Genetic testing

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

You can also get an indeterminant or negative result from genetic testing.

Indeterminant results mean that no pathogenic or likely pathogenic variants were found that are consistent with PI but that one or more variants of unknown significance (VUS) were found. VUS are variants that do not have strong evidence on whether they affect the immune system in a way that causes PI or not. While VUS may be detected in raw genetic data, not all laboratories report them unless the provider ordering the test opts for them to be included. In many cases, your physician will determine whether there is additional testing that can help to determine whether a VUS may be associated with PI, which often includes testing family members.

A negative result means that no pathogenic, likely pathogenic, or VUS variants were found. However, a negative result does not mean that there is no genetic variant underlying 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, such as somatic variants. 

Because WES and WGS cover a large part of a person’s DNA, testing may find variants associated with conditions other than PI. These variants are called secondary findings.

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. These variants cause preventable or treatable genetic conditions that tend to be asymptomatic for long periods of time before striking suddenly, such as familial hypercholesterolemia. The goal of reporting these findings is to alert the individual and their healthcare provider to ‘hidden’ genetic conditions that can be managed if they are caught in time. Increasingly, even panels include the ACMG genes.

The ACMG list is considered 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.

Chorionic villus sampling (CVS) or amniocentesis can obtain a fetal sample for chromosome, genetic, or biochemical testing. CVS is usually scheduled at 10-13 weeks of pregnancy and involves retrieving a tiny sample of the developing placenta from the womb. Amniocentesis is typically performed at 16-17 weeks of pregnancy and involves the withdrawal of amniotic fluid containing fetal cells. Both procedures have a small risk of miscarriage that should be balanced against the benefits of the testing.

Several types of analysis can be done with CVS or amniocentesis samples:

• Gene variant analysis: This method is 100% reliable if the PI-causing variant is known.
• Linkage analysis: If the PI-causing variant is unknown, but the diagnosis is definite, prenatal diagnosis may be possible using linkage analysis. This will be slightly less reliable than gene variant analysis.
• Enzyme analysis: The concentration and/or function of the enzyme affected in a certain PI can be measured. Examples are adenosine deaminase (ADA) and purine nucleoside phosphorylase (PNP), deficiencies which both cause forms of SCID. Both enzymes can be analyzed in a CVS sample taken at 11-12 weeks of gestation.

Noninvasive prenatal screening (NIPS), sometimes called noninvasive prenatal testing (NIPT), analyzes small fragments of DNA circulating in a pregnant woman’s blood. NIPS involves taking a blood sample from the mother and is not associated with any risk of miscarriage.

Unlike most DNA, which lives inside cells, these small DNA fragments float freely outside cells and are called cell-free DNA (cfDNA). cfDNA comes from cells that die off and are broken down so that their contents, including DNA, are released into the bloodstream. During pregnancy, a mother’s blood contains a mix of cfDNA that comes from her cells and cells from the placenta. The placenta is tissue in the uterus that links the fetus and the mother’s blood supply. The DNA in placental cells is usually identical to the DNA of the fetus. 

Because of the technical challenges of determining whether a particular DNA fragment is from the placenta or the mother, NIPS is largely clinically available only for disorders that involve large insertions or deletions of DNA or extra chromosomes. Some clinical labs are working on techniques that allow single-gene variants to be detected through NIPS, but NIPS for single-gene disorders, which includes most genetically-defined PIs, is currently limited.

Analyzing cfDNA from the placenta provides an opportunity for early detection of certain genetic abnormalities without harming the fetus. However, NIPS is a screening instead of a diagnostic test, so it does not give a definitive answer about whether or not a fetus has a genetic condition. The test can only estimate whether the risk of having certain conditions is increased or decreased. If NIPS indicates an increased risk of a genetic condition, more definitive diagnostic testing, such as CVS or amniocentesis, can confirm the results. In addition, the test may detect a genetic condition in the mother.

Pre-implantation genetic diagnosis (PGD) is a useful option for couples who are at high risk of having a child with a genetic disorder. It involves in vitro fertilization (IVF) of a number of eggs, followed by genetic testing of a single cell from each embryo, and subsequent implantation of embryos that do not have the PI-causing gene variant.

Implantation of an unaffected embryo via IVF in individuals with SCID, leukocyte adhesion deficiency (LAD), CGD, and XLA has been previously reported. Evidence also supports the efficacy of PGD in the detection of other immunodeficiencies such as Wiskott-Aldrich syndrome, X-linked hyper IgM syndrome (HIGM), NEMO deficiency, and ataxia-telangiectasia.

Note that the use of donor egg or sperm to conceive a child via in vitro fertilization (IVF) can be carry a risk of PI if the health or carrier status of the donor has not been established.