Cores

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Administrative Core

Simon N. Powell, MD, PhD (core director)

Jorge S. Reis-Filho, MD, PhD (co-core director)

The Administrative Core serves as the operational hub of the SPORE, arranging all SPORE-related functions in scientific review, intra- and inter-SPORE collaborations, financial management of budgeting and monitoring expenses, editorial services as needed, and grant administration.  We also regard the SPORE as a forum for education and mentoring, above and beyond what is directly assisted in the developmental programs, by creating an environment in which new ideas for projects can be discussed with supportive SPORE key personnel.  The Core will coordinate the functions of the internal and external advisory boards and liaise with the Memorial Sloan Kettering Cancer Center (MSK) breast cancer disease management team over identification and monitoring of the cancer patient populations required for this SPORE ,and communicate with our patient advocates about our ongoing results, trials and future planning.


Biostatistics and Computational Genomics Core 

Sohrab Shah, PhD (core director)

Ronglai Shen, PhD (co-core director)

The Biostatistics and Computational Genomics Core will provide support in statistical and computational analysis of sequencing data, biomarker development and validation, pre-clinical study design and analysis to meet the needs of the SPORE Research Projects and interact with other cores and institutional resources to achieve the scientific and translational purposes of the SPORE. The Research Projects in this SPORE require a broad range of statistical and bioinformatics expertise, including tools for the analysis and visualization of whole genome sequencing and single cell sequencing data. The Core will provide a team of dedicated personnel with extensive experience and strong track record of developing innovative statistical and computational methods. We will maintain and expand current tools and pipelines to assist the design and analysis of the SPORE research projects, and provide centralized support for data collection, processing, quality assessment, and normalization procedures to facilitate data integration and downstream analysis and visualization. Importantly, the core will devote significant effort in developing innovative computational tools that aim to detect, quantify, and track genomic signatures of specific DNA repair defects and/or genetic instability at the tumor bulk and single cell levels. In addition, the Core will synergize with the current infrastructure available at Memorial Sloan Kettering Cancer Center to provide the SPORE investigators not only with the state-of-the-art computational biology methods, but also with novel computational tools to address specific analytical challenges germane to the success of the SPORE Research Projects.


Biospecimen Repository and Pathology Core

Jorge S. Reis-Filho, MD, PhD (core director)

George Plitas, MD (co-core director)

The Biospecimen Repository and Pathology Core is designed to provide support for the translational research efforts of the Genomic Instability in Breast Cancer SPORE, serving the SPORE RP1, RP2, and RP3, and developmental research projects. This Core will ensure a seamless integration of the current infrastructure available at Memorial Sloan Kettering Cancer Center (MSKCC), and constitute an essential component of this SPORE project, facilitating and expediting the collection, annotation, storage, distribution, and digital archiving and processing of biospecimens from breast cancer patients with specific patterns of DNA repair defects and/or genetic instability included in the SPORE research projects. This Core was also conceived to provide SPORE investigators with expert histopathologic evaluation of tumor samples from breast cancer patients enrolled in the research protocols, patient-derived xenografts and murine models described in this SPORE application, in conjunction with comparative pathologists from the MSK Laboratory of Comparative Pathology and the Genetically Engineered Mouse Phenotyping Service. The Core will also provide assistance in performing and interpreting immunohistochemical assays, in selecting tissue for microdissection and performing these microdissections, and in the generation of dedicated tissue microarrays. The Core will provide multiplexed immunophenotyping of the tumor and tumor microenvironment from breast cancers and breast cancer models. The specific aims of the Biospecimen Repository and Pathology Core include 1) to maintain and expand the systematic collection, annotation, and storage of bio-specimens for translational research of breast cancers with specific patterns of DNA repair defects and/or genomic instability, 2) to perform expert pathologic evaluation of all human breast cancer and animal models of breast cancer samples with specific patterns of DNA repair defects and/or genomic instability and preparation of appropriate material for use by SPORE investigators, and 3) to perform detailed immunophenotypic characterization of breast cancers and animal models of breast cancers with specific patterns of DNA repair defects and/or genomic instability. By centralizing and standardizing the pathology review of both human and murine breast cancer samples from both clinical and research settings, and by working in conjunction with other cores within MSK on the processing and curation of the biospecimen materials and digital images obtained from the samples included, the Biospecimen Repository and Pathology Core will help mitigate the impact of common confounders in translational research studies. It also will assist in the integration and prioritization of a variety of institutional pathology systems-related development efforts.