Integrated Genomics & Bioinformatics Core: Project Summary/Abstract Modern cancer research relies on a broad array of genome-wide approaches. The mission of the Koch Institute Integrated Genomics & Bioinformatics Core (IGB Core) is to support the acquisition of genomic and gene expression data and the organization and analyses of the resulting large and complex data sets through advanced technology service platforms, state-of-the-art computational infrastructure and expert bioinformatics capabilities. It provides Center Members with integrated and comprehensive services including consultative services and training in experimental design and data analyses and technical pipelines from sample generation and quality control to sequencing and informatic analysis to allow investigation of: mRNA, microRNA and lncRNA expression; splicing events; transcription factor binding sites; epigenetic modifications; point mutations and chromosomal abnormalities; and single cell genomics. In the prior renewal, the Genomics and Bioinformatics Cores were presented as separate entities. We have now combined these into the IGB Core, reflecting the critical importance of integrating genomics data generation with downstream informatic analysis. The IGB Core is an Institutional Shared Resource between the Koch Institute and three other MIT units. During the current period, usage of the IGB Core increased from 80% to 87% of Center Members. To support this demand, the IGB Core expanded sample preparation, quality control and processing, data analysis, and hardware and software capabilities. This includes expanded offerings for ii) sequencing library preparation, including development of multiple high-throughput (HT) protocols; ii) single cell acquisition/sequencing and analysis approaches; iii) long read sequencing services and analysis; and iv) RNAseq and Epigenomics analysis capabilities. The IGB Core also deployed new compute and data storage resources. Core staff provided additional direct support to this CCSG through development of financial and publication database and client-side interfaces. Thus, this Shared Resource is essential to the success of the Koch Institute mission. In the upcoming period, The IGB Core is committed to continued enhancement of genomics technologies and informatics expertise as well as maintaining IT hardware to support these efforts and the KI research community. Planned initiatives include: developing additional HT methods for sequencing library preparation; further strengthening expertise in single cell genomics applications; expanding data storage and compute cluster and/or cloud computing in line with investigator needs; and expanding informatics training offerings to include more hands-on workshop opportunities. This shared Core is of exceptional value to the CCSG because Koch Institute Members account for 47% of the Genomic services usage and 87% of Informatics services usage, but the CCSG contribution to the Core (8%) is comparable to that of the other sponsoring entities (7%) and far less than the costs covered by user chargebacks (78%).

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Center Core Grants (P30)
Project #
2P30CA014051-49
Application #
9937089
Study Section
Subcommittee I - Transistion to Independence (NCI)
Project Start
Project End
Budget Start
2020-05-01
Budget End
2021-04-30
Support Year
49
Fiscal Year
2020
Total Cost
Indirect Cost
Name
Massachusetts Institute of Technology
Department
Type
DUNS #
001425594
City
Cambridge
State
MA
Country
United States
Zip Code
02142
Wu, Connie; Li, Jiahe; Wang, Wade et al. (2018) Rationally Designed Polycationic Carriers for Potent Polymeric siRNA-Mediated Gene Silencing. ACS Nano 12:6504-6514
Perez, Dahlia E; Henle, Andrea M; Amsterdam, Adam et al. (2018) Uveal melanoma driver mutations in GNAQ/11 yield numerous changes in melanocyte biology. Pigment Cell Melanoma Res 31:604-613
Ordovas-Montanes, Jose; Dwyer, Daniel F; Nyquist, Sarah K et al. (2018) Allergic inflammatory memory in human respiratory epithelial progenitor cells. Nature 560:649-654
Lam, Fred C; Morton, Stephen W; Wyckoff, Jeffrey et al. (2018) Enhanced efficacy of combined temozolomide and bromodomain inhibitor therapy for gliomas using targeted nanoparticles. Nat Commun 9:1991
Chiu, Anthony C; Suzuki, Hiroshi I; Wu, Xuebing et al. (2018) Transcriptional Pause Sites Delineate Stable Nucleosome-Associated Premature Polyadenylation Suppressed by U1 snRNP. Mol Cell 69:648-663.e7
Weidberg, Hilla; Amon, Angelika (2018) MitoCPR-A surveillance pathway that protects mitochondria in response to protein import stress. Science 360:
Mead, Benjamin E; Ordovas-Montanes, Jose; Braun, Alexandra P et al. (2018) Harnessing single-cell genomics to improve the physiological fidelity of organoid-derived cell types. BMC Biol 16:62
Nagarajan, Maxwell B; Tentori, Augusto M; Zhang, Wen Cai et al. (2018) Nonfouling, Encoded Hydrogel Microparticles for Multiplex MicroRNA Profiling Directly from Formalin-Fixed, Paraffin-Embedded Tissue. Anal Chem 90:10279-10285
Dayton, Talya L; Gocheva, Vasilena; Miller, Kathryn M et al. (2018) Isoform-specific deletion of PKM2 constrains tumor initiation in a mouse model of soft tissue sarcoma. Cancer Metab 6:6
Chen, Tiffany F; Li, Kevin K; Zhu, Eric F et al. (2018) Artificial Anti-Tumor Opsonizing Proteins with Fibronectin Scaffolds Engineered for Specificity to Each of the Murine Fc?R Types. J Mol Biol 430:1786-1798

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