2015 — 2018 |
Jepsen, Kristen Lynn |
P50Activity Code Description: To support any part of the full range of research and development from very basic to clinical; may involve ancillary supportive activities such as protracted patient care necessary to the primary research or R&D effort. The spectrum of activities comprises a multidisciplinary attack on a specific disease entity or biomedical problem area. These grants differ from program project grants in that they are usually developed in response to an announcement of the programmatic needs of an Institute or Division and subsequently receive continuous attention from its staff. Centers may also serve as regional or national resources for special research purposes. |
Genomics and Genome Engineering Core @ University of California San Diego
RESEARCH CORE A ? SUMMARY The objective of the Genomics and Genome Engineering Core (GGEC) is to provide cutting-edge, reliable and innovative genomic technologies enabling Center investigators to accomplish the individual aims of their research. It also seeks to disseminate new assays and protocols developed by the Center to the scientific community by offering training and education in genomics and genome editing. Doing so enhances the ability of Center Investigators and the wider scientific community to implement these technologies in their research. The GGEC is comprised of three well-established and highly functional facilities on the Torrey Pines research mesa: the UCSD Institute for Genomic Medicine Genomics Center, the UCSD Center for Computational Biology, and the Sanford-Burnham Medical Research Institute Functional Genomics Facility. The GGEC supports the research of the SDCSB faculty through the following four Specific Aims. First, it enables investigators to generate high-throughput genomics datasets by providing the necessary services, expertise, equipment, and training. Second, it provides expertise for processing genomics data, including basic analysis of individual experiments as well as integration of datasets from multiple platforms. Third, it enables loss-of-function (siRNA, shRNA, miRNA inhibitors, CRISPR-Cas9) and gain-of-function (ORFs, miRNA mimics) studies by high-throughput screening in cultured cells. Fourth and finally, it disseminates workflows and assays developed by center investigators to the wider scientific community. GGEC technologies will be highly used by all four SDCSB Research Projects.
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2019 |
Jepsen, Kristen Lynn |
S10Activity Code Description: To make available to institutions with a high concentration of NIH extramural research awards, research instruments which will be used on a shared basis. |
Illumina Novaseq 6000 Sequencing System @ University of California, San Diego
PROJECT SUMMARY/ABSTRACT We are requesting funds for an Illumina NovaSeq 6000 high throughput sequencing system to expand sequencing capacity at the University of California, San Diego (UC San Diego). The NovaSeq 6000 will be placed in the Institute for Genomic Medicine (IGM) Genomics Center, a campus-wide core facility managed by the IGM. The IGM Genomics Center is the only core facility at UC San Diego that offers high throughput sequencing. The highly trained staff of the Genomics Center are experienced with genomics technologies and Illumina sequencing and currently operate an Illumina HiSeq2500 and an Illumina HiSeq4000, both of which are running near capacity (90-95%). Since the IGM Genomics Center was established in 2013, we have seen a steady increase in the demand for sequencing capacity driven by the technological advancements in the field and we must expand our current capacity in order to continue to meet demand. The NovaSeq 6000 will dramatically increase the sequencing throughput capabilities of the Center and shorten turnaround time and also significantly reduce the cost of sequencing licensing additional discovery. The IGM Genomics Center supports the genomics research of hundreds of NIH-supported investigators from UC San Diego, as well as neighboring institutions, in the areas of basic, translational, and clinical biomedical research. We have identified 18 Major and Minor Users across the UC San Diego research community, including investigators from the Division of Biological Sciences, the Jacobs School of Engineering, and from multiple departments within the School of Medicine. The projects of our Users encompass the areas of genetics, epigenetics, single cell genomics and metagenomics and all rely on affordable high throughput sequencing technologies to drive discovery. The sequencing data generated on the NovaSeq 6000 will positively impact studies in a variety of disease areas, including neurological diseases, cardiac disease, diabetes, cancer, inflammatory bowel disease, kidney disease, drug abuse/addiction, obesity and HIV. UC San Diego has demonstrated a strong commitment to the advancement of genomics research and the IGM Genomics Center is determined to continue to provide cutting edge genomics technologies and technical expertise to the local research community. With the support of our institution and our qualified staff, we will ensure that the NovaSeq 6000 will be maintained and used to its full potential.
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2019 — 2021 |
Fisch, Kathleen Marie Frazer, Kelly A Jepsen, Kristen Lynn Laurent, Louise Chang |
U54Activity Code Description: To support any part of the full range of research and development from very basic to clinical; may involve ancillary supportive activities such as protracted patient care necessary to the primary research or R&D effort. The spectrum of activities comprises a multidisciplinary attack on a specific disease entity or biomedical problem area. These differ from program project in that they are usually developed in response to an announcement of the programmatic needs of an Institute or Division and subsequently receive continuous attention from its staff. Centers may also serve as regional or national resources for special research purposes, with funding component staff helping to identify appropriate priority needs. |
Omics Data Generation Center (Odgc) For the Acute to Chronic Pain Signatures (A2cps) Program @ University of California, San Diego
Omics Data Generation Center (ODGC) for the Acute to Chronic Pain Signatures (A2CPS) Program OVERALL PROJECT SUMMARY Chronic pain is a major health concern and one of the most common reasons adults seek medical care. It is associated with substantial morbidity linked to reduced quality of life, restricted mobility, depression, and opioid dependence. The biological mechanisms that prevent the resolution of acute pain after the initial insult and drive the transition from acute to chronic pain are poorly understood. The lack of rigorously validated biomarkers to predict which patients are more susceptible to the transition from acute to chronic pain states is thus a major gap hindering the development and implementation of population-wide and individualized preventive pain interventions. In the A2CPS Consortium, the Clinical Centers will recruit and collect clinical data and biofluid samples from two longitudinal cohorts of 1800 subjects each. Biofluid samples will be collected 0, 3, and 6 months after an acute pain episode, consisting of a specific surgical procedure or a specific musculoskeletal trauma. These samples will be used to generate multi-omic data to validate 40 primary outcome biomarkers indicating susceptibility or resilience to development of chronic pain, as well as to identify new candidate biomarkers. For the proposed A2CPS Omics Data Generation Center (ODGC), Aim 1, which will be executed in Year 1, will involve close collaboration with other components of the A2CPS Consortium to establish the final study design and protocols. All of the A2CPS Program investigators will work together to establish the 40 primary outcome biomarkers. The ODGC and Clinical Center investigators will jointly decide on the specific sample type(s) and collection/processing/storage methods. The ODGC and Data integration Resource Center/Data Coordination Component (DIRC/DCC) investigators will establish Metadata and Data Standards and a workflow for submission of metadata and raw data to the DCC. The Administrative Core of the ODGC will establish a LIMS for sample and data tracking and recording of metadata. The ODGC will work closely with the DIRC/Data Integration and Analysis Component (DIAC) to establish data analysis pipelines. ODGC investigators also anticipate participating in integrative analyses with the DIRC/DIAC aimed at developing pain signatures comprised of multiple biomarker types (including molecular, clinical, psychosocial, and/or imaging biomarkers) indicating susceptibility/resilience to chronic pain, which can be used to develop personalized strategies for prevention and treatment of chronic pain. Aims 2 and 3 will span Years 2-4, with Aim 2 focused on data generation from the ~11,000 biofluid samples that will be collected by the Clinical Centers. Aim 3 will encompass submission of metadata and data to the DIRC/DCC, quality control of the data, and data analysis and interpretation. The primary goal of this project is to establish the A2CPS Omics Data Generation Center to generate genetic variant, metabolomic, lipidomic, proteomic, exRNA, transcriptome, and microbiome data from two pain cohorts to validate 40 primary outcome biomarkers indicating susceptibility or resilience to development of chronic pain and identify novel biosignatures predicting the transition from acute to chronic pain.
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