November 16, 2020
Researchers are sharing valuable genomic data that will help transform the way childhood cancer is treated. Nearly 16,000 children are diagnosed with cancer each year in the U.S. Today, more than 84% of children with cancer survive five years or more, but many will experience lifelong complications from their treatments.
Now, with the help of a one-year, $500,000 grant, a team of scientists from The University of Kansas Cancer Center and Children’s Mercy will contribute information providing critical insights into the genomic diversity of childhood cancers, leading the way to new discoveries. Children’s Mercy is recognized by the National Cancer Institute (NCI) as a consortium partner of KU Cancer Center. The additional funding supplements the cancer center’s current P30 Cancer Center Support Grant.
Under the NCI’s Childhood Cancer Data Initiative (CCDI), organizations are pooling pediatric cancer data in a central repository with the goal of aggregating and sharing with researchers across the globe. Childhood cancer is a rare disease comprising about 1% of all new cancer diagnoses, and so such data can be hard to come by. This problem is exacerbated because there are very rare subtypes of childhood cancer, and centers may see such cases only once every few years.
Midhat Farooqi, MD, PhD, Director of Children’s Mercy’s Molecular Oncology program, faculty member in the Children’s Mercy Department of Pathology and Laboratory Medicine, and a member of the KU Cancer Center’s Drug Discovery, Delivery and Experimental Therapeutics research program, is leading the effort.
“Childhood cancers harbor different molecular alterations relative to adult tumors and are much rarer,” Dr. Farooqi said. “With this grant we can share our data with the broader scientific community and take a vital step forward in the advancement of precision medicine and innovative discovery in pediatric cancer.”
In 2017, Children’s Mercy began banking samples from pediatric cancer patients at multiple disease timepoints, including diagnosis, remission and relapse. Now part of the Children’s Mercy Research Institute Biorepository, the tumor bank at Children’s Mercy houses more than a thousand tumor tissue and normal tissue samples from over 200 pediatric patients. Samples from these patients have undergone comprehensive genomic profiling, including single-cell sequencing – a particularly powerful, data-rich source. These genomic data will be made available to researchers nationally through a repository managed by the NCI.
“Typically, sequencing is done in aggregate – you take a tumor sample containing thousands of tumor cells and study them as a whole,” Dr. Farooqi explained. “Single-cell sequencing lets you examine the distinct gene expression profile of thousands of tumor cells individually. We will also be sharing a computational analysis tool, developed by the Genomic Medicine Center at Children’s Mercy, that allows for the exploration of single-cell data by entry-level users.”
Additional personnel supporting the effort include Linda Cooley, MD, MBA, Division Director for the Clinical Genetics & Genomics Laboratories; Erin Guest, MD, Director of Children’s Mercy’s Cancer Genomics Program and Cancer Center Biorepository; Sahibu Sultan Habeebu MD, PhD, Director of Molecular Pathology at Children’s Mercy; Mark Hoffman, PhD, Children’s Mercy Chief Research Information Officer; Neil Miller, Director of Bioinformatics for Children’s Mercy’s Genomic Medicine Center; and Tomi Pastinen, MD, PhD, Director of the Genomic Medicine Center.
Contributing to the national dataset allows researchers to learn from every child with cancer, advancing treatment and improving quality of life.