In general, indications for genetic analysis can be divided into inherited conditions and acquired conditions. Within inherited conditions, genetic testing can be offered at either the prenatal or postnatal stages. It may involve conventional cytogenetics, FISH, molecular diagnostics, or a combination of these techniques.
Prenatal genetic analysis should be offered to all patients who are at risk of having cytogenetically abnormal progeny. It can be performed on cells obtained by amniocentesis, on chorionic villus biopsy material, or increasingly in “liquid biopsies” on maternal blood paired with next-generation sequencing. Some important indications are the following:
Advanced maternal age (beyond 34 years), which is associated with greater risk of trisomies
Confirmed carrier status for a balanced reciprocal trans-location, robertsonian translocation, or inversion (in such cases, the gametes may be unbalanced, so the progeny would be at risk for chromosomal disorders)
Fetal abnormalities observed on ultrasound, or an abnormal result on routine maternal blood screening
Determination of fetal sex when the patient or partner is a confirmed carrier of an X-linked genetic disorder
Postnatal genetic analysis usually is performed on peripheral blood lymphocytes. Indications are as follows:
Suspicion of a metabolic syndrome
Suspected aneuploidy (e.g., features of Down syndrome) or other syndromic chromosomal abnormality (e.g., deletions, inversions)
Suspected monogenic disease, whether previously described or unknown
Acquired genetic alterations, such as somatic mutations in cancer, are increasingly becoming a large focus area in molecular diagnostics laboratories, especially with the advent of targeted therapies. Although single gene tests (mutations of EGFR or BRAF, amplification of HER2) have been used for a while to inform treatment decisions, the advent of cost-effective next-generation sequencing approaches has now allowed interrogations of large numbers of coding genes (often in the 100s), as well as cancer-relevant translocations, in a single assay. The clinical team typically receives a “genomic report” on the patient’s cancer, including potential molecularly targeted treatment recommendations. Another major focus of molecular diagnostics has been the rapid identification of infectious diseases, such as suspected tuberculosis or virulent pathogens such as Ebola, using DNA-based approaches. In general, these approaches have cut down the time required for diagnosis from weeks to a matter of days. Besides de novo identification of pathogens, molecular diagnostics laboratories can also contribute to the identification of treatment resistance (e.g., acquired mutations in influenza viruses that render them resistant to anti-virals), and to the monitoring of treatment efficacy using assays for “viral load” in the blood. Similar parameters (measuring efficacy of therapy and emergence of resistance) are also widely used in cancer patients.
Because of the rapid advances in molecular diagnostics, terms such as “personalized therapy” and “precision medicine” are being increasingly used to indicate therapy tailored to the needs of the individual patient. It is hoped that such expectations will be met in the foreseeable future. We will now discuss some of the common approaches used in molecular diagnostics laboratories for assessment of inherited and acquired indications.
As already discussed in this chapter, various diseases may occur as a result of copy number abnormalities, at the level of the entire chromosome (trisomy 21), chromosomal segments (22q11 deletion syndrome), or submicroscopic intragenic deletions (WAGR syndrome). Karyotype analysis of chromosomes by G banding remains the classic approach for identifying changes at the chromosomal level; however, as might be expected, the resolution with this technique is fairly low. To identify subchromosomal alterations, both focused analysis of chromosomal regions by FISH and global genomic approaches such as comparative genomic hybridization (CGH) are commonly used.