Prenatal Diagnostic Testing

Introduction

Testing is available for an ever-increasing number of genetic disorders. Although prenatal testing originally focused primarily on Down syndrome, it is now possible to detect a broad range of genetic conditions. Prenatal diagnostic testing is most commonly performed on fetal tissue obtained with amniocentesis or chorionic villus sampling (CVS), although umbilical cord blood obtained through percutaneous sampling is occasionally used. In the early embryo, preimplantation genetic testing (PGT) is also used for genetic diagnosis in families at risk for specific genetic disorders (see Chapter 15 ). The focus of this chapter is on CVS and amniocentesis, as these are the techniques most commonly used for routine prenatal testing.

Prenatal genetic testing is focused on every woman’s values and preferences, which vary greatly. Before undergoing prenatal diagnostic testing, women should understand the benefits and limitations of such testing, the conditions that are being tested for, as well as the conditions that will not be detected, and the risks of the procedure. Prenatal genetic testing can provide reassurance when results are normal, identify disorders for which in utero treatment might be available, improve neonatal outcomes by assuring the best location for delivery and that appropriate pediatric specialists are available to care for affected infants, and can also provide the opportunity for pregnancy termination for women who choose that option.

Fetal genetic disorders that are amenable to prenatal genetic testing include those abnormalities in structure or function that are caused by variants in an individual’s genes, in contrast to those caused primarily by environmental or other disruptive causes; these latter conditions may be best identified by imaging. These distinctions are not always clear, as a genetic predisposition may increase the susceptibility to environmental influences, and some genetic abnormalities may only become apparent under specific environmental conditions or circumstances. Some disorders may have an epigenetic basis; in other words, gene functions may be turned on or silenced by modifications that may depend on the parent of origin or other influences (see Chapter 2 ). With improvements in our ability to study genetics and genomics, it is increasingly appreciated that inheritance and genetics are complex and our understanding is still relatively limited. For this reason, prenatal diagnosis can be complicated, and it is not always possible to predict the outcome based on a prenatal genetic test. It is important that patients understand that prenatal diagnostic testing is possible for many, but not all, genetic disorders.

What Conditions Can Be Diagnosed by Prenatal Genetic Testing?

In general, chromosomal abnormalities and single gene disorders can be identified by analysis of fetal tissue, and it is these categories of conditions that are most often the target of prenatal diagnostic testing. Chromosomal abnormalities are relatively common in pregnancy, and about 1/150 live births has a chromosomal abnormality that causes an abnormal phenotype. About 5% of stillbirths and 5–7% of infant and childhood deaths result from chromosomal abnormalities, and chromosomal abnormalities are commonly associated with structural fetal abnormalities. Copy number variants (CNVs), which can be detected with chromosomal microarray analysis (CMA), are present in about 1–1.7% of structurally normal fetuses and about 6% of those with an abnormality detected by ultrasound.

Chromosomal abnormalities include variations in chromosome number or structure. The most common abnormality of chromosome number found by prenatal testing is aneuploidy, which is the presence of an extra or missing chromosome or chromosomes. It is also possible to have one or more extra sets of chromosomes, as in triploidy or tetraploidy. Abnormalities in chromosome number can be mosaic, in which the abnormal number of chromosomes is not present in all cells (see Chapter 4 ).

In addition to abnormalities of chromosome number, there can also be aberrations in chromosome structure, such as deletions, duplications, translocations, and other rearrangements. In some cases, rearrangements are balanced, meaning the appropriate genomic content is present but rearranged, whereas in other cases, translocations or other rearrangements can result in extra or missing pieces of chromosomes. Balanced translocations most often are associated with a normal phenotype, although they can lead to recurrent miscarriage or an increased risk of abnormal offspring. Deletions and duplications can be quite large, and easily seen by a karyotype, or can be small microdeletions or duplications only detectable with chromosomal microarray analysis (CMA), fluorescence in situ hybridization (FISH), or other specialized methods (see Chapter 6 ) ( Table 14.1 ).

Some genetic disorders, such as cystic fibrosis, hemophilia, and Tay–Sachs disease, are caused by variants in single genes. Diseases caused solely by abnormalities in a single gene are relatively uncommon. The phenotype of some single gene disorders can be impacted by modifying genes, or by combinations of additional genes, as well as by environmental influences and therefore not all individuals who inherit a genetic variant will have the exact same phenotype. Single gene disorders can be detected by prenatal diagnostic testing if the disorder has been diagnosed with certainty and the particular variant within the family has been identified.

The most common congenital anomalies are isolated birth defects, such as heart defects, neural tube defects, and facial clefts. These traits are determined by multiple genes and environmental factors rather than by single genes. Because there is a genetic component, they often recur more commonly within a family. However, because they are not caused by a single gene variant but rather a complex interplay of genetic and environmental factors, prenatal diagnostic genetic testing is not available using specific DNA methods; rather diagnosis is usually made by ultrasound or other imaging. In some cases, an apparently isolated structural anomaly is associated with a cytogenetic abnormality or CNV, therefore karyotyping and/or chromosomal microarray analysis is recommended when one or more structural abnormalities is identified by ultrasound (see Chapter 12 ).

Although most genes are encoded in the nuclear genome, the mitochondria each contain their own genome. Variants can also occur in the mitochondrial DNA, and a number of mitochondrial diseases are due to these disorders. Mitochondria are essential for aerobic respiration, and mitochondrial diseases commonly affect tissues with high-energy requirements, such as the central nervous system, heart, and muscle. Mitochondria are all maternally inherited, and prenatal diagnosis for mitochondrial diseases can be complex and clinical outcomes are difficult to predict, due to variation in the number of abnormal mitochondria and the association with predicted phenotype (see Chapter 2 ).

How Is Prenatal Diagnostic Testing Performed?

Prenatal diagnostic testing refers to genetic testing done on fetal tissue obtained most commonly by amniocentesis or CVS. Less commonly, fetal blood is obtained through percutaneous umbilical blood sampling. Testing of early embryos can also be done in conjunction with in vitro fertilization in a procedure known as preimplantation genetic testing (PGT) (see Chapter 15 ). Finally, fetal cell-free DNA (cfDNA) or potentially nucleated fetal cells can be obtained from the maternal circulation and tested for genetic disorders. However, such techniques at present are considered screening methods and are discussed elsewhere in this book (see Chapter 9 ).

Cytogenetic or karyotype analysis requires viable cells that can be cultured; such cells can be obtained by CVS, amniocentesis, or fetal blood sampling. DNA for molecular testing (including chromosomal microarray analysis) can be obtained from any cell with a nucleus, regardless of viability, including blood lymphocytes, skin, hair, cheek cells or saliva, and paraffin tissue blocks. Cultured amniocytes, chorionic villi, and fetal blood are tissues that can be used for prenatal DNA testing of the fetus; if adequate tissue is obtained, DNA can be extracted without the need for culture. Other fetal tissue biopsy, such as biopsy of fetal skin, muscle, or liver, was done in the past for direct measurement of fetal enzyme activity or other physiologic parameters. Such biopsies have been largely replaced by molecular DNA methods that can directly detect the underlying genetic basis of many congenital disorders (see Table 14.1 ).