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. : rocchi@biologia.uniba.it

Information resources, emerging guidelines, ongoing debates, meetings

Click to download

Blue-Genome new

IntegraGen

Oxford Gene Technology Services

Spectral Genomics

Vysis

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

  1. Technical
    1. Variation in statistics
    2. Variation in performance
    3. Data analysis websites
      1. http://medgen.ugent.be/arrayCGHbase
      2. http://www.bccrc.ca/ArrayCGH/
      3. MANOR (Micro-array NORmalisation) software written in R is available upon request. http://bioinfo.curie.fr/
      4. VAMP (Visualisation and analysis of CGH arrays, transcriptome and other molecular profiles).  http://bioinfo.curie.fr/vamp
      5. CGHPRO  Tool for the normalization, visualization, breakpoint detection and comparative analysis of array-CGH data.  CGHPRO is a stand-alone JAVA application that guides users through the whole process of data analysis. 

        http://www.molgen.mpg.de/~abt_rop/molecular_cytogenetics/ArrayCGH/CGHPRO/

    4. Follow up after array CGH: FISH, others
  1. Quality criteria
    1. Define minimal criteria
    2. Need for reference material?
    3. EQA?
  1. Information resources
    1. Variation in the human genome
      1. http://projects.tcag.ca/variation: Note that this human variation database can be visualised within the Ensembl genome browser by activating in the cytogenetics view, the DAS server called ‘Toronto’ database.  
    2. Clinical information
      1. ECARUCA: http://www.ecaruca.net
      2. DECIPHER: http://www.sanger.ac.uk/Postgenomics/decipher: Note that the DECIPHER database can be visualized within the Ensembl genome browser by activating in the cyotogenetics view, the link ‘DECIPHER’. 
      3.  Others

 

    1. Meetings/Workshops
      1. Marie-Curie conferences and training workshops on array CGH and molecular cytogenetics http://www.medgen.ugent.be/arrayCGH-MC
      2.  
  1. Reporting data
    1. ISCN: 
      1. At the ECA meeting, Lisa Schaeffer presented a draft version of the novel ISCN 2005 nomenclature.  This novel ISCN nomenclature is scheduled to appear in book version at the end of 2005.
    2. Reporting in journals
      1. From July 15-17, a meeting took place at the Wellcome Trust Conference Centre in Hinxton to discuss the need to standardise publication and archiving of array-CGH data.  The meeting brought together representatives from array-providers (Affymetrix, Agilent, Signature Genomics, Niblegen), publishers (Nature Genetics) and scientific and clinical array CGH users.   At this meeting it was decided that all array CGH data should be MIAME complient and all published array CGH data will have to be submitted to MIAME complient data repositories before publication can be accepted.   Currently, these database providers are working on data entry formats for array CGH data.  It can be expected that MIAME compliance will be required by the beginning of 2006.
    3. Storage of patient information

 

  1. A selection of the literature related to the above issues. 

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.