Literature DB >> 21216738

Detecting structural variations in the human genome using next generation sequencing.

Ruibin Xi1, Tae-Min Kim, Peter J Park.   

Abstract

Structural variations are widespread in the human genome and can serve as genetic markers in clinical and evolutionary studies. With the advances in the next-generation sequencing technology, recent methods allow for identification of structural variations with unprecedented resolution and accuracy. They also provide opportunities to discover variants that could not be detected on conventional microarray-based platforms, such as dosage-invariant chromosomal translocations and inversions. In this review, we will describe some of the sequencing-based algorithms for detection of structural variations and discuss the key issues in future development.

Entities:  

Mesh：

Substances：

Year:  2011        PMID： 21216738      PMCID： PMC3080742          DOI： 10.1093/bfgp/elq025

Source DB:  PubMed          Journal:  Brief Funct Genomics        ISSN： 2041-2649            Impact factor:   4.241


  51 in total

1.  Recent segmental duplications in the human genome.

Authors:  Jeffrey A Bailey; Zhiping Gu; Royden A Clark; Knut Reinert; Rhea V Samonte; Stuart Schwartz; Mark D Adams; Eugene W Myers; Peter W Li; Evan E Eichler
Journal:  Science       Date:  2002-08-09       Impact factor: 47.728

2.  MoDIL: detecting small indels from clone-end sequencing with mixtures of distributions.

Authors:  Seunghak Lee; Fereydoun Hormozdiari; Can Alkan; Michael Brudno
Journal:  Nat Methods       Date:  2009-05-31       Impact factor: 28.547

3.  Duplications of noncoding elements 5' of SOX9 are associated with brachydactyly-anonychia.

Authors:  Ingo Kurth; Eva Klopocki; Sigmar Stricker; Jolieke van Oosterwijk; Sebastian Vanek; Jens Altmann; Heliosa G Santos; Jeske J T van Harssel; Thomy de Ravel; Andrew O M Wilkie; Andreas Gal; Stefan Mundlos
Journal:  Nat Genet       Date:  2009-08       Impact factor: 38.330

4.  Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes.

Authors:  Fereydoun Hormozdiari; Can Alkan; Evan E Eichler; S Cenk Sahinalp
Journal:  Genome Res       Date:  2009-05-15       Impact factor: 9.043

5.  Large-scale copy number polymorphism in the human genome.

Authors:  Jonathan Sebat; B Lakshmi; Jennifer Troge; Joan Alexander; Janet Young; Pär Lundin; Susanne Månér; Hillary Massa; Megan Walker; Maoyen Chi; Nicholas Navin; Robert Lucito; John Healy; James Hicks; Kenny Ye; Andrew Reiner; T Conrad Gilliam; Barbara Trask; Nick Patterson; Anders Zetterberg; Michael Wigler
Journal:  Science       Date:  2004-07-23       Impact factor: 47.728

6.  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

7.  A geometric approach for classification and comparison of structural variants.

Authors:  Suzanne Sindi; Elena Helman; Ali Bashir; Benjamin J Raphael
Journal:  Bioinformatics       Date:  2009-06-15       Impact factor: 6.937

8.  PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls.

Authors:  Joel Rozowsky; Ghia Euskirchen; Raymond K Auerbach; Zhengdong D Zhang; Theodore Gibson; Robert Bjornson; Nicholas Carriero; Michael Snyder; Mark B Gerstein
Journal:  Nat Biotechnol       Date:  2009-01-04       Impact factor: 54.908

9.  Transcriptome sequencing to detect gene fusions in cancer.

Authors:  Christopher A Maher; Chandan Kumar-Sinha; Xuhong Cao; Shanker Kalyana-Sundaram; Bo Han; Xiaojun Jing; Lee Sam; Terrence Barrette; Nallasivam Palanisamy; Arul M Chinnaiyan
Journal:  Nature       Date:  2009-01-11       Impact factor: 49.962

10.  CNV-seq, a new method to detect copy number variation using high-throughput sequencing.

Authors:  Chao Xie; Martti T Tammi
Journal:  BMC Bioinformatics       Date:  2009-03-06       Impact factor: 3.169
View more
  16 in total

1.  Reconstructing cancer genomes from paired-end sequencing data.

Authors:  Layla Oesper; Anna Ritz; Sarah J Aerni; Ryan Drebin; Benjamin J Raphael
Journal:  BMC Bioinformatics       Date:  2012-04-19       Impact factor: 3.169

2.  Characterization of structural variants with single molecule and hybrid sequencing approaches.

Authors:  Anna Ritz; Ali Bashir; Suzanne Sindi; David Hsu; Iman Hajirasouliha; Benjamin J Raphael
Journal:  Bioinformatics       Date:  2014-10-28       Impact factor: 6.937

Review 3.  Application of next generation sequencing to human gene fusion detection: computational tools, features and perspectives.

Authors:  Qingguo Wang; Junfeng Xia; Peilin Jia; William Pao; Zhongming Zhao
Journal:  Brief Bioinform       Date:  2012-08-09       Impact factor: 11.622

Review 4.  A beginners guide to SNP calling from high-throughput DNA-sequencing data.

Authors:  André Altmann; Peter Weber; Daniel Bader; Michael Preuss; Elisabeth B Binder; Bertram Müller-Myhsok
Journal:  Hum Genet       Date:  2012-08-11       Impact factor: 4.132

Review 5.  Human genetics and genomics a decade after the release of the draft sequence of the human genome.

Authors:  Nasheen Naidoo; Yudi Pawitan; Richie Soong; David N Cooper; Chee-Seng Ku
Journal:  Hum Genomics       Date:  2011-10       Impact factor: 4.639

6.  Bayesian model to detect phenotype-specific genes for copy number data.

Authors:  Juan R González; Carlos Abellán; Juan J Abellán
Journal:  BMC Bioinformatics       Date:  2012-06-13       Impact factor: 3.169

Review 7.  Sequencing technologies and genome sequencing.

Authors:  Chandra Shekhar Pareek; Rafal Smoczynski; Andrzej Tretyn
Journal:  J Appl Genet       Date:  2011-06-23       Impact factor: 3.240

8.  Connecting Anxiety and Genomic Copy Number Variation: A Genome-Wide Analysis in CD-1 Mice.

Authors:  Julia Brenndörfer; André Altmann; Regina Widner-Andrä; Benno Pütz; Darina Czamara; Erik Tilch; Tony Kam-Thong; Peter Weber; Monika Rex-Haffner; Thomas Bettecken; Andrea Bultmann; Bertram Müller-Myhsok; Elisabeth E Binder; Rainer Landgraf; Ludwig Czibere
Journal:  PLoS One       Date:  2015-05-26       Impact factor: 3.240

9.  SoftSearch: integration of multiple sequence features to identify breakpoints of structural variations.

Authors:  Steven N Hart; Vivekananda Sarangi; Raymond Moore; Saurabh Baheti; Jaysheel D Bhavsar; Fergus J Couch; Jean-Pierre A Kocher
Journal:  PLoS One       Date:  2013-12-16       Impact factor: 3.240

10.  On the power and the systematic biases of the detection of chromosomal inversions by paired-end genome sequencing.

Authors:  José Ignacio Lucas Lledó; Mario Cáceres
Journal:  PLoS One       Date:  2013-04-23       Impact factor: 3.240
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.