Literature DB >> 25892534

Structural variation mutagenesis of the human genome: Impact on disease and evolution.

James R Lupski1.   

Abstract

Watson-Crick base-pair changes, or single-nucleotide variants (SNV), have long been known as a source of mutations. However, the extent to which DNA structural variation, including duplication and deletion copy number variants (CNV) and copy number neutral inversions and translocations, contribute to human genome variation and disease has been appreciated only recently. Moreover, the potential complexity of structural variants (SV) was not envisioned; thus, the frequency of complex genomic rearrangements and how such events form remained a mystery. The concept of genomic disorders, diseases due to genomic rearrangements and not sequence-based changes for which genomic architecture incite genomic instability, delineated a new category of conditions distinct from chromosomal syndromes and single-gene Mendelian diseases. Nevertheless, it is the mechanistic understanding of CNV/SV formation that has promoted further understanding of human biology and disease and provided insights into human genome and gene evolution. Environ. Mol. Mutagen. 56:419-436, 2015.
© 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

Entities:  

Keywords:  DNA replication; chromosome biology; copy number variant; recombination; structural variant

Mesh:

Year:  2015        PMID: 25892534      PMCID: PMC4609214          DOI: 10.1002/em.21943

Source DB:  PubMed          Journal:  Environ Mol Mutagen        ISSN: 0893-6692            Impact factor:   3.216


  134 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.  Molecular genetics of inherited variation in human color vision.

Authors:  J Nathans; T P Piantanida; R L Eddy; T B Shows; D S Hogness
Journal:  Science       Date:  1986-04-11       Impact factor: 47.728

3.  Enriched rearing improves behavioral responses of an animal model for CNV-based autistic-like traits.

Authors:  Melanie Lacaria; Corinne Spencer; Wenli Gu; Richard Paylor; James R Lupski
Journal:  Hum Mol Genet       Date:  2012-04-05       Impact factor: 6.150

4.  Gigantism and acromegaly due to Xq26 microduplications and GPR101 mutation.

Authors:  Giampaolo Trivellin; Adrian F Daly; Fabio R Faucz; Bo Yuan; Liliya Rostomyan; Darwin O Larco; Marie Helene Schernthaner-Reiter; Eva Szarek; Letícia F Leal; Jean-Hubert Caberg; Emilie Castermans; Chiara Villa; Aggeliki Dimopoulos; Prashant Chittiboina; Paraskevi Xekouki; Nalini Shah; Daniel Metzger; Philippe A Lysy; Emanuele Ferrante; Natalia Strebkova; Nadia Mazerkina; Maria Chiara Zatelli; Maya Lodish; Anelia Horvath; Rodrigo Bertollo de Alexandre; Allison D Manning; Isaac Levy; Margaret F Keil; Maria de la Luz Sierra; Leonor Palmeira; Wouter Coppieters; Michel Georges; Luciana A Naves; Mauricette Jamar; Vincent Bours; T John Wu; Catherine S Choong; Jerome Bertherat; Philippe Chanson; Peter Kamenický; William E Farrell; Anne Barlier; Martha Quezado; Ivana Bjelobaba; Stanko S Stojilkovic; Jurgen Wess; Stefano Costanzi; Pengfei Liu; James R Lupski; Albert Beckers; Constantine A Stratakis
Journal:  N Engl J Med       Date:  2014-12-03       Impact factor: 91.245

5.  The DNA replication FoSTeS/MMBIR mechanism can generate genomic, genic and exonic complex rearrangements in humans.

Authors:  Feng Zhang; Mehrdad Khajavi; Anne M Connolly; Charles F Towne; Sat Dev Batish; James R Lupski
Journal:  Nat Genet       Date:  2009-06-21       Impact factor: 38.330

6.  Recurrent reciprocal 1q21.1 deletions and duplications associated with microcephaly or macrocephaly and developmental and behavioral abnormalities.

Authors:  Nicola Brunetti-Pierri; Jonathan S Berg; Fernando Scaglia; John Belmont; Carlos A Bacino; Trilochan Sahoo; Seema R Lalani; Brett Graham; Brendan Lee; Marwan Shinawi; Joseph Shen; Sung-Hae L Kang; Amber Pursley; Timothy Lotze; Gail Kennedy; Susan Lansky-Shafer; Christine Weaver; Elizabeth R Roeder; Theresa A Grebe; Georgianne L Arnold; Terry Hutchison; Tyler Reimschisel; Stephen Amato; Michael T Geragthy; Jeffrey W Innis; Ewa Obersztyn; Beata Nowakowska; Sally S Rosengren; Patricia I Bader; Dorothy K Grange; Sayed Naqvi; Adolfo D Garnica; Saunder M Bernes; Chin-To Fong; Anne Summers; W David Walters; James R Lupski; Pawel Stankiewicz; Sau Wai Cheung; Ankita Patel
Journal:  Nat Genet       Date:  2008-12       Impact factor: 38.330

7.  Microduplications of 16p11.2 are associated with schizophrenia.

Authors:  Shane E McCarthy; Vladimir Makarov; George Kirov; Anjene M Addington; Jon McClellan; Seungtai Yoon; Diana O Perkins; Diane E Dickel; Mary Kusenda; Olga Krastoshevsky; Verena Krause; Ravinesh A Kumar; Detelina Grozeva; Dheeraj Malhotra; Tom Walsh; Elaine H Zackai; Paige Kaplan; Jaya Ganesh; Ian D Krantz; Nancy B Spinner; Patricia Roccanova; Abhishek Bhandari; Kevin Pavon; B Lakshmi; Anthony Leotta; Jude Kendall; Yoon-Ha Lee; Vladimir Vacic; Sydney Gary; Lilia M Iakoucheva; Timothy J Crow; Susan L Christian; Jeffrey A Lieberman; T Scott Stroup; Terho Lehtimäki; Kaija Puura; Chad Haldeman-Englert; Justin Pearl; Meredith Goodell; Virginia L Willour; Pamela Derosse; Jo Steele; Layla Kassem; Jessica Wolff; Nisha Chitkara; Francis J McMahon; Anil K Malhotra; James B Potash; Thomas G Schulze; Markus M Nöthen; Sven Cichon; Marcella Rietschel; Ellen Leibenluft; Vlad Kustanovich; Clara M Lajonchere; James S Sutcliffe; David Skuse; Michael Gill; Louise Gallagher; Nancy R Mendell; Nick Craddock; Michael J Owen; Michael C O'Donovan; Tamim H Shaikh; Ezra Susser; Lynn E Delisi; Patrick F Sullivan; Curtis K Deutsch; Judith Rapoport; Deborah L Levy; Mary-Claire King; Jonathan Sebat
Journal:  Nat Genet       Date:  2009-10-25       Impact factor: 38.330

8.  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

9.  Parental somatic mosaicism is underrecognized and influences recurrence risk of genomic disorders.

Authors:  Ian M Campbell; Bo Yuan; Caroline Robberecht; Rolph Pfundt; Przemyslaw Szafranski; Meriel E McEntagart; Sandesh C S Nagamani; Ayelet Erez; Magdalena Bartnik; Barbara Wiśniowiecka-Kowalnik; Katie S Plunkett; Amber N Pursley; Sung-Hae L Kang; Weimin Bi; Seema R Lalani; Carlos A Bacino; Mala Vast; Karen Marks; Michael Patton; Peter Olofsson; Ankita Patel; Joris A Veltman; Sau Wai Cheung; Chad A Shaw; Lisenka E L M Vissers; Joris R Vermeesch; James R Lupski; Paweł Stankiewicz
Journal:  Am J Hum Genet       Date:  2014-07-31       Impact factor: 11.025

10.  Deletions of recessive disease genes: CNV contribution to carrier states and disease-causing alleles.

Authors:  Philip M Boone; Ian M Campbell; Brett C Baggett; Zachry T Soens; Mitchell M Rao; Patricia M Hixson; Ankita Patel; Weimin Bi; Sau Wai Cheung; Seema R Lalani; Arthur L Beaudet; Pawel Stankiewicz; Chad A Shaw; James R Lupski
Journal:  Genome Res       Date:  2013-05-16       Impact factor: 9.043

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  59 in total

Review 1.  Non-coding genetic variants in human disease.

Authors:  Feng Zhang; James R Lupski
Journal:  Hum Mol Genet       Date:  2015-07-07       Impact factor: 6.150

2.  2018 Victor A. McKusick Leadership Award: Molecular Mechanisms for Genomic and Chromosomal Rearrangements.

Authors:  James R Lupski
Journal:  Am J Hum Genet       Date:  2019-03-07       Impact factor: 11.025

3.  Neurons with Complex Karyotypes Are Rare in Aged Human Neocortex.

Authors:  William D Chronister; Ian E Burbulis; Margaret B Wierman; Matthew J Wolpert; Mark F Haakenson; Aiden C B Smith; Joel E Kleinman; Thomas M Hyde; Daniel R Weinberger; Stefan Bekiranov; Michael J McConnell
Journal:  Cell Rep       Date:  2019-01-22       Impact factor: 9.423

Review 4.  Guidelines for DNA recombination and repair studies: Cellular assays of DNA repair pathways.

Authors:  Hannah L Klein; Giedrė Bačinskaja; Jun Che; Anais Cheblal; Rajula Elango; Anastasiya Epshtein; Devon M Fitzgerald; Belén Gómez-González; Sharik R Khan; Sandeep Kumar; Bryan A Leland; Léa Marie; Qian Mei; Judith Miné-Hattab; Alicja Piotrowska; Erica J Polleys; Christopher D Putnam; Elina A Radchenko; Anissia Ait Saada; Cynthia J Sakofsky; Eun Yong Shim; Mathew Stracy; Jun Xia; Zhenxin Yan; Yi Yin; Andrés Aguilera; Juan Lucas Argueso; Catherine H Freudenreich; Susan M Gasser; Dmitry A Gordenin; James E Haber; Grzegorz Ira; Sue Jinks-Robertson; Megan C King; Richard D Kolodner; Andrei Kuzminov; Sarah Ae Lambert; Sang Eun Lee; Kyle M Miller; Sergei M Mirkin; Thomas D Petes; Susan M Rosenberg; Rodney Rothstein; Lorraine S Symington; Pawel Zawadzki; Nayun Kim; Michael Lisby; Anna Malkova
Journal:  Microb Cell       Date:  2019-01-07

Review 5.  The contribution of CNVs to the most common aging-related neurodegenerative diseases.

Authors:  Giulia Gentile; Valentina La Cognata; Sebastiano Cavallaro
Journal:  Aging Clin Exp Res       Date:  2020-02-06       Impact factor: 3.636

Review 6.  Clinical genomics: from a truly personal genome viewpoint.

Authors:  James R Lupski
Journal:  Hum Genet       Date:  2016-05-25       Impact factor: 4.132

Review 7.  Neurodevelopmental Disorders Associated with Abnormal Gene Dosage: Smith-Magenis and Potocki-Lupski Syndromes.

Authors:  Juanita Neira-Fresneda; Lorraine Potocki
Journal:  J Pediatr Genet       Date:  2015-09-28

8.  Copy number variation arising from gene conversion on the human Y chromosome.

Authors:  Wentao Shi; Andrea Massaia; Sandra Louzada; Ruby Banerjee; Pille Hallast; Yuan Chen; Anders Bergström; Yong Gu; Steven Leonard; Michael A Quail; Qasim Ayub; Fengtang Yang; Chris Tyler-Smith; Yali Xue
Journal:  Hum Genet       Date:  2017-12-05       Impact factor: 4.132

9.  In Utero Exposure to Benzo[a]pyrene Induces Ovarian Mutations at Doses That Deplete Ovarian Follicles in Mice.

Authors:  Ulrike Luderer; Matthew J Meier; Gregory W Lawson; Marc A Beal; Carole L Yauk; Francesco Marchetti
Journal:  Environ Mol Mutagen       Date:  2018-12-21       Impact factor: 3.216

Review 10.  Pituitary gigantism: update on molecular biology and management.

Authors:  Maya B Lodish; Giampaolo Trivellin; Constantine A Stratakis
Journal:  Curr Opin Endocrinol Diabetes Obes       Date:  2016-02       Impact factor: 3.243

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