Whole-genome array CGH evaluation for replacing prenatal karyotyping in Hong Kong

Abstract

Objective: To evaluate the effectiveness of whole-genome array comparative genomic hybridization (aCGH) in prenatal diagnosis in Hong Kong.

Methods: Array CGH was performed on 220 samples recruited prospectively as the first-tier test study. In addition 150 prenatal samples with abnormal fetal ultrasound findings found to have normal karyotypes were analyzed as a 'further-test' study using NimbleGen CGX-135K oligonucleotide arrays.

Results: Array CGH findings were concordant with conventional cytogenetic results with the exception of one case of triploidy. It was found in the first-tier test study that aCGH detected 20% (44/220) clinically significant copy number variants (CNV), of which 21 were common aneuploidies and 23 had other chromosomal imbalances. There were 3.2% (7/220) samples with CNVs detected by aCGH but not by conventional cytogenetics. In the 'further-test' study, the additional diagnostic yield of detecting chromosome imbalance was 6% (9/150). The overall detection for CNVs of unclear clinical significance was 2.7% (10/370) with 0.9% found to be de novo. Eleven loci of common CNVs were found in the local population.

Conclusion: Whole-genome aCGH offered a higher resolution diagnostic capacity than conventional karyotyping for prenatal diagnosis either as a first-tier test or as a 'further-test' for pregnancies with fetal ultrasound anomalies. We propose replacing conventional cytogenetics with aCGH for all pregnancies undergoing invasive diagnostic procedures after excluding common aneuploidies and triploidies by quantitative fluorescent PCR. Conventional cytogenetics can be reserved for visualization of clinically significant CNVs.

Figure 1. A schematic diagram showing the indications for recruitment to the study and CNVs detected in the evaluation study.

The samples were subjected to first-tier test and ‘further-test’, with the clinical indications of testing and findings stated. aCGH, array CGH; CNVs, copy number variants; n, number of samples; DS +ve, Down syndrome screening positive; USS abn, ultrasound abnormality; Anxiety: maternal anxiety. Details on the clinically significant CNVs and CNVs of uncertain clinical significance are listed in Tables 1, 2, 3, 4, 5, 6.

Figure 2. Identical complex chromosomal rearrangements in chromosome 15 found in 2 prenatal samples with different karyotypes and phenotypes.

Sample A karyotype is 46,XY,15q+ dn (Table 3, Case no. 8); Sample B karyotype is 47,XX,+mar from characterization study. Each dot on the X-axis represents one oligonucleotide probe on the respective chromosome position. Two-copy gain is detected at 15q11.2q13.2 with minimum gain of 7.77 Mb. Single copy gain is detected at 15q13.2q13.3 with minimum gain of 1.3 Mb. No probe is located in the segment between the 2 regions of copy gains, therefore the exact number of copy gained is unknown in the segment. The genetic syndromes (red boxes) and genes (green boxes) in the region denoted by Signature Genomics Genoglyphix software are shown in the lower panel.

Figure 3. Proposed workflow for replacing karyotyping with aCGH in prenatal testing in Hong Kong.

Pregnancies with Down syndrome screening positive without ultrasound abnormalities can be subjected to non-invasive prenatal testing; while pregnancies with Down syndrome screening positive in the presence of ultrasound abnormalities can be subjected to invasive test by QF-PCR to exclude common aneuploidy and maternal contamination, followed by aCGH as shown. aCGH, array CGH; DS+ve, Down syndrome screening positive; FISH, fluorescent in-situ hybridization; NIPT, non-invasive prenatal testing; QF-PCR, quantitative fluorescent-polymerase chain reaction for common aneuploidy detection.