Construction and application of a full-coverage, high-resolution, human chromosome 8q genomic microarray for comparative genomic hybridization

Mark Van Duin, Ronald Van Marion, J. E.Vivienne Watson, Pamela L. Paris, Anna Lapuk, Nils Brown, Vanessa V. Oseroff, Donna G. Albertson, Daniel Pinkel, Pieter De Jong, Elizabeth P. Nacheva, Winand Dinjens, Herman Van Dekken, Colin Collins

Research output: Contribution to journalArticle

Abstract

Background: Array-based comparative genomic hybridization (aCGH) enables genome-wide quantitative delineation of genomic imbalances. A high-resolution contig array was developed specifically for chromosome 8q because this chromosome arm is frequently altered in many human cancers. Methods: A minimal tiling path contig of 702 8q-specific bacterial artificial chromosome (BAC) clones was generated with a novel computational tool (BAC Contig Assembler). BAC clones were amplified by degenerative oligonucleotide primer (DOP) polymerase chain reaction and subsequently printed onto glass slides. For validation of the array DNA samples of gastroesophageal and prostate cancer cell lines, and chronic myeloid leukemia specimens were used, which were previously characterized by multicolor fluorescence in situ hybridization and conventional CGH. Results: Single and double copy gains were confidently demonstrated with the 8q array. Single copy loss and high-level amplifications were accurately detected and confirmed by bicolor fluorescence in situ hybridization experiments. The 8q array was further tested with paraffin-embedded prostate cancer specimens. In these archival specimens, the copy number changes were confirmed. In fresh and archival samples, additional alterations were disclosed. In comparison with conventional CGH, the resolution of the detected changes was much improved, which was demonstrated by an amplicon of 0.7 Mb and a deletion of 0.6 Mb, both spanned by only six BAC clones. Conclusions: A comprehensive array is presented, which provides a high-resolution method for mapping copy number alterations on chromosome 8q.

Original languageEnglish (US)
Pages (from-to)10-19
Number of pages10
JournalCytometry Part A
Volume63
Issue number1
DOIs
StatePublished - Jan 2005

Keywords

  • 8q contig
  • Amplification
  • Cancer
  • Chromosomal aberrations
  • Comparative genomic hybridization
  • Deletion
  • Gain
  • Genomic array

ASJC Scopus subject areas

  • Pathology and Forensic Medicine
  • Histology
  • Cell Biology

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