When a submicroscopic gain or loss of chromosomal material is suspected and is beyond the resolution of routine chromosome analysis, CGH microarray should be considered as adjunct testing.

Karyotype analysis on amniotic fluid samples or chorionic villi has limited resolution and there is a delay between sampling and results. Therefore, invasive prenatal diagnosis has been reserved for pregnancies that are at increased risk for a defined genetic disorder, or for common aneuploidies found in liveborns. However, more than 70 disorders are now known to be associated with birth defects or developmental problems that are caused by deletion or duplication of a small chromosomal segment. These conditions and aneuploidies can be detected by array-based comparative genomic hybridization (CGH), which can evaluate the copy number of thousands of genomic regions simultaneously in a single assay. We review current knowledge on benign and pathological genomic copy number variants, principles of array CGH and its use for discovery and diagnosis of genetic diseases. Array CGH has already revolutionized genetic diagnosis in children and adults and is being used increasingly for prenatal diagnosis.

Current Practice for Prenatal Diagnosis of Chromosomal Abnormalities

Currently, invasive prenatal cytogenetic testing by chorionic villus sampling (CVS) or amniocentesis is routinely offered to pregnant women who are at an increased risk of a fetus with the most common aneuploidy associated with neonatal survival, trisomy 21 (Down syndrome), secondarily trisomy 18 and 13. The risk for these conditions is calculated from maternal age, abnormal first- or second-trimester serum screening results, fetal anomalies detected by ultrasound, a family history of cytogenetic disorders or from a combination of these.^[1,2] Less frequently, women are offered DNA-based molecular testing because of an increased risk for a specific Mendelian disorder in their fetus based on family history, abnormal results on parental carrier screening (e.g., for cystic fibrosis, sickle cell anemia or thalassemia), or abnormal prenatal ultrasound findings.

Karyotype analysis of G-banded chromosomal metaphase spreads has been the standard method for prenatal cytogenetic diagnosis since the 1970s. Such conventional cytogenetic analysis can identify all chromosomal aneuploidies and chromosomal aberrations that are microscopically visible. These include deletions, duplications or balanced and unbalanced chromosomal translocations, typically involving chromosomal segments of at least 4–5 Mb in size. Small supernumerary marker chromosomes (SMCs) and mosaic chromosomal abnormalities are also detected. The major limitations of conventional cytogenetic analysis are the low resolution of the G-banding technique, the requirement for cell culture, the extended time from sampling to results and the need for subjective interpretation, which requires skill and limits the possibility for high-throughput automated analysis. Frequently, 10–14 days are needed to obtain results. More importantly, submicroscopic deletions, duplications or other rearrangements are not commonly detectable. This category of structural genomic variants is an increasingly recognized cause of genetic disorders and has been associated with up to 17% of syndromic and nonsyndromic mental retardation.^[3]

Fluorescence in situ hybridization with chromosome-specific probes and, more recently, quantitative fluorescent PCR, is commonly used for the fast detection of the clinically relevant major aneuploidies (sex chromosome aneuploidy and trisomies 13, 21 and 18).^[4,5]FISH with locus-specific probes from selected regions known to harbor a known deletion or duplication syndrome, can also readily be performed. However, it is used less frequently prenatally and only when the fetus is clinically suspected to be at risk for a particular syndrome from a suggestive family history or a typical prenatal ultrasound finding. For example, FISH with a probe in 22q11 in the velocardiofacial/DiGeorge syndrome microdeletion region is offered when a fetal congenital heart defect is detected by prenatal ultrasound.^[6] As only a few probes can be used simultaneously, FISH is of limited benefit as a general prenatal diagnostic tool; for example, when there are nonspecific findings on fetal ultrasound. In addition, the birth defects and developmental problems found in many of the known microdeletion and microduplication syndromes have nonspecific or no prenatal ultrasound findings, and these conditions are rarely detected in low-risk pregnancies.

Microarray-based comparative genomic hybridization (array CGH) is a recently developed method that simultaneously evaluates numerous genomic regions for copy-number losses (deletions), or gains (duplications) and can address many of the limitations of karyotyping and FISH. Array CGH is already widely used for the clinical diagnosis of cytogenetic and genomic disorders in the pediatric population^[7-9] and, more recently, has been evaluated for prenatal diagnosis.^[10-12]