Bibliography on copy number variations (2006)

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  1. Timothy J Aitman, Rong Dong, Timothy J Vyse, Penny J Norsworthy, Michelle D Johnson, Jennifer Smith, Jonathan Mangion, Cheri Roberton-Lowe, Amy J Marshall, Enrico Petretto, Matthew D Hodges, Gurjeet Bhangal, Sheetal G Patel, Kelly Sheehan-Rooney, Mark Duda, Paul R Cook, David J Evans, Jan Domin, Jonathan Flint, Joseph J Boyle, Charles D Pusey, H Terence Cook (2006), "Copy number polymorphism in Fcgr3 predisposes to glomerulonephritis in rats and humans", Nature, 439:851-855.
    [abstract]

  2. Bradley D Anderson, Michael C Gilson, Abigail A Scott, Bryan S Biehl, Jeremy D Glasner, Gireesh Rajashekara, Gary A Splitter, Nicole T Perna (2006), "CGHScan: finding variable regions using high-density microarray comparative genomic hybridization data", BMC Genomics, 7:91.
    [abstract]

  3. Rameen Beroukhim, Ming Lin, Yuhyun Park, Ke Hao, Xiaojun Zhao, Levi A. Garraway, Edward A. Fox, Ephraim P. Hochberg, Ingo K. Mellinghoff, Matthias D. Hofer, Aurelien Descazeaud, Mark A. Rubin, Matthew Meyerson, Wing Hung Wong, William R. Sellers and Cheng Li (2006), "Inferring loss-of-heterozygosity from tumor-only samples using high-density oligonucleotide SNP arrays", PLoS Computational Biology, 2(5):e41.
    [ abstract]

  4. Philippe Broët and Sylvia Richardson (2006), "Detection of gene copy number changes in CGH microarrays using a spatially correlated mixture model", Bioinformatics, 22(8):911-918
    [abstract]

  5. Andrew Carson, Lars Feuk, Mansoor Mohammed, Stephen W Scherer (2006), "Strategies for the detection of copy number and other structural variants in the human genome", Human Genomics, 2(6):403-414.
    [abstract]

  6. EK Cho, J Tchinda, JL Freeman, YJ Chung, WW Cai, C Lee (2006), "Array-based comparative genomic hybridization and copy number variation in cancer research", Cytogenetics and Genome Research, 115:262-272

  7. DF Conrad, TD Andrews, NP Carter, ME Hurles, JK Pritchard (2006), "A high-resolution survey of deletion polymorphism in the human genome", Nature Genetics, 38:75-81.
    [abstract]

  8. Abdallah S Daar, Stephen W Scherer, Robert A Hegele (2006), "Implications of copy-number variation in the human genome: a time for questions" (research highlight), Nature Reviews Genetics, 7:414.
    [html]

  9. JT Den Dunner, SJ White (2006), "MLPA and MAPH: sensitive detection of deletions and duplications", Current Protocols in Human Genetics, Chapter 7, Unit 7.14.

  10. Sharon J Diskin, Thomas Eck, Joel Greshock, Yael P Mosse, Tara Naylor, Christian J Stoeckert Jr., Barbara L Weber, John M Maris, Gregory R Grant (2006), "STAC: A method for testing the significance of DNA copy number aberrations across multiple array-CGH experiments", Genome Research, 16(9):1149-1158.
    [abstract]

  11. DA Engler, G Mohapatra, DN Louis, RA Betensky (2006), "A pseudolikelihood approach for simultaneous analysis of array comparative genomic hybridizations", Biostatistics, 7(3):399-421.
    [abstract]

  12. Lars Feuk, Andrew R Carson, Stephen W Scherer (2006), "Structural variation in the human genome", Nature Reviews Genetics, 7:85-97.

  13. L Feuk, CR Marshall, RF Wintle, SW Scherer (2006), "Structural variants: changing the landscape of chromosomes and design of disease studies", Human Molecular Genetics, 15:R57-R66.
    [ abstract]

  14. Heike Fiegler, Richard Redon, Dan Andrews, Carol Scott, Robert Andrews, Carol Carder, Richard Clark, Oliver Dovey, Peter Ellis, Lars Feuk, Lisa French, Paul Hunt, Dimitrios Kalaitzopoulos, James Larkin, Lyndal Montgomery, George H. Perry, Bob W. Plumb, Keith Porter, Rachel E. Rigby, Diane Rigler, Armand Valsesia, Cordelia Langford, Sean J Humphray, Stephen W Scherer, Charles Lee, Matthew E Hurles, Nigel P Carter (2006), "Accurate and reliable high-throughput detection of copy number variation in the human genome", Genome Research, 16(12):1566-1574.
    [abstract]

  15. Jennifer L Freeman, George H Perry, Lars Feuk, Richard Redon, Steven A McCarroll, David M Altshuler, Hiroyuki Aburatani, Keith W Jones, Chris Tyler-Smith, Matthew E Hurles, Nigel P Carter, Stephen W Scherer, and Charles Lee (2006), "Copy number variation: New insights in genome diversity", Genome Research, 16(6):949-961.
    [abstract]

  16. Brian Gibbons, Parikkhit Datta, Ying Wu, Alan Chan, John AL Armour (2006), "Microarray MAPH: accurate array-based detection of relative copy number in genomic DNA", BMC Genomics, 7:163.
    [abstract]

  17. Violaine Goidts, David N Cooper, Lluis Armengol, Werner Schempp, Jeffrey Conroy, Xavier Estivill, Norma Nowak, Horst Hameister and Hildegard Kehrer-Sawatzki (2006), "Complex patterns of copy number variation at sites of segmental duplications: an important category of structural variation in the human genome", Human Genetics, 120(2):270-284.
    [ abstract]

  18. J Hicks, A Krasnitz, B Lakshmi, NE Navin, M Riggs, E Leibu, D Esposito, J Alexander, J Troge, V Grubor, S Yoon, M Wigler, K Ye, AL Børresen-Dale, B Naume, E Schlicting, L Norton, T Hägerström, L Skoog, G Auer, S Månér, P Lundin, A Zetterberg (2006), "Novel patterns of genome rearrangement and their association with survival in breast cancer", Genome Research, 16(12):1465-1479.

  19. DA Hinds, AP Kloek, M Jen, X Chen, KA Frazer (2006), "Common deletions and SNPs are in linkage disequilibrium in the human genome", Nature Genetics, 38(1):82-85.

  20. Jing Huang, Wen Wei, Joyce Chen, Jane Zhang, Guoying Liu, Xiaojun Di, Rui Mei, Shumpei Ishikawa, Hiroyuki Aburatani, Keith W Jones, Michael H Shapero (2006), "CARAT: A novel method for allelic detection of DNA copy number changes using high density oligonucleotide arrays", BMC Bioinformatics, 7:83.
    [abstract]

  21. Pedro Jares, Elías Campo (2006), "Genomic platforms for cancer research: potential diagnostic and prognostic applications in clinical oncology", Clinical and Translational Oncology, 8(3):161-172.
    [ abstract]

  22. Olli-P Kallioniemi, Anne Kallioniemi, Jim Piper, Jorma Isola, Fred M Waldman, Joe W Gray, Dan Pinkel (2006), "Optimizing comparative genomic hybridization for analysis of DNA sequence copy number changes in solid tumors", Genes, Chromosomes and Cancer, 10(4):231-243.
    [ abstract]

  23. R Khaja, J Zhang, JR MacDonald, Y He, AM Joseph-George, J Wei, MA Rafiq, C Qian, M Shago, L Pantano, H Aburatani, K Jones, R Redon, M Hurles, L Armengol, X Estivill, RJ Mural, C Lee, SW Scherer, L Feuk (2006), "Genome assembly comparison to identify structural variants in the human genome", Nature Genetics, 38:1413-1418

  24. Daisuke Komura, Fan Shen, Shumpei Ishikawa, Karen R. Fitch, Wenwei Chen, Jane Zhang, Guoying Liu, Sigeo Ihara, Hiroshi Nakamura, Matthew E. Hurles, Charles Lee, Stephen W. Scherer, Keith W. Jones, Michael H. Shapero, Jing Huang, Hiroyuki Aburatani (2006), "Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arrays", Genome Research, 16(12):1575-1584.
    [abstract]

  25. Marjolein Kriek, Stefan J White, Karoly Szuhai, Jeroen Knijnenburg, Gert-Jan B van Ommen, Johan T den Dunnen, Martijn H Breuning (2006), "Copy number variation in regions flanked (or unflanked) by duplicons among patients with developmental delay and/or congenital malformations; detection of reciprocal and partial Williams-Beuren duplications", European Journal of Human Genetics, 14:180-189.
    [abstract]

  26. B Lakshmi, IM Hall, C Egan, J Alexander, A Leotta, J Healy, L Zender, MS Spector, W Xue, SW Lowe, M Wigler, R Lucito (2006), "Mouse genomic representational oligonucleotide microarray analysis: detection of copy number variations in normal and tumor specimens", Proceedings of the National Academy of Sciences , 103(30):11234-11239.
    [abstract]

  27. Philippe La Rosa, Eric Viara, Philippe Hupé, Gaëlle Pierron, Stéphane Liva, Pierre Neuvial, Isabel Brito, Séverine Lair, Nicolas Servant, Nicolas Robine, Elodie Manié, Caroline Brennetot, Isabelle Janoueix-Lerosey, Virginie Raynal, Nadège Gruel, Céline Rouveirol, Nicolas Stransky, Marc-Henri Stern, Olivier Delattre, Alain Aurias, François Radvanyi, Emmanuel Barillot (2006), "VAMP: Visualization and analysis of array-CGH, transcriptome and other molecular profiles", Bioinformatics, 22(17):2066-2073.
    [abstract]

  28. Doron Lipson, Yonatan Aumann, Amir Ben-Dor, Nathan Linial, Zohar Yakhini (2006), "Efficient calculation of interval scores for DNA copy number data analysis", Journal of Computational Biology, 13(2): 215-228.
    [ abstract]

  29. Jun Liu, Jaaved Mohammed, James Carter, Sanjay Ranka, Tamer Kahveci, Michael Baudis (2006), "Distance-based clustering of CGH data", Bioinformatics, 22(16):1971-1978.
    [abstract]

  30. Stéphane Liva, Philippe Hupé, Pierre Neuvial, Isabel Brito, Eric Viara, Philippe La Rosa, Emmanuel Barillot (2006), "CAPweb: a bioinformatics CGH array analysis platform", Nucleic Acids Research, 34(web server issue):W477-W481.
    [abstract]

  31. D Locke, A Sharp, S McCarroll, S McGrath, T Newman, Z Cheng, S Schwartz, D Albertson, D Pinkel, D Altshuler (2006), "Linkage disequilibrium and heritability of copy-number polymorphisms within duplicated regions of the human genome", American Journal of Human Genetics, 79(2):275-290.

  32. JC Marioni, NP Thorne, S Tavaré (2006), "BioHMM: a heterogeneous hidden Markov model for segmenting array CGH data", Bioinformatics, 22:1144-1146.
    [abstract]

  33. Steven A McCarroll, Tracy N Hadnott, George H Perry, Pardis C Sabeti, Michael C Zody, Jeffrey C Barrett, Stephanie Dallaire, Stacey B Gabriel, Charles Lee, Mark J Daly, David M Altshuler, The International HapMap Consortium (2006), "Common deletion polymorphisms in the human genome", Nature Genetics, 38:86-92.
    [abstract]

  34. Pierre Neuvial, Philippe Hupé, Isabel Brito, Stéphane Liva, Élodie Manié, Caroline Brennetot, François Radvanyi, Alain Aurias, Emmanuel Barillot (2006), "Spatial normalization of array-CGH data", BMC Bioinformatics, 7:264.
    [abstract]

  35. Tera L Newman, Mark J Rieder, V Anne Morrison, Andrew J Sharp, Joshua D Smith, L James Sprague, Rajinder Kaul, Christopher S Carlson, Maynard V Olson, Deborah A Nickerson and Evan E Eichler (2006), "High-throughput genotyping of intermediate-size structural variation", Human Molecular Genetics, 15(7):1159-1167.
    [abstract]

  36. DQ Nguyen, C Webber, CP Ponting (2006), "Bias of selection on human copy-number variants", PLoS Genetics, 2(2):e20.
    [ abstract]

  37. Karim Ouahchi, Neal Lindeman, Charles Lee (2006), "Copy number variants and pharmacogenomics", Pharmacogenomics, 7(1):25-29.
    [ abstract]

  38. Daniel A Peiffer, Jennie M Le, Frank J Steemers, Weihua Chang, Tony Jenniges, Francisco Garcia, Kirt Haden, Jiangzhen Li, Chad A Shaw, John Belmont, Sau Wai Cheung, Richard M Shen, David L Barker, Kevin L Gunderson (2006), "High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping", Genome Research, 16:1136-1148.
    [abstract]

  39. RJ Pelham, L Rodgers, I Hall, R Lucito, KC Nguyen, N Navin, J Hicks, D Mu, S Powers, M Wigler, D Botstein (2006), "Identification of alterations in DNA copy number in host stromal cells during tumor progression", Proceedings of the National Academy of Sciences , 103(52):19848-19853.
    [abstract]

  40. George H Perry, Joelle Tchinda, Sean D McGrath, Junjun Zhang, Simon R Picker, Angela M Cáceres, A John Iafrate, Chris Tyler-Smith, Stephen W Scherer, Evan E Eichler, Anne C Stone, Charles Lee (2006), "Hotspots for copy number variation in chimpanzees and humans", Proceedings of the National Academy of Sciences , 103(21):8006-8011.
    [abstract]

  41. Richard Redon, Shumpei Ishikawa, Karen R Fitch, Lars Feuk, George H Perry, T Daniel Andrews, Heike Fiegler, Michael H Shapero, Andrew R Carson, Wenwei Chen, Eun Kyung Cho, Stephanie Dallaire, Jennifer L Freeman, Juan R González, Mònica Gratacòs, Jing Huang, Dimitrios Kalaitzopoulos, Daisuke Komura, Jeffrey R MacDonald, Christian R Marshall, Rui Mei, Lyndal Montgomery, Kunihiro Nishimura, Kohji Okamura, Fan Shen, Martin J Somerville, Joelle Tchinda, Armand Valsesia, Cara Woodwark, Fengtang Yang, Junjun Zhang, Tatiana Zerjal, Jane Zhang, Lluis Armengol, Donald F Conrad, Xavier Estivill, Chris Tyler-Smith, Nigel P Carter, Hiroyuki Aburatani, Charles Lee, Keith W Jones, Stephen W Scherer, Matthew E Hurles (2006), "Global variation in copy number in the human genome", Nature, 444:444-454.
    [abstract]

  42. C Rouveirol, N Stransky, Ph Hupé , Ph La Rosa, E Viara, E Barillot and F Radvanyi (2006), "Computation of recurrent minimal genomic alterations from array-CGH data", Bioinformatics, 22(7):849-856.
    [abstract]

  43. 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 (2006), "Discovery of previously unidentified genomic disorders from the duplication architecture of the human genome", Nature Genetics, 38:1038-1042.
    [abstract]

  44. Jason C Ting, Ying Ye, George H Thomas, Ingo Ruczinski, Jonathan Pevsner (2006), "Analysis and visualization of chromosomal abnormalities in SNP data with SNPscan", BMC Bioinformatics, 7:25.
    [abstract]

  45. Alexander Eckehart Urban, Jan O Korbel, Rebecca Selzer, Todd Richmond, April Hacker, George V Popescu, Joseph F Cubells, Roland Green, Beverly S Emanuel, Mark B Gerstein, Sherman M Weissman, Michael Snyder (2006), "High-resolution mapping of DNA copy alterations in human chromosome 22 using high-density tiling oligonucleotide arrays", Proceedings of the National Academy of Sciences , 103(12):4534-4539.
    [abstract]

  46. W N Van Wieringen, J A M Belien, S J Vosse, E M Achame, B Ylstra (2006), "ACE-it: a tool for genome-wide integration of gene dosage and RNA expression data", Bioinformatics, 22(15):1919-1920.
    [abstract]

  47. Chi-Chung Wen, Yuh-Jenn Wu, Yung-Hsiang Huang, Wei-Chen Chen, Shu-Chen Liu, Shih Sheng Jiang, Jyh-Lyh Juang, Chung-Yen Lin, Wen-Tsen Fang, Chao Agnes Hsiung, I-Shou Chang (2006), "A Bayes Regression Approach to Array-CGH Data", Statistical Applications in Genetics and Molecular Biology, 5(1):3.
    [abstract]

  48. Gary M Wilson, Stephane Flibotte, Perseus I Missirlis, Marco A Marra, Steven Jones, Kevin Thornton, Andrew G Clark, and Robert A Holt (2006), "Identification by full-coverage array CGH of human DNA copy number increases relative to chimpanzee and gorilla", Genome Research, 16(2):173-181.
    [abstract]

  49. M Wirtenberger, K Hemminki, B Burwinkel (2006), "Identification of frequent chromosome copy-number polymorphisms by use of high-resolution single-nucleotide-polymorphism arrays", American Journal of Human Genetics, 78(3):520-522.

  50. Bauke Ylstra, Paul van den IJssel, Beatriz Carvalho, Ruud H Brakenhoff, Gerrit A Meijer (2006), "BAC to the future! or oligonucleotides: a perspective for micro array comparative genomic hybridization (array CGH)", Nucleic Acids Research, 34(2):445-450.
    [abstract] [html]