/ABSTACT The Bioinformatics Core will provide services that are vital to many of the projects with in the SPORE in Prostate Cancer, including the application and development of statistical and computational techniques to process next-generation sequencing data from a variety of applications. The Core can apply standard processing algorithms and pipelines to a large number of samples. Additionally, the personnel of this Core have the expertise to create and deploy custom methods and applications as needed by the SPORE researchers. Members of the Core can leverage their experience in processing the large amount of genomic data at Memorial Sloan Kettering Cancer Center (MSKCC) to provide SPORE projects with state-of-the-art- applications with very little development time or effort; thus, greatly reducing the time and cost required for individual projects to develop their own analysis pipelines.
The specific aims of the Bioinformatics Core are:
Aim 1. To develop and provide state-of-the-art genomic analysis pipelines for: ? the detection of variants in targeted-DNA assays, MSK-IMPACT (Integrated Mutation Profiling of Actionable Cancer Targets) and whole exome sequence (WES). This pipeline will detect both single nucleotide changes and small insertion deletions for both somatic- and germline-variant calling scenarios. ? DNA copy number analysis, which can measure both total copy number changes and allele-specific copy number, including loss of heterozygosity (LOH).
Aim 2 : To facilitate the sharing of data generated in the SPORE research projects and enable collaboration of integrative analysis via the MSKCC cBioPortal by collecting, formatting, and importing data generated by these research projects into the cBioPortal.

Public Health Relevance

The Bioinformatics Core forms an integral part of the SPORE in Prostate Cancer as it directly supports the timely conduct of research of SPORE projects. The centralization of various bioinformatics services is designed to streamline requests of SPORE investigators to Core personnel with particular areas of expertise, therefore ensuring that services are provided in an efficient manner and with the highest quality. The Core also carries out research and development to identify new bioinformatic methods and rapidly works to implement and deploy these new techniques to make state-of-the-art computational pipelines available to the research groups in the SPORE and at Memorial Sloan Kettering Cancer Center.

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Specialized Center (P50)
Project #
2P50CA092629-16
Application #
9148026
Study Section
Special Emphasis Panel (ZCA1)
Project Start
2001-09-14
Project End
2021-08-31
Budget Start
2016-09-01
Budget End
2017-08-31
Support Year
16
Fiscal Year
2016
Total Cost
Indirect Cost
Name
Sloan-Kettering Institute for Cancer Research
Department
Type
DUNS #
064931884
City
New York
State
NY
Country
United States
Zip Code
10065
Kinsella, Netty; Stattin, Pär; Cahill, Declan et al. (2018) Factors Influencing Men's Choice of and Adherence to Active Surveillance for Low-risk Prostate Cancer: A Mixed-method Systematic Review. Eur Urol 74:261-280
Li, Weiqiang; Middha, Mridu; Bicak, Mesude et al. (2018) Genome-wide Scan Identifies Role for AOX1 in Prostate Cancer Survival. Eur Urol 74:710-719
Aras, Omer; Pearce, Gillian; Watkins, Adam J et al. (2018) An in-vivo pilot study into the effects of FDG-mNP in cancer in mice. PLoS One 13:e0202482
Sjoberg, Daniel D; Vickers, Andrew J; Assel, Melissa et al. (2018) Twenty-year Risk of Prostate Cancer Death by Midlife Prostate-specific Antigen and a Panel of Four Kallikrein Markers in a Large Population-based Cohort of Healthy Men. Eur Urol 73:941-948
Vickers, Andrew J; Young-Afat, Danny A; Ehdaie, Behfar et al. (2018) Just-in-time consent: The ethical case for an alternative to traditional informed consent in randomized trials comparing an experimental intervention with usual care. Clin Trials 15:3-8
Assel, Melissa; Dahlin, Anders; Ulmert, David et al. (2018) Association Between Lead Time and Prostate Cancer Grade: Evidence of Grade Progression from Long-term Follow-up of Large Population-based Cohorts Not Subject to Prostate-specific Antigen Screening. Eur Urol 73:961-967
Han, SoHyun; Stoyanova, Radka; Lee, Hansol et al. (2018) Automation of pattern recognition analysis of dynamic contrast-enhanced MRI data to characterize intratumoral vascular heterogeneity. Magn Reson Med 79:1736-1744
Vickers, Andrew J; Steineck, Gunnar (2018) Prognosis, Effect Modification, and Mediation. Eur Urol 74:243-245
Kinsella, Netty; Helleman, Jozien; Bruinsma, Sophie et al. (2018) Active surveillance for prostate cancer: a systematic review of contemporary worldwide practices. Transl Androl Urol 7:83-97
Hieronymus, Haley; Murali, Rajmohan; Tin, Amy et al. (2018) Tumor copy number alteration burden is a pan-cancer prognostic factor associated with recurrence and death. Elife 7:

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