SS05 :
Post-genomic medical decision making in cancer
Monday, July 14, 2014, 10:30 a.m. - 12:25 p.m.
Room: Ballroom C
Rachel Karchin, Johns Hopkins University, United States
Melissa Cline, UC Santa Cruz, United States
We are now in an era of unprecedented accumulation of data about the molecular basis of cancer. DNA sequencing of large cohorts of cancer patients has great potential to contribute to medical diagnostics, prognostics, and selection of individualized therapeutic regimens. We believe that bioinformatics analysis is essential for interpretation of the very large and high-dimensional data sets that are now emerging from the Cancer Genome Atlas, International Cancer Genome Consortium, TARGET, PCGP and others. The computational biology and genomics community has an opportunity to make a real difference in outcomes for cancer patients. However, much work remains if we are to truly benefit from this data explosion. Key challenges include:
Accuracy: For genomics to be useful in a clinical setting, the genomic aberrations that are present in the tumor DNA must be detected, and the aberrations that are called as present must be real. This applies to structural rearrangements and indels as well as point mutations.
Identifying actionable aberrations: Given the mutations in a patient's DNA, one must distinguish causative mutations from those of no likely consequence, and must identify the driver mutations that contribute to tumorigenesis. Moreover, given the patient's mutations, one must accurately predict the course of therapy that would most benefit the patient.
Evaluating treatment progression: As treatment progresses, the clinician must continually evaluate the patient for signs of treatment response, resistance and metastasis. Genomics offers the hope for detecting response to treatment earlier, since molecular changes generally presage phenotypic changes. However, detecting molecular responses that are both real and significant is still an open field of research.
Cost versus value: One important factor in clinical decision making is the cost of the care to the patient. At this time, patients cannot assume that their insurance will cover the full cost of genomic testing. In order for testing to be of value to cancer patients, the patients and their doctors must be able to interpret the results.
The purpose of this session is to help bioinformatics scientists understand better the current state of genomics and clinical decision making in cancer. We will have talks from physician scientists who are using genomics in their own decision making or who have taken a leadership role in making genomics-based decision making available to oncologists and their patients. We will discuss the needs of those in the clinical world, provide suggestions as to how computational scientists can get involved, and address some challenges involved when clinicians and computationalists work together.
10:40 AM - 11:10 PM
Benefits of Genomic Medicine: What to Tell the Patient.Head and neck squamous cell carcinoma (HNSCC) encompasses a diverse group of malignancies originating in the oral cavity, oropharynx, larynx and hypopharynx. Due to the heterogeneous nature of HNSCC, discovering a "silver bullet" or single critical biomarker to treat HNSCC, such as imatinib for EGFR-mutated chronic myeloid leukemia (CML), is unlikely. Many HNSCC patients now have the option for tumor profiling, using deep exome sequencing on panels of known driver genes. For patients with substantial financial resources, whole exome sequencing (WES) and whole genome sequencing (WGS) are possible. But, assuming that the patient lives long enough to receive such results, are the benefits to survival and quality of life worth the cost? This presentation will discuss application, potential benefits and current limitations of genomic technology in HNSCC care from perspectives of a practicing physician and patients.
Confirmed speaker:   Dr. Christine Chung
11:10 PM - 11:40 PM
Evaluating Tumor Exome Sequencing in the Oncology Clinic: Lessons from the BASIC3 Study.Modern sequencing technologies can provide genome-scale data to oncologists and geneticists caring for cancer patients. But how well does sequencing technology aid patient care? The BASIC3 (Baylor Advancing Sequencing into Childhood Cancer Care) study is assessing the clinical impact of incorporating CLIA-certified exome sequencing into the care of children with newly diagnosed solid tumors. Tissue samples are submitted for clinical exome sequencing, with the results deposited into the patients' medical records and disclosed to families by their oncologist and a genetic counselor. Oncologists are surveyed on treatment options in the event of recurrence before and after receiving sequencing results. Patients will be followed for two years. This presentation will discuss the clinical utility of exome sequencing, and the response of doctors and patients' families to genetic testing.
Confirmed speaker:   Dr. Donald W. (Will) Parsons
11:40 PM - 12:10 PM
Guiding clinical decision-making with omics data.This talk will address some challenges bioinformatics scientists face in translating genomic data to a form useful for patient outcomes. First, cancer is often studied in silos defined by tissue of origin. However, recent pan-cancer analyses reveal connections across tissues, cell-of-origin signals, and contributions from the tumor microenvironment. Bioinformatics methods that deconvolute these signals may provide insights for treatment decisions. Next, a recent benchmark study revealed that current algorithms to identify DNA sequence changes in tumor genomes have limited concordance with each other. The DREAM somatic mutation calling challenge was recently launched to find the most accurate algorithms to read tumor genomes with high fidelity. Finally, algorithms are sorely needed to interpret the impact of these findings on the genetic pathways of cells. Approaches that can find explanatory models of tumor wiring and re-wiring may provide clues about what points in the networks can be targeted to eliminate or keep in check rogue cancer cells.
Confirmed speaker:    Dr. Josh Stuart
12:10 PM - 12:25 PM Discussion
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