Baylor College of Medicine

Grant to compare large-scale genomic sequencing, standard clinical tests for childhood cancer patients

Dana Benson


Houston, TX -
Media Component
Dr. Sharon Plon, Dr. Will Parsons and Dr. Amy McGuire.

Baylor College of Medicine is one of six U.S. institutions to receive a grant through the National Human Genome Research Institute’s Clinical Sequencing Evidence-Generating Research Consortium, or CSER2. The four-year grant, including $2.8 million for fiscal year 2017, co-funded by the National Cancer Institute, will support Baylor’s new KidsCanSeq program that will compare the results of large-scale genomic testing, such as whole exome sequencing, to targeted clinical tests in childhood cancer patients at five sites across the state that serve a highly diverse patient population, including Texas Children’s Cancer Center.

In addition to Texas Children’s Cancer Center, pediatric patients will be enrolled in KidsCanSeq at the Vannie E. Cook Children’s Cancer Clinic in McAllen, the Children’s Hospital of San Antonio, The University of Texas Health Science Center at San Antonio, and Cook Children’s Health Care System in Fort Worth.

KidsCanSeq follows the Baylor Advancing Sequencing in Childhood Cancer Care (BASIC3) study at Baylor and Texas Children’s Cancer Center, which developed the initial protocols for performing clinical genomic testing of pediatric cancer patients, reporting results and communicating those results to families and oncologists. BASIC3 was part of the NHGRI Clinical Sequencing Exploratory Research program, a precursor to CSER2.

“Through BASIC3 we explored broad questions, such as whether we could conduct large-scale genomic testing in a clinical setting, what kind of results it would generate, and how to communicate the results to families and physicians. KidsCanSeq is focused more on generating specific data on what tests are better or worse than standard tests in pediatric cancer patients,” said the study’s principal investigator Dr. Sharon Plon, professor of pediatrics and of molecular and human genetics at Baylor and director of the Cancer Genetics Clinical and Research Programs at Texas Children’s Hospital.

“BASIC3 was essentially a pilot study, and now that we have a better idea of how to implement broad-scale genetic testing in the clinic, we can focus this study more specifically on determining which patients would be most likely to benefit from it or for whom it would be most likely to impact care,” said Dr. Will Parsons, co-principal investigator and associate professor of pediatrics at Baylor and Texas Children’s Cancer Center. “For example, tumor sequencing of cancer types for which kids are almost always cured at the time of diagnosis is not likely to be as useful as for high-risk and relapsed cancers.”

KidsCanSeq will strive to answer questions such as how effective is a germline and tumor panel of approximately 150 to 200 genes at picking up hereditary genetic factors and tumor-specific actionable information compared with larger scale tests, like whole exome sequencing, which evaluates thousands of genes. Specifically, the study will compare the targeted cancer panel to whole exome sequencing of a blood sample of all enrolled childhood cancer patients to find hereditary factors and to whole exome sequencing, transcriptome sequencing and copy number array of tumor samples for the subset of patients with high-risk or relapsed tumors to find mutations that might guide treatment. This comprehensive set of genomic tests will be performed by a unique collaboration between multiple diagnostic facilities with the involvement of Dr. Richard Gibbs, director of the Human Genome Sequencing Center, Drs. Christine Eng and Shashikant Kulkarni, professors of molecular and human genetics, all of Baylor, and Dr. Angshumoy Roy, assistant professor of pathology & immunology at Baylor and Texas Children’s Hospital.

The program, in which about 900 patients are expected to be enrolled over four years, also will include parent and doctor surveys to determine what they found most useful from the testing as well as the development of video and other educational materials in both English and Spanish. Understanding differences among families from different ethnic or racial backgrounds as well as in different healthcare settings, including large academic medical centers versus smaller clinical settings, also is a goal of KidsCanSeq.

Dr. Amy McGuire, Leon Jaworski Professor of Biomedical Ethics and director of the Center for Medical Ethics and Health Policy at Baylor, also is co-principal investigator of the study. She will investigate the ethics and utility of genomic testing for pediatric cancer patients.

“It is important to study the clinical and psychosocial risks and benefits of any new technology in order to plan for its responsible use,” McGuire said. “We also want to make sure the infrastructure is in place so that oncologists in non-academic settings can understand, effectively communicate and appropriately manage the results of germline and tumor whole exome sequencing.”

Specific aims of the KidsCanSeq study include:

• Assess the clinical utility of large-scale genomic testing by measuring the frequency of diagnostic and/or actionable germline (blood) and tumor findings and the effect on treatment decisions
• Compare uptake by first-degree relatives for familial genetic testing and recommended cancer surveillance by race, ethnicity and clinical settings.
• Describe perceived utility of large scale testing by surveying and interviewing parents and participating pediatric oncologists.
• Work with pediatric cancer stakeholders, including advocates, BASIC3 study parents and national organizations, to create and evaluate the use of culturally sensitive educational materials, including videos in English and Spanish, improved integrated genomic test reports and counseling materials, and compare in-person versus telemedicine exome results disclosure.
• Provide data to guide future application of clinical genomics through three innovative pilot projects focused on health economics, decision support for cancer surveillance and whole genome sequencing.

Drs. Plon, Parsons and McGuire all are members of the NCI-designated Dan L Duncan Comprehensive Cancer Center at Baylor College of Medicine.

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