Literature DB >> 29626206

High-throughput mouse phenomics for characterizing mammalian gene function.

Steve D M Brown1, Chris C Holmes2, Ann-Marie Mallon3, Terrence F Meehan4, Damian Smedley5, Sara Wells6.   

Abstract

We are entering a new era of mouse phenomics, driven by large-scale and economical generation of mouse mutants coupled with increasingly sophisticated and comprehensive phenotyping. These studies are generating large, multidimensional gene-phenotype data sets, which are shedding new light on the mammalian genome landscape and revealing many hitherto unknown features of mammalian gene function. Moreover, these phenome resources provide a wealth of disease models and can be integrated with human genomics data as a powerful approach for the interpretation of human genetic variation and its relationship to disease. In the future, the development of novel phenotyping platforms allied to improved computational approaches, including machine learning, for the analysis of phenotype data will continue to enhance our ability to develop a comprehensive and powerful model of mammalian gene-phenotype space.

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Year:  2018        PMID: 29626206      PMCID: PMC6582361          DOI: 10.1038/s41576-018-0005-2

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN: 1471-0056            Impact factor:   53.242


  132 in total

Review 1.  A mouse phenome project.

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3.  Chd8 Mutation Leads to Autistic-like Behaviors and Impaired Striatal Circuits.

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Journal:  Cell Rep       Date:  2017-04-11       Impact factor: 9.423

4.  SHIRPA, a protocol for behavioral assessment: validation for longitudinal study of neurological dysfunction in mice.

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Review 5.  The construction of transgenic and gene knockout/knockin mouse models of human disease.

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6.  ENU mutagenesis screening for dominant behavioral mutations based on normal control data obtained in home-cage activity, open-field, and passive avoidance tests.

Authors:  Yumiko Wada; Tamio Furuse; Ikuko Yamada; Hiroshi Masuya; Tomoko Kushida; Yoko Shibukawa; Yuji Nakai; Kimio Kobayashi; Hideki Kaneda; Yoichi Gondo; Tetsuo Noda; Toshihiko Shiroishi; Shigeharu Wakana
Journal:  Exp Anim       Date:  2010

7.  A Whole-Genome Analysis Framework for Effective Identification of Pathogenic Regulatory Variants in Mendelian Disease.

Authors:  Damian Smedley; Max Schubach; Julius O B Jacobsen; Sebastian Köhler; Tomasz Zemojtel; Malte Spielmann; Marten Jäger; Harry Hochheiser; Nicole L Washington; Julie A McMurry; Melissa A Haendel; Christopher J Mungall; Suzanna E Lewis; Tudor Groza; Giorgio Valentini; Peter N Robinson
Journal:  Am J Hum Genet       Date:  2016-08-25       Impact factor: 11.025

Review 8.  The functional annotation of mammalian genomes: the challenge of phenotyping.

Authors:  Steve D M Brown; Wolfgang Wurst; Ralf Kühn; John M Hancock
Journal:  Annu Rev Genet       Date:  2009       Impact factor: 16.830

9.  High-fat-diet induced development of increased fasting glucose levels and impaired response to intraperitoneal glucose challenge in the collaborative cross mouse genetic reference population.

Authors:  Hanifa J Abu-Toamih Atamni; Richard Mott; Morris Soller; Fuad A Iraqi
Journal:  BMC Genet       Date:  2016-01-05       Impact factor: 2.797

10.  Genome-wide association of multiple complex traits in outbred mice by ultra-low-coverage sequencing.

Authors:  Jérôme Nicod; Robert W Davies; Na Cai; Carl Hassett; Leo Goodstadt; Cormac Cosgrove; Benjamin K Yee; Vikte Lionikaite; Rebecca E McIntyre; Carol Ann Remme; Elisabeth M Lodder; Jennifer S Gregory; Tertius Hough; Russell Joynson; Hayley Phelps; Barbara Nell; Clare Rowe; Joe Wood; Alison Walling; Nasrin Bopp; Amarjit Bhomra; Polinka Hernandez-Pliego; Jacques Callebert; Richard M Aspden; Nick P Talbot; Peter A Robbins; Mark Harrison; Martin Fray; Jean-Marie Launay; Yigal M Pinto; David A Blizard; Connie R Bezzina; David J Adams; Paul Franken; Tom Weaver; Sara Wells; Steve D M Brown; Paul K Potter; Paul Klenerman; Arimantas Lionikas; Richard Mott; Jonathan Flint
Journal:  Nat Genet       Date:  2016-07-04       Impact factor: 38.330

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  31 in total

Review 1.  Fishing forward and reverse: Advances in zebrafish phenomics.

Authors:  Ricardo Fuentes; Joaquín Letelier; Benjamin Tajer; Leonardo E Valdivia; Mary C Mullins
Journal:  Mech Dev       Date:  2018-08-18       Impact factor: 1.882

2.  High-mobility group nucleosomal binding domain 2 protects against microcephaly by maintaining global chromatin accessibility during corticogenesis.

Authors:  Xue-Ling Gao; Wen-Jia Tian; Bofeng Liu; Jingyi Wu; Wei Xie; Qin Shen
Journal:  J Biol Chem       Date:  2019-11-07       Impact factor: 5.157

Review 3.  Molecular Profiling of the Cardiac Conduction System: the Dawn of a New Era.

Authors:  Sruthi Mantri; Sean M Wu; William R Goodyer
Journal:  Curr Cardiol Rep       Date:  2021-07-01       Impact factor: 2.931

4.  Semantic characterization of adverse outcome pathways.

Authors:  Rong-Lin Wang
Journal:  Aquat Toxicol       Date:  2020-03-30       Impact factor: 4.964

5.  Ontology-based semantic mapping of chemical toxicities.

Authors:  Rong-Lin Wang; Stephen Edwards; Cataia Ives
Journal:  Toxicology       Date:  2018-11-20       Impact factor: 4.221

6.  Missense Mutations in the Human Nanophthalmos Gene TMEM98 Cause Retinal Defects in the Mouse.

Authors:  Sally H Cross; Lisa Mckie; Margaret Keighren; Katrine West; Caroline Thaung; Tracey Davey; Dinesh C Soares; Luis Sanchez-Pulido; Ian J Jackson
Journal:  Invest Ophthalmol Vis Sci       Date:  2019-07-01       Impact factor: 4.799

7.  Multivariate phenotype analysis enables genome-wide inference of mammalian gene function.

Authors:  George Nicholson; Hugh Morgan; Habib Ganjgahi; Steve D M Brown; Ann-Marie Mallon; Chris Holmes
Journal:  PLoS Biol       Date:  2022-08-09       Impact factor: 9.593

8.  A multi-layer functional genomic analysis to understand noncoding genetic variation in lipids.

Authors:  Shweta Ramdas; Jonathan Judd; Sarah E Graham; Stavroula Kanoni; Yuxuan Wang; Ida Surakka; Brandon Wenz; Shoa L Clarke; Alessandra Chesi; Andrew Wells; Konain Fatima Bhatti; Sailaja Vedantam; Thomas W Winkler; Adam E Locke; Eirini Marouli; Greg J M Zajac; Kuan-Han H Wu; Ioanna Ntalla; Qin Hui; Derek Klarin; Austin T Hilliard; Zeyuan Wang; Chao Xue; Gudmar Thorleifsson; Anna Helgadottir; Daniel F Gudbjartsson; Hilma Holm; Isleifur Olafsson; Mi Yeong Hwang; Sohee Han; Masato Akiyama; Saori Sakaue; Chikashi Terao; Masahiro Kanai; Wei Zhou; Ben M Brumpton; Humaira Rasheed; Aki S Havulinna; Yogasudha Veturi; Jennifer Allen Pacheco; Elisabeth A Rosenthal; Todd Lingren; QiPing Feng; Iftikhar J Kullo; Akira Narita; Jun Takayama; Hilary C Martin; Karen A Hunt; Bhavi Trivedi; Jeffrey Haessler; Franco Giulianini; Yuki Bradford; Jason E Miller; Archie Campbell; Kuang Lin; Iona Y Millwood; Asif Rasheed; George Hindy; Jessica D Faul; Wei Zhao; David R Weir; Constance Turman; Hongyan Huang; Mariaelisa Graff; Ananyo Choudhury; Dhriti Sengupta; Anubha Mahajan; Michael R Brown; Weihua Zhang; Ketian Yu; Ellen M Schmidt; Anita Pandit; Stefan Gustafsson; Xianyong Yin; Jian'an Luan; Jing-Hua Zhao; Fumihiko Matsuda; Hye-Mi Jang; Kyungheon Yoon; Carolina Medina-Gomez; Achilleas Pitsillides; Jouke Jan Hottenga; Andrew R Wood; Yingji Ji; Zishan Gao; Simon Haworth; Ruth E Mitchell; Jin Fang Chai; Mette Aadahl; Anne A Bjerregaard; Jie Yao; Ani Manichaikul; Wen-Jane Lee; Chao Agnes Hsiung; Helen R Warren; Julia Ramirez; Jette Bork-Jensen; Line L Kårhus; Anuj Goel; Maria Sabater-Lleal; Raymond Noordam; Pala Mauro; Floris Matteo; Aaron F McDaid; Pedro Marques-Vidal; Matthias Wielscher; Stella Trompet; Naveed Sattar; Line T Møllehave; Matthias Munz; Lingyao Zeng; Jianfeng Huang; Bin Yang; Alaitz Poveda; Azra Kurbasic; Sebastian Schönherr; Lukas Forer; Markus Scholz; Tessel E Galesloot; Jonathan P Bradfield; Sanni E Ruotsalainen; E Warwick Daw; Joseph M Zmuda; Jonathan S Mitchell; Christian Fuchsberger; 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Robin G Walters; Michael V Holmes; Corri Black; Blair H Smith; Aris Baras; Anne E Justice; Julie E Buring; Paul M Ridker; Daniel I Chasman; Charles Kooperberg; Gen Tamiya; Masayuki Yamamoto; David A van Heel; Richard C Trembath; Wei-Qi Wei; Gail P Jarvik; Bahram Namjou; M Geoffrey Hayes; Marylyn D Ritchie; Pekka Jousilahti; Veikko Salomaa; Kristian Hveem; Bjørn Olav Åsvold; Michiaki Kubo; Yoichiro Kamatani; Yukinori Okada; Yoshinori Murakami; Bong-Jo Kim; Unnur Thorsteinsdottir; Kari Stefansson; Jifeng Zhang; Y Eugene Chen; Yuk-Lam Ho; Julie A Lynch; Philip S Tsao; Kyong-Mi Chang; Kelly Cho; Christopher J O'Donnell; John M Gaziano; Peter Wilson; Karen L Mohlke; Timothy M Frayling; Joel N Hirschhorn; Sekar Kathiresan; Michael Boehnke; Pradeep Natarajan; Yan V Sun; Andrew P Morris; Panos Deloukas; Gina Peloso; Themistocles L Assimes; Cristen J Willer; Xiang Zhu; Christopher D Brown
Journal:  Am J Hum Genet       Date:  2022-08-04       Impact factor: 11.043

9.  [An optimized method for embedding undecalcified mouse tibias in plastic blocks].

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Journal:  Nan Fang Yi Ke Da Xue Xue Bao       Date:  2019-09-30

10.  Modeling regulatory network topology improves genome-wide analyses of complex human traits.

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Journal:  Nat Commun       Date:  2021-05-14       Impact factor: 14.919

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