Advanced

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

Zhang, Zhong-Fa; Ruivenkamp, Claudia; Staaf, Johan LU ; Zhu, Hongbo; Barbaro, Michela; Petillo, David; Khoo, Sok Kean; Borg, Åke LU ; Fan, Yao-Shan and Schoumans, Jacqueline (2008) In European Journal of Human Genetics 16(7). p.786-792
Abstract
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... (More)
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. (Less)
Please use this url to cite or link to this publication:
author
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
submicroscopic chromosome aberrations, array platform comparison, copy-number detection
in
European Journal of Human Genetics
volume
16
issue
7
pages
786 - 792
publisher
Nature Publishing Group
external identifiers
  • wos:000256857400005
  • scopus:45749121948
ISSN
1476-5438
DOI
10.1038/ejhg.2008.14
language
English
LU publication?
yes
id
0eadd751-ef09-4f1f-8469-86f4a68e93c0 (old id 1191041)
date added to LUP
2008-09-08 11:04:56
date last changed
2017-01-01 04:35:06
@article{0eadd751-ef09-4f1f-8469-86f4a68e93c0,
  abstract     = {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 &lt;= 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.},
  author       = {Zhang, Zhong-Fa and Ruivenkamp, Claudia and Staaf, Johan and Zhu, Hongbo and Barbaro, Michela and Petillo, David and Khoo, Sok Kean and Borg, Åke and Fan, Yao-Shan and Schoumans, Jacqueline},
  issn         = {1476-5438},
  keyword      = {submicroscopic chromosome aberrations,array platform comparison,copy-number detection},
  language     = {eng},
  number       = {7},
  pages        = {786--792},
  publisher    = {Nature Publishing Group},
  series       = {European Journal of Human Genetics},
  title        = {Detection of submicroscopic constitutional chromosome aberrations in clinical diagnostics: a validation of the practical performance of different array platforms},
  url          = {http://dx.doi.org/10.1038/ejhg.2008.14},
  volume       = {16},
  year         = {2008},
}