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

Patrick G. Buckley, Kiran K. Mantripragada, Magdalena Benetkiewicz, Isabel Tapia-Páez, Teresita Diaz de Ståhl, Magnus Rosenquist, Haider Ali, Caroline Jarbo, Cecilía de Bustos, Carina Hirvelä, Birgitta Sinder Wilén, Ingegerd Fransson, Charlotte Thyr, Britt Inger Johnsson, Carl E.G. Bruder, Uwe Menzel, Martin Hergersberg, Nils Mandahl, Elisabeth Blennow, Anna WedellDavid M. Beare, John E. Collins, Ian Dunham, Donna Albertson, Daniel Pinkel, Boris C. Bastian, A. Fawad Faruqi, Roger S. Lasken, Koichi Ichimura, V. Peter Collins, Jan P. Dumanski

Research output: Contribution to journalReview articlepeer-review

Abstract

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.

Original languageEnglish (US)
Pages (from-to)3221-3229
Number of pages9
JournalHuman Molecular Genetics
Volume11
Issue number25
DOIs
StatePublished - Dec 1 2002

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics
  • Genetics(clinical)

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