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1.  Using previously genotyped controls in genome-wide association studies (GWAS): application to the Stroke Genetics Network (SiGN) 
Genome-wide association studies (GWAS) are widely applied to identify susceptibility loci for a variety of diseases using genotyping arrays that interrogate known polymorphisms throughout the genome. A particular strength of GWAS is that it is unbiased with respect to specific genomic elements (e.g., coding or regulatory regions of genes), and it has revealed important associations that would have never been suspected based on prior knowledge or assumptions. To date, the discovered SNPs associated with complex human traits tend to have small effect sizes, requiring very large sample sizes to achieve robust statistical power. To address these issues, a number of efficient strategies have emerged for conducting GWAS, including combining study results across multiple studies using meta-analysis, collecting cases through electronic health records, and using samples collected from other studies as controls that have already been genotyped and made publicly available (e.g., through deposition of de-identified data into dbGaP or EGA). In certain scenarios, it may be attractive to use already genotyped controls and divert resources to standardized collection, phenotyping, and genotyping of cases only. This strategy, however, requires that careful attention be paid to the choice of “public controls” and to the comparability of genetic data between cases and the public controls to ensure that any allele frequency differences observed between groups is attributable to locus-specific effects rather than to a systematic bias due to poor matching (population stratification) or differential genotype calling (batch effects). The goal of this paper is to describe some of the potential pitfalls in using previously genotyped control data. We focus on considerations related to the choice of control groups, the use of different genotyping platforms, and approaches to deal with population stratification when cases and controls are genotyped across different platforms.
doi:10.3389/fgene.2014.00095
PMCID: PMC4010766  PMID: 24808905
genome-wide association study; case-control study; genetic association study; population stratification; power
2.  Creation of an Open-Access, Mutation-Defined Fibroblast Resource for Neurological Disease Research 
PLoS ONE  2012;7(8):e43099.
Our understanding of the molecular mechanisms of many neurological disorders has been greatly enhanced by the discovery of mutations in genes linked to familial forms of these diseases. These have facilitated the generation of cell and animal models that can be used to understand the underlying molecular pathology. Recently, there has been a surge of interest in the use of patient-derived cells, due to the development of induced pluripotent stem cells and their subsequent differentiation into neurons and glia. Access to patient cell lines carrying the relevant mutations is a limiting factor for many centres wishing to pursue this research. We have therefore generated an open-access collection of fibroblast lines from patients carrying mutations linked to neurological disease. These cell lines have been deposited in the National Institute for Neurological Disorders and Stroke (NINDS) Repository at the Coriell Institute for Medical Research and can be requested by any research group for use in in vitro disease modelling. There are currently 71 mutation-defined cell lines available for request from a wide range of neurological disorders and this collection will be continually expanded. This represents a significant resource that will advance the use of patient cells as disease models by the scientific community.
doi:10.1371/journal.pone.0043099
PMCID: PMC3428297  PMID: 22952635
3.  Dynamic Regulation of cpg15 during Activity-Dependent Synaptic Development in the Mammalian Visual System 
During visual system development, neural activity regulates structural changes in connectivity including axonal branching and dendritic growth. Here we have examined a role for the candidate plasticity gene 15 (cpg15), which encodes an activity-regulated molecule that can promote dendritic growth, in this process. We report that cpg15 is expressed in the cat visual system at relatively high levels in the lateral geniculate nucleus (LGN) but at very low levels in its synaptic target, layer 4 of the visual cortex. Prenatally, when cpg15 mRNA in the LGN is most abundant, expression is insensitive to action potential blockade by tetrodotoxin. Postnatally, activity regulation of cpg15 emerges in the LGN coincident with development of ocular dominance columns in the visual cortex. cpg15 can be detected in layers 2/3 and 5/6 of visual cortex postnatally, and expression in layers 2/3 is activity-regulated during known periods of activity-dependent plasticity for these layers. Localization and regulation of cpg15 expression in the visual system are consistent with a presynaptic role for CPG15 in shaping dendritic arbors of target neurons during activity-dependent synaptic rearrangements, both in development and adulthood.
PMCID: PMC3060705  PMID: 10479700
visual system; cpg15; lateral geniculate nucleus; dendritic growth; visual cortex; neuron
4.  CoAIMs: A Cost-Effective Panel of Ancestry Informative Markers for Determining Continental Origins 
PLoS ONE  2010;5(10):e13443.
Background
Genetic ancestry is known to impact outcomes of genotype-phenotype studies that are designed to identify risk for common diseases in human populations. Failure to control for population stratification due to genetic ancestry can significantly confound results of disease association studies. Moreover, ancestry is a critical factor in assessing lifetime risk of disease, and can play an important role in optimizing treatment. As modern medicine moves towards using personal genetic information for clinical applications, it is important to determine genetic ancestry in an accurate, cost-effective and efficient manner. Self-identified race is a common method used to track and control for population stratification; however, social constructs of race are not necessarily informative for genetic applications. The use of ancestry informative markers (AIMs) is a more accurate method for determining genetic ancestry for the purposes of population stratification.
Methodology/Principal Findings
Here we introduce a novel panel of 36 microsatellite (MSAT) AIMs that determines continental admixture proportions. This panel, which we have named Continental Ancestry Informative Markers or CoAIMs, consists of MSAT AIMs that were chosen based upon their measure of genetic variance (Fst), allele frequencies and their suitability for efficient genotyping. Genotype analysis using CoAIMs along with a Bayesian clustering method (STRUCTURE) is able to discern continental origins including Europe/Middle East (Caucasians), East Asia, Africa, Native America, and Oceania. In addition to determining continental ancestry for individuals without significant admixture, we applied CoAIMs to ascertain admixture proportions of individuals of self declared race.
Conclusion/Significance
CoAIMs can be used to efficiently and effectively determine continental admixture proportions in a sample set. The CoAIMs panel is a valuable resource for genetic researchers performing case-control genetic association studies, as it can control for the confounding effects of population stratification. The MSAT-based approach used here has potential for broad applicability as a cost effective tool toward determining admixture proportions.
doi:10.1371/journal.pone.0013443
PMCID: PMC2955551  PMID: 20976178
5.  Use of calcium imaging for analysis of neuronal gap junction coupling 
Neuroscience letters  2008;445(1):26-30.
We recently used western blots for connexin 36 and neuronal dye coupling with neurobiotin to measure developmental decrease in neuronal gap junction coupling in cell cultures. To ask whether Ca2+ imaging also can be used to measure changes in the amount of neuronal gap junction coupling, we defined a Ca2+ coupling coefficient as the percentage of neurons with bicuculline-induced increases in intracellular Ca2+ that are suppressed by blocking gap junctions. We demonstrate in rat and mouse hypothalamic neuronal cultures that the Ca2+ coupling coefficient decreases during culture development, this decrease is prevented by manipulations that also prevent developmental decrease in neuronal gap junction coupling, and the coefficient is low in cultures lacking connexin 36. The results indicate that Ca2+ imaging is a useful tool to quantify the amount of neuronal gap junction coupling in cultures.
doi:10.1016/j.neulet.2008.08.075
PMCID: PMC2585604  PMID: 18778753
Connexin; gap junctions; calcium imaging; NMDA receptors; CREB; cultures
6.  Synaptic NMDA receptor activity boosts intrinsic antioxidant defences 
Nature neuroscience  2008;11(4):476-487.
Intrinsic antioxidant defences are important for neuronal longevity. We show that synaptic activity, acting via NMDA receptor (NMDAR) signaling, boosts antioxidant defences through changes to the thioredoxin-peroxiredoxin system. Synaptic activity enhances thioredoxin activity, facilitates the reduction of overoxidized peroxiredoxins, and promotes resistance to oxidative stress. Resistance is mediated by coordinated transcriptional changes: synaptic NMDAR activity inactivates a novel FOXO target gene, the thioredoxin inhibitor Txnip. Conversely, NMDAR blockade upregulates Txnip in vivo and in vitro, where it binds thioredoxin and promotes vulnerability to oxidative damage. Synaptic activity also up-regulates the peroxiredoxin re-activating genes Sestrin2 and Sulfiredoxin, via C/EBPβ and AP-1 respectively. Mimicking these expression changes is sufficient to strengthen antioxidant defences. Trans-synaptic stimulation of synaptic NMDARs is crucial for boosting antioxidant defences: chronic bath activation of all (synaptic and extrasynaptic) NMDARs induces no antioxidative effects. Thus, synaptic NMDAR activity may influence the progression of pathological processes associated with oxidative damage.
doi:10.1038/nn2071
PMCID: PMC2556874  PMID: 18344994
7.  Whole genome association studies of neuropsychiatric disease: An emerging era of collaborative genetic discovery 
Family history, which includes both common environmental and genetic effects, is associated with an increased risk for many neuropsychiatric diseases. Investigators have identified several disease-causing mutations for specific neuropsychiatric disorders that display Mendelian segregation. Such discoveries can lead to more rational drug design and improved intervention from a better understanding of the underlying biological mechanisms. However, a key challenge of genetic discovery in human complex diseases, including neuropsychiatric disorders, is that most diseases with genetic components display non-Mendelian patterns of inheritance. Recent advances in human population genetics include high-density genome-wide analyses of single nucleotide polymorphisms (SNPs) that make it possible to study complex genetic contributions to human disease. This approach is currently the most powerful strategy for analyzing the genetics of complex diseases. Genome-wide SNP analyses often require a large collaborative effort to collect, manage, and disseminate the numerous samples and corresponding clinical data. In this review we discuss the use of publicly available biorepositories for the collection and distribution of human genetic material, associated phenotypic information, and their use in genome-wide investigations of human neuropsychiatric diseases.
PMCID: PMC2656297  PMID: 19300590
repository; human; neurology; consent; genetics; bioinformatics
8.  Amyotrophic Lateral Sclerosis: An Emerging Era of Collaborative Gene Discovery 
PLoS ONE  2007;2(12):e1254.
Amyotrophic lateral sclerosis (ALS) is the most common form of motor neuron disease (MND). 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. However, most forms of the disease are not obviously familial. Recent advances in human genetics have enabled genome-wide analyses of single nucleotide polymorphisms (SNPs) that make it possible to study complex genetic contributions to human disease. Genome-wide SNP analyses require a large sample size and thus depend upon collaborative efforts to collect and manage the biological samples and corresponding data. Public availability of biological samples (such as DNA), phenotypic and genotypic data further enhances research endeavors. Here we discuss a large collaboration among academic investigators, government, and non-government organizations which has created a public repository of human DNA, immortalized cell lines, and clinical data to further gene discovery in ALS. This resource currently maintains samples and associated phenotypic data from 2332 MND subjects and 4692 controls. This resource should facilitate genetic discoveries which we anticipate will ultimately provide a better understanding of the biological mechanisms of neurodegeneration in ALS.
doi:10.1371/journal.pone.0001254
PMCID: PMC2100166  PMID: 18060051

Results 1-8 (8)