ISSUES IN MOLECULAR KARYOTYPING/ARRAY CGH
Program of the Permanent Working Group meeting in Istambul (Saturday 7, 16.00-17.00):
Nicole De Leeuw, Nijmegen:
Best practice guidelines for molecular karyotyping and the Nijmegen experience.
Heike Fiegler, Sanger Institute:
The results of the DECIPHER molecular karyotyping EQA
As decided on the ECA meeting in Madrid of this year, we maintain a website with the latest information on array CGH developments. This web site is meant to be an information resourse on clinical implementation on array CGH, emerging guidelines, ongoing debates, meetings, etc… Readers are invited to actively participate in the continuous update of this information. If you feel some information is lacking or if you want to contribute to this site, please do so.
During the last three months the following updates have been made:
1. Philippos Patsalis has sent questionaires addressing basic questions about array CGH to all array CGH providers. Answers to these questionnaires are of interest to array CGH users and the answers are placed on our website. Array CGH providers that have not answered these questions but want to contribute can still contribute.
2. Users of commercial arrays can submit their experiences on the web site. Others can learn from this information.
3. Novel information on nomenclature, data submission, information sources, data analysis websites, etc… has been updated on the website.
Please send useful information, your comments or interesting links to
Joris Vermeesch : Joris.Vermeesch@uz.kuleuven.ac.be
Mariano Rocchi. : email@example.com
Information resources, emerging guidelines, ongoing debates, meetings
Click to download
Oxford Gene Technology Services
Vysis 2005 Microarray Technologies Bibliography
Molecular Karyotyping from a company
Molecular Karyotyping from a customer
Molecular karyotyping, a novel molecular cytogenetic technology with huge diagnostic potential, is likely to be implemented in diagnostic cytogenetic laboratories during the coming years. This website is meant to be a forum for interaction between cytogeneticists on resources and issues related to molecular karyotyping/array CGH.
At the introduction meeting on ECA2005 a number of issues related to array CGH use in clinical diagnostics were raised. These issues are stated below. Upcoming answers/ references/ guidelines/etc.. are indicated next to the questions raised. The current list incomplete and everyone is encouraged to help updating this website. Comments and suggestions can be sent to Mariano Rocchi or Yoris Vermeesch
Buckley, P.G., Mantripragada, K.K., Piotrowski, A., Diaz, d.S. and Dumanski, J.P. Copy-number polymorphisms: mining the tip of an iceberg. Trends Genet 21:315-317, 2005.
Dudoit, S., Gentleman, R.C. and Quackenbush, J. Open source software for the analysis of microarray data. Biotechniques JID - 45-51, 2003.
Fiegler, H., Carr, P., Douglas, E.J., et al. DNA microarrays for comparative genomic hybridization based on DOP-PCR amplification of BAC and PAC clones. Genes Chromosomes Cancer 36:361-374, 2003.
Garnis, C., Coe, B.P., Lam, S.L., MacAulay, C. and Lam, W.L. High-resolution array CGH increases heterogeneity tolerance in the analysis of clinical samples. Genomics 85:790-793, 2005.
Ishkanian, A.S., Malloff, C.A., Watson, S.K., et al. A tiling resolution DNA microarray with complete coverage of the human genome. Nat Genet 36:299-303, 2004.
Menten, B., Pattyn, F., De Preter, K., et al. arrayCGHbase: an analysis platform for comparative genomic hybridization microarrays. BMC Bioinformatics - [aheadofprint] AID - 1471-2105-6-124 [pii] AID - 10.1186/1471-2105-6-124 [doi] PST - aheadofprint 6:1242005.
Myers, C.L., Chen, X. and Troyanskaya, O.G. Visualization-based discovery and analysis of genomic aberrations in microarray data. BMC Bioinformatics [aheadofprint] AID - 1471-2105-6-146 [pii] AID - 10.1186/1471-2105-6-146 [doi] PST - aheadofprint 6:1462005.
Pinkel, D., Segraves, R., Sudar, D., et al. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet 20:207-211, 1998.
Pinkel, D. and Albertson, D.G. Comparative Genomic Hybridization. Annu Rev Genomics Hum Genet /annurev.genom.6.080604.162140 [doi] PST - aheadofprint 2005.
Pinkel, D. and Albertson, D.G. Array comparative genomic hybridization and its applications in cancer. Nat Genet 37 Suppl:S11-S172005.
Pinkel, D. and Albertson, D.G. Comparative Genomic Hybridization. Annu Rev Genomics Hum Genet annurev.genom.6.080604.162140 [doi] PST - aheadofprint 2005.
Price, T.S., Regan, R., Mott, R., et al. SW-ARRAY: a dynamic programming solution for the identification of copy-number changes in genomic DNA using array comparative genome hybridization data. Nucleic Acids Res 33:3455-3464, 1905.
Rauch, A., Ruschendorf, F., Huang, J., et al. Molecular karyotyping using an SNP array for genomewide genotyping. J Med Genet 41:916-922, 2004.
Rosenberg, C., Knijnenburg, J., Bakker, E., et al. Array-CGH detection of micro rearrangements in mentally retarded individuals: Clinical significance of imbalances present both in affected children and normal parents. J Med Genet PST - aheadofprint 2005.
Schaeffer, A.J., Chung, J., Heretis, K., Wong, A., Ledbetter, D.H. and Lese, M.C. Comparative genomic hybridization-array analysis enhances the detection of aneuploidies and submicroscopic imbalances in spontaneous miscarriages. Am J Hum Genet 74:1168-1174, 2004.
Sebat, J., Lakshmi, B., Troge, J., et al. Large-scale copy number polymorphism in the human genome. Science 305:525-528, 2004.
Sharp, A.J., Locke, D.P., McGrath, S.D., et al. Segmental duplications and copy-number variation in the human genome. Am J Hum Genet 77:78-88, 2005.
Shaw-Smith, C., Redon, R., Rickman, L., et al. Microarray based comparative genomic hybridisation (array-CGH) detects submicroscopic chromosomal deletions and duplications in patients with learning disability/mental retardation and dysmorphic features. J Med Genet 41:241-248, 2004.
Snijders, A.M., Nowak, N., Segraves, R., et al. Assembly of microarrays for genome-wide measurement of DNA copy number. Nat Genet 29:263-264, 2001.
Solinas-Toldo, S., Lampel, S., Stilgenbauer, S., et al. Matrix-based comparative genomic hybridization: biochips to screen for genomic imbalances. Genes Chromosomes Cancer 20:399-407, 1997.
Tuzun, E., Sharp, A.J., Bailey, J.A., et al. Fine-scale structural variation of the human genome. Nat Genet aheadofprint 2005.
Vermeesch, J.R., Melotte, C., Froyen, G., et al. Molecular Karyotyping: Array CGH Quality Criteria for Constitutional Genetic Diagnosis. J Histochem Cytochem 53:413-422, 2005.
Vissers, L.E., de Vries, B.B., Osoegawa, K., et al. Array-based comparative genomic hybridization for the genomewide detection of submicroscopic chromosomal abnormalities. Am J Hum Genet 73:1261-1270, 2003.