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Human Molecular Genetics, 2002, Vol. 11, No. 25 3221-3229
© 2002 Oxford University Press

A full-coverage, high-resolution human chromosome 22 genomic microarray for clinical and research applications

Patrick G. Buckley1,{ddagger}, Kiran K. Mantripragada1,{ddagger}, Magdalena Benetkiewicz1, Isabel Tapia-Páez2, Teresita Diaz de Ståhl1, Magnus Rosenquist1, Haider Ali1, Caroline Jarbo1, Cecilía de Bustos1, Carina Hirvelä1, Birgitta Sinder Wilén1, Ingegerd Fransson2, Charlotte Thyr1, Britt-Inger Johnsson1, Carl E.G. Bruder1,{dagger}, Uwe Menzel1, Martin Hergersberg3, Nils Mandahl4, Elisabeth Blennow2, Anna Wedell2, David M. Beare5, John E. Collins5, Ian Dunham5, Donna Albertson6, Daniel Pinkel6, Boris C. Bastian6, A. Fawad Faruqi7, Roger S. Lasken7, Koichi Ichimura8, V. Peter Collins8 and Jan P. Dumanski1,*

1Department of Genetics and Pathology, Rudbeck laboratory, Uppsala University, 751 85 Uppsala, Sweden, 2Department of Molecular Medicine, CMM building, Karolinska Hospital, 171 76 Stockholm, Sweden, 3Zentrum für Labormedizin, Kantonsspital Aarau, CH-5001 Aarau, Switzerland, 4Department of Clinical Genetics, Lund University Hospital, Lund, Sweden, 5The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK, 6UCSF Comprehensive Cancer Center, Box 0808, University of California, San Francisco, CA 94143-0128, USA, 7Molecular Staging, Inc., 300 George Street, 7th Floor, New Haven, CT 06511, USA and 8Department of Pathology, Division of Molecular Histopathology, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 2QQ, UK

Received August 20, 2002; Accepted October 1, 2002

We have constructed the first comprehensive microarray representing a human chromosome for analysis of DNA copy number variation. This chromosome 22 array covers 34.7 Mb, representing 1.1% of the genome, with an average resolution of 75 kb. To demonstrate the utility of the array, we have applied it to profile acral melanoma, dermatofibrosarcoma, DiGeorge syndrome and neurofibromatosis 2. We accurately diagnosed homozygous/heterozygous deletions, amplifications/gains, IGLV/IGLC locus instability, and breakpoints of an imbalanced translocation. We further identified the 14-3-3 eta isoform as a candidate tumor suppressor in glioblastoma. Two significant methodological advances in array construction were also developed and validated. These include a strictly sequence defined, repeat-free, and non-redundant strategy for array preparation. This approach allows an increase in array resolution and analysis of any locus; disregarding common repeats, genomic clone availability and sequence redundancy. In addition, we report that the application of phi29 DNA polymerase is advantageous in microarray preparation. A broad spectrum of issues in medical research and diagnostics can be approached using the array. This well annotated and gene-rich autosome contains numerous uncharacterized disease genes. It is therefore crucial to associate these genes to specific 22q-related conditions and this array will be instrumental towards this goal. Furthermore, comprehensive epigenetic profiling of 22q-located genes and high-resolution analysis of replication timing across the entire chromosome can be studied using our array.

* To whom correspondence should be addressed at: Department of Genetics and Pathology, Rudbeck laboratory 3rd floor, Uppsala University, Dag Hammarskjölds väg 20, 751 85 Uppsala, Sweden. Fax: +46 18558931; Email: jan.dumanski{at}genpat.uu.se

{dagger} Present address: AstraZenenca R&D, Transgenics and Comparative Genomics, 43183 Mölndal, Sweden.

{ddagger} The authors wish it to be known that, in their opinion, these two authors should be considered as joint First Authors.


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