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  1. Article ; Online: A society-wide conversation is needed about germline genome editing using CRISPR.

    Birney, Ewan

    Nature medicine

    2024  Volume 30, Issue 1, Page(s) 30–32

    MeSH term(s) Gene Editing ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; CRISPR-Cas Systems/genetics ; Germ Cells
    Language English
    Publishing date 2024-01-05
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1220066-9
    ISSN 1546-170X ; 1078-8956
    ISSN (online) 1546-170X
    ISSN 1078-8956
    DOI 10.1038/s41591-023-02681-1
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  2. Article ; Online: Mendelian Randomization.

    Birney, Ewan

    Cold Spring Harbor perspectives in medicine

    2022  Volume 12, Issue 4

    Abstract: Mendelian randomization borrows statistical techniques from economics to allow researchers to analyze the effects of the environment, drug treatments, and other factors on human biology and disease. Taking advantage of the fact that genetic variation is ... ...

    Abstract Mendelian randomization borrows statistical techniques from economics to allow researchers to analyze the effects of the environment, drug treatments, and other factors on human biology and disease. Taking advantage of the fact that genetic variation is randomized among children from the same parents, it allows genetic variants known to influence factors like alcohol consumption or low-density lipoprotein (LDL) levels to be used as instrumental variables that can disentangle the effects of these factors on outcomes such as pregnancy or cardiovascular disease, respectively. There are caveats to analyses using Mendelian randomization and related techniques that researchers should be aware of, but they are increasingly powerful tools for solving problems in epidemiology and human biology.
    MeSH term(s) Cardiovascular Diseases/genetics ; Child ; Genetic Variation ; Humans ; Mendelian Randomization Analysis/methods ; Risk Factors
    Language English
    Publishing date 2022-05-17
    Publishing country United States
    Document type Journal Article ; Review
    ISSN 2157-1422
    ISSN (online) 2157-1422
    DOI 10.1101/cshperspect.a041302
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  3. Article ; Online: The International Human Genome Project.

    Birney, Ewan

    Human molecular genetics

    2021  Volume 30, Issue R2, Page(s) R161–R163

    Abstract: The human genome project was conceived and executed as an international project, due to both pragmatic and principled reasons. This internationality has served the project well, with the resulting human genome being freely available for all researchers ... ...

    Abstract The human genome project was conceived and executed as an international project, due to both pragmatic and principled reasons. This internationality has served the project well, with the resulting human genome being freely available for all researchers in all countries. Over time the reference human genome will likely have to evolve to a graph genome, and tap into more diverse sequences worldwide. A similar international mindset underpins data analysis for the interpretation of the human genome from basic to clinical research.
    MeSH term(s) Animals ; Databases, Genetic ; Genetics, Medical/trends ; Genome, Human ; Human Genome Project ; Humans ; Internationality ; Research/trends
    Language English
    Publishing date 2021-07-15
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 1108742-0
    ISSN 1460-2083 ; 0964-6906
    ISSN (online) 1460-2083
    ISSN 0964-6906
    DOI 10.1093/hmg/ddab198
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    Zs.A 3469: Show issues Location:
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  4. Article ; Online: The Convergence of Research and Clinical Genomics.

    Birney, Ewan

    American journal of human genetics

    2019  Volume 104, Issue 5, Page(s) 781–783

    MeSH term(s) Biomedical Research ; Genomics/methods ; Humans ; Interdisciplinary Communication
    Language English
    Publishing date 2019-05-03
    Publishing country United States
    Document type Journal Article
    ZDB-ID 219384-x
    ISSN 1537-6605 ; 0002-9297
    ISSN (online) 1537-6605
    ISSN 0002-9297
    DOI 10.1016/j.ajhg.2019.04.003
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  5. Article ; Online: CNest: A novel copy number association discovery method uncovers 862 new associations from 200,629 whole-exome sequence datasets in the UK Biobank.

    Fitzgerald, Tomas / Birney, Ewan

    Cell genomics

    2022  Volume 2, Issue 8, Page(s) 100167

    Abstract: Copy number variation (CNV) is known to influence human traits, having a rich history of research into common and rare genetic disease, and although CNV is accepted as an important class of genomic variation, progress on copy-number-based genome-wide ... ...

    Abstract Copy number variation (CNV) is known to influence human traits, having a rich history of research into common and rare genetic disease, and although CNV is accepted as an important class of genomic variation, progress on copy-number-based genome-wide association studies (GWASs) from next-generation sequencing (NGS) data has been limited. Here we present a novel method for large-scale copy number analysis from NGS data generating robust copy number estimates and allowing copy number GWASs (CN-GWASs) to be performed genome-wide in discovery mode. We provide a detailed analysis in the UK Biobank resource and a specifically designed software package. We use these methods to perform CN-GWAS analysis across 78 human traits, discovering over 800 genetic associations that are likely to contribute strongly to trait distributions. Finally, we compare CNV and SNP association signals across the same traits and samples, defining specific CNV association classes.
    Language English
    Publishing date 2022-08-10
    Publishing country United States
    Document type Journal Article
    ISSN 2666-979X
    ISSN (online) 2666-979X
    DOI 10.1016/j.xgen.2022.100167
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  6. Article ; Online: Using Nanocompore to Identify RNA Modifications from Direct RNA Nanopore Sequencing Data.

    Mulroney, Logan / Birney, Ewan / Leonardi, Tommaso / Nicassio, Francesco

    Current protocols

    2023  Volume 3, Issue 2, Page(s) e683

    Abstract: RNA modifications can alter the behavior of RNA molecules depending on where they are located on the strands. Traditionally, RNA modifications have been detected and characterized by biophysical assays, mass spectrometry, or specific next-generation ... ...

    Abstract RNA modifications can alter the behavior of RNA molecules depending on where they are located on the strands. Traditionally, RNA modifications have been detected and characterized by biophysical assays, mass spectrometry, or specific next-generation sequencing techniques, but are limited to specific modifications or are low throughput. Nanopore is a platform capable of sequencing RNA strands directly, which permits transcriptome-wide detection of RNA modifications. RNA modifications alter the nanopore raw signal relative to the canonical form of the nucleotide, and several software tools detect these signal alterations. One such tool is Nanocompore, which compares the ionic current features between two different experimental conditions (i.e., with and without RNA modifications) to detect RNA modifications. Nanocompore is not limited to a single type of RNA modification, has a high specificity for detecting RNA modifications, and does not require model training. To use Nanocompore, the following steps are needed: (i) the data must be basecalled and aligned to the reference transcriptome, then the raw ionic current signals are aligned to the sequences and transformed into a Nanocompore-compatible format; (ii) finally, the statistical testing is conducted on the transformed data and produces a table of p-value predictions for the positions of the RNA modifications. These steps can be executed with several different methods, and thus we have also included two alternative protocols for running Nanocompore. Once the positions of RNA modifications are determined by Nanocompore, users can investigate their function in various metabolic pathways. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol: RNA modification detection by Nanocompore Alternate Protocol 1: RNA modification detection by Nanocompore with f5c Alternate Protocol 2: RNA modification detection by Nanocompore using Nextflow.
    MeSH term(s) Nanopore Sequencing/methods ; Nanopores ; RNA/chemistry ; RNA/genetics ; RNA/metabolism ; Sequence Analysis, RNA ; High-Throughput Nucleotide Sequencing/methods
    Chemical Substances RNA (63231-63-0)
    Language English
    Publishing date 2023-02-25
    Publishing country United States
    Document type Journal Article
    ISSN 2691-1299
    ISSN (online) 2691-1299
    DOI 10.1002/cpz1.683
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  7. Article ; Online: From genetic variation to precision medicine.

    Sergouniotis, Panagiotis I / Fitzgerald, Tomas / Birney, Ewan

    Cambridge prisms. Precision medicine

    2023  Volume 1, Page(s) e7

    Abstract: Genetics has been an important tool for discovering new aspects of biology across life. In humans, there is growing momentum behind the application of this knowledge to drive innovation in clinical care, most notably through developments in precision ... ...

    Abstract Genetics has been an important tool for discovering new aspects of biology across life. In humans, there is growing momentum behind the application of this knowledge to drive innovation in clinical care, most notably through developments in precision medicine. Nowhere has the impact of genetics on clinical practice been more striking than in the field of rare disorders. For most of these conditions, individual disease susceptibility is influenced by DNA sequence variation in a single or a small number of genes. In contrast, most common disorders are multifactorial and are caused by a complex interplay of multiple genetic, environmental and stochastic factors. The longstanding division of human disease genetics into rare and common components has obscured the continuum of human traits and echoes aspects of the century-old debate between the Mendelian and biometric views of human genetics. In this article, we discuss the differences in data and concepts between rare and common disease genetics. Opportunities to unify these two areas are noted and the importance of adopting a holistic perspective that integrates diverse genetic and environmental factors is discussed.
    Language English
    Publishing date 2023-01-24
    Publishing country England
    Document type Journal Article
    ISSN 2752-6143
    ISSN (online) 2752-6143
    DOI 10.1017/pcm.2022.11
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  8. Article ; Online: Personalized profiles for disease risk must capture all facets of health.

    McCarthy, Mark / Birney, Ewan

    Nature

    2021  Volume 597, Issue 7875, Page(s) 175–177

    MeSH term(s) Diet ; Disease Susceptibility ; Environment ; Exercise ; Gene-Environment Interaction ; Genetic Variation ; Health Status ; Holistic Health/trends ; Humans ; Multifactorial Inheritance ; Precision Medicine/methods ; Precision Medicine/trends ; Risk Assessment/methods ; Socioeconomic Factors
    Language English
    Publishing date 2021-09-06
    Publishing country England
    Document type Journal Article
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/d41586-021-02401-0
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    Zs.MO 244: Show issues

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  9. Article ; Online: The Mighty Fruit Fly Moves into Outbred Genetics.

    Birney, Ewan

    PLoS genetics

    2016  Volume 12, Issue 11, Page(s) e1006388

    MeSH term(s) Animals ; Drosophila ; Drosophila melanogaster ; Larva
    Language English
    Publishing date 2016-11-03
    Publishing country United States
    Document type Journal Article ; Comment
    ZDB-ID 2186725-2
    ISSN 1553-7404 ; 1553-7390
    ISSN (online) 1553-7404
    ISSN 1553-7390
    DOI 10.1371/journal.pgen.1006388
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  10. Article: Journey to the genetic interior. Interview by Stephen S Hall.

    Birney, Ewan

    Scientific American

    2012  Volume 307, Issue 4, Page(s) 80–2, 84

    MeSH term(s) Computational Biology ; DNA, Intergenic ; Gene Expression Regulation ; Genome, Human ; Humans
    Chemical Substances DNA, Intergenic
    Language English
    Publishing date 2012-10
    Publishing country United States
    Document type Interview
    ZDB-ID 246-x
    ISSN 1946-7087 ; 0036-8733
    ISSN (online) 1946-7087
    ISSN 0036-8733
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