Experience with microarray-based comparative genomic hybridization for prenatal diagnosis in over 5000 pregnancies

Abstract

Objective: To demonstrate the usefulness of microarray testing in prenatal diagnosis based on our laboratory experience.

Methods: Prenatal samples received from 2004 to 2011 for a variety of indications (n = 5003) were tested using comparative genomic hybridization-based microarrays targeted to known chromosomal syndromes with later versions of the microarrays providing backbone coverage of the entire genome.

Results: The overall detection rate of clinically significant copy number alterations (CNAs) among unbiased, nondemise cases was 5.3%. Detection rates were 6.5% and 8.2% for cases referred with abnormal ultrasounds and fetal demise, respectively. The overall rate of findings with unclear clinical significance was 4.2% but would reduce to 0.39% if only de novo CNAs were considered. In cases with known chromosomal rearrangements in the fetus or parent, 41.1% showed CNAs related to the rearrangements, whereas 1.3% showed clinically significant CNAs unrelated to the karyotype. Finally, 71% of the clinically significant CNAs found by microarray were below the resolution of conventional karyotyping of fetal chromosomes.

Conclusions: Microarray analysis has advantages over conventional cytogenetics, including the ability to more precisely characterize CNAs associated with abnormal karyotypes. Moreover, a significant proportion of cases studied by array will show a clinically significant CNA even with apparently normal karyotypes.

Figure 1

An 18.9-Mb 2q24q31 deletion identified by microarray in a specimen with a 46, XY karyotype. Microarray plots show a single-copy loss of 806 oligonucleotide probes from the long arm of chromosome 2, identified in cultured amniocytes from a fetus referred with a diaphragmatic hernia, Dandy Walker malformation, ventricular septal defect, and lower limb abnormalities. The deletion includes several disease-associated genes (green boxes), including epilepsy-associated SCN1A and SCN2A and limb abnormality-associated HOXD genes. Probes are ordered on the x-axis according to physical mapping positions (hg18), with the most distal 2p probes to the left and the most distal 2q probes to the right. Values along the y-axis represent log₂ ratios of patient:control signal intensities. Results are visualized using Genoglyphix (Signature Genomics)

Figure 2

Homozygous deletions of recessive loci in prenatal specimens. (A) Microarray plot showing a complex pattern of heterozygous and homozygous deletion of 5 oligonucleotide probes from the short arm of chromosome 16 over the alpha thalassemia locus at 16p13.3, identified in cultured amniocytes from a fetus referred with edema. Probes are ordered on the x-axis according to physical mapping positions (hg18), with the most distal 16p13.3 probes to the left and the most proximal 16p13.3 probes to the right. Values along the y-axis represent log₂ ratios of patient:control signal intensities. Parental samples were unavailable for array comparative genomic hybridization, but blood work was suggestive of both parents being carriers for alpha thalassemia. (B) Microarray plots from parents and fetus in a prenatal case referred for a family history of intellectual disability. After fetal testing, inspection of this region in the parents showed that the father has a single-copy loss of 3 probes, overlapping ERCC8, a gene associated with Cockayne syndrome, and NDUFAF2, a gene associated with mitochondrial complex I deficiency. The mother has a complex finding of a heterozygous deletion of a single probe within ERCC8 and a more distal heterozygous deletion within NDUFAF2. The fetus inherited both deletions and is therefore predicted to have homozygous loss-of-function of ERCC8 and NDUFAF2. Probes are arranged as in (A), with the most proximal 5q12.1 probes to the left and the most distal 5q12.1 probes to the right. Genes within the region are shown as green boxes. Results are visualized using Genoglyphix (Signature Genomics)