Bibliography on copy number variations (2009)

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  1. KA Aldinger (2009), "Copy number variation at 1q21.1 results in a spectrum of developmental abnormalities", Clinical Genetics, 75(5):425-427.

  2. C Alkan, JM Kidd, T Marques-Bonet, G Aksay, F Antonacci, F Hormozdiari, JO Kitzman, C Baker, M Malig, O Mutlu, SC Sahinalp, RA Gibbs, EE Eichler (2009), "Personalized copy number and segmental duplication maps using next-generation sequencing", Nature Genetics, 41(10):1061-1067.

  3. J Almagro-Garcia, M Manske, C Carret, S Campino, S Auburn, BL Macinnis, G Maslen, A Pain, CI Newbold, DP Kwiatkowski, Tg Clark (2009), "SnoopCGH: software for visualizing comparative genomic hybridization data", Bioinformatics, 25(20):2732-2733

  4. MF Arlt, JG Mulle, VM Schaibley, RL Ragland, SG Durkin, ST Warren, TW Glover (2009), "Replication stress induces genome-wide copy number changes in human cells that resemble polymorphic and pathogenic variants", American Journal of Human Genetics, 84(3):339-350.
    [abstract]

  5. L Armengol, S Villatoro, JR González, L Pantano, M García-Aragones, R Rabionet, M Caceres, X Estivill (2009), "Identification of copy number variants defining genomic differences among major human groups", PLoS One, 4:e7230.

  6. SA Bakar, EJ Hollox, JA Armour (2009), "Allelic recombination between distinct genomic locations generates copy number diversity in human beta-defensins", Proceedings of National Academy of Sciences, 106(3):853-858.

  7. Henrik Bengtsson, Amrita Ray, Paul Spellman, Terence P Speed (2009), "A single-sample method for normalizing and combining full-resolution copy numbers from multiple platforms, labs and analysis methods", Bioinformatics, 25(7):861-867.
    [abstract]

  8. Henrik Bengtsson, Pratyaksha Wirapati, Terence P Speed (2009) "A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays including GenomeWideSNP 5 & 6", Bioinformatics, 25(17):2149-2156.
    [ abstract]

  9. B Banerjee, DN Peiris, SH Koo, P Chui, EJ Lee, MP Hande (2009), "Genomic imbalances in key ion channel genes and telomere shortening in sudden cardiac death victims", Cytogenetics and Genome Research, 122(3-4):350-355.

  10. Willemijn B Breunis, Edwin van Mirre, Judy Geissler, Nadja Laddach, Gertjan Wolbink, Ellen van der Schoot, Masja de Haas, Martin de Boer, Dirk Roos, Taco W Kuijpers (2009), "Copy number variation at the FCGR locus includes FCGR3A, FCGR2C and FCGR3B but not FCGR2A and FCGR2B", Human Mutation, 30(5):E640-E650.
    [ abstract]

  11. HA Bruce, Sachs N, Rudnicki DD, Lin SG, Willour VL, Cowell JK, Conroy J, McQuaid DE, Rossi M, Gaile DP, Nowak NJ, Holmes SE, Sklar P, Ross CA, Delisi LE, Margolis RL. (2009), "Long tandem repeats as a form of genomic copy number variation: structure and length polymorphism of a chromosome 5p repeat in control and schizophrenia populations", Psychiatric Genetics, 19(2):64-71.

  12. Eva Budinska, Eva Gelnarova, and Michael G. Schimek (2009), "MSMAD: a computationally efficient method for the analysis of noisy array CGH data", Bioinformatics, 25(6):703-713.
    [abstract]

  13. K Buysse, B Delle Chiaie, R Van Coster, B Loeys, A De Paepe, G Mortier, F Speleman, B Menten (2009), "Challenges for CNV interpretation in clinical molecular karyotyping: Lessons learned from a 1001 sample experience", European Journal of Medical Geneics, to appear.

  14. IH Cheeseman, Gomez-Escobar N, Carret CK, Ivens A, Stewart LB, Tetteh KK, Conway DJ. (2009), "Gene copy number variation throughout the Plasmodium falciparum genome", BMC Genomics, 10:353.

  15. Ken Chen, John W Wallis, Michael D McLellan, David E Larson, Joelle M Kalicki, Craig S Pohl, Sean D McGrath, Michael C Wendl, Qunyuan Zhang, Devin P Locke, Xiaoqi Shi, Robert S Fulton, Timothy J Ley, Richard K Wilson, Li Ding, Elaine R Mardis (2009), "BreakDancer: an algorithm for high-resolution mapping of genomic structural variation", Nature Methods, 6:677-681.
    [ abstract]

  16. Derek Y Chiang, Gad Getz, David B Jaffe, Michael J T O'Kelly, Xiaojun Zhao, Scott L Carter, Carsten Russ, Chad Nusbaum, Matthew Meyerson, Eric S Lander (2009), " High-resolution mapping of copy-number alterations with massively parallel sequencing", Nature Methods, 6:99-103.
    [ abstract]

  17. R Colobran, N Casamitjana, A Roman, R Faner, E Pedrosa, JI Arostegui, R Pujol-Borrell, M Juan, E Palou (2009), "Copy number variation in the CCL4L gene is associated with susceptibility to acute rejection in lung transplantation", Genes and Immunity, to appear.

  18. DF Conrad, D Pinto, R Redon, L Feuk, O Gokcumen, Y Zhang, J Aerts, TD Andrews, C Barnes, P Campbell, T Fitzgerald, M Hu, CH Ihm, K Kristiansson, DG Macarthur, JR Macdonald, I Onyiah, AW Pang, S Robson, K Stirrups, A Valsesia, K Walter, J Wei, The Wellcome Trust Case Control Consortium, C Tyler-Smith, NP Carter, C Lee, SW Scherer, ME Hurles (2009), "Origins and functional impact of copy number variation in the human genome", Nature, to appear.

  19. HN Cukier, MA Pericak-Vance, JR Gilbert, DJ Hedges (2009), "Sample degradation leads to false-positive copy number variation calls in multiplex real-time polymerase chain reaction assays", Analytical Biochemistry, 386(2):288-290.
    [ abstract]

  20. R De Cid, E Riveira-Munoz, PL Zeeuwen, J Robarge, W Liao, EN Dannhauser, E Giardina, PE Stuart, R Nair, C Helms, G Escaramís, E Ballana, G Martín-Ezquerra, M den Heijer, M Kamsteeg, I Joosten, EE Eichler, C Lázaro, RM Pujol, L Armengol, G Abecasis, JT Elder, G Novelli, JA Armour, PY Kwok, A Bowcock, J Schalkwijk, X Estivill (2009), "Deletion of the late cornified envelope LCE3B and LCE3C genes as a susceptibility factor for psoriasis", Nature Genetics, 41(2):211-215.

  21. JD Degenhardt, P de Candia, A Chabot, S Schwartz, L Henderson, B Ling, M Hunter, Z Jiang, RE Palermo, M Katze, EE Eichler, M Ventura, J Rogers, P Marx, Y Gilad, CD Bustamante (2009), "Copy number variation of CCL3-like genes affects rate of progression to simian-AIDS in Rhesus Macaques (Macaca mulatta)", PLoS Genetics, 5(1):e1000346.

  22. NG De Groot, CM Heijmans, N De Groot, GG Doxiadis, N Otting, RE Bontrop (2009), "The chimpanzee Mhc-DRB region revisited: Gene content, polymorphism, pseudogenes, and transcripts", Molecular Immunology, to appear.

  23. F Demichelis, SR Setlur, R Beroukhim, S Perner, JO Korbel, CJ Lafargue, D Pflueger, C Pina, MD Hofer, A Sboner, MA Svensson, DS Rickman, A Urban, M Snyder, M Meyerson, C Lee, MB Gerstein, R Kuefer, MA Rubin (2009), "Distinct genomic aberrations associated with ERG rearranged prostate cancer", Genes, Chromosomes & Cancer, 48(4):366-380.

  24. FY Deng, LJ Zhao, YF Pei, BY Sha, XG Liu, H Yan, L Wang, TL Yang, RR Recker, CJ Papasian, HW Deng (2009), "Genome-wide copy number variation association study suggested VPS13B gene for osteoporosis in Caucasians", Osteoporosis International, to appear.

  25. LM Dibbens, S Mullen, I Helbig, HC Mefford, MA Bayly, S Bellows, C Leu, H Trucks, T Obermeier, M Wittig, A Franke, H Caglayan, Z Yapici, EPICURE Consortium, T Sander, EE Eichler, IE Scheffer, JC Mulley, SF Berkovic (2009), "Familial and sporadic 15q13.3 microdeletions in Idiopathic Generalized Epilepsy: Precedent for Disorders with Complex Inheritance", Human Molecular Genetics, to appear.

  26. Sharon J Diskin, Cuiping Hou, Joseph T Glessner, Edward F Attiyeh, Marci Laudenslager, Kristopher Bosse, Kristina Cole, Yaël P Mossé, Andrew Wood, Jill E Lynch, Katlyn Pecor, Maura Diamond, Cynthia Winter, Kai Wang, Cecilia Kim, Elizabeth A Geiger, Patrick W McGrady, Alexandra I F Blakemore, Wendy B London, Tamim H Shaikh, Jonathan Bradfield, Struan F A Grant,, Hongzhe Li, Marcella Devoto,,0, Eric R Rappaport, Hakon Hakonarson, John M Maris (2009), "Copy number variation at 1q21.1 associated with neuroblastoma", Nature, 459:987-991.
    [ abstract]

  27. GG Doxiadis, N de Groot, EM Dauber, PH van Eede, I Fae, R Faner, G Fischer, Z Grubic, NM Lardy, W Mayr, E Palou, W Swelsen, K Stingl, II Doxiadis, RE Bontrop (2009), "High resolution definition of HLA-DRB haplotypes by a simplified microsatellite typing technique", Tissue Antigens, to appear.

  28. J Du, RD Bjornson, ZD Zhang, Y Kong, M Snyder, MB Gerstein (2009), "Integrating sequencing technologies in personal genomics: optimal low cost reconstruction of structural variants", PLoS Computational Biology, 5(7):e1000432.

  29. L Edelmann, K Hirschhorn (2009), "Clinical utility of array CGH for the detection of chromosomal imbalances associated with mental retardation and multiple congenital anomalies", Annals of New York Academy of Sciences, 1151:157-166.

  30. J Elia, X Gai, H M Xie, J C Perin, E Geiger, J T Glessner, M D'arcy, R deBerardinis, E Frackelton, C Kim, F Lantieri, B M Muganga, L Wang, T Takeda, E F Rappaport, S F A Grant, W Berrettini, M Devoto, T H Shaikh, H Hakonarson, P S White (2009), "Rare structural variants found in attention-deficit hyperactivity disorder are preferentially associated with neurodevelopmental genes", Molecular Psychistry, 15:637-646.
    [ abstract]

  31. D Etemadmoghadam, A Defazio, R Beroukhim, C Mermel, J George, G Getz, R Tothill, A Okamoto, MB Raeder, AOCS Study Group, P Harnett, S Lade, LA Akslen, AV Tinker, B Locandro, K Alsop, YE Chiew, N Traficante, S Fereday, D Johnson, S Fox, W Sellers, M Urashima, HB Salvesen, M Meyerson, D Bowtell (2009), "Integrated genome-wide DNA copy number and expression analysis identifies distinct mechanisms of primary chemoresistance in ovarian carcinomas", Clinical Cancer Research, 15(4):1417-1427.

  32. I Faik, EG de Carvalho, JF Kun (2009), "Parasite-host interaction in malaria: genetic clues and copy number variation", Genome Medicine, 1(9):82.

  33. BA Fernandez, W Roberts, B Chung, R Weksberg, S Meyn, P Szatmari, AM Joseph-George, S Mackay, K Whitten, B Noble, C Vardy, V Crosbie, S Luscombe, E Tucker, L Turner, CR Marshall, SW Scherer (2009), "Phenotypic spectrum associated with de novo and inherited deletions and duplications at 16p11.2 in individuals ascertained for diagnosis of autism spectrum disorder", Journal of Medical Genetics, to appear.

  34. I Filges, B Röthlisberger, C Noppen, N Boesch, F Wenzel, J Necker, F Binkert, AR Huber, K Heinimann, P Miny (2009), "Familial 14.5 Mb interstitial deletion 13q21.1-13q21.33: clinical and array-CGH study of a benign phenotype in a three-generation family", American Journal of Medical Genetics A, 149A(2):237-241.

  35. JL Freeman, C Ceol, H Feng, DM Langenau, C Belair, HM Stern, A Song, BH Paw, AT Look, Y Zhou, LI Zon, C Lee (2009), "Construction and application of a zebrafish array CGH platform", Genes Chromosomes & Cancer, 48(2):155-170.
    [ abstract]

  36. C Giachini, F Nuti, DJ Turner, I Laface, Y Xue, F Daguin, G Forti, C Tyler-Smith, C Krausz (2009), "TSPY1 copy number variation influences spermatogenesis and shows differences among Y lineages", Journal of Clinical Endocrinology and Metabolism, 94(10):4016-4022

  37. 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 (2009), "Autism genome-wide copy number variation reveals ubiquitin and neuronal genes", Nature, 459:569-573.
    [ abstract]

  38. G Gornalusse, S Mummidi, W He, G Silvestri, M Bamshad, SK Ahuja (2009), "CCL3L Copy number variation and the co-evolution of primate and viral genomes", PLoS Genetics, 5(1):e1000359.

  39. V Grubor, A Krasnitz, JE Troge, JL Meth, B Lakshmi, JT Kendall, B Yamrom, G Alex, D Pai, N Navin, LA Hufnagel, YH Lee, K Cook, SL Allen, KR Rai, RN Damle, C Calissano, N Chiorazzi, M Wigler, D Esposito (2009), "Novel genomic alterations and clonal evolution in chronic lymphocytic leukemia revealed by representational oligonucleotide microarray analysis (ROMA)", Blood, 113(6):1294-1303.
    [ abstract]

  40. FD Hannes, Sharp AJ, Mefford HC, de Ravel T, Ruivenkamp CA, Breuning MH, Fryns JP, Devriendt K, Van Buggenhout G, Vogels A, Stewart H, Hennekam RC, Cooper GM, Regan R, Knight SJ, Eichler EE, Vermeesch JR (2009), "Recurrent reciprocal deletions and duplications of 16p13.11: the deletion is a risk factor for MR/MCA while the duplication may be a rare benign variant", Journal of Medical Genetics, 46(4):223-232.

  41. PJ Hastings, G Ira, JR Lupski (2009), "A microhomology-mediated break-induced replication model for the origin of human copy number variation", PLoS Genetics, 5(1):e1000327.

  42. PJ Hastings, James R Lupski, Susan M Rosenberg, Grzegorz Ira (2009), "Mechanisms of change in gene copy number", Nature Reviews Genetics, 10:551-564.
    [ abstract]

  43. EL Heinzen, AC Need, KM Hayden, O Chiba-Falek, AD Roses, WJ Strittmatter, JR Burke, CM Hulette, KA Welsh-Bohmer, DB Goldstein (2009), "Genome-Wide scan of copy number variation in late-onset Alzheimer's disease", Journal of Alzheimer's Disease, to appear.

  44. I Helbig, HC Mefford, AJ Sharp, M Guipponi, M Fichera, A Franke, H Muhle, C de Kovel, C Baker, S von Spiczak, KL Kron, I Steinich, AA Kleefuss-Lie, C Leu, V Gaus, B Schmitz, KM Klein, PS Reif, F Rosenow, Y Weber, H Lerche, F Zimprich, L Urak, K Fuchs, M Feucht, P Genton, P Thomas, F Visscher, GJ de Haan, RS Mřller, H Hjalgrim, D Luciano, M Wittig, M Nothnagel, CE Elger, P Nürnberg, C Romano, A Malafosse, BP Koeleman, D Lindhout, U Stephani, S Schreiber, EE Eichler, T Sander (2009), "15q13.3 microdeletions increase risk of idiopathic generalized epilepsy", Nature Genetics, 41(2):160-162

  45. Charlotte N Henrichsen, Evelyne Chaignat, Alexandre Reymond (2009), "Copy number variants, diseases and gene expression", Human Molecular Genetics, 18(R1):R1-R8.
    [ abstract]

  46. Charlotte N Henrichsen, Nicolas Vinckenbosch, Sebastian Zöllner, Evelyne Chaignat, Sylvain Pradervand, Frédéric Schütz, Manuel Ruedi, Henrik Kaessmann, Alexandre Reymond (2009), "Segmental copy number variation shapes tissue transcriptomes", Nature Genetics, 41:424-429.
    [ abstract]

  47. Daniel S Herman, G Kees Hovingh, Oleg Iartchouk, Heidi L Rehm, Raju Kucherlapati, J G Seidman, Christine E Seidman (2009), "Filter-based hybridization capture of subgenomes enables resequencing and copy-number detection", Nature Methods, 6(7):507-510.
    [ abstract]

  48. EJ Hollox, JC Detering, T Dehnugara (2009), "An integrated approach for measuring copy number variation at the FCGR3 (CD16) locus", Human Mutation, 30(3):477-484.

  49. F Hormozdiari, C Alkan, EE Eichler, SC Sahinalp (2009), "Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes", Genome Research, 19(7):1270-1278.

  50. R Stephanie Huang, Peixian Chen, Steve Wisel, Shiwei Duan, Wei Zhang, Edwin H Cook, Soma Das, Nancy J Cox, M Eileen Dolan (2009), "Population-specific GSTM1 copy number variation", Human Molecular Genetics, 18(2):366-372.
    [ abstract]

  51. I Ionita-Laza, AJ Rogers, C Lange, BA Raby, C Lee (2009), "Genetic association analysis of copy-number variation (CNV) in human disease pathogenesis", Genomics, 93(1):22-26.
    [ abstract]

  52. A Itsara, GM Cooper, C Baker, S Girirajan, J Li, D Absher, RM Krauss, RM Myers, PM Ridker, DI Chasman, H Mefford, P Ying, DA Nickerson, EE Eichler (2009), "Population analysis of large copy number variants and hotspots of human genetic disease", American Journal of Human Genetics, 84(2):148-161.

  53. FD Jacob, Ramaswamy V, Andersen J, Bolduc FV. (2009), "Atypical Rett syndrome with selective FOXG1 deletion detected by comparative genomic hybridization: case report and review of literature", European Journal of Human Genetics, to appear.

  54. HC Jeung, SY Rha, CH Park, CK Im, SJ Shin, JB Ahn, SH Noh, JK Roh, HC Chung (2009), "Copy number changes can be a predictor for hemoglobin reduction after S-1 monotherapy in gastric cancer", International Journal of Oncology, 34(3):787-796.

  55. MJ Kas, C Gelegen, LC Schalkwyk, DA Collier (2009), "Interspecies comparisons of functional genetic variations and their implications in neuropsychiatry", American Journal of Medical Genetics, B, 150(3):309-317.
    [ abstract]

  56. KY Kim, GY Lee, J Kim, HC Jeung, HC Chung, SY Rha (2009), "Identification of significant regional genetic variations using continuous CNV values in aCGH data", Genomics, to appear.

  57. JO Korbel, A Abyzov, XJ Mu, N Carriero, P Cayting, Z Zhang, M Snyder, MB Gerstein (2009), "PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data", Genome Biology, 10(2):R23.

  58. Kuan-Ting Kuo, Bin Guan, Yuanjian Feng, Tsui-Lien Mao, Xu Chen, Natini Jinawath, Yue Wang, Robert J Kurman, Ie-Ming Shih, Tian-Li Wang, (2009), "Analysis of DNA Copy Number Alterations in ovarian serous tumors identifies new molecular genetic changes in low-grade and high-grade carcinomas", Cancer Research, 69:4036-4042.

  59. Thomas LaFramboise, Wendy Winckler, Roman K. Thomas (2009), "A flexible rank-based framework for detecting copy number aberrations from array data", Bioinformatics, 25(6):722-728.
    [abstract]

  60. SR Lalani, JV Thakuria, GF Cox, X Wang, W Bi, Bray MS, Shaw C, Cheung SW, Chinault AC, Boggs BA, Ou Z, Brundage EK, Lupski JR, Gentile J, Waisbren S, Pursley A, Ma L, Khajavi M, Zapata G, Friedman R, Kim JJ, Towbin JA, Stankiewicz P, Schnittger S, Hansmann I, Ai T, Sood S, Wehrens XH, Martin JF, Belmont JW, Potocki L. (2009), "20p12.3 microdeletion predisposes to Wolff-Parkinson-White syndrome with variable neurocognitive deficits", Journal of Medical Genetics, to appear.

  61. ML Landsverk, EK Ruzzo, HC Mefford, K Buysse, JG Buchan, EE Eichler, EM Petty, EA Peterson, DM Knutzen, K Barnett, MR Farlow, J Caress, GJ Parry, D Quan, KL Gardner, M Hong, Z Simmons, TD Bird, PF Chance, MC Hannibal (2009), "Duplication within the SEPT9 gene associated with a founder effect in North American families with Hereditary Neuralgic Amyotrophy", Human Molecular Genetics, to appear.

  62. CH Lee, CC Wu, YN Wu, HS Chiang (2009), "Gene copy number variations in Asian patients with congenital bilateral absence of the vas deferens", Human Reproduction, 24(3):748-755.

  63. C Le Caignec, R Redon (2009), "Copy number variation goes clinical", Genome Biology, 10(1):301.

  64. L Li, AA McCormack, JM Nicholson, A Fabarius, R Hehlmann, RK Sachs, PH Duesberg (2009), "Cancer-causing karyotypes: chromosomal equilibria between destabilizing aneuploidy and stabilizing selection for oncogenic function", Cancer Genetics and Cytogenetics, 188(1):1-25

  65. Wentian Li, Annette Lee, Peter K Gregersen (2009), "Copy-number-variation and copy-number-alteration region detection by cumulative plots", BMC Bioinformatics, 10(suppl 1):S67.
    [ abstract]

  66. Wennuan Liu, Jishan Sun, Ge Li, Yi Zhu, Scott Zhang, Seong-Tae Kim, Jielin Sun, Fredrik Wiklund, Kathleen Wiley, Sarah D Isaacs, Pär Stattin, Jianfeng Xu, David Duggan, John D Carpten, William B Isaacs, Henrik Grönberg, S Lilly Zheng, Bao-Li Chang (2009), "Association of a Germ-Line Copy Number Variation at 2p24.3 and Risk for Aggressive Prostate Cancer", Cancer Research, 69:2176-2179.
    [ abstract]

  67. M Mamtani, JM Anaya, W He, SK Ahuja (2009), "Association of copy number variation in the FCGR3B gene with risk of autoimmune diseases", Genes and Immunity, to appear.

  68. J Margareto, O Leis, E Larrarte, IC Pomposo, JM Garibi, JV Lafuente (2009), "DNA copy number variation and gene expression analyses reveal the implication of specific oncogenes and genes in GBM", Cancer Investigation, to appear.

  69. KJ McKernan, Peckham HE, Costa G, McLaughlin S, Tsung E, Fu Y, Clouser C, Dunkan C, Ichikawa J, Lee C, Zhang Z, Sheridan A, Fu H, Ranade S, Dimilanta E, Sokolsky T, Zhang L, Hendrickson C, Li B, Kotler L, Stuart J, Malek J, Manning J, Antipova A, Perez D, Moore M, Hayashibara K, Lyons M, Beaudoin R, Coleman B, Laptewicz M, Sanicandro A, Rhodes M, De La Vega F, Gottimukkala RK, Hyland F, Reese M, Yang S, Bafna V, Bashir A, Macbride A, Aklan C, Kidd JM, Eichler EE, Blanchard AP (2009), "Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two base encoding", Genome Research, 19(9):1527-1541.

  70. Paul Medvedev, Monica Stanciu, Michael Brudno (2009), "Computational methods for discovering structural variation with next-generation sequencing", Nature Methods, 6(suppl):S13-S20.
    [ abstract]

  71. HC Mefford, Cooper GM, Zerr T, Smith JD, Baker C, Shafer N, Thorland EC, Skinner C, Schwartz CE, Nickerson DA, Eichler EE. (2009), "A method for rapid, targeted CNV genotyping identifies rare variants associated with neurocognitive disease", Genome Research, 19(9):1579-1585.

  72. HC Mefford, EE Eichler (2009), "Duplication hotspots, rare genomic disorders, and common disease", Current Opinion in Genetics and Development, 19(3):196-204.

  73. Renée X Menezes, Marten Boetzer, Melle Sieswerda, Gert-Jan B van Ommen, Judith M Boer (2009), "Integrated analysis of DNA copy number and gene expression microarray data using gene sets", BMC Bioinformatics, 10:203
    [abstract]

  74. M Milanese, L Segat, LC Arraes, A Garzino-Demo, S Crovella (2009), "Copy number variation of defensin genes and HIV infection in Brazilian children", Journal of Acquired Immune Deficiency Syndromes, to appear.

  75. Charles G Mullighan, J Racquel Collins-Underwood, Letha A A Phillips, Michael G Loudin, Wei Liu, Jinghui Zhang, Jing Ma, Elaine Coustan-Smith, Richard C Harvey, Cheryl L Willman, Fady M Mikhail, Julia Meyer, Andrew J Carroll, Richard T Williams, Jinjun Cheng, Nyla A Heerema0, Giuseppe Basso, Andrea Pession, Ching-Hon Pui, Susana C Raimondi, Stephen P Hunger, James R Downing, William L Carroll, Karen R Rabin (2009), "Rearrangement of CRLF2 in B-progenitor? and Down syndrome?associated acute lymphoblastic leukemia", Nature Genetics, 41:1243-1246.
    [ abstract]

  76. SC Nagamani, A Erez, C Eng, Z Ou, C Chinault, L Workman, J Coldwell, P Stankiewicz, A Patel, JR Lupski, SW Cheung (2009), "Interstitial deletion of 6q25.2-q25.3: a novel microdeletion syndrome associated with microcephaly, developmental delay, dysmorphic features and hearing loss", European Journal of Human Genetics, to appear.

  77. AC Need, DK Attix, JM McEvoy, ET Cirulli, KL Linney, P Hunt, D Ge, EL Heinzen, JM Maia, KV Shianna, ME Weale, LF Cherkas, G Clement, TD Spector, G Gibson, DB Goldstein (2009), "A Genome-wide Study of Common SNPs and CNVs in Cognitive Performance in the CANTAB battery", Human Molecular Geneics, to appear.

  78. TJ Nicholas, Z Cheng, M Ventura, K Mealey, EE Eichler, JM Akey (2009), "The genomic architecture of segmental duplications and associated copy number variants in dogs", Genome Research, to appear.

  79. Björn Nilsson, Mikael Johansson, Fatima Al-Shahrour, Anne E Carpenter, Benjamin L Ebert (2009), "Ultrasome: efficient aberration caller for copy number studies of ultra-high resolution", Bioinformatics, 25(8):1078-1079.
    [abstract]

  80. Marianne S. Nřrskov, Ruth Frikke-Schmidt, Steffen Loft, Anne Tybjćrg-Hansen (2009), "High-throughput genotyping of copy number variation in Glutathione S-Transferases M1 and T1 using real-time PCR in 20,687 individuals", Clinical Biochemistry, 42(3):201-209.
    [ abstract]

  81. J Ohashi (2009), "A practical case-control association test for detecting a susceptibility allele at a copy number variation locus", Journal of Human Genetics, to appear.

  82. LD Orozco, Cokus SJ, Ghazalpour A, Ingram-Drake L, Wang S, van Nas A, Che N, Araujo JA, Pellegrini M, Lusis AJ. (2009), "Copy number variation influences gene expression and metabolic traits in mice", Human Molecular Genetics, 18(21):4118-4129.

  83. V Plagnol (2009), "Association tests and software for copy number variant data", Human Genomics, 3(2):191-194.

  84. Matthew J Rose-Zerilli, Sheila J Barton, A John Henderson, Seif O Shaheen, John W Holloway (2009), "Copy-number variation genotyping of GSTT1 and GSTM1 gene deletions by real-time PCR", Clinical Chemistry, 55:1680-1685.
    [ abstract]

  85. Oscar M Rueda, Ramon Diaz-Uriarte (2009), "Detection of recurrent copy number alterations in the genome: taking among-subject heterogeneity seriously", BMC Bioinformatics, 10:308.
    [abstract]

  86. RB Scharpf, G Parmigiani, J Pevsner, I Ruczinski (2009), "Hidden Markov models for the assessment of chromosomal alterations using high-throughput SNP arrays", Annals of Applied Statistics, 2(2):687-713.

  87. H Schaschl, TJ Aitman, TJ Vyse (2009), "Copy number variation in the human genome and its implication in autoimmunity", Clinical and Experimental Immunology, to appear.

  88. BY Sha, TL Yang, LJ Zhao, XD Chen, Y Guo, Y Chen, F Pan, ZX Zhang, SS Dong, XH Xu, HW Deng (2009), "Genome-wide association study suggested copy number variation may be associated with body mass index in the Chinese population", Journal of Human Genetics, to appear.

  89. S.P. Shah (2009), "Computational methods for identification of recurrent copy number alteration patterns by array CGH", Cytogenetic and Genome Research, 123(1-4):343-351.
    [ abstract]

  90. Tamim H Shaikh, Xiaowu Gai, Juan C Perin, Joseph T Glessner, Hongbo Xie, Kevin Murphy, Ryan O'Hara, Tracy Casalunovo, Laura K Conlin, Monica D'arcy, Edward C Franckelton, Elizabeth A Geiger, Chad Haldeman-Englert, Marcin Imielinski, Cecelia E Kim, Livija Medne, Kiran Annaiah, Jonathan Bradfield, Elvira Dabaghyan, Andrew Eckert, Chioma C Onyiah, Svetlana Ostapenko, F George Otieno, Erin Santa, Julie L Shaner, Robert Skraban, Ryan M Smith, Josephine Elia, Elizabeth Goldmuntz, Nancy B Spinner, Elaine H Zackai, Rosetta M Chiavacci, Robert Grundmeier, Eric F Rappaport, Struan FA Grant, Peter S White, Hakon Hakonarson (2009), "High-resolution mapping and analysis of copy number variations in the human genome: a data resource for clinical and research applications", Genome Research, to appear.

  91. AJ Sharp (2009), "Emerging themes and new challenges in defining the role of structural variation in human disease", Human Mutation, 30(2):135-144.

  92. SM Singh, CA Castellani, RL O'Reilly (2009), "Copy number variation showers in schizophrenia: an emerging hypothesis", Molecular Psychiatry, to appear.

  93. JJ Smith, F Antonacci, EE Eichler, CT Amemiya (2009), "Programmed loss of millions of base pairs from a vertebrate genome", Proceedings of National Academy of Sciences, 106(27):11212-11217.

  94. Philip J Stephens, David J McBride, Meng-Lay Lin, Ignacio Varela, Erin D Pleasance, Jared T Simpson, Lucy A Stebbings, Catherine Leroy, Sarah Edkins, Laura J Mudie, Chris D Greenman, Mingming Jia, Calli Latimer, Jon W Teague, King Wai Lau, John Burton, Michael A Quail, Harold Swerdlow, Carol Churcher, Rachael Natrajan, Anieta M Sieuwerts, John W M Martens, Daniel P Silver, Anita Langerřd, Hege E G Russnes, John A Foekens, Jorge S Reis-Filho, Laura van't Veer, Andrea L Richardson, Anne-Lise Břrresen-Dale, Peter J Campbell, P Andrew Futreal, Michael R Stratton (2009), "Complex landscapes of somatic rearrangement in human breast cancer genomes", Nature, 462:1005-1010.
    [ abstract]

  95. S Sulong, AV Moorman, JA Irving, JC Strefford, ZJ Konn, MC Case, L Minto, KE Barber, H Parker, SL Wright, AR Stewart, S Bailey, NP Bown, AG Hall, CJ Harrison (2009), "A comprehensive analysis of the CDKN2A gene in childhood acute lymphoblastic leukaemia reveals genomic deletion, copy number neutral loss of heterozygosity and association with specific cytogenetic subgroups", Blood, 113(1):100-107.
    [ abstract]

  96. YV Sun, Peyser PA, Kardia SL. (2009), "A common copy number variation on chromosome 6 association with the gene expression level of endothelin 1 in transformed B lymphocytes from three racial groups", Circulation and Cardiovascular Genetics, 2(5):483-488.

  97. GW Tam, R Redon, NP Carter, SG Grant (2009), "The role of DNA copy number variation in schizophrenia", Biological Psychiatry, to appear.

  98. R Thomas, C Rebbeck, AM Leroi, A Burt, M Breen (2009), "Extensive conservation of genomic imbalances in canine transmissible venereal tumors (CTVT) detected by microarray-based CGH analysis", Chromosome Research, to appear.

  99. Z Tian, T Hwang, R Kuang (2009), "A hypergraph-based learning algorithm for classifying gene expression and arrayCGH data with prior knowledge", Bioinformatics, 25(21):2831-2838.

  100. J Tyson, TM Majerus, S Walker, JA Armour (2009), "Quadruplex MAPH: improvement of throughput in high-resolution copy number screening", BMC Genomics, 10:453

  101. BW Van Bon, Mefford HC, Menten B, Koolen DA, Sharp AJ, Nillesen WM, Innis JW, de Ravel TJ, Mercer CL, Fichera M, Stewart H, Connell LE, Ounap K, Lachlan K, Castle B, Van der Aa N, van Ravenswaaij C, Nobrega MA, Serra-Juhé C, Simonic I, de Leeuw N, Pfundt R, Bongers EM, Baker C, Finnemore P, Huang S, Maloney VK, Crolla JA, van Kalmthout M, Elia M, Vandeweyer G, Fryns JP, Janssens S, Foulds N, Reitano S, Smith K, Parkel S, Loeys B, Woods CG, Oostra A, Speleman F, Pereira AC, Kurg A, Willatt L, Knight SJ, Vermeesch JR, Romano C, Barber JC, Mortier G, Perez-Jurado LA, Kooy F, Brunner HG, Eichler EE, Kleefstra T, de Vries BB (2009), "Further delineation of the 15q13 microdeletion and duplication syndromes: a clinical spectrum varying from non-pathogenic to a severe outcome", Journal of Medical Genetics, to appear.

  102. IB Van den Veyver, A Patel, CA Shaw, AN Pursley, SH Kang, MJ Simovich, PA Ward, S Darilek, A Johnson, SE Neill, W Bi, LD White, CM Eng, JR Lupski, SW Cheung, AL Beaudet (2009), "Clinical use of array comparative genomic hybridization (aCGH) for prenatal diagnosis in 300 cases", Prenatal Diagnosis, 29(1):29-39.

  103. Wessel N. Van Wieringen, Mark A. Van De Wiel (2009), "Nonparametric testing for DNA copy number induced differential mRNA gene expression", Biometrics, 65(1):19-29.
    [ abstract]

  104. JB Vincent, A Noor, C Windpassinger, PJ Gianakopoulos, T Schwarzbraun, SE Alfred, B Stachowiak, SW Scherer, W Roberts, K Wagner, PM Kroisel, E Petek (2009), "Characterization of a de novo translocation t(5;18)(q33.1;q12.1) in an autistic boy identifies a breakpoint close to SH3TC2, ADRB2, and HTR4 on 5q, and within the desmocollin gene cluster on 18q". American Journal of Medical Genetics B, to appear.

  105. S Walker, S Janyakhantikul, JA Armour (2009), "Multiplex Paralogue Ratio Tests for accurate measurement of multiallelic CNVs", Genomics, 93(1):98-103.
    [ abstract]

  106. K Wang, J Li, S Li, L Bolund, C Wiuf (2009), "Estimation of tumor heterogeneity using CGH array data", BMC Bioinformatics, 10:12.

  107. LY Wang, A Abyzov, JO Korbel, M Snyder, M Gerstein (2009), "MSB: a mean-shift-based approach for the analysis of structural variation in the genome", Genome Research, 19(1):106-117.

  108. Anja Weise, Kristin Mrasek, Mkrtchyan Hasmik, Madeleine Gross, Sophie Hinreiner, Witthuhn Vera, Thomas Liehr (2009), "Parental origin determination FISH: Pod-FISH", in Fluorescence in Situ Hybriduzation (FISH) -- Application Guide, ed. T Liehr, pp 293-297 (Springer).

  109. Laura Winchester, Christopher Yau, Jiannis Ragousis (2009), "Comparing CNV detection methods for SNP arrays", Briefings in Functional Genomics and Proteomics, 8(5):353-366.
    [ abstract]

  110. CC Wu, S Shete, WV Chen, B Peng, AT Lee, J Ma, PK Gregersen, CI Amos (2009), "Detection of disease-associated deletions in case-control studies using SNP genotypes with application to rheumatoid arthritis", Human Genetics, to appear.

  111. B Xu, A Woodroffe, L Rodriguez-Murillo, JL Roos, EJ van Rensburg, GR Abecasis, JA Gogos, M Karayiorgou (2009), "Elucidating the genetic architecture of familial schizophrenia using rare copy number variant and linkage scans", Proceedings of National Academy of Sciences, 106(39):16746-16751.

  112. J Yan, F Zhang, E Brundage, A Scheuerle, B Lanpher, RP Erickson, Z Powis, HB Robinson, PL Trapane, D Stachiw-Hietpas, KM Keppler-Noreuil, SR Lalani, T Sahoo, AC Chinault, A Patel, SW Cheung, JR Lupski (2009), "Genomic duplication resulting in increased copy number of genes encoding the sister chromatid cohesion complex conveys clinical consequences distinct from Cornelia de Lange", Journal of Medical Genetics, to appear.

  113. S Yoon, Z Xuan, V Makarov, K Ye, J Sebat (2009), "Sensitive and accurate detection of copy number variants using read depth of coverage", Genome Research, 19(9):1586-1592

  114. F Zhang, W Gu, ME Hurles, JR Lupski (2009), "Copy number variation in human health, disease, and evolution", Annual Review of Genomics and Human Genetics, 10:451-481.

  115. YX Zhang, Zhang YP, Gu Y, Guan FJ, Li SL, Xie JS, Shen Y, Wu BL, Ju W, Jenkins EC, Brown WT, Zhong N (2009), "Genetic analysis of first-trimester miscarriages with a combination of cytogenetic karyotyping, microsatellite genotyping and arrayCGH", Clinical Genetics, 75(2):133-140.

  116. Y Zhao, M Marotta, EE Eichler, C Eng, H Tanaka (2009), "Linkage disequilibrium between two high-frequency deletion polymorphisms: implications for association studies involving the glutathione-S transferase (GST) genes", PLoS Genetics, 5(5):e1000472.