NINDS-Genome-Wide Genotyping in Parkinson's Disease: First Stage Analysis and Public Release of Data
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ABSTRACT:
PROVIDER: PRJNA75681 | ENA |
REPOSITORIES: ENA
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Project description:<p>Epidemiological studies have estimated a cumulative prevalence of PD of greater than 1 per thousand. When prevalence is
limited to senior populations, this proportion increases nearly 10-fold. The estimated genetic risk ratio for PD is
approximately 1.7 (70% increased risk for PD if a sibling has PD) for all ages, and increases over 7-fold for those under
age 66 years. The role for genes contributing to the risk of PD is therefore significant.</p>
<p>This study utilized the well characterized <a href="./study.cgi?id=phs000003">collection of North American Caucasians
with Parkinson's disease</a>, and <a href="./study.cgi?id=phs000004">neurologically normal controls</a> from the sample
population which are banked in the National Institute of Neurological Disorders and Stroke (NINDS Repository) collection
for a first stage whole genome analysis. Genome-wide, single nucleotide polymorphism (SNP) genotyping of these publicly
available samples was originally done in 267 Parkinson's disease patients and 270 controls, and this has been extended
to include genome wide genotyping in 939 Parkinson's disease cases and 802 controls.</p>
<p>The NINDS repository was established in 10-2001 towards the goal of developing standardized, broadly useful diagnostic
and other clinical data and a collection of DNA and cell line samples to further advances in gene discovery of neurological
disorders. All samples, phenotypic, and genotypic data are available to the research community including to academics and
industry scientists. In addition, well characterized neurologically normal control subjects are a part of the collection.
This collection formed the basis of this first stage study by Fung et al., and the expanded study by Simon-Sanchez et al.
The genotyping data was generated and provided by the laboratory of Dr. Andrew Singleton NIA, and Dr. John Hardy
NIA (NIH Intramural, funding from NIA and NINDS).</p>
<p><b>Important links to apply for individual-level data</b>
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<li><a href="http://dbgap.ncbi.nlm.nih.gov/aa/wga.cgi?view_pdf&stacc=phs000089.v3.p2" target="_blank">Data Use Certification Requirements (DUC)</a></li>
<li><a href="http://view.ncbi.nlm.nih.gov/dbgap-controlled" target="_blank">Apply here for controlled access to individual level data</a></li>
<li><a href="GetPdf.cgi?id=phd000577" target="_blank">Participant Protection Policy FAQ</a></li>
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</p>
| phs000089.v3.p2 | EGA
Project description:National Institute of Neurological Disorders and Stroke (NINDS) Repository Parkinson's Disease Collection
| PRJNA75381 | ENA
Project description:Genome-wide genotyping in amyotrophic lateral sclerosis and neurologically normal controls: first stage analysis and public release of data
| PRJNA75709 | ENA
Project description:NINDS CIDR Genotyping and Sequencing of Families with Juvenile Myoclonic Epilepsy
| PRJNA276719 | ENA
Project description:The cardinal clinical features of Parkinson's disease result from selective loss of midbrain dopaminergic neurons. The goal of this experiment is to determine the gene expression profiles of these neurons by studying untreated rat substantia nigra pars compacta (SNc) and ventral tegmental area (VTA) dopaminergic neurons using laser capture microscopy to obtain region-specific neuronal mRNA. WARNING: These data are identical to those represented in GEO Series GSE1837.
2004-03-29 | GSE1157 | GEO
Project description:BackgroundNeuroprotection for Parkinson's disease (PD) remains elusive. Biomarkers hold the promise of removing roadblocks to therapy development. The National Institute of Neurological Disorders and Stroke has therefore established the Parkinson's Disease Biomarkers Program to promote discovery of PD biomarkers for use in phase II and III clinical trials.MethodsUsing a novel consortium design, the Parkinson's Disease Biomarker Program is focused on the development of clinical and laboratory-based biomarkers for PD diagnosis, progression, and prognosis. Standardized operating procedures and pooled reference samples were created to allow cross-project comparisons and assessment of batch effects. A web-based Data Management Resource facilitates rapid sharing of data and biosamples across the research community for additional biomarker projects.ResultsEleven consortium projects are ongoing, seven of which recruit participants and obtain biosamples. As of October 2014, 1,082 participants have enrolled (620 PD, 101 with other causes of parkinsonism, 23 essential tremor, and 338 controls), 1,040 of whom have at least one biosample. Six thousand eight hundred ninety-eight total biosamples are available from baseline, 6-, 12-, and 18-month visits: 1,006 DNA, 1,661 RNA, 1,419 whole blood, 1,382 plasma, 1,200 serum, and 230 cerebrospinal fluid (CSF). Quality control analysis of plasma, serum, and CSF samples indicates that almost all samples are high quality (24 of 2,812 samples exceed acceptable hemoglobin levels).ConclusionsBy making samples and data widely available, using stringent operating procedures based on existing standards, hypothesis testing for biomarker discovery, and providing a resource that complements existing programs, the Parkinson's Disease Biomarker Program will accelerate the pace of PD biomarker research. © 2015 International Parkinson and Movement Disorder Society.
| S-EPMC4824671 | biostudies-literature
Project description:Detailed analysis of disease-affected tissue provides insight into molecular mechanisms contributing to pathogenesis. Substantia nigra, striatum and cortex are functionally connected with increasing degrees of alpha-synuclein pathology in Parkinson's disease. Functional and causal pathway analysis of gene expression and proteomic alterations in these three regions revealed pathways that correlated with deposition of alpha-synuclein. Microarray and RNAseq experiments revealed previously unidentified causal changes related to oligodendrocyte function and synaptic vesicle release and other changes were reflected across all brain regions. Importantly a subset of these changes were replicated in Parkinson's disease blood. Proteomic assessment revealed alterations in mitochondria and vesicular transport proteins that preceded gene gene expression changes indicating defects in translation and/or protein turnover. Our combined approach of proteomics, RNAseq and microarray analyses provides a comprehensive view of the molecular changes that accompany alpha-synculein pathology in Parkinson's disease, and may be instrumental in understanding and diagnosing Parkinson's disease progression. Substantia Nigra (3 normal, 3 PD), Striatum (6 normal, 6 PD), Cortex (5 normal, 5 PD), Cortex non-PD neurodegeneration (2 normal, 3 DLB). Note Sample X201264 was used both for Cortex normal and for Cortex nonPD normal
2014-09-01 | E-GEOD-54282 | biostudies-arrayexpress
Project description:Detailed analysis of disease-affected tissue provides insight into molecular mechanisms contributing to pathogenesis. Substantia nigra, striatum and cortex are functionally connected with increasing degrees of alpha-synuclein pathology in Parkinson's disease. Functional and causal pathway analysis of gene expression and proteomic alterations in these three regions revealed pathways that correlated with deposition of alpha-synuclein. Microarray and RNAseq experiments revealed previously unidentified causal changes related to oligodendrocyte function and synaptic vesicle release and other changes were reflected across all brain regions. Importantly a subset of these changes were replicated in Parkinson's disease blood. Proteomic assessment revealed alterations in mitochondria and vesicular transport proteins that preceded gene gene expression changes indicating defects in translation and/or protein turnover. Our combined approach of proteomics, RNAseq and microarray analyses provides a comprehensive view of the molecular changes that accompany alpha-synculein pathology in Parkinson's disease, and may be instrumental in understanding and diagnosing Parkinson's disease progression.
2014-09-01 | GSE54282 | GEO
Project description:Biomarkers for Parkinson's disease (PD) diagnosis, prognostication and clinical trial cohort selection are an urgent need. While many promising markers have been discovered through the National Institute of Neurological Disorders and Stroke Parkinson's Disease Biomarker Program (PDBP) and other mechanisms, no single PD marker or set of markers are ready for clinical use. Here we discuss the current state of biomarker discovery for platforms relevant to PDBP. We discuss the role of the PDBP in PD biomarker identification and present guidelines to facilitate their development. These guidelines include: harmonizing procedures for biofluid acquisition and clinical assessments, replication of the most promising biomarkers, support and encouragement of publications that report negative findings, longitudinal follow-up of current cohorts including the PDBP, testing of wearable technologies to capture readouts between study visits and development of recently diagnosed (de novo) cohorts to foster identification of the earliest markers of disease onset.
| S-EPMC5619098 | biostudies-literature