Medical Genetics

Non-invasive prenatal detection of fetal aneuploidies by cell-free DNA, also called non-invasive prenatal testing (NIPT) and non-invasive prenatal screening (NIPS), is a method of non-invasive fetal DNA testing done through a maternal blood sample. NIPT testing for common aneuploidies, microdeletions and sex chromosome disorders is clinically available to patients in Canada. NIPT is a highly sensitive and specific screening test, but is not diagnostic. Even in high-risk populations, there can be false positive NIPT results. Genetic counselling, along with confirmatory testing via amniocentesis or chorionic villus sampling, should be done prior to using the result to impact management of a pregnancy.

Three types of potentially medically-relevant DTC-GT are available: (1) assessment of risk for common multifactorial diseases (e.g., diabetes, etc.); (2) targeted mutation analysis for single gene disorders; and, (3) sequencing. Some DTC-GT companies state that they do not guarantee the accuracy or reliability of their tests. Many of the significant genetic risk and protective factors for multifactorial conditions have not been identified. This leads to greatly divergent risk interpretations between companies, even when performed on the same individual. For targeted mutation analysis and sequencing, the specific test may not include all clinically relevant genes or mutations; resulting in false reassurance. Genetic changes that are only weakly associated with disease may be reported, leading to anxiety or inappropriate additional testing. When making medical decisions based on results of genetic testing, the test should meet the recommendations made by the Canadian College of Medical Geneticists in 2012. Not all DTC-GT meet these recommendations.

Microarray is the first line test for individuals with intellectual disability/developmental delay without a recognizable syndrome. Indeed, a microarray has a much higher detection rate (15 – 20%) compared to a karyotype (3 – 4%) in individuals presenting for this clinical indication. A karyotype remains important in limited clinical situations where a specific numerical or structural chromosomal syndrome, such as Down syndrome, is suspected.

Whole exome sequencing (WES) is a powerful test for individuals suspected of having an underlying genetic diagnosis. However, WES increases the likelihood of unexpected findings, which may or may not be clinically significant. Further, due to methodological limitations, WES may not always be the correct test to order as WES will not detect all genetic causes of disease (for example, it will not detect chromosomal structural differences). Both informative and uninformative results can lead to complex patient and family psychosocial repercussions, and could impair future insurability. Genetic counselling facilitates informed decision-making. Given complexity of results, WES should only be ordered after counselling by a qualified health care provider.

Carrier testing is primarily useful in the reproductive period to determine the risk of an individual having a child affected by the condition for which testing is being considered. Knowing that a child is a carrier of an X-linked or autosomal recessive condition usually does not alter medical care in the pediatric years since most carriers are unaffected. Thus, in most situations, there is not a medical indication for carrier testing in a child. Undertaking carrier testing of a child violates the right of the child to make his or her own decision about testing and could potentially impair future insurability. An exception could be made for a mature adolescent who may be able to understand the reproductive implications of carrier testing after appropriate genetic counselling.

Rapid genomic tests are increasingly available both pre- and postnatally and can decrease time to diagnosis compared to standard tests. Yet, there is often an added cost to their use and their utility and cost-effectiveness are not entirely established. Before pursuing testing in an expedited timeframe, gathering a patient’s values and preferences is crucial, particularly as it relates to potential decision points in a pregnancy. While genetic information may be valued at an earlier stage in a disease course and rapid results may be preferred by patients, balancing the potential increased cost against conventional genetic turnaround times is particularly important when results are not expected to have immediate management implications.

When there is a specific condition suspected based on clinical features or where clinical criteria are available, targeted testing is more appropriate than broad panel or genomic testing.  The advantages of targeted testing are that the gene(s) or chromosomal region(s) being tested are well known to be associated with specific risks, often have management guidelines available if a pathogenic variant is found, and it is simpler to convey the specific limitations and benefits of doing targeted testing. The analytic validity, clinical validity and clinical utility are important domains in genetic testing evaluation and are easier to determine for a targeted test rather than for a broad or genomic test where the phenotype may not be anticipated, or the gene may be of moderate or low risk. Broad panel or genomic tests increase anxiety with increased number of variants of uncertain significance (VUS), increase the risk of  misinterpretation or misattribution to less well understood gene or genomic region, and lead to increased costs of unnecessary screening and surgeries.

Genome-wide diagnostic testing, including whole exome sequencing and microarray analysis, has become widely used as a first-line test for patients with a variety of clinical presentations.  While these broad tests can provide a good diagnostic yield, they also have technical limitations and are unable to reliably diagnose some specific genetic conditions, including spinal muscular atrophy (SMA), congenital adrenal hyperplasia (CAH), Facioscapulohumeral Muscular Dystrophy (FSHD), imprinting disorders (Beckwith-Wiedemann syndrome, Prader-Willi syndrome, Angelman syndrome, Russel-Silver syndrome, etc.), and repeat expansion disorders (Fragile X syndrome and related disorders, Huntington disease, Myotonic Dystrophy, Friedreich’s ataxia, Spinocerebellar ataxia, etc.), among others.  The mechanism underlying the condition must be considered to determine whether a test can rule out or rule in a diagnosis; if a disorder is being considered as part of the differential diagnosis and cannot reliably be detected by genome-based testing, then a disease- or gene-specific molecular diagnostic test is required.  When an incorrect test is ordered, it may give a false sense of reassurance if a negative result is returned, and it could delay diagnosis for the patient.  In addition, this is potentially a poor use of resources.

Assessment of an increased risk of inherited disease should be available to all individuals considering a pregnancy.  Genetic counselling for possible carrier screening should be offered to individuals identified as being at elevated risk of transmission of an inherited condition based on family history, ethnic background, or past medical/obstetrical history. When the a priori risk is elevated, carrier testing may be offered. Expanded carrier testing using large panels yields few carrier pairs (at most 1% even with larger panels) and therefore is not recommended as a routine test at this time. Additionally, the utilization of limited laboratory, clinical and genetic counselling resources requires stewardship. Since the evidence is limited, routine carrier screening of all individuals is not recommended at this time. However, this may be revisited if evidence of effectiveness and efficiency is established and implementation strategies are proposed.

Whole exome sequencing (WES) is a next generation sequencing method that includes the protein-coding sequence of the genome.  WES covers >99% of sequence variants, and several studies have demonstrated that >98% of relevant sequence variants identified on targeted panels were identified on WES. Most clinical laboratories use the same sequencing methods for WES and gene panels.  Thus, the additional diagnostic yield of panel sequencing after WES is likely to be low.

Intellectual developmental disorders (IDD) affect 2.5% of the population. Inherited metabolic disorders (IMD’s) may present with IDD and often other neurologic or systemic features and some IMD’s are treatable.  Despite years of implementing a biochemical testing algorithm on a research basis in one province, the yield of testing was not increased for IMD’s.

There are significant harms associated with over-investigation.  Although the cost of biochemical testing is inexpensive compared to molecular or specialized tests, it is still a significant burden on the health care system.  The cost of the tests is not the only consideration, since significant human resources are required for pre-test counselling, coordination of sample collection, transport and analysis, interpretation of results and follow-up.  Even more importantly, there may be harm to children and families subjected to further blood draws and urine tests, extending the diagnostic odyssey as repeat testing is often required for a positive or uncertain result. There is extensive literature on the harms of false positives from newborn screening, but this is balanced against the yield of testing for treatable IMD’s on the newborn screen and efficacy of early intervention.  Similar data of the benefits of screening all children with IDD for IMD’s does not exist.

There are well-recognized red flags suggestive of an IMD in children with IDD and it would be appropriate to do targeted metabolic testing in those situations (so called “intellectual disability plus”).  Consideration should also be given to patients who did not have newborn screening (NBS) for IMD.  Further biochemical testing may also be a valuable tool when molecular testing is negative or uncertain, to provide functional evidence of pathogenicity.

Watchful waiting refers to a policy of taking no immediate action with respect to a situation or course of events but of following its development intently. Different areas in medicine employ watchful waiting and have found it not to impact patient outcome in select situations. Given the increased availability, genetic testing is often requested early in a patient’s presentation.  However, genetic conditions and our ability to understand and diagnose them frequently evolve over time. Early investigation may result in increased cost due to repeated application of non-targeted testing, with concomitant increased likelihood of detecting variants of uncertain significance, as well as poorer result interpretation for reports reliant on complete phenotyping. When the phenotype is incomplete or unclear, and there are no red flags, such as deteriorating patient status, potential for change in management, or information necessary for timely reproductive counseling, watchful waiting may be appropriate.