CSER: Evaluating Utility and Improving Implementation of Genomic Sequencing for Pediatric Cancer Patients in the Diverse Population and Healthcare Settings of Texas: The KidsCanSeq Study

Through this Clinical Sequencing Evidence-Generating Research (CSER) with Enhanced Diversity project we are completing a clinical study (The Texas KidsCanSeq Study) comparing the results of targeted cancer panel sequencing versus genome-scale testing in pediatric cancer patients across diverse clinical settings. We will compare the targeted pediatric cancer panel to germline whole exome sequencing (WES) of unselected childhood cancer patients. We will also compare an RNA/DNA targeted pediatric cancer panel versus WES, transcriptome sequencing and copy number array of FFPE tumor samples for the subset of patients with high-risk tumors. Exome sequencing is performed from a blood or saliva sample of the pediatric age (0-18) patient. We are building on our success completing the CSER program BASIC3 exome sequencing trial (which included 60% Hispanic and African-American patients from a single large academic center) in this large multi-institutional study of an even more diverse patient population from six pediatric oncology healthcare settings across Texas. Data from the Texas KidsCanSeq study will be submitted through the CSER Data Coordinating Center for access in NIH-supported databases.]]>
Inclusion Criteria: Children less than 18 years of age with newly-diagnosed or recurrent solid tumors (CNS and non-CNS), lymphomas, and rare histiocytic disorders who plan to receive primary longitudinal oncology care at a Texas KidsCanSeq institution. Parents of KidsCanSeq study patients Exclusion Criteria:Subjects without at least one parent who speaks either English or Spanish. Subjects diagnosed with benign non-CNS solid tumors, e.g. neurofibroma. Subjects with a history of prior allogeneic bone marrow or stem cell transplant.]]>
Participant recruitment was complete as of July 31st, 2021. The majority of participants were recruited from the Texas Children's Hospital main site, with the next highest recruitment at Cook Children's Hospital in Fort Worth and the remainder from one of the other four sites in Texas: Children's Hospital of San Antonio, University of Texas Health - San Antonio, and University of Texas MD Anderson Cancer Center. A total of 581 subjects were enrolled and sequencing of DNA from blood or saliva sample completed. The majority (n=578) had both exome and panel sequencing, however, 3 participants received panel-only due to specimen quality/quantity. A total of 490 subjects entered the Germline plus Tumor arm of the study due to having a high-risk cancer diagnosis or having recurrent or relapsed tumors. Of this group there was sufficient DNA and RNA analysis for 326 RNA/DNA Pediatric Tumor Mutation Panels, 245 tumor exomes and 252 tumor transcriptomes.]]>