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Vol. 135, No. 3-4, 2011
Issue release date: December 2011
Section title: Paper
Cytogenet Genome Res 2011;135:212–221
(DOI:10.1159/000331273)

SNP Array Analysis in Constitutional and Cancer Genome Diagnostics – Copy Number Variants, Genotyping and Quality Control

de Leeuw N. · Hehir-Kwa J.Y. · Simons A. · Geurts van Kessel A. · Smeets D.F. · Faas B.H.W. · Pfundt R.
Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands

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Article / Publication Details

First-Page Preview
Abstract of Paper

Published online: 9/16/2011

Number of Print Pages: 10
Number of Figures: 1
Number of Tables: 1

ISSN: 1424-8581 (Print)
eISSN: 1424-859X (Online)

For additional information: http://www.karger.com/CGR

Abstract

Array-based comparative genomic hybridization analysis of genomic DNA was first applied in postnatal diagnosis for patients with intellectual disability (ID) and/or congenital anomalies (CA). Genome-wide single-nucleotide polymorphism (SNP) array analysis was subsequently implemented as the first line diagnostic test for ID/CA patients in our laboratory in 2009, because its diagnostic yield is significantly higher than that of routine cytogenetic analysis. In addition to the detection of copy number variations, the genotype information obtained with SNP array analysis enables the detection of stretches of homozygosity and thereby the possible identification of recessive disease genes, mosaic aneuploidy, or uniparental disomy. Patient-parent (trio) information analysis is used to screen for the presence of any form of uniparental disomy in the patient and can determine the parental origin of a de novo copy number variation. Moreover, the outcome of a genotype analysis is used as a final quality control by ruling out potential sample mismatches due to non-paternity or sample mix-up. SNP array analysis is now also used in our laboratory for patients with disorders for which locus heterogeneity is known (homozygosity pre-screening), in prenatal diagnosis in case of structural ultrasound anomalies, and for patients with leukemia. In this report, we summarize our array findings and experiences in the various diagnostic applications and demonstrate the power of a SNP-based array platform for molecular karyotyping, because it not only significantly improves the diagnostic yield in both constitutional and cancer genome diagnostics, but it also enhances the quality of the diagnostic laboratory workflow.


  

Author Contacts

Nicole de Leeuw
Department of Human Genetics, Radboud University Nijmegen Medical Centre
PO Box 9101
NL–6500 HB Nijmegen (The Netherlands)
Tel. +31 24 361 4104, E-Mail n.deleeuw@antrg.umcn.nl

  

Article Information

Published online: September 16, 2011
Number of Print Pages : 10
Number of Figures : 1, Number of Tables : 1, Number of References : 58

  

Publication Details

Cytogenetic and Genome Research

Vol. 135, No. 3-4, Year 2011 (Cover Date: December 2011)

Journal Editor: Schmid M. (Würzburg)
ISSN: 1424-8581 (Print), eISSN: 1424-859X (Online)

For additional information: http://www.karger.com/CGR


Article / Publication Details

First-Page Preview
Abstract of Paper

Published online: 9/16/2011

Number of Print Pages: 10
Number of Figures: 1
Number of Tables: 1

ISSN: 1424-8581 (Print)
eISSN: 1424-859X (Online)

For additional information: http://www.karger.com/CGR


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