?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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Wogksch, Matthew D; Howell, Carrie R; Wilson, Carmen L et al. (2018) Physical fitness in survivors of childhood Hodgkin lymphoma: A report from the St. Jude Lifetime Cohort. Pediatr Blood Cancer :e27506
Nishii, Rina; Moriyama, Takaya; Janke, Laura J et al. (2018) Preclinical evaluation of NUDT15-guided thiopurine therapy and its effects on toxicity and antileukemic efficacy. Blood 131:2466-2474
Fernandez-Pineda, Israel; Davidoff, Andrew M; Lu, Lu et al. (2018) Impact of ovarian transposition before pelvic irradiation on ovarian function among long-term survivors of childhood Hodgkin lymphoma: A report from the St. Jude Lifetime Cohort Study. Pediatr Blood Cancer 65:e27232
Stewart, Elizabeth; McEvoy, Justina; Wang, Hong et al. (2018) Identification of Therapeutic Targets in Rhabdomyosarcoma through Integrated Genomic, Epigenomic, and Proteomic Analyses. Cancer Cell 34:411-426.e19
Broniscer, Alberto; Hwang, Scott N; Chamdine, Omar et al. (2018) Bithalamic gliomas may be molecularly distinct from their unilateral high-grade counterparts. Brain Pathol 28:112-120
Quinn, Melissa; Fannin, J T; Sciasci, Joseph et al. (2018) Pentamidine for Prophylaxis against Pneumocystis jirovecii Pneumonia in Pediatric Oncology Patients Receiving Immunosuppressive Chemotherapy. Antimicrob Agents Chemother 62:
Halalsheh, Hadeel; Kaste, Sue C; Navid, Fariba et al. (2018) The role of routine imaging in pediatric cutaneous melanoma. Pediatr Blood Cancer 65:e27412
Wang, Lu; Hiler, Daniel; Xu, Beisi et al. (2018) Retinal Cell Type DNA Methylation and Histone Modifications Predict Reprogramming Efficiency and Retinogenesis in 3D Organoid Cultures. Cell Rep 22:2601-2614
Vanarotti, Murugendra; Evison, Benjamin J; Actis, Marcelo L et al. (2018) Small-molecules that bind to the ubiquitin-binding motif of REV1 inhibit REV1 interaction with K164-monoubiquitinated PCNA and suppress DNA damage tolerance. Bioorg Med Chem 26:2345-2353
Sabin, N D; Cheung, Y T; Reddick, W E et al. (2018) The Impact of Persistent Leukoencephalopathy on Brain White Matter Microstructure in Long-Term Survivors of Acute Lymphoblastic Leukemia Treated with Chemotherapy Only. AJNR Am J Neuroradiol 39:1919-1925

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