Applying Results of CMA Testing

A negative result means that the laboratory did not find clinically significant copy number variants. This rules out most well-described microdeletion/microduplication syndromes, but it does not rule out a genetic cause for your patient’s features.

Remember that CMA detects extra or missing genetic material. CMA does not detect material that is present in the right amount but not working properly. CMA will miss genetic conditions that are caused by small changes in gene sequence. In addition, some conditions have more than one genetic cause. For example, Angelman syndrome is typically caused by a deletion of the gene, but a small percentage of cases are caused by a change in the sequence of the gene. Finally, some CNVs may not be detectable with current technology.

Are there findings the lab does NOT report?

Yes. A negative CMA result does not necessarily mean an absence of copy number variants. Some CNVs are not reported because they are below the laboratory’s reporting size threshold or located in a chromosome region that is unlikely to have clinical significance.  Also, some CNVs are known to be benign and, therefore, are not typically reported.

In addition, recessive genes within a reported CNV may not be explicitly discussed in the test report unless a child’s features indicate a particular recessive condition is likely. This is one reason it is important to provide the laboratory with a thorough description of the child’s features. You should also check back with the laboratory when new clinical information emerges, to determine if this changes interpretation.

What do I do next?

When searching for an explanation for a child’s features, a negative result can be frustrating for families and health care providers alike. However, a negative CMA result is not necessarily the end of the road.

If your patient strongly fits the profile of a specific syndrome, but has a negative CMA result, it may be time for more targeted testing. A consultation with a genetics specialist can help you select the right test. Likewise, if your patient has a unique set of findings, but you don’t recognize a particular syndrome, a genetics specialist may be of help in identifying a diagnostic pathway.

CMA testing and other genome-wide technologies are improving at a rapid rate. Current CMA platforms can detect more CNVs than those from even just 5 years ago. Check back with the laboratory to determine whether their technology has improved enough to justify repeat testing.

Finally, a patient without a genetic or clinical diagnosis of a specific condition should be managed based on symptoms, using family history to guide additional testing.

This classification means that the CNV is known to cause disease. In some cases, the variant is clearly associated with the patient’s findings. In other cases, a variant is an incidental finding, indicating an additional medical concern unrelated to the reason for testing.

How does the lab know it is pathogenic?

The laboratory looks for one or more of the following:

• The variant has been previously and repeatedly associated with specific features
• The variant was inherited from a parent with the same features as the patient
• Neither parent has the variant, indicating it occurred as a new mutation (new mutations are generally more likely to be disease causing)
• The variant is large in size and/or contains many critical genes

What does the variant mean for my patient?

Read the laboratory’s interpretation section thoroughly. Most reports include evidence to support the association between a variant and the patient’s features. There may be specific prognostic and management information available when a variant is associated with a well-described syndrome. 

Determining the prognosis and next steps is more complicated when a variant is novel or rare. The variant may be clearly pathogenic, but little is known about clinical outcomes. Laboratories will often list the genes found in the variant region and provide comments about the potential clinical consequences of those for which data is available.

Occasionally, a variant is associated with a health concern that is unrelated to the original indication for testing. There are two ways this can occur:

• The variant causes BOTH the presenting features and another unsuspected condition. For example, a deletion may include genes that result in intellectual disability but also contains a gene that is associated with cardiomyopathy later in life.
• The variant is not associated with the presenting features, but causes a different, unsuspected condition. For example, a variant may increase risk for cardiomyopathy, but does not explain a patient’s intellectual disability.

The lab will usually report any clearly pathogenic variants, whether or not they are associated with the patient’s findings. The health care provider who ordered testing is responsible for determining the appropriate process for follow-up on incidental findings.  Some health consequences of incidental findings may not need to be addressed until adulthood (e.g. cancer predisposition).  However, if these results are not disclosed appropriately, future healthcare providers may not realize the risk and screening may not take place.  If an incidental variant was inherited, this would have health implications for that parent.

When is parental testing needed?

Parental testing clarifies whether a pathogenic variant was a new mutation or inherited, and therefore if siblings and other relatives are at risk. Parents may be only subtly affected, or may be asymptomatic carriers of a balanced chromosome rearrangement that became unbalanced in the child. Therefore, if you aren’t familiar with the diagnosis, don’t assume a lack of parental symptoms means parental testing isn’t needed.  Lab reports should provide some guidance for this.

What do I do next?

The genetic variants detected by CMA cause a wide spectrum of conditions. What these diagnoses typically have in common is their syndromic nature, involving multiple body systems.  Microdeletions and microduplications may span multiple genes, affecting different tissues, or include one critical gene that is expressed ubiquitously in the body.

The syndromic nature of these conditions means that management may involve multiple screening protocols and referral to specialists, most frequently cardiology, neurology, and orthopedics. Although many syndromes involve intellectual disability, the cognitive profile for a specific condition may be distinct and indicate a particular therapeutic or educational approach.

Management recommendations are available for some of the more common and well-described syndromes. Case reports, literature reviews and phenotype databases may help with rare variants. Use any literature cited on the lab report as a starting place. The following resources also provide information about natural history and management recommendations for specific syndromes or gene variants:

• GeneReviews
• Online Mendelian Inheritance in Man (OMIM)
• National Guidelines Clearinghouse
• Unique: Understanding chromosome disorders
• Genetic Education Materials for School Success (GEMSS)

When parental testing has indicated that a pathologic variant was inherited, family cascade screening is warranted. This refers to a step-wise process in which all first-degree relatives of an affected individual are evaluated or tested for the condition.

This classification means that the pathogenicity of the variant can neither be confirmed nor ruled out. VUS are not unique to CMA. For example, VUS can occur on traditional chromosome testing (karyotype), or in single gene sequencing. However, because CMA is genome-wide, and we are still learning about copy number variants, the chance of finding a VUS is higher.

Why can’t the significance be determined?

A VUS is typically a rare or novel variant. There are a number of reasons that the significance of a variant may not be able to be determined, including the following.

• If previous reports of the variant exist, associations with clinical features may be weak or mixed.
• The function of the genes involved in the deletion or duplication are unknown.
• It is unknown whether loss of function (deletion) or overexpression (duplication) is the mechanism for a particular clinical finding.

Did the variant cause my patient’s condition?

The relationship between a VUS and the phenotype is unknown until more is learned about the variant. Although it is tempting to believe any genetic variant is the explanation for a child’s condition, it is very important not to over-interpret a VUS.

In some cases, there may be tentative evidence that suggests, but does not confirm the nature of a variant. In these cases a VUS may be classified as “likely benign” or “likely pathogenic”. Parental testing can help classify a VUS as “likely benign” or “likely pathogenic.” Finding a VUS in a normal parent reduces, but does not eliminate the chance that the variant is responsible for the child’s features. Keep in mind that there is a chance the variant is disease-causing in the child, but is expressed differently in the parent (variable expression and reduced penetrance). 

What can I do with a VUS result?

Unfortunately, a VUS is not a clinically useful finding. Changes in management or reproductive planning based solely on a VUS are not recommended and could be potentially harmful. A patient with a VUS should be managed based on symptoms, using family history to guide additional screening.

The interpretation of a VUS is likely to change over time as more evidence emerges. Consider scheduling periodic follow-up appointments with patients who have a VUS. Check back with the laboratory to determine whether the classification of a VUS has changed.

One type of CMA, the SNP array,compares single nucleotide polymorphisms (SNPs) on both copies of each chromosome. These SNPs are expected to be mostly distinct, reflecting the genetic differences of the parents. When SNPs are identical, they are said to be homozygous. Large segments of homozygosity are atypical and may suggest another cause of the patient's features.

Regions of homozygosity confined to a single chromosome may suggest uniparental disomy. This refers to the inheritance of a complete chromosome pair, or portion of a chromosome, from a single parent.  Uniparental disomy involving imprinted chromosomes is known to affect development. Multiple regions of homozygosity indicate that parents share more genetic information than would be expected by chance, suggesting that they may be biologically related (consanguinity).

What is the clinical implication of excessive homozygosity?

Regions of homozygosity increase the risk for recessive disease.  When a region of homozygosity occurs in areas of genetic imprinting, there is increased risk for diseases that involve imprinting, such as Prader Willi syndrome.

This classification means that the variant is not associated with the patient’s clinical findings or any other known medical condition.  It may be a well-documented variant commonly found in the general population. This is essentially a “negative” result. See caveats about interpreting negative results above.

Some labs will list benign variants in a separate section or addendum. Look for other terms such as “common polymorphism” and “normal variation”.  Some laboratories do not report benign variants of certain sizes or in certain chromosomal locations.

How does the lab know it is benign?

In some cases, the report may provide evidence to support the classification, including descriptions from the literature and data from the lab’s patient population. In general, a laboratory looks for evidence that:

• The variant is common in the general population of healthy individuals
• The variant is present in a parent who shows no sign of the condition (see section on parental testing)
• Variant is small in size and/or lacking in critical genes.