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About the Authors


Christine McCusker, MD

Christine McCusker is a practicing allergist/immunologist and a clinician researcher and educator at the Children’s Hospital. She is a Clinician Scientist and Associate Professor at McGill University is Division Director for Pediatric Allergy, Immunology and Dermatology at the Montreal Children’s Hospital. Her fundamental research lab focuses on the role of early life environments in the education of the immune. She runs the pediatric transdisciplinary center for biotherapeutics, studying secondary immune deficiencies in patients receiving biologic treatments. 


Sarife Saker, MD

Dr. Saker is an allergist and immunologist in Montreal. She completed her medical degree and residency in general pediatrics at Université de Sherbrooke. She then finished her clinical immunology and allergy fellowship at McGill University. Dr. Saker has an active interest in medical education, and her clinical and research interests are focused on inborn errors of immunity, immunogenomics, food allergy and oral immunotherapy. She will pursue a postdoctoral training in immunogenomics at the Boston Children’s Hospital and an MMSc in Immunology at Harvard Medical School.

Clinical vignette

An 18-year-old male presented with eczema at the age of 6 months. During infancy he also developed multiple food allergies, and progressed with asthma, and allergic rhinitis over time. He had significant dermatitis, frequent acute otitis media, and upper/lower respiratory tract infections often requiring antibiotics.  At 3 years of age, he had an Influenza A related pericardial effusion. He was noted to have eosinophilia of 12.5 x 109/L (30%) and elevated IgE (4320 ug/L).

At 4 years of age, he was admitted with a left lobar pneumonia, pansinusitis and was positive for adenovirus. IgE was elevated (9600 ug/L) and he was noted to have persistent eosinophilia 26.9 x 109/L (60%), poor specific antibody response to vaccines, normal levels of IgG, IgA and IgM and normal lymphocyte subsets but with decreased T-cell proliferation. He was diagnosed with combined immunodeficiency and treated with intravenous immunoglobulin (IVIg) replacement and antibiotic prophylaxis.

Over the next few years, he developed eosinophilic dermatitis, esophagitis and pneumonitis, severe asthma, recurrent otitis media and sinusitis, and generalized flat warts. He had dysgammaglobulinemia with low IgA and IgM and high IgE levels (up to 25000 ug/L). Profound lymphopenia developed with very low T-cells; normal B-cell counts but poor antibody responses. 

He was ultimately diagnosed with hyper-IgE syndrome secondary to DOCK8 deficiency. While waiting for a matched donor for hematopoietic stem cell transplant (HSCT), he developed squamous cell carcinoma of the skin and died at the age of 21 years. This case highlights how the presentation with common allergic conditions may be early signs of important inborn errors of immunity.


Human inborn errors of immunity (IEI), referred to as primary immunodeficiency disorders (PID), are a heterogeneous group of disorders, characterized by an increased susceptibility to infection, autoimmune, autoinflammatory, allergic and/or malignant diseases1. To date, more than 400 disorders have been genetically identified2. Most identified IEI are monogenic variants which result in loss of expression, loss-of-function (LOF; amorphic/hypomorphic), or gain-of-function
(GOF; hypermorphic) of the encoded protein3,4


IEI are common. There is an estimated prevalence of 1 in 1000 to 1 in 5000 live births7 as illustrated in Figure 19, with the exception of IgA deficiency (prevalence of 1 in 500 in Caucasians8). These conditions may present at any age, although children between the ages of 5 to 19 have the highest prevalence rate (Figure 210,11). There is a 1:1 ratio in the gender disposition of IEI per a recent study in the US.

Figure 1. Distribution of major PID groups; Adapted from the Manual of Allergy and Clinical Immunology, 2021

Figure 2. Prevalence of PID by age groups; Adapted from Stiehm’s Immune Deficiencies Inborn Errors of Immunity, 2020

Clinical approach to IEI

The immunologic variations of IEI is increasingly complex and a systematic approach for patients with suspected IEI, as described in the questionnaire below17 is a useful tool for the clinician (Figure 3).

Figure 3. Questionnaire adapted from Stiehm’s Immune Deficiencies, Inborn Errors of Immunity, 2020

Investigations into IEI, should be initiated based on clinical presentations of recurrent infections or evidence of immune dysregulation. Unexplained lymphopenia or persistently abnormal levels of other leukocytes should also prompt investigations. Secondary causes of potential immunodeficiency, including infection, immunosuppressive therapies or malignancy, are also considerations for evaluation of immune function18,19.

IEI classification 

There are eight categories of IEI per the Expert Committee of the International Union of Immunological Societies (IUIS) (Table 12,23). Recently, an IEI classification of two major categories has been proposed: Primary Immune Deficiency Disorders (PIDD) and Primary Immune Regulatory Disorders (PIRD)24. Seventy percent of identified disorders are classified as PIDD25, and are infection dominant conditions. PIRD are dominated by immune-mediated pathologies (autoimmunity, lymphoproliferation, autoinflammation/hyperinflammation, malignancy and severe atopy)24. Defining the precise nature of the PIRD is key to directing clinical management and selecting targeted therapies26,27.

Clinical presentation 

Infections with atypical severity or pathogens, and/or increased frequency are often the first manifestations of IEI. Unusual or early onset autoimmunity, lymphoproliferation or autoinflammation1 are also suggestive features of IEI. The main categories of IEI, as well as their clinical presentation, are described in Table 12,23

IEI may mimic common childhood diseases, including eczematous dermatitis and food allergies. Atopic conditions may result from an underlying immunodeficiency or immune dysregulation28. Mechanistically, the development of atopy includes skin barrier disruption, mast cell dysregulation, tolerance failure and impaired T-cell receptor signaling29. The classic triad of eczema, elevated serum IgE and eosinophilia are hallmarks of conditions including atopy, hyper-IgE syndromes (HIES), Omenn syndrome and Wiskott-Aldrich syndrome30. The differentiation of these conditions in patients with severe atopic dermatitis is still challenging. Findings directing investigations include increased frequency of infection, severity at presentation and comorbidities such as thrombocytopenia. A high index of suspicion is key31.

Table 1. Simplify classification of IEI; adapted from the International Union of Immunological Societies: 2019 Expert Committee on IEI

Clinical vignette

The clinical case of early onset of severe atopy with frequent sinopulmonary infections, unusual severe viral illnesses, eosinophilia, and high serum IgE are key elements suggestive of a combined immunodeficiency, particularly hyper-IgE syndromes. HIES is a multi-systemic syndrome characterized by recurrent skin abscesses, pneumonia with pneumatocele formation, eczematous dermatitis, and elevated IgE levels. However, autosomal dominant and autosomal recessive forms of the disease differ significantly in their clinical features, as shown in Table 2.

Table 2. Clinical features of HIES; Adapted from Castagnoli et al. World Allergy Organization Journal (2021)

Investigating IEI

Early diagnosis of IEI is critical for prevention of disease-associated morbidity and mortality. This requires a high index of clinical suspicion and early treatment dramatically improves life expectancy and quality of life1,32.

Laboratory investigations, prompted by the clinical phenotype, are described in Table 3. Commonly available tests include complete blood count (CBC) and smear, which may reveal signs of lymphopenia or neutropenia. Additionally, both levels of cells and proteins, as well as their function should be evaluated. For example, a patient may have normal levels of IgG, but additional evaluation of specific antibodies post-vaccination may demonstrate a functional failure (Table 4).

Table 3. Laboratory testing according to the IEI clinical phenotype; courtesy of McCusker, MD and Saker, MD

Evaluating antibody responses

Clinical manifestations such as recurrent sinopulmonary infections and those involving encapsulated bacteria should prompt an evaluation for both primary B cell defects and combined immune disorders34,35. Initial screening tests should include a CBC with differential and immunoglobulin quantification such as total IgG, IgA, IgM, and IgE. There are no strict standards for pathologically low immunoglobulin levels, although a serum IgG below 3 g/L in an adolescent or adult and values below the age-matched range in children warrant further evaluation1. Albumin levels will rule out protein loss as the underlying cause of hypogammaglobulinemia.

If serum immunoglobulins are detectable, specific antibody response to protein antigens (diphtheria and tetanus vaccines) and polysaccharide antigens (23-valent polysaccharide vaccine) and/or presence of isohemagglutinins should be assessed. Ideally, specific antibody levels are measured pre-immunization and 3 to 4-weeks post-vaccination. Guidelines for normal responses are available to guide clinicians36. There are 2 methods defining sufficient response to pneumococcal vaccination. Protection against infection and colonization is associated with antibody concentrations of 1.3 mg/mL or greater. Most patients can mount a 2-4-fold increase over baseline titers post-vaccination if the preimmunization levels are <4. For the diagnosis of immunodeficiency, the general standards of normal responses are at least a 4-fold increase or a level ≥ to 1.3 µg/ml of at least 4 pneumococcal serotypes postimmunization. Vaccine response cannot be reliably evaluated in patients who have received immunoglobulin replacement therapy within the past 4 to 6 months. Other useful tests to evaluate the B cell compartment are listed in Table 4.

Table 4. Laboratory testing to evaluate IEI; courtesy of McCusker, MD and Saker, MD

Evaluating T cells

A history of prolonged viral infections, opportunistic infections, autoimmunity and failure to thrive (in the setting of an affected infant or young child) suggest a possible T cell defect­. Initial evaluation includes a CBC focusing on the white blood cell count and absolute lymphocyte count as up to 75% of circulating lymphocytes are T cells. Particularly in infants, lymphopenia may suggest a T cell developmental defect or marked T cell destruction and should prompt immediate immunological evaluation for potentially life-threatening conditions, such as a severe combined immune deficiency (SCID). Low lymphocyte count in isolation, as a screen for SCID, is not adequate as this will fail to identify infants with “leaky (hypomorphic) SCID”37, who may have normal or even elevated T cell numbers yet profound deficiency in T cell function. Other causes of T cell lymphopenia, including HIV infection or mechanical loss of lymphocytes (e.g., intestinal lymphangiectasia) also should be rapidly ruled out.

Newborn screening for severe combined immune deficiency (SCID)

The evaluation for SCID may be initiated by an abnormal newborn screening test which measures the number of copies of T cell restriction excision circles (TRECs), formed during T cell development42. TREC screening alone is not diagnostic for SCID, but requires immediate additional evaluation, including lymphocyte subset immunophenotyping to confirm a failure of T cell development. This is typically followed by lymphocyte proliferation, testing for maternal chimerism, and ultimately genotyping43.

Importantly, TREC screening identifies classic forms of SCID characterized by <300 T cells/mm3 at birth, but it fails to capture atypical SCID due to hypomorphic mutations in known SCID genes, as shown in Table 544.

NBS, Newborn screen; TREC, T-cell receptor excision circle.
Table 5. Newborn screening for SCID: Test results and possible diagnosis; Adapted from Knight V. et al., 2021

Evaluation of complement systems

Specific clinical presentations prompt evaluation of complement defects including encapsulated bacterial infection and angioedema44. The complement system is activated by three pathways: the classical, the alternative, and the lectin pathways, all of which converge at C3 to activate a common final pathway (the membrane attack complex). The three complement pathways should be functionally assessed.

Defects of C3 result in susceptibility to encapsulated bacterial infections, whereas defects of C5 to C9 are associated specifically with Neisseria sp. infections. C1, C2 or C4 complement deficiency are associated with infection and autoimmunity, such as systemic lupus erythematosus47. Functional tests of individual components are available in specialized laboratories (Table 4).

Evaluation of phagocytes

Recurrent bacterial and/or fungal infections involving the skin and deep organs are suggestive of a neutrophil defect44. Assessment should begin with a CBC for the absolute neutrophil count and a peripheral blood smear for cellular morphology. Several genetic IEI have been identified leading to neutropenia.

Assays of neutrophil function should also be considered. Neutrophil migration to sites of infection and pus production are compromised in leukocyte adhesion deficiency (LAD) and neutrophil killing activity is affected in chronic granulomatous disease (CGD). Rapid screening for CGD can be achieved using the dihydrorhodamine 123 (DHR) assay52. Other tests to evaluate the phagocyte compartment are listed in Table 4.

Evaluating natural killer (NK) cells

Recurrent viral infections and primary hemophagocytic lymphohistiocytosis, suggest a possible NK cell defect44,53. NK cell evaluation is done in specialized laboratories (Table 4). Classical NK deficiency results when both the number and function of the NK cells are profoundly reduced, whereas, in functional NK deficiency, only the cytotoxic capacity is abnormal in the setting of normal NK-cell counts.

Genetic testing

Access to genetic testing has become an essential and indispensable tool. Gene discovery has accelerated with significant advances including whole exome and whole genome sequencing. As a result, there are currently more than 400 immune disorders genetically identified2.

The contribution of genetic testing has significant impact on patient care with a shorter time to definitive diagnosis, the identification of asymptomatic family members and better family planning decisions. Genetic testing allows for the identification of molecular defects, allows the use of targeted therapies and increases our understanding of molecular pathways crucial for immune functions.

Despite these benefits, the emergence of broad-based sequencing approaches, has also introduced new challenges. The vast amount of genetic information obtained through sequencing, particularly in the form of variants of unknown significance, is problematic due to the need for functional assessments, not always readily available, and the need of genetic counselling.


Investigation of immune function is essential for accurate diagnoses in patients with recurrent and/or unusual infections as well as those with features of immune dysregulation. Many new diagnostic tools have been added to our medical armamentarium in recent years yet the diagnosis of IEI still relies on the combination of clinical acumen to identify patients at risk, leading to appropriate laboratory and genetic tests. The early evaluation of immune function provides not only critical diagnostic information, but also guides clinical decisions regarding appropriate therapies and prevention of disease-associated morbidity and mortality.

As illustrated in this article and by the clinical vignette, infection may not be the significant presenting feature for IEI. Patients for whom there are clinical suspicions for IEI should be evaluated with screening tests followed by directed protein/cellular and genetic testing. As this remains an evolving field, patients may need to be re-evaluated as our understanding progresses.


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