Application of SNP array for rapid prenatal diagnosis: implementation, genetic counselling and diagnostic flow

Abstract

We report on the validation and implementation of the HumanCytoSNP-12 array (Illumina) (HCS) in prenatal diagnosis. In total, 64 samples were used to validate the Illumina platform (20 with a known (sub) microscopic chromosome abnormality, 5 with known maternal cell contamination (MCC) and 39 normal control samples). There were no false-positive or false-negative results. In addition to the diagnostic possibilities of arrayCGH, the HCS allows detection of regions of homozygosity (ROH), triploidy and helps recognising MCC. Moreover, in two cases of MCC, a deletion was correctly detected. Furthermore we found out that only about 50 ng of DNA is required, which allows a reporting time of only 3 days. We also present a prospective pilot study of 61 fetuses with ultrasound abnormalities and a normal karyotype tested with HCS. In 4 out of 61 (6.5%) fetuses, a clinically relevant abnormality was detected. We designed and present pre-test genetic counselling information on categories of possible test outcomes. On the basis of this information, about 90% of the parents chose to be informed about adverse health outcomes of their future child at infancy and childhood, and 55% also about outcomes at an adult stage. The latter issue regarding the right of the future child itself to decide whether or not to know this information needs to be addressed.

Figure 1

Current diagnostic flow.

Figure 2

Whole genome view of Human CytoSNP-12 profiles in Nexus 5.0. Both log ratios (above) and B allele frequencies (BAF) (below) is shown. The upper panel shows a profile of triploidy 69,XXX. The log ratio is normal; however, the BAF indicates a duplication of all chromosomes. There is no normal frequency at ∼0.5, but two at ∼0.4 and ∼0.6. The DNA input was 117 ng, the QC=0.071. The middle panel shows a normal male profile. The log ratio is about 0 (except for X) and the BAF shows three lines (upper and lower (∼1.0 and ∼0.0) – homozygosity, middle (∼0.5) – heterozygosity). The DNA input was 164 ng, the QC=0.038. The lower panel presents a profile with an indication for MCC. BAF shows additional BAF at ∼0.1 and ∼0.9 on all chromosomes. The DNA input is 202 ng, the QC=0.047.

Figure 3

The 17q deletion in a sample with MCC (case 5, Supplementary Material) shown on a chromosome plot from Nexus 5.0. The deletion in 17q24.3 was correctly identified by Nexus 5.0 in both clear and blood-stained AF. The upper panel shows the chromosome 17 plot of a sample with a 17q deletion and with MCC (uncultured blood-stained AF, DNA input 118 ng, QC=0.067). The lower panel shows the chromosome 17 plot of the same patient sample with a 17q deletion, but the array assay is performed on uncultured clear AF (DNA input 54 ng, QC=0.07).