Personalized copy number and segmental duplication maps using next-generation sequencing

Alkan, Can, Kidd, Jeffrey M, Marques-Bonet, Tomas, Aksay, Gozde, Antonacci, Francesca, Hormozdiari, Fereydoun, Kitzman, Jacob O, Baker, Carl, Malig, Maika, Mutlu, Onur, Sahinalp, S Cenk, Gibbs, Richard A, Eichler, Evan E·2009·Nature Genetics
DOI 10.1038/ng.437

Cited by (748)

Items 201–300 of 748

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  3. Hobbes: optimized gram-based methods for efficient read alignment
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  6. Detecting structural variations in the human genome using next generation sequencing
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  7. A robust benchmark for germline structural variant detection
    Justin M. Zook, Nancy Fisher Hansen, Nathan D. Olson, Lesley M. Chapman, James C. Mullikin, Chunlin Xiao, Stephen T. Sherry, Sergey Koren, Adam M. Phillippy, Paul Christopher Boutros et al. · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
  8. Evaluation and Comparison of Multiple Aligners for Next-Generation Sequencing Data Analysis
    Jing Shang, Fei Zhu, Wanwipa Vongsangnak, Yifei Tang, Wenyu Zhang, Bairong Shen · 2014 · BioMed Research International
  9. Genomic neighbourhood and the regulation of gene expression
    Subhajyoti De, M. Madan Babu · 2010 · Current Opinion in Cell Biology
  10. Response to Comments on “Widespread RNA and DNA Sequence Differences in the Human Transcriptome”
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  11. Computational and Bioinformatics Frameworks for Next‐Generation Whole Exome and Genome Sequencing
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  12. Correlating Multiallelic Copy Number Polymorphisms with Disease Susceptibility
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  13. rSW-seq: Algorithm for detection of copy number alterations in deep sequencing data
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  14. Comparative genomics reveals convergent rates of evolution in ant–plant mutualisms
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  15. CNV-TV: A robust method to discover copy number variation from short sequencing reads
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  17. CHESS 3: an improved, comprehensive catalog of human genes and transcripts based on large-scale expression data, phylogenetic analysis, and protein structure
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  19. Inter‐varietal structural variation in grapevine genomes
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  21. Genome-wide approaches to schizophrenia
    Jubao Duan, Alan R. Sanders, Pablo V. Gejman · 2010 · Brain Research Bulletin
  22. Complex and multi-allelic copy number variation in human disease
    Christina L. Usher, Steven A. McCarroll · 2015 · Briefings in Functional Genomics
  23. Digital Genotyping of Macrosatellites and Multicopy Genes Reveals Novel Biological Functions Associated with Copy Number Variation of Large Tandem Repeats
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  24. DNA copy number, including telomeres and mitochondria, assayed using next-generation sequencing
    John C. Castle, Matthew C. Biery, Heather K. Bouzek, Tao Xie, Ronghua Chen, Kira M. S. Misura, Stuart Jackson, Christopher D. Armour, Jason Michael Johnson, Carol A. Rohl et al. · 2010 · BMC Genomics
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  26. Massively Parallel Sequencing Approaches for Characterization of Structural Variation
    Daniel C. Koboldt, David E. Larson, Ken Chen, Li Ding, Richard K. Wilson · 2011 · Methods in molecular biology
  27. The impact and origin of copy number variations in the Oryza species
    Zetao Bai, Jinfeng Chen, Yi Liao, Meijiao Wang, Rong Liu, Song Ge, Rod A. Wing, Mingsheng Chen · 2016 · BMC Genomics
  28. Genome-wide copy number variation (CNV) detection in Nelore cattle reveals highly frequent variants in genome regions harboring QTLs affecting production traits
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  31. Copy number variation in chemokine superfamily: the complex scene ofCCL3L–CCL4Lgenes in health and disease
    Roger Colobrán, Edurne Pedrosa, Laura Carretero-Iglesia, Manel Juan · 2010 · Clinical & Experimental Immunology
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    Stefan Wilkening, Manu M. Tekkedil, Gen Lin, Emilie S. Fritsch, Wu Wei, Julien Gagneur, David W. Lazinski, Andrew Camilli, Lars Michael Steinmetz · 2013 · BMC Genomics
  33. Improving detection of copy-number variation by simultaneous bias correction and read-depth segmentation
    Jin Szatkiewicz, Weibo Wang, Patrick F. Sullivan, Wei William Wang, Wei Sun · 2012 · Nucleic Acids Research
  34. On genomic repeats and reproducibility
    Can Fırtına, Can Alkan · 2016 · Bioinformatics
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    Xiong Zhang, Bo Liu, Fen Zou, Danyu Shen, Zhiyuan Yin, Rongbo Wang, Feng He, Yuanchao Wang, Brett M. Tyler, Wei Fan et al. · 2019 · Frontiers in Microbiology
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  38. A Survey of Computational Tools to Analyze and Interpret Whole Exome Sequencing Data
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  39. Gene amplification, radiation sensitivity and DNA double-strand breaks
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  41. Gene Transposition Causing Natural Variation for Growth in Arabidopsis thaliana
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  43. Main Memory Scaling: Challenges and Solution Directions
    Onur Mutlu · 2015 · Springer eBooks
  44. How do alignment programs perform on sequencing data with varying qualities and from repetitive regions?
    Xiaoqing Yu, Kishore Guda, Joseph E. Willis, Martina L. Veigl, Zhenghe Wang, Sanford D. Markowitz, Mark D. Adams, Shuying Sun · 2012 · BioData Mining
  45. Accounting for GC-content bias reduces systematic errors and batch effects in ChIP-seq data
    Mingxiang Teng, Rafael A. Irizarry · 2017 · Genome Research
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    Petr Dmitriev, Ekaterina V. Kiseleva, Olga Kharchenko, Evgeny G. Ivashkin, Andrey Pichugin, Philippe Dessen, Thomas Robert, Frédérique Coppée, Alexandra Belayew, Gilles Carnac et al. · 2016 · Oncotarget
  47. Whole genome sequencing for quantifying germline mutation frequency in humans and model species: Cautious optimism
    Marc A. Beal, Travis C. Glenn, Christopher M. Somers · 2011 · Mutation Research/Reviews in Mutation Research
  48. Diagnostic accuracy of random massively parallel sequencing for non-invasive prenatal detection of common autosomal aneuploidies: a collaborative study in Europe
    Markus Stümm, Michael Entezami, Karsten Haug, Cornelia Blank, M Wüstemann, Bernt Schulze, Gisela Raabe‐Meyer, Maja Hempel, M. Schelling, Eva Ostermayer et al. · 2013 · Prenatal Diagnosis
  49. SVseq: an approach for detecting exact breakpoints of deletions with low-coverage sequence data
    Jin Zhang, Yufeng Wu · 2011 · Bioinformatics
  50. Challenges in studying genomic structural variant formation mechanisms: The short‐read dilemma and beyond
    Megumi Onishi‐Seebacher, Jan O. Korbel · 2011 · BioEssays
  51. Suitability of Different Mapping Algorithms for Genome-Wide Polymorphism Scans with Pool-Seq Data
    Robert Kofler, Anna Maria Langmüller, Pierre Nouhaud, Kathrin Anna Otte, Christian Schlötterer · 2016 · G3 Genes Genomes Genetics
  52. Expansion of a 12-kb VNTR containing the REXO1L1 gene cluster underlies the microscopically visible euchromatic variant of 8q21.2
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  53. Genome-wide sequence analyses of ethnic populations across Russia
    Daria V. Zhernakova, Vladimir B. Brukhin, Sergey V. Malov, Tarás K. Oleksyk, Klaus‐Peter Koepfli, Anna S. Zhuk, Pavel V. Dobrynin, Sergei F. Kliver, Nikolay Cherkasov, Gaik Tamazian et al. · 2019 · Genomics
  54. Non-invasive prenatal testing (NIPT) by low coverage genomic sequencing: Detection limits of screened chromosomal microdeletions
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  56. Whole genome association studies in complex diseases: where do we stand?
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  57. Discovery of tandem and interspersed segmental duplications using high-throughput sequencing
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  58. Unravelling the genetic basis of renal diseases; from single gene to multifactorial disorders
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  59. Speeding Up Large-Scale Next Generation Sequencing Data Analysis with pBWA
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  60. Genetic Diversity of Seven Cattle Breeds Inferred Using Copy Number Variations
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  61. Inversion variants in human and primate genomes
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  62. Critical role of bioinformatics in translating huge amounts of next-generation sequencing data into personalized medicine
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  63. Reduced Representation Methods for Subgenomic Enrichment and Next-Generation Sequencing
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  64. Detection of breed-specific copy number variations in domestic chicken genome
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  65. SeGraM
    Damla Senol Cali, Konstantinos Kanellopoulos, Joël Lindegger, Zülal Bingöl, Gurpreet Singh Kalsi, Ziyi Zuo, Can Fırtına, Meryem Banu Cavlak, Jeremie S. Kim, Nika Mansouri Ghiasi et al. · 2022 · Proceedings - International Symposium on Computer Architecture/Proceedings
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  68. Non invasive prenatal diagnosis of fetal aneuploidy using cell free fetal DNA
    Barbara Renga · 2018 · European Journal of Obstetrics & Gynecology and Reproductive Biology
  69. Copy Number Variation
    Aurélien Macé, Zoltán Kutalik, Armand Valsesia · 2018 · Methods in molecular biology
  70. Transcriptomic and genomic structural variation analyses on grape cultivars reveal new insights into the genotype-dependent responses to water stress
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  71. Analysis of copy number variants in the cattle genome
    James Kijas, W. Barendse, Wes Barris, Blair E. Harrison, Russell J. McCulloch, Sean M. McWilliam, Vicki Whan · 2011 · Gene
  72. Whole-Genome Sequencing of Individuals from a Founder Population Identifies Candidate Genes for Asthma
    Catarina D. Campbell, Kiana Mohajeri, Maika Malig, Fereydoun Hormozdiari, Benjamin Nelson, Gaixin Du, Kristen M Patterson, Celeste S. Eng, Dara G. Torgerson, Donglei Hu et al. · 2014 · PLoS ONE
  73. CNOGpro: detection and quantification of CNVs in prokaryotic whole-genome sequencing data
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  74. Copy Number Variations in Pancreatic Cancer: From Biological Significance to Clinical Utility
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  75. Advances in BAC-Based Physical Mapping and Map Integration Strategies in Plants
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  76. On the Power and the Systematic Biases of the Detection of Chromosomal Inversions by Paired-End Genome Sequencing
    José Ignacio Lucas‐Lledó, Mario Cáceres · 2013 · PLoS ONE
  77. Accurate estimation of short read mapping quality for next-generation genome sequencing
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  78. Applications of the pipeline environment for visual informatics and genomics computations
    Ivo D. Dinov, Federica Torri, Fabio M. Macciardi, Petros Petrosyan, Zhizhong Liu, Alen Zamanyan, Paul Eggert, Jonathan Pierce, Alex Genco, James A. Knowles et al. · 2011 · BMC Bioinformatics
  79. PuffAligner: a fast, efficient and accurate aligner based on the Pufferfish index
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  80. cnvHiTSeq: integrative models for high-resolution copy number variation detection and genotyping using population sequencing data
    Evangelos Bellos, Michael R. Johnson, Lachlan Coin · 2012 · Genome biology
  81. lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data
    Ehsan Haghshenas, S. Cenk Şahinalp, Faraz Hach · 2018 · Bioinformatics
  82. Allele-Specific Droplet Digital PCR Combined with a Next-Generation Sequencing-Based Algorithm for Diagnostic Copy Number Analysis in Genes with High Homology: Proof of Concept Using Stereocilin
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  83. Gene inactivation and its implications for annotation in the era of personal genomics.
    S. Balasubramanian, L. Habegger, A. Frankish, D. Macarthur, R. Harte, C. Tyler-Smith, J. Harrow, M. Gerstein · 2011 · Genes & Development
  84. Investigating and Correcting Plasma DNA Sequencing Coverage Bias to Enhance Aneuploidy Discovery
    Dineika Chandrananda, Natalie Thorne, Devika Ganesamoorthy, Damien L. Bruno, Yuval Benjamini, Terence Paul Speed, Howard Robert Slater, Melanie Bahlo · 2014 · PLoS ONE
  85. Genome‐wide copy number variation in the bovine genome detected using low coverage sequence of popular beef breeds,
    Brittney N. Keel, John W. Keele, W. M. Snelling · 2016 · Animal Genetics
  86. Rapid and accurate large-scale genotyping of duplicated genes and discovery of interlocus gene conversions
    Xander Nuttle, John Huddleston, Brian J. O’Roak, Francesca Antonacci, Marco Fichera, Corrado Romano, Jay Shendure, Evan E. Eichler · 2013 · Nature Methods
  87. De-ubiquitination of ELK-1 by USP17 potentiates mitogenic gene expression and cell proliferation
    Charles E. Ducker, Leo Kam Yuen Chow, Janice Saxton, Jürgen Handwerger, Alexander McGregor, Thomas Strahl, Robert Layfield, Peter E. Shaw · 2019 · Nucleic Acids Research
  88. Whole genome sequencing–based copy number variations reveal novel pathways and targets in Alzheimer's disease
    Ming Chen, Minghui Wang, Qian Wang, Ryan A. Neff, Erming Wang, Qi Shen, Joseph S. Reddy, Xue Wang, Mariet Allen, Nilüfer Ertekin‐Taner et al. · 2021 · Alzheimer s & Dementia
  89. Evidence for somatic gene conversion and deletion in bipolar disorder, Crohn's disease, coronary artery disease, hypertension, rheumatoid arthritis, type-1 diabetes, and type-2 diabetes
    Kenneth Andrew Ross · 2011 · BMC Medicine
  90. Toolkit for automated and rapid discovery of structural variants
    Arda Söylev, Can Koçkan, Fereydoun Hormozdiari, Can Alkan · 2017 · Methods
  91. Genomic reproducibility in the bioinformatics era
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  92. SomatiCA: Identifying, Characterizing and Quantifying Somatic Copy Number Aberrations from Cancer Genome Sequencing Data
    Mengjie Chen, Murat Günel, Hongyu Zhao · 2013 · PLoS ONE
  93. Modeling the next generation sequencing sample processing pipeline for the purposes of classification
    Noushin Ghaffari, Mohammadmahdi R. Yousefi, Charles D. Johnson, Ivan V. Ivanov, Edward R. Dougherty · 2013 · BMC Bioinformatics
  94. Increased CNV-Region deletions in mild cognitive impairment (MCI) and Alzheimer's disease (AD) subjects in the ADNI sample
    Guia Guffanti, Federica Torri, Jerod M. Rasmussen, Andrew P. Clark, Anita Lakatos, Jessica A. Turner, James H. Fallon, Andrew J. Saykin, Michael Walter Weiner, Marquis P. Vawter et al. · 2013 · Genomics
  95. Accelerated Seeding for Genome Sequence Alignment with Enumerated Radix Trees
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  96. Non-Invasive Prenatal Detection of Trisomy 13 Using a Single Nucleotide Polymorphism- and Informatics-Based Approach
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  97. Methylation analysis by DNA immunoprecipitation
    Kelsie L. Thu, Larissa A. Pikor, Jennifer Y. Kennett, Carlos E. Alvarez, Wan L. Lam · 2009 · Journal of Cellular Physiology
  98. Gene duplication and dosage effects during the early emergence of C4 photosynthesis in the grass genus Alloteropsis
    Matheus E. Bianconi, Luke T. Dunning, Jose J Moreno-Villena, Colin P. Osborne, Pascal‐Antoine Christin · 2018 · Journal of Experimental Botany
  99. Next-Generation Sequencing Technologies and Fragment Assembly Algorithms
    Heewook Lee, Haixu Tang · 2012 · Methods in molecular biology
  100. Parallelizing Exact and Approximate String Matching via Inclusive Scan on a GPU
    Mitani Yasuaki, Fumihiko Ino, Kenichi Hagihara A · 2016 · IEEE Transactions on Parallel and Distributed Systems