Dataset Information

National Institute of Neurological Disorders and Stroke (NINDS) Repository Neurologically Normal Control Collection

ABSTRACT:

The NINDS repository (http://ccr.coriell.org/ninds/) was established in October 2001 with the goal of developing standardized, broadly useful diagnostic and other clinical data, as well as a collection of DNA and cell line samples to further advance gene discovery of neurological disorders. All samples and both phenotypic and genotypic data are available to the research community including academic and industry scientists. A set of samples from individuals who do not have neurological disease was felt to be essential to allow gene discovery in neurological disorders to proceed. Towards this goal, the NINDS has and is collecting samples and phenotypic data on neurologically normal individuals. The data being collected includes demographic, ethnic, and exclusion of neurological disease information. Variables were measured using the Control Clinical Data Elements form. As of June 2007, there are a total of 2157 publicly available and an additional >2000 which will be added to the publicly available biomaterials collection shortly.

Blood samples were drawn from neurologically normal, unrelated, individuals at many different sites. Spouses, convenience controls, and population controls were all included in this collection. Each participant underwent a detailed medical history interview and had no family history on specific query of Alzheimer's disease, amyotrophic lateral sclerosis, ataxia, autism, bipolar disorder, brain aneurysm, dementia, dystonia, or Parkinson's disease. Folstein Mini-mental state examination scores ranged from 26-30 and are available on a subset of individuals. All participants were interviewed for family history in detail and specifically had no first degree relative with any of the following: amyotrophic lateral sclerosis, ataxia, autism, brain aneurysm, dystonia, Parkinson's disease, and schizophrenia.

A subset of neurologically normal control subjects was utilized in NINDS Parkinson's Disease, NINDS Amyotrophic Lateral Sclerosis and Controls and NINDS Ischemic Stroke Genetics Study (ISGS).

PROVIDER: phs000004.v1.p1 | EGA |

REPOSITORIES: EGA

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Publications

Genome-wide SNP assay reveals structural genomic variation, extended homozygosity and cell-line induced alterations in normal individuals.

Simon-Sanchez Javier J Scholz Sonja S Fung Hon-Chung HC Matarin Mar M Hernandez Dena D Gibbs J Raphael JR Britton Angela A de Vrieze Fabienne Wavrant FW Peckham Elizabeth E Gwinn-Hardy Katrina K Crawley Anthony A Keen Judith C JC Nash Josefina J Borgaonkar Digamber D Hardy John J Singleton Andrew A

Human molecular genetics 20061120 1

The recent hapmap effort has placed focus on the application of genome-wide SNP analysis to assess the contribution of genetic variability, particularly SNPs, to traits such as disease. Here, we describe the utility of genome-wide SNP analysis in the direct detection of extended homozygosity and structural genomic variation. We use this approach to assess the frequency of genomic alterations resulting from the lymphoblast immortalization and culture processes commonly used in cell repositories. ...[more]

PMID: 17116639

Publication: 1/2

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Project description:The National Institute of Neurological Disorders and Stroke (NINDS) Human Genetics Resource Center: DNA and Cell Line Repository (<a href="http://ccr.coriell.org/Sections/Collections/NINDS/?SsId=10">the NINDS Repository</a>), banks phenotypic data and biological samples, including from individuals with motor neuron disease, in order to facilitate gene discovery in neurological disorders. Those samples are used in a number of studies, and genotyping data from studies using this resource are encouraged to be shared via dbGaP. Many studies have already shared data in this fashion, which in turn, can be linked back to the biologicals banked at the NINDS Repository. Motor Neuron Disease is characterized by selective degeneration of the motor neurons of the spinal cord, brainstem, or motor cortex. Clinical subtypes are distinguished by the major site of degeneration. In Amyotrophic Lateral Sclerosis (ALS), there is involvement of upper, lower, and brainstem motor neurons. In progressive muscular atrophy and related syndromes, the motor neurons in the spinal cord are primarily affected. With progressive bulbar palsy, the initial degeneration occurs in the brainstem. In primary lateral sclerosis, the cortical neurons are affected in isolation (Adams et al, Principles of Neurology, 6th ed, p 1089). The Motor Neuron Disease Collection of DNA and cell lines in the NINDS Repository is largely Amyotrophic Lateral Sclerosis cases (others include progressive muscular atrophy, primary lateral sclerosis, progressive bulbar palsy, Kennedy's disease). Amyotrophic lateral sclerosis (ALS) is the most common form of motor neuron disease (MND). Although ALS is the most common MND, it is still a relatively rare disease with an incidence of around 1.6 per 100,000 in the United States. It is currently incurable and treatment is largely limited to supportive care. Family history is associated with an increased risk of ALS, and many Mendelian causes have been discovered (including SOD1). However, most forms of the disease are not obviously familial. It is suspected that the sporadic forms of neurodegenerative disorders are caused by multiple genetic variants that individually make relatively weak contributions to risk. There is also an associated Control collection (see <a href="./study.cgi?study_id=phs000004.v1.p1">dbGaP</a> and <a href="http://ccr.coriell.org/Sections/Collections/NINDS/Population.aspx?PgId=194&coll=ND"> Coriell</a>). Studies in motor Neuron Disease may use cases from the NINDS repository, controls from the NINDS repository, as well as cases, and controls, from other sources. A subset of subjects from The National Institute of Neurological Disorders and Stroke (NINDS) Human Genetics Resource Center: DNA and Cell Line Repository (the NINDS Repository): Motor Neuron/Amyotrophic Lateral Sclerosis (ALS) Study was utilized in the <a href="./study.cgi?id=phs000101">Genome-wide genotyping in amyotrophic lateral sclerosis and neurologically normal controls: first stage analysis and public release of data</a> study. Note: The publication <a href="http://www.ncbi.nlm.nih.gov/pubmed/19193627" target="_blank">Chio et al., 2009</a> states that "Raw sample-level genotype data from the initial GWAS study ... are available for download through the dbGAP portal (<a href="./study.cgi?id=phs000006" target="_blank">phs000006.v1.p1</a>)". Instead, please follow this link: <a href="./study.cgi?study_id=phs000101.v1.p1">phs000101.v1.p1</a>.

Project description: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. 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. 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). Important links to apply for individual-level data <ol> <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> </ol>

Project description:The third leading cause of death in the United States, stroke is an acute neurological event leading to death of neural tissues. Although the majority of strokes are ischemic strokes, meaning there is oxygen deprivation to the brain, almost 20% of strokes are hemorrhagic, resulting from bleeding into the brain. Stroke is a complex disorder and likely multigenic in nature, resulting from a combination of genetic and environmental factors. These well characterized risk factors that contribute to the incidence of stroke include hypertension, cardiac disease, sickle cell disease, hyperhomocysteinemia, family history of stroke and smoking. ISGS aim is to perform a prospective genetic association study of ischemic stroke focusing on the hemostatic system. ISGS is a 5-center case-control study of first-ever ischemic stroke cases and concurrent controls individually matched for age, sex and recruitment site. This data includes that from subjects both banked in the <a href="http://ccr.coriell.org/Sections/Collections/NINDS/?SsId=10"> NINDS repository</a> with biologicals publicly available, and those whose samples are not banked/not available.  This study utilized the <a href="./study.cgi?id=phs000005">NINDS Repository Cerebrovascular/Stroke Study</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.

Dataset Information

National Institute of Neurological Disorders and Stroke (NINDS) Repository Neurologically Normal Control Collection

Publications

Genome-wide SNP assay reveals structural genomic variation, extended homozygosity and cell-line induced alterations in normal individuals.

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