Literature DB >> 31729472

Structural variation in the sequencing era.

Steve S Ho1, Alexander E Urban2,3, Ryan E Mills4,5.   

Abstract

Identifying structural variation (SV) is essential for genome interpretation but has been historically difficult due to limitations inherent to available genome technologies. Detection methods that use ensemble algorithms and emerging sequencing technologies have enabled the discovery of thousands of SVs, uncovering information about their ubiquity, relationship to disease and possible effects on biological mechanisms. Given the variability in SV type and size, along with unique detection biases of emerging genomic platforms, multiplatform discovery is necessary to resolve the full spectrum of variation. Here, we review modern approaches for investigating SVs and proffer that, moving forwards, studies integrating biological information with detection will be necessary to comprehensively understand the impact of SV in the human genome.

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Mesh:

Year:  2019        PMID: 31729472      PMCID: PMC7402362          DOI: 10.1038/s41576-019-0180-9

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


  200 in total

1.  Integrated detection and population-genetic analysis of SNPs and copy number variation.

Authors:  Steven A McCarroll; Finny G Kuruvilla; Joshua M Korn; Simon Cawley; James Nemesh; Alec Wysoker; Michael H Shapero; Paul I W de Bakker; Julian B Maller; Andrew Kirby; Amanda L Elliott; Melissa Parkin; Earl Hubbell; Teresa Webster; Rui Mei; James Veitch; Patrick J Collins; Robert Handsaker; Steve Lincoln; Marcia Nizzari; John Blume; Keith W Jones; Rich Rava; Mark J Daly; Stacey B Gabriel; David Altshuler
Journal:  Nat Genet       Date:  2008-09-07       Impact factor: 38.330

2.  Paternally inherited cis-regulatory structural variants are associated with autism.

Authors:  William M Brandler; Danny Antaki; Madhusudan Gujral; Morgan L Kleiber; Joe Whitney; Michelle S Maile; Oanh Hong; Timothy R Chapman; Shirley Tan; Prateek Tandon; Timothy Pang; Shih C Tang; Keith K Vaux; Yan Yang; Eoghan Harrington; Sissel Juul; Daniel J Turner; Bhooma Thiruvahindrapuram; Gaganjot Kaur; Zhuozhi Wang; Stephen F Kingsmore; Joseph G Gleeson; Denis Bisson; Boyko Kakaradov; Amalio Telenti; J Craig Venter; Roser Corominas; Claudio Toma; Bru Cormand; Isabel Rueda; Silvina Guijarro; Karen S Messer; Caroline M Nievergelt; Maria J Arranz; Eric Courchesne; Karen Pierce; Alysson R Muotri; Lilia M Iakoucheva; Amaia Hervas; Stephen W Scherer; Christina Corsello; Jonathan Sebat
Journal:  Science       Date:  2018-04-20       Impact factor: 47.728

3.  DNA template strand sequencing of single-cells maps genomic rearrangements at high resolution.

Authors:  Ester Falconer; Mark Hills; Ulrike Naumann; Steven S S Poon; Elizabeth A Chavez; Ashley D Sanders; Yongjun Zhao; Martin Hirst; Peter M Lansdorp
Journal:  Nat Methods       Date:  2012-10-07       Impact factor: 28.547

4.  Comprehensive mapping of long-range interactions reveals folding principles of the human genome.

Authors:  Erez Lieberman-Aiden; Nynke L van Berkum; Louise Williams; Maxim Imakaev; Tobias Ragoczy; Agnes Telling; Ido Amit; Bryan R Lajoie; Peter J Sabo; Michael O Dorschner; Richard Sandstrom; Bradley Bernstein; M A Bender; Mark Groudine; Andreas Gnirke; John Stamatoyannopoulos; Leonid A Mirny; Eric S Lander; Job Dekker
Journal:  Science       Date:  2009-10-09       Impact factor: 47.728

5.  An integrative probabilistic model for identification of structural variation in sequencing data.

Authors:  Suzanne S Sindi; Selim Onal; Luke C Peng; Hsin-Ta Wu; Benjamin J Raphael
Journal:  Genome Biol       Date:  2012       Impact factor: 17.906

6.  HySA: a Hybrid Structural variant Assembly approach using next-generation and single-molecule sequencing technologies.

Authors:  Xian Fan; Mark Chaisson; Luay Nakhleh; Ken Chen
Journal:  Genome Res       Date:  2017-01-19       Impact factor: 9.043

7.  Long-read single-molecule maps of the functional methylome.

Authors:  Hila Sharim; Assaf Grunwald; Tslil Gabrieli; Yael Michaeli; Sapir Margalit; Dmitry Torchinsky; Rani Arielly; Gil Nifker; Matyas Juhasz; Felix Gularek; Miguel Almalvez; Brandon Dufault; Sreetama Sen Chandra; Alexander Liu; Surajit Bhattacharya; Yi-Wen Chen; Eric Vilain; Kathryn R Wagner; Jonathan Pevsner; Jeff Reifenberger; Ernest T Lam; Alex R Hastie; Han Cao; Hayk Barseghyan; Elmar Weinhold; Yuval Ebenstein
Journal:  Genome Res       Date:  2019-03-07       Impact factor: 9.043

8.  Tandem-genotypes: robust detection of tandem repeat expansions from long DNA reads.

Authors:  Satomi Mitsuhashi; Martin C Frith; Takeshi Mizuguchi; Satoko Miyatake; Tomoko Toyota; Hiroaki Adachi; Yoko Oma; Yoshihiro Kino; Hiroaki Mitsuhashi; Naomichi Matsumoto
Journal:  Genome Biol       Date:  2019-03-19       Impact factor: 13.583

9.  DELLY: structural variant discovery by integrated paired-end and split-read analysis.

Authors:  Tobias Rausch; Thomas Zichner; Andreas Schlattl; Adrian M Stütz; Vladimir Benes; Jan O Korbel
Journal:  Bioinformatics       Date:  2012-09-15       Impact factor: 6.937

10.  PBHoney: identifying genomic variants via long-read discordance and interrupted mapping.

Authors:  Adam C English; William J Salerno; Jeffrey G Reid
Journal:  BMC Bioinformatics       Date:  2014-06-10       Impact factor: 3.169

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  90 in total

Review 1.  Towards improved genetic diagnosis of human differences of sex development.

Authors:  Emmanuèle C Délot; Eric Vilain
Journal:  Nat Rev Genet       Date:  2021-06-03       Impact factor: 53.242

2.  CNVxplorer: a web tool to assist clinical interpretation of CNVs in rare disease patients.

Authors:  Francisco Requena; Hamza Hadj Abdallah; Alejandro García; Patrick Nitschké; Sergi Romana; Valérie Malan; Antonio Rausell
Journal:  Nucleic Acids Res       Date:  2021-07-02       Impact factor: 16.971

Review 3.  Computational analysis of cancer genome sequencing data.

Authors:  Isidro Cortés-Ciriano; Doga C Gulhan; Jake June-Koo Lee; Giorgio E M Melloni; Peter J Park
Journal:  Nat Rev Genet       Date:  2021-12-08       Impact factor: 53.242

Review 4.  Omics-Facilitated Crop Improvement for Climate Resilience and Superior Nutritive Value.

Authors:  Tinashe Zenda; Songtao Liu; Anyi Dong; Jiao Li; Yafei Wang; Xinyue Liu; Nan Wang; Huijun Duan
Journal:  Front Plant Sci       Date:  2021-12-01       Impact factor: 5.753

Review 5.  Clonal expansion in non-cancer tissues.

Authors:  Nobuyuki Kakiuchi; Seishi Ogawa
Journal:  Nat Rev Cancer       Date:  2021-02-24       Impact factor: 60.716

6.  Ecological basis and genetic architecture of crypsis polymorphism in the desert clicker grasshopper (Ligurotettix coquilletti).

Authors:  Timothy K O'Connor; Marissa C Sandoval; Jiarui Wang; Jacob C Hans; Risa Takenaka; Myron Child; Noah K Whiteman
Journal:  Evolution       Date:  2021-08-17       Impact factor: 3.694

7.  Simple and reliable detection of CRISPR-induced on-target effects by qgPCR and SNP genotyping.

Authors:  Isabel Weisheit; Joseph A Kroeger; Rainer Malik; Benedikt Wefers; Peter Lichtner; Wolfgang Wurst; Martin Dichgans; Dominik Paquet
Journal:  Nat Protoc       Date:  2021-02-17       Impact factor: 13.491

Review 8.  Classical, Molecular, and Genomic Cytogenetics of the Pig, a Clinical Perspective.

Authors:  Brendan Donaldson; Daniel A F Villagomez; W Allan King
Journal:  Animals (Basel)       Date:  2021-04-27       Impact factor: 2.752

9.  Detection of copy number variants in African goats using whole genome sequence data.

Authors:  Wilson Nandolo; Gábor Mészáros; Maria Wurzinger; Liveness J Banda; Timothy N Gondwe; Henry A Mulindwa; Helen N Nakimbugwe; Emily L Clark; M Jennifer Woodward-Greene; Mei Liu; George E Liu; Curtis P Van Tassell; Benjamin D Rosen; Johann Sölkner
Journal:  BMC Genomics       Date:  2021-05-29       Impact factor: 3.969

Review 10.  Towards population-scale long-read sequencing.

Authors:  Wouter De Coster; Matthias H Weissensteiner; Fritz J Sedlazeck
Journal:  Nat Rev Genet       Date:  2021-05-28       Impact factor: 53.242

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