Structural and Functional Bioinformatics Group

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Now showing 1 - 5 of 296
  • Article

    Influence of autozygosity on common disease risk across the phenotypic spectrum.

    (Elsevier BV, 2023-09-26) Malawsky, Daniel S; van Walree, Eva; Jacobs, Benjamin M; Heng, Teng Hiang; Huang, Qin Qin; Sabir, Ataf H; Rahman, Saadia; Sharif, Saghira Malik; Khan, Ahsan; Mirkov, Maša Umićević; 23andMe Research Team; Genes & Health Research Team; Kuwahara, Hiroyuki; Gao, Xin; Alkuraya, Fowzan S; Posthuma, Danielle; Newman, William G; Griffiths, Christopher J; Mathur, Rohini; van Heel, David A; Finer, Sarah; O'Connell, Jared; Martin, Hilary C; Computational Bioscience Research Center (CBRC); Computer, Electrical and Mathematical Science and Engineering (CEMSE) Division; Computer Science Program; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.; Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Department of Complex Trait Genetics Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU Amsterdam, Amsterdam, the Netherlands.; Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK; Wolfson Institute of Population Health, Queen Mary University of London, London, UK.; West Midlands Regional Clinical Genetics Unit, Birmingham Women's and Children's NHS FT, Birmingham, UK; Institute of Cancer and Genomics, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.; Queen Square Institute of Neurology, University College London, London, UK.; Yorkshire Regional Genetics Service, Leeds Teaching Hospitals NHS Trust, Leeds, UK.; Waltham Forest Council, Waltham Forest Town Hall, Forest Road, Walthamstow E17 4JF, UK.; Congenica Limited, BioData Innovation Centre, Wellcome Genome Campus, Hinxton, UK.; Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.; Department of Complex Trait Genetics Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU Amsterdam, Amsterdam, the Netherlands.; Division of Evolution, Infection and Genomics, Faculty of Biology, Medicine and Human Sciences, University of Manchester, Manchester M13 9PL, UK; Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester M13 9WL, UK.; Wolfson Institute of Population Health, Queen Mary University of London, London, UK; MRC and Asthma UK Centre in Allergic Mechanisms of Asthma, King's College London, London, UK.; Wolfson Institute of Population Health, Queen Mary University of London, London, UK.; Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK.; 23andMe, Inc., Sunnyvale, CA, USA.

    Autozygosity is associated with rare Mendelian disorders and clinically relevant quantitative traits. We investigated associations between the fraction of the genome in runs of homozygosity (FROH) and common diseases in Genes & Health (n = 23,978 British South Asians), UK Biobank (n = 397,184), and 23andMe. We show that restricting analysis to offspring of first cousins is an effective way of reducing confounding due to social/environmental correlates of FROH. Within this group in G&H+UK Biobank, we found experiment-wide significant associations between FROH and twelve common diseases. We replicated associations with type 2 diabetes (T2D) and post-traumatic stress disorder via within-sibling analysis in 23andMe (median n = 480,282). We estimated that autozygosity due to consanguinity accounts for 5%–18% of T2D cases among British Pakistanis. Our work highlights the possibility of widespread non-additive genetic effects on common diseases and has important implications for global populations with high rates of consanguinity.

  • Article

    Repetitive DNA sequence detection and its role in the human genome

    (Springer Science and Business Media LLC, 2023-09-19) Liao, Xingyu; Zhu, Wufei; Zhou, Juexiao; Li, Haoyang; Xu, Xiaopeng; Zhang, Bin; Gao, Xin; Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955, Saudi Arabia; Computer, Electrical and Mathematical Science and Engineering (CEMSE) Division; Computational Bioscience Research Center (CBRC); Computer Science Program; Department of Endocrinology, Yichang Central People’s Hospital, The First College of Clinical Medical Science, China Three Gorges University, 443000, Yichang, P.R. China

    Repetitive DNA sequences playing critical roles in driving evolution, inducing variation, and regulating gene expression. In this review, we summarized the definition, arrangement, and structural characteristics of repeats. Besides, we introduced diverse biological functions of repeats and reviewed existing methods for automatic repeat detection, classification, and masking. Finally, we analyzed the type, structure, and regulation of repeats in the human genome and their role in the induction of complex diseases. We believe that this review will facilitate a comprehensive understanding of repeats and provide guidance for repeat annotation and in-depth exploration of its association with human diseases.

  • Preprint

    CryoAlign: feature-based method for global and local 3D alignment of EM density maps

    (arXiv, 2023-09-17) He, Bintao; Zhang, Fa; Feng, Chenjie; Yang, Jianyi; Gao, Xin; Han, Renmin; Computer Science Program; Computational Bioscience Research Center (CBRC); Computer, Electrical and Mathematical Science and Engineering (CEMSE) Division; Research Center for Mathematics and Interdisciplinary Sciences, Shandong University, Qingdao 266237, China; School of Medical Technology, Beijing Institute of Technology; College of Medical Information and Engineering, Ningxia Medical University, Yinchuan 750004, China

    Advances on cryo-electron imaging technologies have led to a rapidly increasing number of density maps. Alignment and comparison of density maps play a crucial role in interpreting structural information, such as conformational heterogeneity analysis using global alignment and atomic model assembly through local alignment. Here, we propose a fast and accurate global and local cryo-electron microscopy density map alignment method CryoAlign, which leverages local density feature descriptors to capture spatial structure similarities. CryoAlign is the first feature-based EM map alignment tool, in which the employment of feature-based architecture enables the rapid establishment of point pair correspondences and robust estimation of alignment parameters. Extensive experimental evaluations demonstrate the superiority of CryoAlign over the existing methods in both alignment accuracy and speed.

  • Software

    JoshuaChou2018/DeepTR: Deep Learning Enhanced Tandem Repeat Variation Identification via Multi-Modal Conversion of Nanopore Reads Alignment

    (Github, 2023-07-25) Liao, Xingyu; Zhou, Juexiao; Zhang, Bin; Li, Xingyi; Xu, Xiaopeng; Li, Haoyang; Gao, Xin; Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia; Computer, Electrical and Mathematical Science and Engineering (CEMSE) Division; Computational Bioscience Research Center (CBRC); Computer Science Program; School of computer science, Northwestern Polytechnical University, Xi’an, Shaanxi 710072, China

    Deep Learning Enhanced Tandem Repeat Variation Identification via Multi-Modal Conversion of Nanopore Reads Alignment

  • Software

    JoshuaChou2018/DeepTR: Deep Learning Enhanced Tandem Repeat Variation Identification via Multi-Modal Conversion of Nanopore Reads Alignment

    (Github, 2023-07-25) Liao, Xingyu; Zhou, Juexiao; Zhang, Bin; Li, Xingyi; Xu, Xiaopeng; Li, Haoyang; Gao, Xin; Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia; Computer, Electrical and Mathematical Science and Engineering (CEMSE) Division; Computational Bioscience Research Center (CBRC); Computer Science Program; School of computer science, Northwestern Polytechnical University, Xi’an, Shaanxi 710072, China

    Deep Learning Enhanced Tandem Repeat Variation Identification via Multi-Modal Conversion of Nanopore Reads Alignment