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  1. Article ; Online: Understanding how non-coding genomic polymorphisms affect gene expression.

    Koester, S E / Insel, T R

    Molecular psychiatry

    2016  Volume 21, Issue 4, Page(s) 448–449

    Abstract: ... to the research community. The project is testing the role of genomic variation in altering gene expression across ...

    Abstract The NIH Common Fund GTEx project is designed to serve as a data and post-mortem tissue resource to the research community. The project is testing the role of genomic variation in altering gene expression across a wide array of tissues in a large number of human post-mortem donors. Both data and tissue samples are available to the research community for additional studies.
    MeSH term(s) Brain/metabolism ; Brain/physiology ; Gene Expression ; Gene Expression Regulation ; Genome-Wide Association Study ; Genomics/methods ; Humans ; Mental Disorders/genetics ; Mental Health ; Polymorphism, Genetic
    Language English
    Publishing date 2016-04
    Publishing country England
    Document type Journal Article
    ZDB-ID 1330655-8
    ISSN 1476-5578 ; 1359-4184
    ISSN (online) 1476-5578
    ISSN 1359-4184
    DOI 10.1038/mp.2015.226
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

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  2. Article: Understanding the Dynamics of Gene Regulatory Systems; Characterisation and Clinical Relevance of cis-Regulatory Polymorphisms.

    Cowie, Philip / Ross, Ruth / MacKenzie, Alasdair

    Biology

    2013  Volume 2, Issue 1, Page(s) 64–84

    Abstract: Modern genetic analysis has shown that most polymorphisms associated with human disease are non ... gene expression. It has been hypothesised that many diseases may be due to polymorphisms within CRSs that alter ... an understanding of the functions of CRSs, and how they are affected by SNPs and epigenetic modification, is ...

    Abstract Modern genetic analysis has shown that most polymorphisms associated with human disease are non-coding. Much of the functional information contained in the non-coding genome consists of cis-regulatory sequences (CRSs) that are required to respond to signal transduction cues that direct cell specific gene expression. It has been hypothesised that many diseases may be due to polymorphisms within CRSs that alter their responses to signal transduction cues. However, identification of CRSs, and the effects of allelic variation on their ability to respond to signal transduction cues, is still at an early stage. In the current review we describe the use of comparative genomics and experimental techniques that allow for the identification of CRSs building on recent advances by the ENCODE consortium. In addition we describe techniques that allow for the analysis of the effects of allelic variation and epigenetic modification on CRS responses to signal transduction cues. Using specific examples we show that the interactions driving these elements are highly complex and the effects of disease associated polymorphisms often subtle. It is clear that gaining an understanding of the functions of CRSs, and how they are affected by SNPs and epigenetic modification, is essential to understanding the genetic basis of human disease and stratification whilst providing novel directions for the development of personalised medicine.
    Language English
    Publishing date 2013-01-09
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2661517-4
    ISSN 2079-7737
    ISSN 2079-7737
    DOI 10.3390/biology2010064
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Understanding the Dynamics of Gene Regulatory Systems; Characterisation and Clinical Relevance of cis-Regulatory Polymorphisms

    Cowie, Philip / Ross, Ruth / MacKenzie, Alasdair

    Biology. 2013 Jan. 09, v. 2, no. 1

    2013  

    Abstract: Modern genetic analysis has shown that most polymorphisms associated with human disease are non ... gene expression. It has been hypothesised that many diseases may be due to polymorphisms within CRSs that alter ... an understanding of the functions of CRSs, and how they are affected by SNPs and epigenetic modification, is ...

    Abstract Modern genetic analysis has shown that most polymorphisms associated with human disease are non-coding. Much of the functional information contained in the non-coding genome consists of cis-regulatory sequences (CRSs) that are required to respond to signal transduction cues that direct cell specific gene expression. It has been hypothesised that many diseases may be due to polymorphisms within CRSs that alter their responses to signal transduction cues. However, identification of CRSs, and the effects of allelic variation on their ability to respond to signal transduction cues, is still at an early stage. In the current review we describe the use of comparative genomics and experimental techniques that allow for the identification of CRSs building on recent advances by the ENCODE consortium. In addition we describe techniques that allow for the analysis of the effects of allelic variation and epigenetic modification on CRS responses to signal transduction cues. Using specific examples we show that the interactions driving these elements are highly complex and the effects of disease associated polymorphisms often subtle. It is clear that gaining an understanding of the functions of CRSs, and how they are affected by SNPs and epigenetic modification, is essential to understanding the genetic basis of human disease and stratification whilst providing novel directions for the development of personalised medicine.
    Keywords alleles ; allelic variation ; epigenetics ; gene expression ; genetic analysis ; genomics ; human diseases ; medicine ; signal transduction ; single nucleotide polymorphism
    Language English
    Dates of publication 2013-0109
    Size p. 64-84.
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article
    ZDB-ID 2661517-4
    ISSN 2079-7737
    ISSN 2079-7737
    DOI 10.3390/biology2010064
    Database NAL-Catalogue (AGRICOLA)

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  4. Article ; Online: Understanding the Dynamics of Gene Regulatory Systems; Characterisation and Clinical Relevance of cis-Regulatory Polymorphisms

    Philip Cowie / Ruth Ross / Alasdair MacKenzie

    Biology, Vol 2, Iss 1, Pp 64-

    2013  Volume 84

    Abstract: Modern genetic analysis has shown that most polymorphisms associated with human disease are non ... gene expression. It has been hypothesised that many diseases may be due to polymorphisms within CRSs that alter ... an understanding of the functions of CRSs, and how they are affected by SNPs and epigenetic modification, is ...

    Abstract Modern genetic analysis has shown that most polymorphisms associated with human disease are non-coding. Much of the functional information contained in the non-coding genome consists of cis-regulatory sequences (CRSs) that are required to respond to signal transduction cues that direct cell specific gene expression. It has been hypothesised that many diseases may be due to polymorphisms within CRSs that alter their responses to signal transduction cues. However, identification of CRSs, and the effects of allelic variation on their ability to respond to signal transduction cues, is still at an early stage. In the current review we describe the use of comparative genomics and experimental techniques that allow for the identification of CRSs building on recent advances by the ENCODE consortium. In addition we describe techniques that allow for the analysis of the effects of allelic variation and epigenetic modification on CRS responses to signal transduction cues. Using specific examples we show that the interactions driving these elements are highly complex and the effects of disease associated polymorphisms often subtle. It is clear that gaining an understanding of the functions of CRSs, and how they are affected by SNPs and epigenetic modification, is essential to understanding the genetic basis of human disease and stratification whilst providing novel directions for the development of personalised medicine.
    Keywords gene regulation ; cis-regulatory variation ; non-coding DNA ; chromatin ; signal transduction ; drug response stratification ; cell specificity ; context dependency ; ENCODE consortium ; Biology (General) ; QH301-705.5
    Subject code 621
    Language English
    Publishing date 2013-01-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article: From GWAS to Gene: Transcriptome-Wide Association Studies and Other Methods to Functionally Understand GWAS Discoveries.

    Li, Binglan / Ritchie, Marylyn D

    Frontiers in genetics

    2021  Volume 12, Page(s) 713230

    Abstract: ... have unknown functions. The valley between non-coding GWAS discoveries and downstream affected genes ... genomic regulatory roles that non-coding regions play in the transcriptional activities of genes. In this review ... or traits. The majority of GWAS discoveries are located in non-coding regions of the human genome and ...

    Abstract Since their inception, genome-wide association studies (GWAS) have identified more than a hundred thousand single nucleotide polymorphism (SNP) loci that are associated with various complex human diseases or traits. The majority of GWAS discoveries are located in non-coding regions of the human genome and have unknown functions. The valley between non-coding GWAS discoveries and downstream affected genes hinders the investigation of complex disease mechanism and the utilization of human genetics for the improvement of clinical care. Meanwhile, advances in high-throughput sequencing technologies reveal important genomic regulatory roles that non-coding regions play in the transcriptional activities of genes. In this review, we focus on data integrative bioinformatics methods that combine GWAS with functional genomics knowledge to identify genetically regulated genes. We categorize and describe two types of data integrative methods. First, we describe fine-mapping methods. Fine-mapping is an exploratory approach that calibrates likely causal variants underneath GWAS signals. Fine-mapping methods connect GWAS signals to potentially causal genes through statistical methods and/or functional annotations. Second, we discuss gene-prioritization methods. These are hypothesis generating approaches that evaluate whether genetic variants regulate genes via certain genetic regulatory mechanisms to influence complex traits, including colocalization, mendelian randomization, and the transcriptome-wide association study (TWAS). TWAS is a gene-based association approach that investigates associations between genetically regulated gene expression and complex diseases or traits. TWAS has gained popularity over the years due to its ability to reduce multiple testing burden in comparison to other variant-based analytic approaches. Multiple types of TWAS methods have been developed with varied methodological designs and biological hypotheses over the past 5 years. We dive into discussions of how TWAS methods differ in many aspects and the challenges that different TWAS methods face. Overall, TWAS is a powerful tool for identifying complex trait-associated genes. With the advent of single-cell sequencing, chromosome conformation capture, gene editing technologies, and multiplexing reporter assays, we are expecting a more comprehensive understanding of genomic regulation and genetically regulated genes underlying complex human diseases and traits in the future.
    Language English
    Publishing date 2021-09-30
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2606823-0
    ISSN 1664-8021
    ISSN 1664-8021
    DOI 10.3389/fgene.2021.713230
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