Computational Biology Genomics Laboratory
Providing laboratory support and NGS services to the Department of Computational Biology and collaborative partners
Overview
The Computational Biology Genomics Laboratory (CBGL) is a wet lab dedicated to supporting the research activities of the Department of Computational Biology. In service of that mission, the CBGL validates (and formulates methods to validate) the models and approaches developed by the department’s computationalists; imports and optimizes technologies that could help generate new ideas and code; and previews and evaluates emerging technologies for their potential utility. The lab supports a wide range of activities in genomics, including next-generation sequencing (NGS), the acquisition of single-cell data, and the use of image-based technologies to delineate the relationship between cells and tissues. These activities are carried out to further the development of computational methods intended to increase understanding of cancer biology.
Impact
The CBGL is physically embedded within the Department of Computational Biology, providing rapid iterative data generation to facilitate algorithm testing and development. The lab has generated data sets and provided technical expertise for projects both internal to the Department of Computational Biology and in collaboration with outside departments and institutions. These projects include follow-up studies of patients treated at St. Jude Children’s Research Hospital (the St. Jude Life (SJLIFE) study) and elsewhere (the Childhood Cancer Survivor Study (CCSS); an investigation of the fundamental mechanisms of DNA structure and variation driving pediatric cancer (3D Genome Consortium); the identification of therapeutic targets in pediatric cancer (iTARGETS); and the generation of data to investigate the potential role of the epigenome in cancer dependency screens (Pediatric Cancer Dependencies Accelerator (PedDep)).
Capabilities
The CBGL is equipped to perform a broad range of activities in support of members of the department. Its primary focus is on NGS for the purpose of studying variation in the genome and transcriptome; other frequent activities include primary tissue processing for spatial transcriptomics, single-cell multiomics, and CRISPR screens of cell lines. These activities are enhanced through the lab’s routine leverage of the technology and expertise of St Jude’s numerous core facilities.
Selected publications
About the director
John Easton, PhD
Dr. John Easton began his career at St. Jude Children’s Research Hospital over thirty years ago. After receiving his Ph.D. in cell biology and anatomy from the University of Alabama at Birmingham College of Medicine, he joined St. Jude Children’s Research Hospital as a postdoctoral researcher for the (former) Department of Molecular Pharmacology. He later worked as an associate scientist in the Department of Pathology, where he developed diagnostic assays for patient testing. In 2010, Dr. Easton was selected to manage the validation laboratory for the Pediatric Cancer Genome Project. That work involved confirming DNA variants identified from the whole genome sequencing data generated at Washington University as well as mRNA sequencing to identify potential cancer-driving fusion transcripts. He became Director of the CBGL when the Department of Computational Biology was established in 2015.
