Severe Combined Immunodeficiencies - SCID

Severe combined immunodeficiencies (SCIDs) are genetic disorders characterized by blocked T-lymphocyte differentiation or function and often are associated with abnormal development of other lymphocyte lineages (B cells and natural killer [NK] cells). SCID is also commonly referred to as "bubble boy disease." About 92% of U.S. newborns are now screened for SCID by molecular laboratory testing (Immune Deficiency Foundation [IDF], 2017).

Diagnosis

Indications for Testing

In infants or children (Joint Task Force on Practice Parameters, Bonilla, 2015)
- Chronic diarrhea
- Failure to thrive
- Recurrent, persistent, or severe viral, fungal, or bacterial infections
- Pneumocystis jiroveci infection

Criteria for Diagnosis

Primary Immune Deficiency Treatment Consortium Diagnostic Criteria for

SCID, Leaky SCID, Omenn Syndrome, and Reticular Dysgenesis
Typical SCID	Leaky SCID	Omenn Syndrome	Reticular Dysgenesis
Absence of or very low CD3 T-cell number (<300/µL), and no or very low T-cell function (<10% LLN), based on PHA response, OR	Reduced CD3 T-cell number	Skin rash, generalized	Absence of T cells or very low T-cell number (<300/µL)
Presence of maternal-origin T cells	No maternal engraftment	No maternal engraftment	No or very low T-cell function (<10% LLN), based on PHA response
	<30% of LLN T-cell function, based on PHA response	CD3 cells detectable at level of ≥300/µL	Severe neutropenia (ANC <200/µL)
	<30% of LLN T-cell function, based on PHA response	Absent/low T-cell proliferation (≤30% of normal) to antigens to which patient has been exposed	Sensorineural deafness and/or no granulopoiesis found in bone marrow exam and/or deleterious AK2 mutation
ANC, absolute neutrophil count; LLN, lower level of normal; PHA, phytohemagglutinin Source: Adapted from Shearer, PIDTC, 2014

Laboratory Testing

Screen for underlying diseases associated with immunodeficiency
- CBC – presence of lymphopenia (total lymphocyte count of ≤3,400 cells/µL at birth, ≤3,900 cells/µL at 5-6 months, and ≤1,000 cells/µL in adults) (Immune Deficiency Foundation [IDF], 2015)
  - Normal lymphocyte count does not rule out SCIDs
- HIV testing – rule out HIV infection
Screen for other immunodeficiencies
- T-cell and B-cell immunodeficiency profile testing
  - Testing at minimum should include CD3, CD4, CD8, CD19, CD45RA, CD45RO, natural killer (NK) cell, and CD4:CD8 ratio
- Quantitative immunoglobulins
- Lymphocyte proliferation induced by mitogens – will be abnormal
  - Test requires at least 4-5 days for results
  - Anti-CD3/anti-CD28/IL-2-induced lymphocyte proliferation test may be useful, specifically in the context of IL-2-receptor signaling defects
- Neutrophil function testing
- Complement testing
Analyte/enzyme testing may be considered prior to genetic testing
- Adenosine deaminase, purine nucleoside phosphorylase
Molecular diagnosis
- Available for prenatal/postnatal testing for SCID
- Genetic testing – see lists in Background

Background

Epidemiology

Incidence – >1/58,000 births (Joint Task Force on Practice Parameters, Bonilla, 2015)
Age – median 4-7 months
Sex – M:F, equal, except for X-linked forms

Identified Forms of SCID

Combined Immunodeficiencies (Based on the Classification Update from the International Union of Immunological Societies Primary Immunodeficiency Diseases Committee, Picard, 2018^a)
Gene	T Cells	B Cells	NK Cells	Genetics	Associated Features
T-negative/B-positive SCID
IL2RG	Very low	Normal to high	Low	XL	Impaired cytokine-mediated signaling
JAK3	Very low	Normal to high	Low	AR	Impaired cytokine-mediated signaling
IL7R	Very low	Normal to high	Normal	AR	Impaired cytokine-mediated signaling
PTPRC	Very low	Normal	n/a	AR	—
CD3D	Very low	Normal	Normal	AR	CD3-delta deficiency
CD3E	Very low	Normal	Normal	AR	CD3-epsilon deficiency
CD247	Very low	Normal	Normal	AR	—
CORO1A	Very low	Normal	n/a	AR	Detectable thymus, EBV
LAT	Normal to low number	Normal to low	n/a	AR	Adenopathy, splenomegaly, recurrent infections, autoimmunity
T-negative/B-negative SCID
RAG1^b	Very low	Very low	Normal	AR	Associated with Omenn syndrome
RAG2^b	Very low	Very low	Normal	AR	Associated with Omenn syndrome
DCLRE1C^b	Very low	Very low	Normal	AR	Radiation sensitivity; Omenn syndrome
PRKDC	Very low	Very low	Normal	AR	Radiation sensitivity; microcephaly
NHEJ1	Very low	Very low	Normal	AR	Radiation sensitivity; microcephaly
LIG4	Very low	Very low	Normal	AR	Radiation sensitivity; microcephaly
AK2	Very low	Normal to low	n/a	AR	Granulocytopenia and deafness; reticular dysgenesis
ADA^b	Very low	Low, decreasing	Low	AR	Bone defects; may have pulmonary alveolar proteinosis; cognitive defects
^aSources in addition to the International Union of Immunological Societies Primary Immunodeficiency Diseases Committee report (Picard, 2018) include Cossu (2010) and van der Burg (2011) ^bGene included on Primary Antibody Deficiency Panel, Sequencing and Deletion/Duplication – ARUP test code 2011156 ADA, adenosine deaminase; AR, autosomal recessive; EBV, Epstein-Barr virus; n/a, not applicable; NK, natural killer; XL, X-linked

Combined Immunodeficiencies Typically Less Profound Than SCID^a
Gene	T Cells	B Cells	Genetics	Comment
DOCK2	Low	Normal	AR	Impaired interferon response in hematopoietic and nonhematopoietic cells; normal NK numbers but defective function
CD40LG^b	Normal to low	sIgM+ and sIgD+ B cells present, other surface isotype positive B cells absent	XL	Neutropenia; thrombocytopenia; hemolytic anemia; liver/biliary tract disease; opportunistic infections
CD40^b	Normal	IgM+ and IgD+ cells present, other isotypes absent	AR	Neutropenia; GI and liver/biliary tract disease; opportunistic infections
ICOS^b	Normal	Normal	AR	Recurrent infections; autoimmunity; gastroenteritis; granulomas in some cases
PNP	Progressive decrease	Normal	AR	Autoimmune hemolytic anemia; neurological impairment
CD3G	Normal number; low TCR expression	Normal	AR	—
CD8A	Absent CD8, normal CD4 cells	Normal	AR	Recurrent infections; may be asymptomatic
ZAP70	Low CD8, normal CD4 cells	Normal	AR	In some cases, immune dysregulation, autoimmunity
TAP1, TAP2, or TAPBP	Low CD8, normal CD4 cells	Normal	AR	Vasculitis; pyoderma gangrenosum
B2M	—	Normal	AR	—
CIITA, RFXANK, RFX5, RFXAP	Low CD4 cells	Normal	AR	Respiratory and GI infections; liver/biliary tract disease
ITK	Progressive decrease	Normal	AR	EBV-associated B-cell lymphoproliferation, lymphoma; normal or low IgG
MAGT1	Low CD4 cells	Normal	XL	EBV infection; lymphoma; viral infections; respiratory and GI infections
DOCK8	Low	Low; low CD27+ memory B cells	AR	Eosinophilia; recurrent infections; severe atopy; cutaneous viral, staphylococcal, and fungal infections; cancer susceptibility; low/impaired function NK cells
RHOH	Normal number	Normal	AR	HPV infection; lymphoma; lung granulomas; molluscum contagiosum
SH2D1A^b	Normal or increased activated T cells	Reduced memory B cells	XL	Clinical and immunologic features induced by EBV infection; HLH; lymphoproliferation; aplastic anemia; lymphoma; hypogammaglobulinemia
RMRP	Varies from severely low to normal; impaired lymphocyte proliferation	Normal	AR	Short-limbed dwarfism with metaphyseal dysostosis; sparse hair; bone marrow failure; autoimmunity; cancer/lymphoma susceptibility; impaired spermatogenesis; neuronal dysplasia of the intestine
STK4	Low	Low	AR	Recurrent bacterial, viral/HPV, and candidal infections; intermittent neutropenia; EBV lymphoproliferation; lymphoma; congenital heart disease; autoimmune cytopenias
TRAC	Absent TCR alpha beta cells	Normal	AR	Recurrent viral, bacterial, and fungal infections; immune dysregulation autoimmunity; diarrhea
LCK	Low CD4+ and T regulatory cells	Normal	AR	Recurrent infections; immune dysregulation; autoimmunity
MALT1	Normal number	Normal	AR	Bacterial, fungal, and viral infections
CARD11^b	Normal number	Normal predominance of transitional B cells	AD, AR	Pneumocystis jirovecii pneumonia, bacterial and viral infections
BCL10	Normal number	Normal number	AR	Recurrent bacterial and viral infections; candidiasis; gastroenteritis
BCL11B	Low	Normal	AD	Congenital abnormalities, neonatal teeth, facies abnormalities, absent corpus callosum, neurocognitive defects
IL21	Normal number	Low	AR	Severe onset early colitis; sinopulmonary infections
IL21R^b	Normal number	Normal number	AD	Recurrent infections; susceptibility to cryptosporidium and pneumocystis infections and liver disease
TNFRSF4	Normal number	Normal number	AR	Kaposi sarcoma; impaired immunity to HHV8
IKBKB	Normal number	Normal number	AR	Recurrent bacterial, viral, and fungal infections; opportunistic infections
PIK3CD^b	—	Low or absent pro-B cells	AD	Severe bacterial infections; EBV
LRBA^b	Normal/decreased CD4 number	Low or normal number	AR	Recurrent infections; IBD; autoimmunity; EBV infection
CD27^b	Normal	No memory B cells	AR	Clinical and immunologic features triggered by EBV infection; HLH; aplastic anemia; lymphoma; hypogammaglobulinemia; low iNKT cells
RELB	Normal number	—	AR	Recurrent infections
MSN	Normal number	Low number	XL	Recurrent infections with bacteria, varicella, neutropenia
TFRC	Normal number	Normal number, low memory B cells	AR	Recurrent infections, neutropenia, thrombocytopenia
MAP3K14	Normal number	Low	AR	Recurrent bacterial, viral, and Cryptosporidium infections; low NK cell number
CTPS1	Normal or decreased	Normal or decreased	AR	Recurrent/chronic viral infections (particularly EBV, VZV), lymphoproliferation; B-cell NHL
^aBased on the International Union of Immunological Societies Primary Immunodeficiency Diseases Committee report (Picard, 2018); see original source for additional detail about T-cell and B-cell status and function ^bGene included on Primary Antibody Deficiency Panel, Sequencing and Deletion/Duplication– ARUP test code 2011156 AD, autosomal dominant; AR, autosomal recessive; CMV, cytomegalovirus; EBV, Epstein-Barr virus; GI, gastrointestinal; HHV8, human herpesvirus 8; HLH, hemophagocytic lymphohistiocytoses; HPV, human papillomavirus; IBD, irritable bowel disease; iNK, invariant natural killer; NHL, non-Hodgkin lymphoma; NK, natural killer; TEMRA, terminal differentiated effector memory cells; Treg, regulatory T cells; VZV, varicella-zoster virus; XL, X-linked

Pathophysiology

Blockage in T-lymphocyte differentiation or growth and variable abnormal development of other lymphocyte lineages

Clinical Presentation

Most newborns appear normal
Early onset of severe infections
- Earliest are Pneumocystis jirovecii, viral (also fungal), followed in many cases at 4-6 months by bacterial infection
Growth failure
Persistent diarrhea
Desquamative skin rash, elevated liver enzymes, and gastrointestinal bleeding
Occurrence of graft-versus-host disease upon exposure to maternal lymphocytes, during delivery, or by nonirradiated blood transfusion
- Most prominent in skin and liver
- May be associated with autoimmune thrombocytopenia or pancytopenia
- Rejection of hematopoietic stem cell transplant from father or other donor
Omenn syndrome – atypical SCIDs associated with hypomorphic mutations

ARUP Laboratory Tests

Assess thymic function in suspected severe combined immunodeficiencies (SCIDs), DiGeorge syndrome (22q11.2 deletion syndrome), and other T-cell immune deficiency disorders

Evaluate immune reconstitution during highly active antiviral therapy (HAART) in HIV patients and post chemotherapy and hematopoietic cell transplant

2010179

CD4+ T-Cell Recent Thymic Emigrants (RTEs) 2010179

Method

Quantitative Flow Cytometry

Useful for assessing primary T-cell immunodeficiency disorders

0095862

Lymphocyte Subset Panel 6 - Total Lymphocyte Enumeration with CD45RA and CD45RO 0095862

Method

Quantitative Flow Cytometry

Test enumerates the percent and absolute cell count of lymphocyte subsets in whole blood for CD3 (total T cells), CD4 (helper T cells), CD45RA (naive helper T cells), CD45RO (memory helper T cells), CD8 (cytotoxic T cells), CD4:CD8 ratio, CD19 (B cells), natural killer (NK) cells

Evaluate NK- and NKT-cell subsets

2013805

Natural Killer Cell and Natural Killer T-Cell Panel 2013805

Method

Semi-Quantitative Flow Cytometry

Panel includes:

Pct CD3-CD16-/+CD56br/dim (total NK cells)
Abs CD3-CD16-/+CD56br/dim (total NK cells)
Pct CD3-CD16+CD56dim (cytotoxic NK cells)
Abs CD3-CD16+CD56dim (cytotoxic NK cells)
Pct CD3-CD16-CD56br (cyto secreting NK cells)
Abs CD3-CD16-CD56br (cyto secreting NK cells)
Pct CD3-CD57+ (CD57 NK cells)
Abs CD3-CD57+ (CD57 NK cells)
Pct CD3+CD56+ (CD56 NKT cells)
Abs CD3+CD56+ (CD56 NKT cells)
Pct CD3+CD57+ (CD57 NKT cells)
Abs CD3+CD57+ (CD57 NKT cells)
Pct CD45+CD3+ (T cells)
Abs CD45+CD3+ (T cells)
Pct CD45+CD3- (Non T cells)
Abs CD45+CD3- (Non T cells)
NKT-cell panel interpretation

Evaluate NK cells in patients with suspected immune deficiency

0092404

Natural Killer Cells Enumeration 0092404

Method

Quantitative Flow Cytometry

Acceptable lymphocyte subset panel for the investigation of primary immunodeficiency disorders

0095899

Lymphocyte Subset Panel 7 - Congenital Immunodeficiencies 0095899

Method

Quantitative Flow Cytometry

Assess B-cell subsets in immunodeficiencies (eg, common variable immunodeficiency [CVID], B-cell reconstitution after bone marrow, or hematopoietic stem cell transplantation)

Supports the diagnosis of CVID and may help predict the clinical phenotype

Assess B-cell reconstitution after bone marrow or hematopoietic stem cell transplantation

Measures B cells (CD19+), total memory B cells (CD19+/CD27+), class-switched memory B cells (CD19+/CD27+/IgD-/IgM-), nonswitched/marginal zone memory B cells (CD19+/CD27+/IgD+/IgM+), IgM only memory B cells, and naive B cells (CD19+/CD27-/IgD+)

Not recommended for rituximab monitoring; refer to B-cell CD20 expression

Refer to Additional Technical Information document for further content

3002216

B Cell Subset Analysis 3002216

Method

Flow Cytometry

Initial test in the workup of immunoglobulin disorders

In adults and children >15 years with suspected hypogammaglobulinemia, order in conjunction with serum protein electrophoresis and immunofixation to rule out plasma cell dyscrasia

0050630

Immunoglobulins (IgA, IgG, IgM), Quantitative 0050630

Method

Quantitative Immunoturbidimetry

Assist in diagnosis of innate immunodeficiencies when genetic defects of the innate immune system are suspected in individuals negative for other immunodeficiencies (eg, no detectable abnormality of antibody function, complement activity, neutrophil function, or cell-mediated immunity)

Results should be interpreted in conjunction with the individual’s clinical status

0051589

Toll-Like Receptor Function 0051589

Method

Cell Culture/Quantitative Multiplex Bead Assay

Preferred genetic test for individual with clinical phenotype of primary antibody deficiency (eg, agammaglobulinemia, hyper-IgM syndrome, or CVID)

Refer to Test Fact Sheet for complete list of genes tested

Refer to Test Fact Sheet for complete list of limitations

2011156

Primary Antibody Deficiency Panel, Sequencing and Deletion/Duplication 2011156

Method

Massively Parallel Sequencing/Sequencing

Evaluate patients with suspected immunodeficiency diseases, including SCID

Panel includes testing for phytohemagglutinin, concanavalin A, pokeweed mitogen, Candida antigen, and tetanus antigen

Time sensitive

0096056

Lymphocyte Antigen and Mitogen Proliferation Panel 0096056

Method

Cell Culture

Related Tests

Rule out HIV

2006526

Human Immunodeficiency Virus (HIV) Combo Antigen/Antibody (HIV-1/O/2) by CIA, with Reflex to HIV-1 Antibody Confirmation by Western Blot 2006526

Method

Qualitative Chemiluminescent Immunoassay /Qualitative Western Blot

Reflex pattern: if HIV-1,2 combo antigen/antibodies screen is repeatedly reactive, then HIV-1 antibody confirmation by Western Blot will be added

Primarily for evaluating recall antigen responses in patients with suspected cellular immune dysfunction, such as primary and secondary immunodeficiencies

Other uses include monitoring lymphocyte recovery and competence after hematopoietic stem cell transplantation and monitoring lymphocyte function during immunosuppressive therapy

Do not order for patients younger than 3 months unless clinical history of candidiasis is present

0096055

Lymphocyte Antigen Proliferation 0096055

Method

Cell Culture

Primarily for evaluating lymphocyte function in patients with suspected cellular immune dysfunction, such as primary and secondary immunodeficiencies

Other uses include monitoring lymphocyte recovery and competence after hematopoietic stem cell transplantation and monitoring lymphocyte function during immunosuppressive therapy

0096043

Lymphocyte Mitogen Proliferation 0096043

Method

Cell Culture

Monitor engraftment of maternal T cells in patients with SCID prior to allogenic stem cell transplantation

2014694

Maternal T Cell Engraftment in SCID, Pre-Engraftment Specimen 2014694

Method

Polymerase Chain Reaction/Fragment Analysis

May be used as a marker of severe combined immunodeficiencies (SCIDs); lack of adenosine deaminase (ADA) allows deoxyadenosine to accumulate and kill lymphocytes

If patient has been recently transfused, ADA deficiency may be masked; interpret results with caution

Heterozygotes cannot be identified by this test; if clinical suspicion remains, consider testing to determine ADA genotype

0083001

Adenosine Deaminase, RBC 0083001

Method

Kinetic Spectrophotometry

Monitor engraftment of maternal T cells in patients with SCID prior to allogenic stem cell transplantation

2014699

Maternal T Cell Engraftment in SCID 2014699

Method

Polymerase Chain Reaction/Fragment Analysis

2014704