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Array comparative genomic hybridization in prenatal diagnosis of first trimester pregnancies at high risk for chromosomal anomalies

Isabel Filges13*, Anjeung Kang2, Vanessa Klug1, Friedel Wenzel1, Karl Heinimann1, Sevgi Tercanli2 and Peter Miny1

Author Affiliations

1 Dr. med. Isabel Filges, Division of Medical Genetics, University Children’s Hospital and Department of Biomedicine, University of Basel, Burgfelderstrasse 101, Building J, CH-4055, Basel, Switzerland

2 Ultrasound Unit, Department of Obstetrics and Gynecology, University Hospital, Basel, Switzerland

3 Department of Medical Genetics, BC Children’s and Women’s Hospital, Child and Family Research Institute, University of British Columbia, Box 153, 4480 Oak Street, Vancouver, BC V6H 3V4, Canada

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Molecular Cytogenetics 2012, 5:38  doi:10.1186/1755-8166-5-38

Published: 17 September 2012



To describe the diagnostic performance of array comparative genomic hybridization (aCGH) as a potential first line diagnostic method in first trimester high risk pregnancies.


In a retrospective study we performed aCGH using a targeted array BAC platform (Constitutional Chip® 4.0, PerkinElmer, Turku Finland, median resolution 600 kB) and the Affymetrix Cytogenetics® Whole Genome 2.7 M array (at a resolution of 400kB) on 100 anonymized prenatal samples from first trimester high risk pregnancies with normal conventional karyotype. We studied the technical feasibility and turn-around-time as well as the detection rate of pathogenic submicroscopic chromosome anomalies and CNVs of unknown significance.


We obtained results in 98 of 100 samples in 3 to a maximum of 5 days after DNA extraction. At the given resolution we did not identify any additional pathogenic CNVs but two CNVs of unknown significance in the chromosomal regions 1q21.1q21.2 (deletion) and 5p15.33 (duplication) (2%).


In accordance with a growing number of reports this study supports the concept that aCGH at a resolution of 400-600kB may be used as a first line prenatal diagnostic test with high diagnostic safety and rapid turn-around time in high-risk first trimester pregnancies. Detection rate of CNVs of unknown significance, considered as a major hindrance for replacing conventional karyotyping by aCGH, is 2%, but the diagnosis of additional submicroscopic anomalies in this heterogeneous group of patients seems to be rare.

Prenatal diagnosis; Array comparative genomic hybridization; ArrayCGH; aCGH; First trimester; High risk; CVS