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CSER: Incorporation of Genomic Sequencing into Pediatric Cancer Care

ABSTRACT:

This project includes data derived from subjects enrolled in the BASIC3 (Baylor College of Medicine Advancing Sequencing in Childhood Cancer Care) study. BASIC3 is a National Genome Human Research Institute (NHGRI) and National Cancer Institute-funded Clinical Sequencing Exploratory Research (CSER) consortium project that focused on prospective implementation of clinical whole exome sequencing in the pediatric oncology clinic. The primary study objective were to integrate information from CLIA-certified germline and tumor exome sequencing into the care of newly diagnosed solid tumor patients at Texas Children's Cancer Center, and to perform parallel evaluation of the impact of tumor and germline exomes on families and physicians.

Blood and frozen tumor (if available) samples were collected from children undergoing surgery or biopsy of newly diagnosed solid tumors and subjected to exome sequencing in a CLIA-certified laboratory. Germline and tumor (if applicable) exome sequencing reports were generated and submitted into the electronic health record and returned to each patient/family by their primary oncologist.

In addition to the clinical exome sequencing, specific (optional) consent was requested for research sequencing studies. If this consent was obtained then research studies of some of the children and parents participating in the BASIC3 study (including tumor transcriptome and whole genome sequencing of blood and/or tumor) are performed.

The Clinical Sequencing Exploratory Research Consortium Cohort is utilized in the following dbGaP sub-study. To view molecular data, and derived variables collected in this sub-study, please click on the following sub-studies below or in the "Sub-study" box located on the right hand side of this top-level study page phs001383 Clinical Sequencing Exploratory Research Consortium Cohort.

phs001026 BASIC3
phs001878 GMKF BASIC3

PROVIDER: phs001683 | dbGaP |

REPOSITORIES: dbGaP

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Project description:Whole genome sequencing (WGS) and whole exome sequencing (WES) services are currently available to and being utilized by physicians and their patients in both research and clinical settings, and recently to anyone in the general public via direct-to-consumer companies. But the widespread availability and use of WGS and WES in the practice of clinical medicine is imminent. In the very near future, sequencing of individual genomes will be inexpensive and ubiquitous, and patients will be looking to the medical establishment for interpretations, insight and advice to improve their health. Developing standards and procedures for the use of WGS information in clinical medicine is an urgent need, but there are numerous obstacles related to integrity and storage of WGS data, interpretation and responsible clinical integration. The MedSeq Project is an exploratory trial of WGS in clinical medicine. At the conclusion of this study, we will have helped create innovative protocols and novel outcome measures that can be applied safely in future large-scale multi-site randomized clinical trials with larger numbers of physicians from broad specialties and with more economically and ethnically diverse patients. Together with our colleagues from across the nation through the U01 consortium formed as a result of this funding from the NIH, we will have invented a process of implementation and evaluation whereby the fruits of the Human Genome Project can be applied for the first time to the daily practice of medicine for the betterment of human health. The objectives of the MedSeq Project are to: <ol> <li>Recruit, consent and enroll 2 study groups:</li> <ol type="a"> <li>10 primary care physicians and 100 of their healthy middle-aged patients </li> <li>10 cardiologists and 100 of their patients with cardiomyopathy.</li> </ol> <li>Randomize each study group to receive standard of care versus standard of care plus WGS.</li> <li>Monitor the entire protocol for subject safety.</li> <li>Only half the enrolled patients were selected for sequencing. Fifty subjects were selected from the primary care cohort and fifty were selected from the cardiomyopathy cohort. Whole genome sequencing was performed at 30x coverage in Illumina's CLIA-certified laboratory on these 100 individuals.</li> <li>Generate and optimize an algorithm for interpreting WGS data covering the spectrum of human genetic variation, in terms of both previously reported and novel variants likely to influence the health of patients.</li> <li>Create patient reports and provide an interface for communicating clinically relevant genomic information to practicing physicians.</li> <li>Describe physicians' and patients' attitudes toward, and preferences for, the disclosure of WGS results at the start of the study.</li> <li>Evaluate physicians' experiences with receiving and interpreting patients' genetic test results and how they communicate these results to their patients.</li> <li>Explore how patients respond to and use WGS results by administering validated scales of psychological impact, personal utility, and behavioral responses, as well as economic and health outcomes.</li> </ol> Although we do not have a large enough sample size for statistical comparisons of outcomes, we will conduct exploratory comparisons: Exploratory Hypotheses: <ul> <li>Patients who receive WGS results will show equivalent levels of distress compared to patients who receive family history only.</li> <li>Patients with higher genetic literacy and better understanding will report greater satisfaction and less decisional regret.</li> <li>Patients who receive WGS will (a) be more likely to change health behaviors and (b) utilize more health care resources than those who do not receive WGS.</li> </ul>

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CSER: Incorporation of Genomic Sequencing into Pediatric Cancer Care

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