Bioinformatics and Biotechnology Shared Resource Core

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PROJECT SUMMARY/ABSTRACT—Bioinformatics and Biotechnology Shared Resource The goal of the Bioinformatics and Biotechnology Shared Resource (BBSR) is to provide the latest innovative, high-throughput biotechnology and bioinformatics methods and approaches to support the cancer research of SJCCC members. The Bioinformatics team provides expert data analysis by utilizing a SJCCC genomic-analysis infrastructure developed and validated through the Pediatric Cancer Genome Project. The Biotechnology team provides state-of-the-art high-throughput genomic assays of RNA and DNA samples by using 3 complementary platforms: genome sequencing, Sanger sequencing, and microarray analysis. The BBSR is directed by Dr. Jinghui Zhang (CBP), Chair of the Department of Computational Biology, who has more than 20 years of research experience in genetic variant characterization in the human genome. She is recognized worldwide for her expertise in the development of novel algorithms, data visualizations, and analyses for deciphering sequence- variation data in pediatric cancer. She is assisted by Dr. Geoffrey Neale, who is responsible for management and scientific oversight of the biotechnology laboratories. He has more than 25 years of experience in scientific management and the investigation of pediatric cancer using molecular techniques. The BBSR is further staffed by a group of PhD-level expert scientists with varied specialization and domain knowledge to support SJCCC projects. Services include technical and analytical support for state-of-the-art molecular profiling, such as next- generation sequencing, microarrays, single-cell sequencing, and CRISPR screening, as well as expert consultation and advisory support. The impact of the BBSR on SJCCC research is evidenced by the significant contribution to publications, many in high-impact journals such as the New England Journal of Medicine, Nature, Nature Genetics, Cell, and Lancet. During the project period, the BBSR supported all 5 SJCCC Programs, resulting in 418 publications, which represent 20.2% of the total publications from the SJCCC during this period. The BBSR was used by 65 SJCCC members, 70% (n=46) of whom have cancer-relevant, peer-reviewed funding. In the next project period, the BBSR will actively evaluate new technology and analytical methods. New standard services and technology, such as Novaseq, will be introduced for SJCCC members. We will also continue to work with the SJCCC Programs to establish new molecular-profiling technology and to pursue bioinformatics method development in areas including network analysis; long-read technology (PacBio and Oxford Nanapore); single-cell RNA-Seq (DropSeq) and VDJ solution from 10X Genomics; and long-range chromatin-interaction assays (eg., Hi-C, HiChip, and Capture-C). Finally, we will continue deploying workflows to the newly established St. Jude Cloud platform, a Blue Sky initiative, to provide bench scientists within the SJCCC and around the world with direct access to sophisticated bioinformatics pipelines.