Literature DB >> 26924765

Mechanisms underlying structural variant formation in genomic disorders.

Claudia M B Carvalho1,2, James R Lupski1,3,4,5.   

Abstract

With the recent burst of technological developments in genomics, and the clinical implementation of genome-wide assays, our understanding of the molecular basis of genomic disorders, specifically the contribution of structural variation to disease burden, is evolving quickly. Ongoing studies have revealed a ubiquitous role for genome architecture in the formation of structural variants at a given locus, both in DNA recombination-based processes and in replication-based processes. These reports showcase the influence of repeat sequences on genomic stability and structural variant complexity and also highlight the tremendous plasticity and dynamic nature of our genome in evolution, health and disease susceptibility.

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Year:  2016        PMID: 26924765      PMCID: PMC4827625          DOI: 10.1038/nrg.2015.25

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


  164 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.  Break-induced replication occurs by conservative DNA synthesis.

Authors:  Roberto A Donnianni; Lorraine S Symington
Journal:  Proc Natl Acad Sci U S A       Date:  2013-07-29       Impact factor: 11.205

Review 3.  Complex human chromosomal and genomic rearrangements.

Authors:  Feng Zhang; Claudia M B Carvalho; James R Lupski
Journal:  Trends Genet       Date:  2009-06-25       Impact factor: 11.639

4.  Frequent Interchromosomal Template Switches during Gene Conversion in S. cerevisiae.

Authors:  Olga Tsaponina; James E Haber
Journal:  Mol Cell       Date:  2014-07-24       Impact factor: 17.970

5.  Characterization of 26 deletion CNVs reveals the frequent occurrence of micro-mutations within the breakpoint-flanking regions and frequent repair of double-strand breaks by templated insertions derived from remote genomic regions.

Authors:  Ye Wang; Peiqiang Su; Bin Hu; Wenjuan Zhu; Qibin Li; Ping Yuan; Jiangchao Li; Xinyuan Guan; Fucheng Li; Xiangyi Jing; Ru Li; Yongling Zhang; Claude Férec; David N Cooper; Jun Wang; Dongsheng Huang; Jian-Min Chen; Yiming Wang
Journal:  Hum Genet       Date:  2015-03-20       Impact factor: 4.132

6.  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

7.  Mechanisms for nonrecurrent genomic rearrangements associated with CMT1A or HNPP: rare CNVs as a cause for missing heritability.

Authors:  Feng Zhang; Pavel Seeman; Pengfei Liu; Marian A J Weterman; Claudia Gonzaga-Jauregui; Charles F Towne; Sat Dev Batish; Els De Vriendt; Peter De Jonghe; Bernd Rautenstrauss; Klaus-Henning Krause; Mehrdad Khajavi; Jan Posadka; Antoon Vandenberghe; Francesc Palau; Lionel Van Maldergem; Frank Baas; Vincent Timmerman; James R Lupski
Journal:  Am J Hum Genet       Date:  2010-05-20       Impact factor: 11.025

8.  Recombination between similar but not identical DNA sequences during yeast transformation occurs within short stretches of identity.

Authors:  C Mézard; D Pompon; A Nicolas
Journal:  Cell       Date:  1992-08-21       Impact factor: 41.582

9.  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

10.  Chromosome rearrangements via template switching between diverged repeated sequences.

Authors:  Ranjith P Anand; Olga Tsaponina; Patricia W Greenwell; Cheng-Sheng Lee; Wei Du; Thomas D Petes; James E Haber
Journal:  Genes Dev       Date:  2014-11-01       Impact factor: 11.361

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  234 in total

1.  Discovery and quality analysis of a comprehensive set of structural variants and short tandem repeats.

Authors:  David Jakubosky; Erin N Smith; Matteo D'Antonio; Marc Jan Bonder; William W Young Greenwald; Agnieszka D'Antonio-Chronowska; Hiroko Matsui; Oliver Stegle; Stephen B Montgomery; Christopher DeBoever; Kelly A Frazer
Journal:  Nat Commun       Date:  2020-06-10       Impact factor: 14.919

2.  Pronounced maternal parent-of-origin bias for type-1 NF1 microdeletions.

Authors:  Lisa Neuhäusler; Anna Summerer; David N Cooper; Victor-F Mautner; Hildegard Kehrer-Sawatzki
Journal:  Hum Genet       Date:  2018-05-05       Impact factor: 4.132

3.  The Genomics of Arthrogryposis, a Complex Trait: Candidate Genes and Further Evidence for Oligogenic Inheritance.

Authors:  Davut Pehlivan; Yavuz Bayram; Nilay Gunes; Zeynep Coban Akdemir; Anju Shukla; Tatjana Bierhals; Burcu Tabakci; Yavuz Sahin; Alper Gezdirici; Jawid M Fatih; Elif Yilmaz Gulec; Gozde Yesil; Jaya Punetha; Zeynep Ocak; Christopher M Grochowski; Ender Karaca; Hatice Mutlu Albayrak; Periyasamy Radhakrishnan; Haktan Bagis Erdem; Ibrahim Sahin; Timur Yildirim; Ilhan A Bayhan; Aysegul Bursali; Muhsin Elmas; Zafer Yuksel; Ozturk Ozdemir; Fatma Silan; Onur Yildiz; Osman Yesilbas; Sedat Isikay; Burhan Balta; Shen Gu; Shalini N Jhangiani; Harsha Doddapaneni; Jianhong Hu; Donna M Muzny; Eric Boerwinkle; Richard A Gibbs; Konstantinos Tsiakas; Maja Hempel; Katta Mohan Girisha; Davut Gul; Jennifer E Posey; Nursel H Elcioglu; Beyhan Tuysuz; James R Lupski
Journal:  Am J Hum Genet       Date:  2019-06-20       Impact factor: 11.025

4.  Characterization of large in-frame von Willebrand factor deletions highlights differing pathogenic mechanisms.

Authors:  Ashley Cartwright; Simon J Webster; Annika de Jong; Richard J Dirven; Lisa D S Bloomer; Ahlam M Al-Buhairan; Ulrich Budde; Christer Halldén; David Habart; Jenny Goudemand; Ian R Peake; Jeroen C J Eikenboom; Anne C Goodeve; Daniel J Hampshire
Journal:  Blood Adv       Date:  2020-07-14

5.  Toward Recovering Allele-specific Cancer Genome Graphs.

Authors:  Ashok Rajaraman; Jian Ma
Journal:  J Comput Biol       Date:  2018-04-16       Impact factor: 1.479

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.  Non-homologous DNA end joining and alternative pathways to double-strand break repair.

Authors:  Howard H Y Chang; Nicholas R Pannunzio; Noritaka Adachi; Michael R Lieber
Journal:  Nat Rev Mol Cell Biol       Date:  2017-05-17       Impact factor: 94.444

8.  Homolog-Dependent Repair Following Dicentric Chromosome Breakage in Drosophila melanogaster.

Authors:  Jayaram Bhandari; Travis Karg; Kent G Golic
Journal:  Genetics       Date:  2019-05-03       Impact factor: 4.562

Review 9.  Implications of germline copy-number variations in psychiatric disorders: review of large-scale genetic studies.

Authors:  Masahiro Nakatochi; Itaru Kushima; Norio Ozaki
Journal:  J Hum Genet       Date:  2020-09-21       Impact factor: 3.172

10.  Clinical genomics and contextualizing genome variation in the diagnostic laboratory.

Authors:  James R Lupski; Pengfei Liu; Pawel Stankiewicz; Claudia M B Carvalho; Jennifer E Posey
Journal:  Expert Rev Mol Diagn       Date:  2020-10-10       Impact factor: 5.225

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