Core C: The Statistical Analysis and Bioinformatics Core of the University of Miami (UM) Udall Center builds on our experience in analysis of genes in PD over the previous twelve years. The goal of the Core is to support the needs of the Projects by applying powerful next-generation sequence analysis approaches, bioinformatics techniques, and established statistical analyses. The Core has integrated informatics, bioinformatics and statistical support. It takes advantage of existing resources within UM in the Hussman Institute for Human Genomics (HIHG) and Center for Computational Science (CCS). The core is lead by Dr. Beecham who is the director of informatics at the HIHG, an expert in genetic association analysis. He replaces Dr. Martin as PI, and has been a Project PI in our Udall Center since its inception. She remains on the core as a co-investigator. Members of the data management, computer, statistical, and bioinformatics staff of the HIHG staff will form the nucleus of the Statistical Analysis and Bioinformatics Core, addressing the projects'needs through the following specific aims: ? To provide the informatics to support database management, storage, and rapid retrieval of family history, clinical, risk factor, genotypic, DNA sequence and RNA expression data for the projects and clinical core. ? To provide analytical support for next-generation sequencing. We will provide support for the entire pipeline of next-generation sequencing data analysis;from data generation to statistical analysis and interpretation. The analyses include quality control, assembly, alignment, variant calling, functional annotation, and phenotype association analyses. ? To provide additional statistical analysis support for all projects and cores. We will conduct various analyses, including quality control, association analysis, parametric and non-parametric linkage, gene-gene and gene-environment interaction, biological pathway analysis, and copy-number variant detection and association.

Agency
National Institute of Health (NIH)
Institute
National Institute of Neurological Disorders and Stroke (NINDS)
Type
Specialized Center (P50)
Project #
5P50NS071674-04
Application #
8539101
Study Section
Special Emphasis Panel (ZNS1-SRB-E)
Project Start
Project End
Budget Start
2013-09-01
Budget End
2014-08-31
Support Year
4
Fiscal Year
2013
Total Cost
$186,645
Indirect Cost
$57,821
Name
University of Miami School of Medicine
Department
Type
DUNS #
052780918
City
Coral Gables
State
FL
Country
United States
Zip Code
33146
Rawlik, Konrad; Rowlatt, Amy; Tenesa, Albert (2016) Imputation of DNA Methylation Levels in the Brain Implicates a Risk Factor for Parkinson's Disease. Genetics 204:771-781
Lubbe, Steven J; Escott-Price, Valentina; Brice, Alexis et al. (2016) Is the MC1R variant p.R160W associated with Parkinson's? Ann Neurol 79:159-61
Nuytemans, Karen; Maldonado, Lizmarie; Ali, Aleena et al. (2016) Overlap between Parkinson disease and Alzheimer disease in ABCA7 functional variants. Neurol Genet 2:e44
El Hokayem, Jimmy; Cukier, Holly N; Dykxhoorn, Derek M (2016) Blood Derived Induced Pluripotent Stem Cells (iPSCs): Benefits, Challenges and the Road Ahead. J Alzheimers Dis Parkinsonism 6:
Esanov, Rustam; Belle, Kinsley C; van Blitterswijk, Marka et al. (2016) C9orf72 promoter hypermethylation is reduced while hydroxymethylation is acquired during reprogramming of ALS patient cells. Exp Neurol 277:171-7
Lubbe, S J; Escott-Price, V; Brice, A et al. (2016) Rare variants analysis of cutaneous malignant melanoma genes in Parkinson's disease. Neurobiol Aging 48:222.e1-222.e7
Hossein-Nezhad, Arash; Fatemi, Roya Pedram; Ahmad, Rili et al. (2016) Transcriptomic Profiling of Extracellular RNAs Present in Cerebrospinal Fluid Identifies Differentially Expressed Transcripts in Parkinson's Disease. J Parkinsons Dis 6:109-17
Xiong, Nian; Li, Nuomin; Martin, Eden et al. (2016) hVMAT2: A Target of Individualized Medication for Parkinson's Disease. Neurotherapeutics 13:623-34
Zeier, Zane; Esanov, Rustam; Belle, Kinsley C et al. (2015) Bromodomain inhibitors regulate the C9ORF72 locus in ALS. Exp Neurol 271:241-50
Pastori, Chiara; Kapranov, Philipp; Penas, Clara et al. (2015) The Bromodomain protein BRD4 controls HOTAIR, a long noncoding RNA essential for glioblastoma proliferation. Proc Natl Acad Sci U S A 112:8326-31

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