials of sera and almost 150,000 vials of lymphocytes for cellular assays. Serial serum samples obtained from patients during regular clinic visits or according to multicenter trial protocols enable the immediate study of the relationship of tumor markers to the course of disease. Many specimens are linked to extended follow-up data and clinical outcomes, making them invaluable for correlative studies. The annotated specimen bank and electronic clinical database are used in tandem for prospective and retrospective investigations of prognosis, recurrence, and tumor biology. All specimens and linked data are coded to preserve donor confidentiality.

In accordance with the National Cancer Institute’s resource sharing policies, JWCI is committed to making its melanoma specimen repository available for collaborative studies with external researchers. Investigators interested in obtaining specimens should email us a brief description of the type and number of specimens needed. If specimens are available, we will ask for a research proposal detailing the proposed use of the specimens and justification for sample size. Proposals are reviewed based on clinical and scientific import, preliminary data, statistical support showing feasibility, and demonstration that use of this unique and limited resource is crucial to the research proposed.

Evidence of funding is not required to submit a proposal but must be obtained before specimens can be released.

In addition, the authorization for use of specimens is not considered final until the applicant signs a specimen use agreement to comply with standard procedures for data analysis, data confidentiality, authorship, and intellectual property sharing. Finally, evidence of IRB approval for the proposal is required before release of samples.

Requests for specimen amounts that would exhaust the repository supply or curtail specimen access by John Wayne Cancer Institute investigators will not be honored. Specimens are provided for research purposes only. Specimens and their products shall not be sold (or distributed free of charge) to third parties.