Non‐targeted whole genome 250K SNP array analysis as replacement for karyotyping in fetuses with structural ultrasound anomalies: evaluation of a one‐year experience

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Abstract
Objective We evaluated both clinical and laboratory aspects of our new strategy offering quantitative fluorescence (QF)‐PCR followed by non‐targeted whole genome 250K single‐nucleotide polymorphism array analysis instead of routine karyotyping for prenatal diagnosis of fetuses with structural anomalies. Methods Upon the detection of structural fetal anomalies, parents were offered a choice between QF‐PCR and 250K single‐nucleotide polymorphism array analysis (QF/array) or QF‐PCR and routine karyotyping (QF/karyo). Results Two hundred twenty fetal samples were included. In 153/220 cases (70%), QF/array analysis was requested. In 35/153 (23%), an abnormal QF‐PCR result was found. The remaining samples were analyzed by array, which revealed clinically relevant aberrations, including two known microdeletions, in 5/118 cases. Inherited copy number variants were detected in 11/118 fetuses, copy number variants with uncertain clinical relevance in 3/118 and homozygous stretches in 2/118. In 67/220 (30%) fetuses, QF/karyo was requested: 23/67 (34%) were abnormal with QF‐PCR, and in 3/67, an abnormal karyotype was found. Conclusion Even though QF/array does not reveal a high percentage of submicroscopic aberrations in fetuses with unselected structural anomalies, it is preferred over QF/karyo, as it provides a whole genome scan at high resolution, without additional tests needed and with a low chance on findings not related to the ultrasound anomalies. © 2012 John Wiley & Sons, Ltd.