Literature DB >> 23329113

Phenotypic impact of genomic structural variation: insights from and for human disease.

Joachim Weischenfeldt1, Orsolya Symmons, François Spitz, Jan O Korbel.   

Abstract

Genomic structural variants have long been implicated in phenotypic diversity and human disease, but dissecting the mechanisms by which they exert their functional impact has proven elusive. Recently however, developments in high-throughput DNA sequencing and chromosomal engineering technology have facilitated the analysis of structural variants in human populations and model systems in unprecedented detail. In this Review, we describe how structural variants can affect molecular and cellular processes, leading to complex organismal phenotypes, including human disease. We further present advances in delineating disease-causing elements that are affected by structural variants, and we discuss future directions for research on the functional consequences of structural variants.

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Year:  2013        PMID： 23329113     DOI： 10.1038/nrg3373

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


  146 in total

1.  Discovery of previously unidentified genomic disorders from the duplication architecture of the human genome.

Authors:  Andrew J Sharp; Sierra Hansen; Rebecca R Selzer; Ze Cheng; Regina Regan; Jane A Hurst; Helen Stewart; Sue M Price; Edward Blair; Raoul C Hennekam; Carrie A Fitzpatrick; Rick Segraves; Todd A Richmond; Cheryl Guiver; Donna G Albertson; Daniel Pinkel; Peggy S Eis; Stuart Schwartz; Samantha J L Knight; Evan E Eichler
Journal:  Nat Genet       Date:  2006-08-13       Impact factor: 38.330

2.  Segmental copy number variation shapes tissue transcriptomes.

Authors:  Charlotte N Henrichsen; Nicolas Vinckenbosch; Sebastian Zöllner; Evelyne Chaignat; Sylvain Pradervand; Frédéric Schütz; Manuel Ruedi; Henrik Kaessmann; Alexandre Reymond
Journal:  Nat Genet       Date:  2009-03-08       Impact factor: 38.330

3.  High frequencies of de novo CNVs in bipolar disorder and schizophrenia.

Authors:  Dheeraj Malhotra; Shane McCarthy; Jacob J Michaelson; Vladimir Vacic; Katherine E Burdick; Seungtai Yoon; Sven Cichon; Aiden Corvin; Sydney Gary; Elliot S Gershon; Michael Gill; Maria Karayiorgou; John R Kelsoe; Olga Krastoshevsky; Verena Krause; Ellen Leibenluft; Deborah L Levy; Vladimir Makarov; Abhishek Bhandari; Anil K Malhotra; Francis J McMahon; Markus M Nöthen; James B Potash; Marcella Rietschel; Thomas G Schulze; Jonathan Sebat
Journal:  Neuron       Date:  2011-12-22       Impact factor: 17.173

4.  Split-hand/split-foot malformation 3 (SHFM3) at 10q24, development of rapid diagnostic methods and gene expression from the region.

Authors:  Robert Lyle; Uppala Radhakrishna; Jean-Louis Blouin; Sarantis Gagos; David B Everman; Corinne Gehrig; Celia Delozier-Blanchet; Jitendra V Solanki; Uday C Patel; Swapan K Nath; Fiorella Gurrieri; Giovanni Neri; Charles E Schwartz; Stylianos E Antonarakis
Journal:  Am J Med Genet A       Date:  2006-07-01       Impact factor: 2.802

5.  Network- and attribute-based classifiers can prioritize genes and pathways for autism spectrum disorders and intellectual disability.

Authors:  Yan Kou; Catalina Betancur; Huilei Xu; Joseph D Buxbaum; Avi Ma'ayan
Journal:  Am J Med Genet C Semin Med Genet       Date:  2012-04-12       Impact factor: 3.908

6.  Towards a comprehensive structural variation map of an individual human genome.

Authors:  Andy W Pang; Jeffrey R MacDonald; Dalila Pinto; John Wei; Muhammad A Rafiq; Donald F Conrad; Hansoo Park; Matthew E Hurles; Charles Lee; J Craig Venter; Ewen F Kirkness; Samuel Levy; Lars Feuk; Stephen W Scherer
Journal:  Genome Biol       Date:  2010-05-19       Impact factor: 13.583

7.  Autism genome-wide copy number variation reveals ubiquitin and neuronal genes.

Authors:  Joseph T Glessner; Kai Wang; Guiqing Cai; Olena Korvatska; Cecilia E Kim; Shawn Wood; Haitao Zhang; Annette Estes; Camille W Brune; Jonathan P Bradfield; Marcin Imielinski; Edward C Frackelton; Jennifer Reichert; Emily L Crawford; Jeffrey Munson; Patrick M A Sleiman; Rosetta Chiavacci; Kiran Annaiah; Kelly Thomas; Cuiping Hou; Wendy Glaberson; James Flory; Frederick Otieno; Maria Garris; Latha Soorya; Lambertus Klei; Joseph Piven; Kacie J Meyer; Evdokia Anagnostou; Takeshi Sakurai; Rachel M Game; Danielle S Rudd; Danielle Zurawiecki; Christopher J McDougle; Lea K Davis; Judith Miller; David J Posey; Shana Michaels; Alexander Kolevzon; Jeremy M Silverman; Raphael Bernier; Susan E Levy; Robert T Schultz; Geraldine Dawson; Thomas Owley; William M McMahon; Thomas H Wassink; John A Sweeney; John I Nurnberger; Hilary Coon; James S Sutcliffe; Nancy J Minshew; Struan F A Grant; Maja Bucan; Edwin H Cook; Joseph D Buxbaum; Bernie Devlin; Gerard D Schellenberg; Hakon Hakonarson
Journal:  Nature       Date:  2009-04-28       Impact factor: 49.962

Review 8.  Karyotype, ploidy, and gene dosage.

Authors:  Jonathan Hodgkin
Journal:  WormBook       Date:  2005-06-25

9.  Large recurrent microdeletions associated with schizophrenia.

Authors:  Hreinn Stefansson; Dan Rujescu; Sven Cichon; Olli P H Pietiläinen; Andres Ingason; Stacy Steinberg; Ragnheidur Fossdal; Engilbert Sigurdsson; Thordur Sigmundsson; Jacobine E Buizer-Voskamp; Thomas Hansen; Klaus D Jakobsen; Pierandrea Muglia; Clyde Francks; Paul M Matthews; Arnaldur Gylfason; Bjarni V Halldorsson; Daniel Gudbjartsson; Thorgeir E Thorgeirsson; Asgeir Sigurdsson; Adalbjorg Jonasdottir; Aslaug Jonasdottir; Asgeir Bjornsson; Sigurborg Mattiasdottir; Thorarinn Blondal; Magnus Haraldsson; Brynja B Magnusdottir; Ina Giegling; Hans-Jürgen Möller; Annette Hartmann; Kevin V Shianna; Dongliang Ge; Anna C Need; Caroline Crombie; Gillian Fraser; Nicholas Walker; Jouko Lonnqvist; Jaana Suvisaari; Annamarie Tuulio-Henriksson; Tiina Paunio; Timi Toulopoulou; Elvira Bramon; Marta Di Forti; Robin Murray; Mirella Ruggeri; Evangelos Vassos; Sarah Tosato; Muriel Walshe; Tao Li; Catalina Vasilescu; Thomas W Mühleisen; August G Wang; Henrik Ullum; Srdjan Djurovic; Ingrid Melle; Jes Olesen; Lambertus A Kiemeney; Barbara Franke; Chiara Sabatti; Nelson B Freimer; Jeffrey R Gulcher; Unnur Thorsteinsdottir; Augustine Kong; Ole A Andreassen; Roel A Ophoff; Alexander Georgi; Marcella Rietschel; Thomas Werge; Hannes Petursson; David B Goldstein; Markus M Nöthen; Leena Peltonen; David A Collier; David St Clair; Kari Stefansson
Journal:  Nature       Date:  2008-09-11       Impact factor: 49.962

10.  Hereditary mixed polyposis syndrome is caused by a 40-kb upstream duplication that leads to increased and ectopic expression of the BMP antagonist GREM1.

Authors:  Emma Jaeger; Simon Leedham; Annabelle Lewis; Stefania Segditsas; Martin Becker; Pedro Rodenas Cuadrado; Hayley Davis; Kulvinder Kaur; Karl Heinimann; Kimberley Howarth; James East; Jenny Taylor; Huw Thomas; Ian Tomlinson
Journal:  Nat Genet       Date:  2012-05-06       Impact factor: 38.330
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  202 in total

Review 1.  Genomics of Immune Diseases and New Therapies.

Authors:  Michael Lenardo; Bernice Lo; Carrie L Lucas
Journal:  Annu Rev Immunol       Date:  2015-12-23       Impact factor: 28.527

Review 2.  Massively parallel sequencing: the new frontier of hematologic genomics.

Authors:  Jill M Johnsen; Deborah A Nickerson; Alex P Reiner
Journal:  Blood       Date:  2013-09-10       Impact factor: 22.113

3.  Primate genome architecture influences structural variation mechanisms and functional consequences.

Authors:  Omer Gokcumen; Verena Tischler; Jelena Tica; Qihui Zhu; Rebecca C Iskow; Eunjung Lee; Markus Hsi-Yang Fritz; Amy Langdon; Adrian M Stütz; Pavlos Pavlidis; Vladimir Benes; Ryan E Mills; Peter J Park; Charles Lee; Jan O Korbel
Journal:  Proc Natl Acad Sci U S A       Date:  2013-09-06       Impact factor: 11.205

Review 4.  Topology of mammalian developmental enhancers and their regulatory landscapes.

Authors:  Wouter de Laat; Denis Duboule
Journal:  Nature       Date:  2013-10-24       Impact factor: 49.962

5.  Influence of genetic diversity of seventeen Beauveria bassiana isolates from different hosts on virulence by comparative genomics.

Authors:  Zhengkun Zhang; Yang Lu; Wenjing Xu; Li Sui; Qian Du; Yangzhou Wang; Yu Zhao; Qiyun Li
Journal:  BMC Genomics       Date:  2020-06-30       Impact factor: 3.969

6.  Identification of large rearrangements in cancer genomes with barcode linked reads.

Authors:  Li C Xia; John M Bell; Christina Wood-Bouwens; Jiamin J Chen; Nancy R Zhang; Hanlee P Ji
Journal:  Nucleic Acids Res       Date:  2018-02-28       Impact factor: 16.971

Review 7.  Adaptive potential of genomic structural variation in human and mammalian evolution.

Authors:  David W Radke; Charles Lee
Journal:  Brief Funct Genomics       Date:  2015-05-23       Impact factor: 4.241

8.  Advances in computer simulation of genome evolution: toward more realistic evolutionary genomics analysis by approximate bayesian computation.

Authors:  Miguel Arenas
Journal:  J Mol Evol       Date:  2015-03-26       Impact factor: 2.395

9.  Characterization of intermediate-sized insertions using whole-genome sequencing data and analysis of their functional impact on gene expression.

Authors:  Saeideh Ashouri; Jing Hao Wong; Hidewaki Nakagawa; Mihoko Shimada; Katsushi Tokunaga; Akihiro Fujimoto
Journal:  Hum Genet       Date:  2021-05-12       Impact factor: 4.132

10.  Exome sequencing and arrayCGH detection of gene sequence and copy number variation between ILS and ISS mouse strains.

Authors:  Laura Dumas; C Michael Dickens; Nathan Anderson; Jonathan Davis; Beth Bennett; Richard A Radcliffe; James M Sikela
Journal:  Mamm Genome       Date:  2014-02-20       Impact factor: 2.957
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