An Overview of GeneticTesting

Diagnostic Techniques in Clinical Genetics

There are many methods used in clinical genetic testing, each of which has strengths and limitations. These methods are applied to particular clinical-use cases such as newborn screening, carrier testing, noninvasive prenatal screening, presymptomatic testing, diagnostic testing, and pharmacogenomics. Each method is optimized to address a specific type of genetic variation, and the methods are somewhat overlapping and largely complementary. Tandem mass spectrometry (MS) has a significant role in expansion of newborn screening. A karyotype is used to detect aneuploidies, large deletions or duplications, and chromosomal rearrangements. Fluorescence in situ hybridization (FISH) detects microdeletions and microduplications (although with less fidelity) but requires a correct hypothesis about which probe to use to detect the cytogenetic anomaly. By contrast, a chromosomal microarray (CMA) is hypothesis free and provides high resolution to detect small copy-number variants throughout the genome in a single test. Sanger sequencing was the traditional method to sequence and identify single-nucleotide variations and insertions/deletions of a few bases. With the development of next-generation sequencing (NGS) and massive parallel sequencing, the cost/base of sequencing decreased and throughput increased dramatically, making feasible the sequencing of panels of genes to diagnose genetically heterogeneous diseases for conditions such as cardiomyopathies and hereditary cancer. Exome sequencing (ES) assesses only coding regions of most genes in the genome whereas genome sequencing (GS) assesses both coding and noncoding regions. ES and GS offer versatility and can be used to assess sequence-level variants and, with appropriate analysis copy number, variants and structural variants in the case of GS.

A summary comparing the different clinical genetic testing methods is provided in Table 77.1 .

Chromosomal Disorders and Karyotyping

Chromosome disorders are an important category of genetic disease, occurring in approximately 1 of every 150 live births. They are a common cause of intellectual disability and pregnancy loss. Chromosomal disorders can be divided into two groups: numerical and structural abnormalities. Numerical abnormalities result from the gain or loss of one or more chromosomes, referred to as an aneuploidy (e.g., trisomy, monosomy, or tetrasomy), or the addition of one or more complete haploid genomes, referred to as polyploidy (e.g., triploidy, tetraploidy).

Structural chromosome abnormalities can be unbalanced (the rearrangement causes a gain or loss of chromosomal material) or balanced (the rearrangement does not produce a loss or gain of chromosome material). Unbalanced abnormalities of chromosomes cause congenital anomalies and neurodevelopmental disorders more commonly than do balanced rearrangements. Structural alterations can be caused by translocations (reciprocal or Robertsonian translocations), ring chromosomes, insertions, deletions, or complex rearrangements.

Mosaicism

Mosaicism is the presence of at least two cell populations derived from the same zygote. Mitotic nondisjunction, trisomy rescue, or occurrence of a somatic new mutation can lead to the development of genetically different cell lines within the body. Mosaicism is possible for any type of genetic change, from a chromosome to a single nucleotide. Mosaicism can affect any cells or tissue within a developing embryo at any point after conception through adulthood. In gonadal mosaicism, the mosaic cells are restricted to the gonads and do not have a clinically observable phenotype but can be passed on to multiple progeny in the next generation. If the mosaic cells are found only in the placenta and absent in the embryo, this is known as confined placental mosaicism, which may be detectable on a chorionic villus sample and may be associated with intrauterine growth restriction but not with congenital anomalies, neurodevelopmental disorders, or any other phenotype if the genetic anomaly is not present in the fetus.