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Genomic SNP array as a gold standard for prenatal diagnosis of foetal ultrasound abnormalities

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Author(s): Srebniak Malgorzata I | Boter Marjan | Oudesluijs Gretel O | Cohen-Overbeek Titia | Govaerts Lutgarde CP | Diderich Karin EM | Oegema Renske | Knapen Maarten FCM | van de Laar Ingrid MBH | Joosten Marieke | Van Opstal Diane | Galjaard Robert-Jan H

Journal: Molecular Cytogenetics
ISSN 1755-8166

Volume: 5;
Issue: 1;
Start page: 14;
Date: 2012;
Original page

Keywords: Genomic SNP array | Prenatal diagnosis | Foetal abnormalities | Submicroscopic aberrations

ABSTRACT
Abstract Background We have investigated whether replacing conventional karyotyping by SNP array analysis in cases of foetal ultrasound abnormalities would increase the diagnostic yield and speed of prenatal diagnosis in clinical practice. Findings/results From May 2009 till June 2011 we performed HumanCytoSNP-12 array (HCS) (http://www.Illumina.com) analysis in 207 cases of foetal structural abnormalities. HCS allows detecting unbalanced genomic abnormalities with a resolution of about 150/200 kb. All cases were selected by a clinical geneticist after excluding the most common aneuploidies by RAD (rapid aneuploidy detection). Pre-test genetic counselling was offered in all cases. In 24/207 (11,6%) foetuses a clinically relevant genetic abnormality was detected. Only 8/24 abnormalities would have been detected if only routine karyotyping was performed. Submicroscopic abnormalities were found in 16/207 (7,7%) cases. The array results were achieved within 1-2 weeks after amniocentesis. Conclusions Prenatal SNP array testing is faster than karyotyping and allows detecting much smaller aberrations (~0.15 Mb) in addition to the microscopic unbalanced chromosome abnormalities detectable with karyotyping (~ > 5 Mb). Since karyotyping would have missed 66% (16/24) of genomic abnormalities in our cohort, we propose to perform genomic high resolution array testing assisted by pre-test counselling as a primary prenatal diagnostic test in cases of foetal ultrasound abnormalities.
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