?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.

National Institute of Health (NIH)
National Cancer Institute (NCI)
Center Core Grants (P30)
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Subcommittee I - Transistion to Independence (NCI)
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St. Jude Children's Research Hospital
United States
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Donohoe, Clare; Bosi, Judy K; Sykes, April et al. (2018) Clinical Characteristics of Children and Adolescents Undergoing Hematopoietic Cell Transplantation Who Develop Oral Mucositis. Oncol Nurs Forum 45:457-462
Green, Daniel M; Wang, Mingjuan; Krasin, Matthew J et al. (2018) Serum ALT elevations in survivors of childhood cancer. A report from the St. Jude Lifetime Cohort Study. Hepatology :
Kirchhoff, Anne C; Nipp, Ryan; Warner, Echo L et al. (2018) ""Job Lock"" Among Long-term Survivors of Childhood Cancer: A Report From the Childhood Cancer Survivor Study. JAMA Oncol 4:707-711
Crom, Deborah B; Ness, Kirsten K; Martinez, Larry R et al. (2018) Workplace experiences and turnover intention among adult survivors of childhood cancer. J Cancer Surviv 12:469-478
Bishop, Michael W; Advani, Shailesh M; Villarroel, Milena et al. (2018) Health-Related Quality of Life and Survival Outcomes of Pediatric Patients With Nonmetastatic Osteosarcoma Treated in Countries With Different Resources. J Glob Oncol :1-11
Heitzer, Andrew M; Ashford, Jason M; Hastings, Camden et al. (2018) Neuropsychological outcomes of patients with low-grade glioma diagnosed during the first year of life. J Neurooncol :
Tsujimoto, Shinichi; Osumi, Tomoo; Uchiyama, Meri et al. (2018) Diplotype analysis of NUDT15 variants and 6-mercaptopurine sensitivity in pediatric lymphoid neoplasms. Leukemia 32:2710-2714
Li, Liyuan; Qian, Maoxiang; Chen, I-Hsuan et al. (2018) Acquisition of Cholangiocarcinoma Traits during Advanced Hepatocellular Carcinoma Development in Mice. Am J Pathol 188:656-671
Dvorak, Christopher C; Satwani, Prakash; Stieglitz, Elliot et al. (2018) Disease burden and conditioning regimens in ASCT1221, a randomized phase II trial in children with juvenile myelomonocytic leukemia: A Children's Oncology Group study. Pediatr Blood Cancer 65:e27034
Pui, Ching-Hon (2018) To delay or not to delay, that is the question for patients with acute lymphoblastic leukemia who do not receive prophylactic cranial irradiation. Cancer 124:4442-4446

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