Interpretation of genomic copy number variants using DECIPHER.
作者： Manuel Corpas , Eugene Bragin , Stephen Clayton , Paul Bevan , Helen V. Firth
DOI: 10.1002/0471142905.HG0814S72
关键词:
摘要: Many patients suffering from developmental disorders have submicroscopic deletions or duplications affecting the copy number of dosage-sensitive genes disrupting normal gene expression. these changes are novel extremely rare, making clinical interpretation problematic and genotype/phenotype correlations difficult. Identification sharing a genomic rearrangement having phenotypes in common increases certainty diagnosis allows characterization new syndromes. The DECIPHER database is an online repository genotype phenotype data whose chief objective to facilitate association variation with enable (CNV). This unit shows how can be used (1) search for consented defined chromosomal location, (2) navigate regions interest using in-house visualization tools Ensembl genome browser, (3) analyze affected prioritize them according their likelihood haploinsufficiency, (4) upload patient aberrations phenotypes, (5) create printouts at different levels detail. By following this protocol, clinicians researchers alike will able learn characterize patients' imbalances DECIPHER.
sci-hub.se 参考文章(15)
M Baraitser, K Tomiwa, J Wilson, R Winter, A database of genetically determined neurological conditions for clinicians. Journal of Neurology, Neurosurgery, and Psychiatry. ,vol. 52, pp. 106- 107 ,(1989) , 10.1136/JNNP.52.1.106
Pawel Stankiewicz, Arthur L Beaudet, Use of array CGH in the evaluation of dysmorphology, malformations, developmental delay, and idiopathic mental retardation Current Opinion in Genetics & Development. ,vol. 17, pp. 182- 192 ,(2007) , 10.1016/J.GDE.2007.04.009
Donald F. Conrad, , Dalila Pinto, Richard Redon, Lars Feuk, Omer Gokcumen, Yujun Zhang, Jan Aerts, T. Daniel Andrews, Chris Barnes, Peter Campbell, Tomas Fitzgerald, Min Hu, Chun Hwa Ihm, Kati Kristiansson, Daniel G. MacArthur, Jeffrey R. MacDonald, Ifejinelo Onyiah, Andy Wing Chun Pang, Sam Robson, Kathy Stirrups, Armand Valsesia, Klaudia Walter, John Wei, Chris Tyler-Smith, Nigel P. Carter, Charles Lee, Stephen W. Scherer, Matthew E. Hurles, Origins and functional impact of copy number variation in the human genome Nature. ,vol. 464, pp. 704- 712 ,(2010) , 10.1038/NATURE08516
Helen V. Firth, Shola M. Richards, A. Paul Bevan, Stephen Clayton, Manuel Corpas, Diana Rajan, Steven Van Vooren, Yves Moreau, Roger M. Pettett, Nigel P. Carter, DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources American Journal of Human Genetics. ,vol. 84, pp. 524- 533 ,(2009) , 10.1016/J.AJHG.2009.03.010
N. Le Meur, M. Holder-Espinasse, S. Jaillard, A. Goldenberg, S. Joriot, P. Amati-Bonneau, A. Guichet, M. Barth, A. Charollais, H. Journel, S. Auvin, C. Boucher, J.-P. Kerckaert, V. David, S. Manouvrier-Hanu, P. Saugier-Veber, T. Frebourg, C. Dubourg, J. Andrieux, D. Bonneau, MEF2C haploinsufficiency caused by either microdeletion of the 5q14.3 region or mutation is responsible for severe mental retardation with stereotypic movements, epilepsy and/or cerebral malformations Journal of Medical Genetics. ,vol. 47, pp. 22- 29 ,(2010) , 10.1136/JMG.2009.069732
Hartmut Engels, Eva Wohlleber, Alexander Zink, Juliane Hoyer, Kerstin U Ludwig, Felix F Brockschmidt, Dagmar Wieczorek, Ute Moog, Birgit Hellmann-Mersch, Ruthild G Weber, Lionel Willatt, Martina Kreiß-Nachtsheim, Helen V Firth, Anita Rauch, A novel microdeletion syndrome involving 5q14.3-q15: clinical and molecular cytogenetic characterization of three patients European Journal of Human Genetics. ,vol. 17, pp. 1592- 1599 ,(2009) , 10.1038/EJHG.2009.90
Helen V Firth, Caroline F Wright, None, The Deciphering Developmental Disorders (DDD) study. Developmental Medicine & Child Neurology. ,vol. 53, pp. 702- 703 ,(2011) , 10.1111/J.1469-8749.2011.04032.X
Sylvie Jaillard, Séverine Drunat, Claude Bendavid, Azzedine Aboura, Amandine Etcheverry, Hubert Journel, Andrée Delahaye, Laurent Pasquier, Dominique Bonneau, Annick Toutain, Lydie Burglen, Agnès Guichet, Eva Pipiras, Brigitte Gilbert-Dussardier, Brigitte Benzacken, Dominique Martin-Coignard, Catherine Henry, Albert David, Josette Lucas, Jean Mosser, Véronique David, Sylvie Odent, Alain Verloes, Christèle Dubourg, Identification of gene copy number variations in patients with mental retardation using array-CGH: Novel syndromes in a large French series. European Journal of Medical Genetics. ,vol. 53, pp. 66- 75 ,(2010) , 10.1016/J.EJMG.2009.10.002
E. A. Bruford, M. J. Lush, M. W. Wright, T. P. Sneddon, S. Povey, E. Birney, The HGNC Database in 2008: a resource for the human genome Nucleic Acids Research. ,vol. 36, pp. 445- 448 ,(2007) , 10.1093/NAR/GKM881
Ryan E Mills, Klaudia Walter, Chip Stewart, Robert E Handsaker, Ken Chen, Can Alkan, Alexej Abyzov, Seungtai Chris Yoon, Kai Ye, R Keira Cheetham, Asif Chinwalla, Donald F Conrad, Yutao Fu, Fabian Grubert, Iman Hajirasouliha, Fereydoun Hormozdiari, Lilia M Iakoucheva, Zamin Iqbal, Shuli Kang, Jeffrey M Kidd, Miriam K Konkel, Joshua Korn, Ekta Khurana, Deniz Kural, Hugo YK Lam, Jing Leng, Ruiqiang Li, Yingrui Li, Chang-Yun Lin, Ruibang Luo, Xinmeng Jasmine Mu, James Nemesh, Heather E Peckham, Tobias Rausch, Aylwyn Scally, Xinghua Shi, Michael P Stromberg, Adrian M Stütz, Alexander Eckehart Urban, Jerilyn A Walker, Jiantao Wu, Yujun Zhang, Zhengdong D Zhang, Mark A Batzer, Li Ding, Gabor T Marth, Gil McVean, Jonathan Sebat, Michael Snyder, Jun Wang, Kenny Ye, Evan E Eichler, Mark B Gerstein, Matthew E Hurles, Charles Lee, Steven A McCarroll, Jan O Korbel, 1000 Genomes Project, None, Mapping copy number variation by population-scale genome sequencing Nature. ,vol. 470, pp. 59- 65 ,(2011) , 10.1038/NATURE09708