The Georgia Cancer Center's Bioinformatics Shared Resource provides expertise in integrative computational-based analysis solutions to basic, clinical, and translational research applications.
Bioinformatics support ranges in scope from simple consultations to more in-depth collaborations. We require the participation of the investigator during the course of our data analysis because we believe that input into the biological parameters are tantamount to success of the analysis.
Campus users have access to several advanced computing servers owned by the Georgia Cancer Center, including a High Performance Computing Server (HPC) that has 544 total compute cores and an aggregated memory of 2.9TB. The system is composed of 15 PowerEdge R430 1U systems (128 GB RAM each node), 1 PowerEdge R830 (high memory 1024 GB RAM node), and a high-speed 40GbE interconnect for intraserver communication. The HPC also houses 652 TB RAW storage capacity known as Qumulo, allowing the functionalities of effective management and maintenance as well as highly efficient analysis of large data sets, and is committed to the Bioinformatics Shared Resource. Training or a knowledge of Linux is required to use the HPC server.
Booking of server time is done through ilab. iLab allows researchers, PIs, financial managers, and core managers to ensure that they are using valid payment information (Chart Field Combination or CFC) at each step of the request and billing process for core facilities. Financial managers assign CFCs to lab members who will order services from AU cores. Researchers can order services with valid CFC, and core managers can bill for these services knowing that they are using valid CFCs.
Assess the quality of sequencing for various kinds of metrics
Motifs from peaks
Generate a table and figure for gene fusion
Cellranger and Loupe cell browser by 10X Genomics
Ding J, Li T, Wang X, Zhao E, Choi J, Yang L, Zha Y, Dong Z, Huang S, Asara JM, Cui H, Ding H-F. The histone H3 methyltransferase G9A epigenetically activates the serine-glycine synthesis pathway to sustain cancer cell survival and proliferation. (2013). Cell Metab. 3;18(6):896-907.
Ren M, Qin H, Ren R, Cowell JK. (2013) Ponatinib suppresses the development of myeloid and lymphoid malignancies associated with FGFR1 abnormalities. 27(1):32-40.
Ren M, Qin H, Kitamura E, Cowell JK. (2013). Dysregulated signaling pathways in the development of CNTRL-FGFR1-induced myeloid and lymphoid malignancies associated with FGFR1 in human and mouse models. 8:122(6):1007-16.
Pathania R, Ramachandran S, Elangovan S, Padia R, Yang P, Cinghu S, Veeranan-Karmegam R, Arjunan P, Gnana-Prakasam JP, Sadanand F, Pei L, Chang CS, Choi JH, Shi H, Manicassamy S, Prasad PD, Sharma S, Ganapathy V, Jothi R, Thangaraju M. (2015). DNMT1 is essential for mammary and cancer stem cell maintenance and tumorigenesis. Nat Commun. 24;6:6910.
John K Cowell, Haiyang Qin, Chang-Sheng Chang, Eiko Kitamura, Mingqiang Ren. (2016). A model of BCR-FGFR1 driven human AML in immunocompromised mice. British Journal of Haematology. 175(3): 542-545
Drewry M, Helwa I, Allingham RR, Hauser MA, Liu Y. (2016). miRNA profile in three different normal human ocular tissues by miRNA-seq. Invest Ophthalmol vis Sci. 1;57(8):3731-9
Pathania R, Ramachandran S, Mariappan G, Thakur P, Shi H, Choi JH, Manicassamy S, Kolhe R, Prasad PD, Sharma S, Lokeshwar BL, Ganapathy V, Thangaraju M. (2016). Combined Inhibition of DNMT and HDAC blocks the tumorigenicity of cancer stem-like cells and attenuates mammary tumor growth. Cancer Res. 1;76(11):3224-35.
Zhu X, Hu T, Ho MH, Wang Y, Yu M, Patel N, Pi W, Choi JH, Xu H, Kutlar F, Ganapathy V, Kutlar A, Tuan D. (2017). Hydroxyurea differentially modulates activator and repressors of γ-globin gene in erythroblasts of responsive and non-responsive patients with sickle cell disease in correlation with Index of Hydroxyurea Responsiveness.102(12):1995-2004.
Hu T, Chong Y, Qin H, Kitamura E, Chang C-S, Silva J, Ren M, Cowell JK. (2018). The miR-17/92 cluster is involved in the molecular etiology of the SCLL syndrome driven by the BCR-FGFR1 chimeric kinase. Oncogene, 37(14), 1926-1938.
Hu T, Chong Y, Lu S, Wang R, Qin H, Silva J, Kitamura E, Chang C-S, Hawthorn L, Cowell JK. (2018). MicroRNA339 promotes development of Stem Cell Leukemia/Lymphoma syndrome through downregulation of the BCL2L11 and BAX pro-apoptotic genes. Cancer Research, 1;78(13):3522-3531
Chang C-S, Kitamura E, Johnson J, Bollag R, Hawthorn L. (2018). Genomic analysis of racial differences in triple negative breast cancer. Genomics S0888-7543(18)30045-4
Hu T, Chong Y, Qin H, Kitamura E, Chang C-S, Silva J, Ren M, Cowell JK. (2018). The miR-17/92 cluster is involvedin the molecular etiology of the SCLL syndrome driven by the BCR-FGFR1 chimeric kinase. Oncogene 78 (13)
Silva J, Chang C-S, Hu T, Qin H, Kitamura M, Hawthorn L, Ren M, Cowell JK. (2018). Distinct signaling programs associated with progression of FGFR1 driven leukemia in a mouse model of stem cell leukemia lymphoma syndrome. S0888-7543(18)30273-8.
Khaled ML, Bykhovskaya Y, Yablonski SER, Li H, Drewry MD, Aboobakar IF, Estes A, Gao XR, Stamer WD, Xu H, Allingham RR, Hauser MA, Rabinowitz YS, Liu Y. (2018). Differential Expression of Coding and Long Noncoding RNAs in Keratoconus-Affected Corneas. Invest Ophthalmol Vis Sci. 1;59(7):2717-2728.
Chong Y, Liu Y, Lu S, Cai B, Gin H, Chang CS, Ren M, Cowell JK, Hu T. (2019). Critical individual roles of the BCR and FGFR1 kinase domains in BCR-FGFR1-driven stem cell leukemia/lymphoma syndrome. Int J Cancer.PMID:31525277
Silva J, Chang C-S, Hu T, Qin H, Kitamura M, Hawthorn L, Ren M, Cowell JK. (2019). Distinct signaling programs associated with progression of FGFR1 driven leukemia in a mouse model of stem cell leukemia lymphoma syndrome. Genomics 111 (6) 1566
Yu M, Guo G, Huang L, Deng L, Chang C-S, Achyut BR, Canning M, Xu N, Arbab AS, Bollag RJ, Rodriguez PC, Mellor AL, Shi H, Munn DH, Cui Y, CD73 on cancer-associated fibroblasts enhanced by the A2B-mediated feedforward circuit enforces an immune checkpoint. Nat Commu 2020; 11: 515
Kitamura E, Cowell JK, Chang C-S, Hawthorn L (2020) Variant profiles of Genes Mapping to Chromosome 16q Loss in Willms Tumors Reveals Link to Cilia-Related Genes and Pathways. Genes & Cancer 2020 Dec. 31; 11(3-4): 137-153
Silva J, Hawthorn L, Cowell JK. (2020) Inactivation of Lgi1 in murine neuronal precursor cells leads to dysregulation of axon guidance pathways. Genomics. 112(2):1167-1172
Yun Liu, Baohuan Cai, Yating Chong, Chesley-Anne Kemp, Su Lu, Chang-Sheng Chang, Mingqiang Ren, John Cowell, Tianxiang Hu Downregulation of PUMA underlies resistance to FGFR1 inhibitors in the stem cell leukemia/lymphoma syndrome Cell Death & Disease (884) Oct. 2020
Madhav D. S., Rafal P., Huidong S., Anita S., Zuzana J.B., Yuisef Z., Austin G., Chang-Sheng Chang, Sudharshan E., William T. C., Roni J. B., Ravibdra K., Ramses S., Tracy L.M., Paulo R., Jessica M., Bruce R. B., Theodore S. J., David H. M. BTK and IDO in tumor-associated dendritic cells create a metabolic checkpoint that suppresses mTOR-driven maturation July 2021 accepted in Immunity
American Society of Human Genetics (ASHG), Oct. 2020, San Diego, CA, USA, "Genome Wide Association analysis using whole exome sequencing data on Wilms tumor" Chang-Sheng Chang, E. Kitamura, L. Hawthorn
American Society of Human Genetics (ASHG), Oct. 15-19 2019, Houston, TX, USA, "Network Pathways Leading to Discover Biomarker Candidates Based on Genomic profiles of Racial Differences in TNBC" Chang-Sheng Chang, E. Kitamura, L. Hawthorn
IWCLL2019, Sept. 20-23 2019, Edinburgh, UK, "Modulation of SF3B1 causes global intron retention and down-regulation of B cell pathway in CLL", Q. Han, Chang-Sheng Chang, Huidong Shi
Research Data Management Symposium, March 20th 2019, Augusta GA "Georgia Cancer Center High Performance Computing (HPC) Server" Chang-Sheng Chang
American Society of Hematology (ASH) Annual Meeting, 1-4 Dec, 2018, San Diego "Transcriptome sequencing reveals alternative splicing patterns and an increased sensitivity to spliceosome inhibition associated MYD88L265P mutation in chronic lymphocytic leukemia" Shuchao Qin, Chang-Sheng Chang, Huidong Shi
World Cancer Congress, Moscow Russia, 2018 "Genomic Analysis of Racial Differences in Triple Negative Breast Cancer Outcomes" LesleyAnn Hawthorn, Chang-Sheng Chang
AS Clinical Oncology, Chicago June 2017 "PIK3 Mutation and Effect of Aspirin Use in Breast Cancer" Shou-Ching Tang, Priyanka Raval, Chang-Sheng Chang, Sangmi Kim
2nd Global Insight Conference on Breast Cancer 2017, Rome, Italy "Genomic Analysis of Racial Differences in Triple Negative Breast Cancer" LesleyAnn Hawthorn, Chang-Sheng Chang
Pathania R, Kolhe RB, Ramachandran S, Mariappan G, Thakur P, Prasad PD, Ganapathy V. (2016) Combination of DNMT and HDAC inhibitors reprogram cancer stem cell signaling to overcome drug resistance. AACR, Abstract#3325.
Drewry M, Helwa I, Allingham RR, Hauser MA, Liu Y. (2016). miRNA-seq in four different normal human ocular tissues. ARVO
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