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  1. Article ; Online: Lyp breakdown and autoimmunity.

    Behrens, Timothy W

    Nature genetics

    2011  Volume 43, Issue 9, Page(s) 821–822

    MeSH term(s) Animals ; Autoimmune Diseases/genetics ; Autoimmune Diseases/immunology ; Dendritic Cells/immunology ; Lymphocyte Activation ; Male ; Protein Tyrosine Phosphatase, Non-Receptor Type 22/genetics ; Protein Tyrosine Phosphatase, Non-Receptor Type 22/metabolism
    Chemical Substances Protein Tyrosine Phosphatase, Non-Receptor Type 22 (EC 3.1.3.48) ; Ptpn22 protein, mouse (EC 3.1.3.48)
    Language English
    Publishing date 2011-08-29
    Publishing country United States
    Document type News ; Comment
    ZDB-ID 1108734-1
    ISSN 1546-1718 ; 1061-4036
    ISSN (online) 1546-1718
    ISSN 1061-4036
    DOI 10.1038/ng.914
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Thinking differently about lupus.

    Wuster, Arthur / Behrens, Timothy W

    eLife

    2016  Volume 5

    Abstract: A search for the genetic causes of an autoimmune disease called systemic lupus erythematosus reveals a new twist on an old story. ...

    Abstract A search for the genetic causes of an autoimmune disease called systemic lupus erythematosus reveals a new twist on an old story.
    MeSH term(s) Genetic Predisposition to Disease ; Humans ; Lupus Erythematosus, Systemic/genetics
    Language English
    Publishing date 2016--29
    Publishing country England
    Document type Journal Article ; Comment
    ZDB-ID 2687154-3
    ISSN 2050-084X ; 2050-084X
    ISSN (online) 2050-084X
    ISSN 2050-084X
    DOI 10.7554/eLife.15352
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: STXBP6

    Lim, Che Kang / Bronson, Paola G / Varade, Jezabel / Behrens, Timothy W / Hammarström, Lennart

    Frontiers in genetics

    2021  Volume 12, Page(s) 736235

    Abstract: Immunoglobulin A Deficiency (IgAD) is a polygenic primary immune deficiency, with a strong genetic association to the human leukocyte antigen (HLA) region. Previous genome-wide association studies (GWAS) have identified five non-HLA risk loci ( ...

    Abstract Immunoglobulin A Deficiency (IgAD) is a polygenic primary immune deficiency, with a strong genetic association to the human leukocyte antigen (HLA) region. Previous genome-wide association studies (GWAS) have identified five non-HLA risk loci (
    Language English
    Publishing date 2021-12-17
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2606823-0
    ISSN 1664-8021
    ISSN 1664-8021
    DOI 10.3389/fgene.2021.736235
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Personalizing medicine for autoimmune and inflammatory diseases.

    Chan, Andrew C / Behrens, Timothy W

    Nature immunology

    2013  Volume 14, Issue 2, Page(s) 106–109

    Abstract: Therapies that target molecular pathways do not provide uniform benefits for all patients at present. New transformative therapies for autoimmune and inflammatory diseases require greater molecular understanding of patient subsets and the ability to ... ...

    Abstract Therapies that target molecular pathways do not provide uniform benefits for all patients at present. New transformative therapies for autoimmune and inflammatory diseases require greater molecular understanding of patient subsets and the ability to personalize targeted therapies for each subset.
    MeSH term(s) Antineoplastic Agents/economics ; Antineoplastic Agents/therapeutic use ; Autoimmune Diseases/genetics ; Autoimmune Diseases/immunology ; Autoimmune Diseases/therapy ; Genetic Heterogeneity ; Humans ; Immunosuppressive Agents/economics ; Immunosuppressive Agents/therapeutic use ; Inflammation/genetics ; Inflammation/immunology ; Inflammation/therapy ; Molecular Targeted Therapy ; Neoplasms/genetics ; Neoplasms/immunology ; Neoplasms/therapy ; Precision Medicine
    Chemical Substances Antineoplastic Agents ; Immunosuppressive Agents
    Language English
    Publishing date 2013-01-18
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2016987-5
    ISSN 1529-2916 ; 1529-2908
    ISSN (online) 1529-2916
    ISSN 1529-2908
    DOI 10.1038/ni.2473
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: geneAttribution: trait agnostic identification of candidate genes associated with noncoding variation.

    Wuster, Arthur / Chang, Diana / Behrens, Timothy W / Bhangale, Tushar R

    Bioinformatics (Oxford, England)

    2017  Volume 33, Issue 4, Page(s) 599–600

    Abstract: Motivation: We have developed geneAttribution, an R package that assigns candidate causal gene(s) to a risk variant identified by a genetic association study such as a GWAS. The method combines user-supplied functional annotation such as expression ... ...

    Abstract Motivation: We have developed geneAttribution, an R package that assigns candidate causal gene(s) to a risk variant identified by a genetic association study such as a GWAS. The method combines user-supplied functional annotation such as expression quantitative trait loci (eQTL) or Hi-C genome conformation data and reports the most likely candidate genes. In the absence of annotation data, geneAttribution relies on the distances between the genes and the input variant.
    Availability and implementation: The package is freely available from http://www.bioconductor.org/ . A quick-start vignette is included with the package.
    Contact: wustera@gene.com.
    Language English
    Publishing date 2017-02-15
    Publishing country England
    Document type Journal Article
    ZDB-ID 1422668-6
    ISSN 1367-4811 ; 1367-4803
    ISSN (online) 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btw698
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  6. Article ; Online: TRAPing a new gene for autoimmunity.

    Behrens, Timothy W / Graham, Robert R

    Nature genetics

    2011  Volume 43, Issue 2, Page(s) 90–91

    MeSH term(s) Acid Phosphatase/genetics ; Alleles ; Autoantibodies/chemistry ; Autoimmune Diseases/genetics ; Autoimmunity ; Brain/metabolism ; Genes, Recessive ; HLA Antigens/metabolism ; Humans ; Isoenzymes/genetics ; Lupus Erythematosus, Systemic/genetics ; Mutation ; Osteochondrodysplasias/genetics ; Osteopontin/genetics ; Phosphorylation ; Risk ; Syndrome ; Tartrate-Resistant Acid Phosphatase
    Chemical Substances Autoantibodies ; HLA Antigens ; Isoenzymes ; Osteopontin (106441-73-0) ; Acid Phosphatase (EC 3.1.3.2) ; Tartrate-Resistant Acid Phosphatase (EC 3.1.3.2)
    Language English
    Publishing date 2011-01-27
    Publishing country United States
    Document type News ; Comment
    ZDB-ID 1108734-1
    ISSN 1546-1718 ; 1061-4036
    ISSN (online) 1546-1718
    ISSN 1061-4036
    DOI 10.1038/ng0211-90
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  7. Article: geneAttribution: trait agnostic identification of candidate genes associated with noncoding variation

    Wuster, Arthur / Chang, Diana / Behrens, Timothy W / Bhangale, Tushar R

    Bioinformatics. 2017 Feb. 15, v. 33, no. 4

    2017  

    Abstract: Motivation: We have developed geneAttribution, an R package that assigns candidate causal gene(s) to a risk variant identified by a genetic association study such as a GWAS. The method combines user-supplied functional annotation such as expression ... ...

    Abstract Motivation: We have developed geneAttribution, an R package that assigns candidate causal gene(s) to a risk variant identified by a genetic association study such as a GWAS. The method combines user-supplied functional annotation such as expression quantitative trait loci (eQTL) or Hi-C genome conformation data and reports the most likely candidate genes. In the absence of annotation data, geneAttribution relies on the distances between the genes and the input variant. Availability and Implementation: The package is freely available from http://www.bioconductor.org/. A quick-start vignette is included with the package. Contact: wustera@gene.com
    Keywords bioinformatics ; computer software ; genes ; quantitative trait loci ; risk
    Language English
    Dates of publication 2017-0215
    Size p. 599-600.
    Publishing place Oxford University Press
    Document type Article
    ZDB-ID 1468345-3
    ISSN 1460-2059 ; 1367-4811 ; 1367-4803
    ISSN (online) 1460-2059 ; 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btw698
    Database NAL-Catalogue (AGRICOLA)

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  8. Article ; Online: ADAR and hnRNPC deficiency synergize in activating endogenous dsRNA-induced type I IFN responses.

    Herzner, Anna-Maria / Khan, Zia / Van Nostrand, Eric L / Chan, Sara / Cuellar, Trinna / Chen, Ronald / Pechuan-Jorge, Ximo / Komuves, Laszlo / Solon, Margaret / Modrusan, Zora / Haley, Benjamin / Yeo, Gene W / Behrens, Timothy W / Albert, Matthew L

    The Journal of experimental medicine

    2021  Volume 218, Issue 9

    Abstract: Cytosolic double-stranded RNA (dsRNA) initiates type I IFN responses. Endogenous retroelements, notably Alu elements, constitute a source of dsRNA. Adenosine-to-inosine (A-to-I) editing by ADAR induces mismatches in dsRNA and prevents recognition by MDA5 ...

    Abstract Cytosolic double-stranded RNA (dsRNA) initiates type I IFN responses. Endogenous retroelements, notably Alu elements, constitute a source of dsRNA. Adenosine-to-inosine (A-to-I) editing by ADAR induces mismatches in dsRNA and prevents recognition by MDA5 and autoinflammation. To identify additional endogenous dsRNA checkpoints, we conducted a candidate screen in THP-1 monocytes and found that hnRNPC and ADAR deficiency resulted in synergistic induction of MDA5-dependent IFN responses. RNA-seq analysis demonstrated dysregulation of Alu-containing introns in hnRNPC-deficient cells via utilization of unmasked cryptic splice sites, including introns containing ADAR-dependent A-to-I editing clusters. These putative MDA5 ligands showed reduced editing in the absence of ADAR, providing a plausible mechanism for the combined effects of hnRNPC and ADAR. This study contributes to our understanding of the control of repetitive element-induced autoinflammation and suggests that patients with hnRNPC-mutated tumors might maximally benefit from ADAR inhibition-based immunotherapy.
    MeSH term(s) Adenosine Deaminase/genetics ; Adenosine Deaminase/metabolism ; Alu Elements ; CRISPR-Cas Systems ; Cytosol/physiology ; Heterogeneous-Nuclear Ribonucleoprotein Group C/genetics ; Heterogeneous-Nuclear Ribonucleoprotein Group C/metabolism ; Humans ; Interferon Type I/genetics ; Interferon Type I/metabolism ; Interferon-Induced Helicase, IFIH1/genetics ; Interferon-Induced Helicase, IFIH1/metabolism ; Introns ; MCF-7 Cells ; Membrane Proteins/genetics ; Membrane Proteins/metabolism ; RNA Editing ; RNA, Double-Stranded/metabolism ; RNA-Binding Proteins/genetics ; RNA-Binding Proteins/metabolism ; THP-1 Cells
    Chemical Substances HNRNPC protein, human ; Heterogeneous-Nuclear Ribonucleoprotein Group C ; IFI27 protein, human ; Interferon Type I ; Membrane Proteins ; RNA, Double-Stranded ; RNA-Binding Proteins ; ADAR protein, human (EC 3.5.4.37) ; Adenosine Deaminase (EC 3.5.4.4) ; IFIH1 protein, human (EC 3.6.1.-) ; Interferon-Induced Helicase, IFIH1 (EC 3.6.4.13)
    Language English
    Publishing date 2021-07-23
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 218343-2
    ISSN 1540-9538 ; 0022-1007
    ISSN (online) 1540-9538
    ISSN 0022-1007
    DOI 10.1084/jem.20201833
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: Genetics of autoimmune diseases--disorders of immune homeostasis.

    Gregersen, Peter K / Behrens, Timothy W

    Nature reviews. Genetics

    2006  Volume 7, Issue 12, Page(s) 917–928

    Abstract: In the past few years, our extensive knowledge of the mammalian immune system and our increasing ability to understand the genetic causes of complex human disease have opened a window onto the pathways that lead to autoimmune disorders. In addition to ... ...

    Abstract In the past few years, our extensive knowledge of the mammalian immune system and our increasing ability to understand the genetic causes of complex human disease have opened a window onto the pathways that lead to autoimmune disorders. In addition to the well-established role of genetic variation that affects the major histocompatibility complex, a number of rare and common variants that affect a range of immunological pathways are now known to have important influences on the phenotypic diversity that is seen among autoimmune diseases. Recent studies have also highlighted a previously unanticipated interplay between the innate and adaptive immune system, providing a new direction for research in this field.
    MeSH term(s) Animals ; Autoimmune Diseases/genetics ; Autoimmunity ; Homeostasis/immunology ; Humans ; Immune System
    Language English
    Publishing date 2006-12
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 2035157-4
    ISSN 1471-0064 ; 1471-0056
    ISSN (online) 1471-0064
    ISSN 1471-0056
    DOI 10.1038/nrg1944
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  10. Article ; Online: Identifying and mitigating batch effects in whole genome sequencing data.

    Tom, Jennifer A / Reeder, Jens / Forrest, William F / Graham, Robert R / Hunkapiller, Julie / Behrens, Timothy W / Bhangale, Tushar R

    BMC bioinformatics

    2017  Volume 18, Issue 1, Page(s) 351

    Abstract: Background: Large sample sets of whole genome sequencing with deep coverage are being generated, however assembling datasets from different sources inevitably introduces batch effects. These batch effects are not well understood and can be due to ... ...

    Abstract Background: Large sample sets of whole genome sequencing with deep coverage are being generated, however assembling datasets from different sources inevitably introduces batch effects. These batch effects are not well understood and can be due to changes in the sequencing protocol or bioinformatics tools used to process the data. No systematic algorithms or heuristics exist to detect and filter batch effects or remove associations impacted by batch effects in whole genome sequencing data.
    Results: We describe key quality metrics, provide a freely available software package to compute them, and demonstrate that identification of batch effects is aided by principal components analysis of these metrics. To mitigate batch effects, we developed new site-specific filters that identified and removed variants that falsely associated with the phenotype due to batch effect. These include filtering based on: a haplotype based genotype correction, a differential genotype quality test, and removing sites with missing genotype rate greater than 30% after setting genotypes with quality scores less than 20 to missing. This method removed 96.1% of unconfirmed genome-wide significant SNP associations and 97.6% of unconfirmed genome-wide significant indel associations. We performed analyses to demonstrate that: 1) These filters impacted variants known to be disease associated as 2 out of 16 confirmed associations in an AMD candidate SNP analysis were filtered, representing a reduction in power of 12.5%, 2) In the absence of batch effects, these filters removed only a small proportion of variants across the genome (type I error rate of 3%), and 3) in an independent dataset, the method removed 90.2% of unconfirmed genome-wide SNP associations and 89.8% of unconfirmed genome-wide indel associations.
    Conclusions: Researchers currently do not have effective tools to identify and mitigate batch effects in whole genome sequencing data. We developed and validated methods and filters to address this deficiency.
    MeSH term(s) Genome-Wide Association Study/methods ; Genotype ; High-Throughput Nucleotide Sequencing ; Humans ; Macular Degeneration/genetics ; Macular Degeneration/pathology ; Phenotype ; Polymorphism, Single Nucleotide ; Principal Component Analysis ; Sequence Analysis, DNA ; Software
    Language English
    Publishing date 2017-07-24
    Publishing country England
    Document type Journal Article
    ZDB-ID 2041484-5
    ISSN 1471-2105 ; 1471-2105
    ISSN (online) 1471-2105
    ISSN 1471-2105
    DOI 10.1186/s12859-017-1756-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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