Prenatal diagnosis of chromosome abnormalities: past, present, and future.

For decades, conventional chromosome analysis using G-banded karyotyping has been the gold standard for detecting cytogenetic abnormalities in fetuses for prenatal diagnosis and pregnancy loss. Although chromosome studies easily identify such chromosome abnormalities as aneuploidy (gain or loss of an entire chromosome), balanced rearrangements, and large unbalanced structural rearrangements, they have limited resolution. Pathogenic copy number changes smaller than approximately 5–10 Mb are not detectable; however, recent advances in chromosomal microarray (CMA) analysis now allow the detection of chromosomal deletions and duplications at much higher resolutions (down to only a few kilobases, depending on the microarray), producing a higher diagnostic yield. In fact, a recently published study that compared standard karyotyping with postnatal CMA testing for patients with unexplained developmental delay, autism spectrum disorders, or multiple congenital anomalies demonstrated an increased diagnostic yield of about 12%–15% with CMA analysis, vs. 4% with karyotyping. These findings led to the recommendation by the American College of Medical Genetics that CMA testing replace chromosome analysis as the first-tier test for such patients (1, 2 ). Given these findings in the postnatal setting, the incremental diagnostic yields of CMA analysis and chromosome analysis are now being evaluated for prenatal genetic testing. Recent publications in the New England Journal of Medicine have described approaches to answering this question, not only with prenatal samples (3 ) but also with stillbirths (defined as pregnancy loss at or after 20 weeks’ gestation) (4 ). The multicenter study by Wapner et al. successfully analyzed 4182 samples of amniotic fluid and chorionic villi with both chromosome and CMA analysis (3 ). The women were tested for indications that included advanced maternal age, a positive result in maternal-serum screening, and fetal anomalies detected on ultrasonography. CMA was equally efficacious in identifying all aneuploidies and unbalanced rearrangements that had been identified by karyotyping. This methodology, however, was unable to detect balanced translocations and triploidy. These features are known limitations of this type of testing, although truly balanced rearrangements are rarely clinically relevant for the fetus. Nevertheless, microarrays that use probes to interrogate singlenucleotide polymorphisms in addition to copy number changes can, in fact, detect triploidy. In samples with a normal karyotype, CMA analysis detected clinically relevant copy number changes in 6% of pregnancies with structural anomalies identified by ultrasound and in 1.7% of pregnancies with an older maternal age and positive results in serum screening tests. These results demonstrate—as in the postnatal setting—that CMA analysis has greater clinical utility than chromosome studies. Karyotype analysis reveals an abnormality in approximately 6% to 13% of stillbirths; however, 25% to 60% of stillbirths remain unexplained, even after postmortem examination and karyotype analysis. Therefore, the Stillbirth Collaborative Research Network conducted a population-based study to determine whether CMA analysis would yield additional genetic diagnoses (4 ). In this study, CMA yielded a result (whether normal or abnormal) in 87.4% of the 532 samples analyzed, whereas chromosome studies yielded a result only 70.5% of the time. Chromosome analyses were able to identify clinically relevant abnormalities in 5.8% of stillbirths, whereas CMA detected aneuploidy or a pathogenic copy number variant (CNV) in 8.3% of samples. Including CNVs of uncertain clinical relevance increases the abnormalitydetection rate for CMA to 13%, a 122.6% increase compared with karyotype analyses. Although CMA was unable to detect 2 low-level mosaic cases ( 10%), the authors point out that the clinical implications of these 2 low-level mosaic cases are unclear; hence, CMAs have increased clinical utility in cases of miscarriage as well as for prenatal diagnosis. The increased diagnostic yield is the primary benefit of CMA, but CMA has additional benefits compared with karyotyping. First, CMA is performed on genomic DNA, often without the need to culture the 1 Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN. * Address correspondence to this author at: Hilton 971, 200 First St. SW, Rochester, MN 55905. Fax 507-284-0043; e-mail [email protected]. Received April 22, 2013; accepted June 20, 2013. Previously published online at DOI: 10.1373/clinchem.2013.204149 2 Nonstandard abbreviations: CMA, chromosomal microarray; CNV, copy number variant; VUS, CNV of uncertain clinical significance; ICCG, International Collaboration for Clinical Genomics. Clinical Chemistry 59:1