Carrier Screening: Sequencing or Genotyping?

Kelli.jpg

With the plethora of commercial laboratories offering preconception and prenatal genetic carrier screening, it is worthwhile to review some basic aspects of the laboratory analyses behind these tests. Genetic carrier screening is typically carried out by one of two methodologies – genotyping and sequencing. Genotyping employs the testing strategy of identifying only the known, higher frequency mutations. Such methodologies are relatively inexpensive to perform, as well as conducive to rapid turnaround times. However, a limitation of genotyping is that the section of targeted mutations, and their frequencies, are frequently based on selected populations, and therefore are not necessarily applicable to every individual.

Sequencing methodologies, in contrast, analyze every base in the DNA sequence that codes for the functional component of the gene (and usually a bit more than that as well). In principle, this strategy for screening identifies most, if not all, variants in a gene – including known mutations that are both relatively common as well as the ones that are rarer. In addition, sequencing may uncover previously unreported variants, whose pathogenicity (or lack thereof) may not be established. Such a change is called a VOUS: Variant Of Unknown Significance. While such a result frequently leaves the clinician in a predicament, an increasing number of sophisticated algorithms are available that may permit us to make cautious predictions about phenotypic effects.

It is important to be aware that not all sequencing panels are created equal. Some sequencing panels are very limited in the number of genes selected for analysis. Others may sequence the majority of the targeted listed genes, but not all of them; they may even include genotyping methods for a select subset of genes. These modifications are often for ‘technical reasons’ such as a limitation of a laboratory’s ability to automate every step or reduce efficiencies of their turnaround time. Thus, rather than remove a targeted gene from an advertised gene set, a non-sequencing workaround is inserted. These distinctions are not always evident in the representation of a carrier screening panel by some of the commercial laboratories.

IMG’s Experience:

We have recently compared the impact of offering sequencing-based expanded carrier screening panels to a very similar panel that uses a targeted, genotype-based methodology (which was in use at IMG prior to May 2015). The current panel offered by IMG covers 75 conditions, including cystic fibrosis, spinal muscular atrophy, and fragile X. This selection of heritable disorders has been customized by our physicians and counselors based on of the severity of developmental problems or their potential treatability so that parents may anticipate and be prepared. Some of these assays are done in the IMG molecular laboratory, so as to ensure that all tests on the panel have the maximum possible sequencing data. Over the past six months, the shift to a fully sequenced panel has resulted in the identification of >50% more carriers for one or more autosomal recessive conditions because the mutation analysis is not restricted to only the ‘most frequently found’ variants.

As always, genetic carrier screening performed through our services is accompanied by extensive pre-test genetic counseling, so that patients can make informed choices in this rather complex area. Some of the genes and mutations that we have all previously associated only with certain ethnic or racial backgrounds are being identified in individuals who are not from that traditionally at-risk ancestry. Carrier screening has become pan-ethnic, to be sure.

Reflex Testing:

When a carrier is identified through screening, we recommend ‘reflex’ testing of the partner by sequencing of the relevant gene to assure all possible mutations are identified. In this way, all possible mutations and variants can be screened for, providing the most thorough evaluation of a couple’s risk status of having an affected offspring. Additionally, we can do this at a lower cost than an entire sequencing panel offered by any commercial laboratory that we are aware of.

If you happen to have a patient previously identified as a carrier, IMG can help you and your patients with the genetic counseling and reflex single gene sequencing; please call us if you have questions about how such couples are managed.

The counseling for expanded genetic carrier screening, particularly the pre-test counseling, has become increasingly complex. The amount of information that a patient or couple has to learn in a short-term encounter is considerable – the nature of the conditions being screened for (without discussing each condition specifically), the implications of a positive finding, the follow-up steps, the serious exploration of how such screening itself aligns with the individual or couple’s values and concerns, and all the questions that accompany these dimensions. All of these are addressed by us during a patient’s counseling session, an approach endorsed by ACOG and ACMG.