Genetic testing

Panel testing is the most widely available type of genetic testing. It looks for variants in a limited number of genes, typically several hundred, that are already known to be related to a particular diagnosis or set of diagnoses. While this is the most limited type of genetic test, it is focused on known PIs and genetic variants and will provide a genetic diagnosis for many PIs caused by variants in single genes.

However, it is possible to get a false negative result from a panel. This means that the person has a PI caused by a gene variant, but the panel test did not find the variant. A false negative result can happen if the panel does not ‘cover’ the variant the person has. For example, the panel may not include all of the genes associated with PI or may not cover all parts of the genes it does include.

Note that panels for the same diagnosis can differ between different testing laboratories and the details of what a panel does and does not cover affect the results. Some panels only include the most common genes linked to a disorder; others may not be updated with genes that have only recently been linked to a condition. Often, panels only include the parts of a gene that code for its protein or other molecule (known as ‘exons’), which means that variants in non-coding regions may be missed. While most genetic variants associated with PI are in exons, variants in these non-coding regions can also cause PI.

Whole exome sequencing (WES) is broader than panel testing and picks up variants in all of the exons of all 20,000+ human genes [2]. In addition to what panels find, WES can turn up variants in genes that:

• Are linked to PI but are not included in available panel tests.
• Have not previously been linked to PI but have a known function in the immune system.
• Have not been previously linked to PI or the immune system.

Since WES turns up many variants in many genes, how the data are analyzed is key to getting useful information. A study in the United Kingdom of more than 49,000 people found that each person, on average, had thousands of variants identified by WES [3]. If WES only finds variants in genes that haven’t been linked to PI before, it can be difficult to make sense of the data. In this case, your provider or a genetic counselor may be able to recommend a research study to help make sense of the data, if one is available.

In the past, healthcare providers generally used WES as a second-tier test when panel testing did not identify a PI-causing variant, but it’s being used as a first-tier test more and more often. Like panels, WES returns only variants in exons, not variants in non-coding DNA. The analysis of WES data also prioritizes genes most relevant to the condition for which the person is being tested.

Whole genome sequencing (WGS) is the most complete type of genetic testing available. WGS sequences all of a person’s DNA, including exons, non-coding bits in a gene called introns, and non-coding regions between genes. In addition to the types of variants WES can detect, WGS can also detect:

• Structural variants, which are large pieces of DNA that are duplicated, deleted, or in the wrong place. For example, 22q11.2 deletion syndrome can be diagnosed with WGS but is generally not detected by WES [4].
• Non-coding areas within and between genes, which may have sequences important for turning genes on and off.

Again, how WGS data is analyzed is critical to getting useful information. WGS turns up even more variants than WES, which means even more potential leads to follow up. Similar to WES, individuals may need to enroll in research studies to interpret WGS results that do not reveal an obvious PI-causing variant.

Chromosomal microarray testing (CMA) looks broadly to see if pieces of DNA are missing (deletions) or if there are ‘extra’ copies of DNA (duplications). The duplications and deletions CMA detects are typically much larger than what sequencing-based tests detect. CMA testing may be used alone or in combination with other types of genetic testing [5]. Some of the reasons a healthcare provider may order CMA include:

• Testing for certain PIs that are caused by deletions in a person’s DNA like 22q11.2 deletion syndrome, Jacobsen syndrome (chromosome 11q deletion syndrome), chromosome 10p12-p14 deletion syndrome, and deletions in chromosome 14q32 associated with antibody deficiency.
• For individuals with neurodevelopmental disorders and immune deficiency, including a CMA with other genetic testing can help determine if a single diagnosis accounts for all of the person’s symptoms. 
• Added on to panel or WES testing, CMA can determine if one copy of a gene has missing pieces, which might not be detected with the other tests.

In genetic testing, getting a positive test result means that the test found a genetic variant that causes PI. In the report, this variant may be labeled pathogenic or likely pathogenic. This means that there is strong scientific evidence that the variant found in your DNA disrupts the immune system in a way that causes PI symptoms.

A positive test result can also mean that you are a carrier for PI. This means that you have one copy of a genetic variant that is associated with a condition, but it is not enough to cause the condition. Knowing you are a carrier may influence your family planning decisions.

Indeterminate results in genetic testing mean that no pathogenic or likely pathogenic variants were found that cause PI but that one or more VUSs were found. While VUSs may be detected in raw genetic data, not all laboratories report them unless the provider ordering the test asks for them to be included. In many cases, your healthcare provider will decide whether there is additional testing that can help to determine whether a VUS may be linked to PI, which often includes testing family members.

For genetic testing, a negative result means that no pathogenic, likely pathogenic, or VUSs were found. However, a negative result does not mean that there is no genetic variant causing your PI. There are certain types of variants, such as those involving large sections of DNA, that standard sequencing methods do not detect well. In addition, specialized analysis of the raw data may be necessary to detect some genetic causes of PI.

Because WES and WGS cover a large part of a person’s DNA, testing may find variants linked to conditions other than PI. These variants are called secondary or incidental findings. In general, testing laboratories do not look for or report most secondary findings. 

However, the American College of Medical Genetics and Genomics (ACMG) recommends that all laboratories look for and return secondary findings of pathogenic variants within a limited list of genes if individuals or their caregivers choose to receive these results [9]. These variants are linked to conditions like inherited cancers or heart disease where early treatment can help. The goal of reporting these findings is to alert the person and their healthcare provider to ‘hidden’ genetic conditions that can be managed if they are caught in time. Even panels sometimes include the ACMG genes.

The ACMG list is a minimum list of secondary findings that should be reported for WES and WGS, but some laboratories may offer additional secondary findings if the ordering provider opts in.

On the other hand, it’s important to understand that results that show a risk for conditions that are not treatable, or that only cause problems later in life, are usually not reported to avoid causing unnecessary worry.