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Detection of submicroscopic constitutional chromosome aberrations in clinical diagnostics: a validation of the practical performance of different array platforms

Author:
  • Zhong-Fa Zhang
  • Claudia Ruivenkamp
  • Johan Staaf
  • Hongbo Zhu
  • Michela Barbaro
  • David Petillo
  • Sok Kean Khoo
  • Åke Borg
  • Yao-Shan Fan
  • Jacqueline Schoumans
Publishing year: 2008
Language: English
Pages: 786-792
Publication/Series: European Journal of Human Genetics
Volume: 16
Issue: 7
Document type: Journal article
Publisher: Nature Publishing Group

Abstract english

For several decades etiological diagnosis of patients with idiopathic mental retardation (MR) and multiple congenital anomalies (MCA) has relied on chromosome analysis by karyotyping. Conventional karyotyping allows a genome-wide detection of chromosomal abnormalities but has a limited resolution. Recently, array-based comparative genomic hybridization (array CGH) technologies have been developed to evaluate DNA copy-number alterations across the whole-genome at a much higher resolution. It has proven to be an effective tool for detection of submicroscopic chromosome abnormalities causing congenital disorders and has recently been adopted for clinical applications. Here, we investigated four high-density array platforms with a theoretical resolution <= 100 kb: 33K tiling path BAC array, 500K Affymetrix SNP array, 385K NimbleGen oligonucleotide array and 244K Agilent oligonucleotide array for their robustness and implementation in our diagnostic setting. We evaluated the practical performance based on the detection of 10 previously characterized abnormalities whose size ranged from 100 kb to 3 Mb. Furthermore, array data analysis was performed using four computer programs developed for each corresponding platform to test their effective ability of reliable copy-number detection and their user-friendliness. All tested platforms provided sensitive performances, but our experience showed that accurate and user-friendly computer programs are of crucial importance for reliable copy-number detection.

Keywords

  • Medical Genetics
  • submicroscopic chromosome aberrations
  • array platform comparison
  • copy-number detection

Other

Published
  • ISSN: 1476-5438
Åke Borg
Åke Borg
E-mail: ake [dot] borg [at] med [dot] lu [dot] se

Principal investigator

Oncology and Pathology, MV

+46 46 275 25 52

MV 404 C21B2

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Project manager

Familial Breast Cancer

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Professor

Oncology and Pathology, MV

MV 404 C21C2

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