Primary Antibody Deficiency Panel, Sequencing and Deletion/Duplication

Content Review: May 2022 Last Update:

Determine the genetic etiology of a primary antibody deficiency in affected individuals.

If a familial sequence variant has been previously identified, targeted sequencing for that variant may be appropriate; refer to the Laboratory Test Directory for additional information.

Primary antibody deficiency (PAD) syndromes are a group of rare genetic disorders affecting antibody (immunoglobulin) production. Three categories of primary antibody deficiencies include common variable immunodeficiency (CVID), agammaglobulinemia, and hyper-IgM syndrome. Symptoms may include unusual, opportunistic, or severe infections that typically affect multiple organs/organ systems. Other signs may include sepsis, failure to thrive, splenomegaly, autoimmune conditions, and neutropenia. Agammaglobulinemia and hyper-IgM syndrome usually occur within the first 2 years of life. CVID manifests at all ages, but most often in the second and third decade. Molecular testing is used to determine the genetic etiology of PAD in affected individuals.

Genetics

Genes

See Genes Tested table for genes included in the panel.

Incidence

Estimated at 1/10,000

Inheritance

X-linked, autosomal dominant, or autosomal recessive, depending on the causative gene

Test Interpretation

Methodology

This test is performed using the following sequence of steps:

  • Selected genomic regions, primarily coding exons and exon-intron boundaries, from the targeted genes are isolated from extracted genomic DNA using a probe-based hybrid capture enrichment workflow.
  • Enriched DNA is sequenced by massively parallel sequencing (MPS; also known as next generation sequencing [NGS]) followed by paired-end read alignment and variant calling using a custom bioinformatics pipeline. The pipeline includes an algorithm for the detection of large (single exon-level or larger) deletions and duplications.
  • Sanger sequencing is performed as necessary to fill in regions of low coverage and in certain situations, to confirm variant calls.
  • Large deletion/duplication calls made using MPS are confirmed by an orthogonal exon-level microarray when sample quality and technical conditions allow.

Clinical Sensitivity

  • Agammaglobulinemia, 90% 
  • Hyper-IgM syndrome, 75-80% 
  • CVID, 20% 

Analytic Sensitivity

For massively parallel sequencing:

Variant Class Analytic Sensitivity (PPA) Estimatea (%)
and 95% Credibility Region (%)		 Analytic Specificity (NPA) (%)

SNVs

>99 (96.9-99.4)

>99.9

Deletions 1-10 bpb

93.8 (84.3-98.2)

>99.9

Insertions 1-10 bpb

94.8 (86.8-98.5)

>99.9

Exon-levelc deletions

97.8 (90.3-99.8) [2 exons or larger]

62.5 (38.3-82.6) [single exon]

>99.9

Exon-levelc duplications

83.3 (56.4-96.4) [3 exons or larger]

>99.9

aGenes included on this test are a subset of a larger methods-based validation from which the PPA values are derived. These values do not apply to testing performed by multiplex ligation-dependent probe amplification (MLPA).

bVariants greater than 10 bp may be detected, but the analytic sensitivity may be reduced.

cIn most cases, a single exon deletion or duplication is less than 450 bp and 3 exons span a genomic region larger than 700 bp.

bp, base pairs; NPA, negative percent agreement; PPA, positive percent agreement; SNVs, single nucleotide variants

Limitations

  • A negative result does not exclude a PAD syndrome.
  • Diagnostic errors can occur due to rare sequence variations.
  • Interpretation of this test result may be impacted if the individual has had an allogeneic stem cell transplantation.
  • The following will not be evaluated:
    • Variants outside the coding regions and intron-exon boundaries of the targeted genes
    • Regulatory region variants and deep intronic variants
    • Breakpoints of large deletions/duplications
    • Deletions/duplications in NFKBIA and TCF3
    • Translocations
    • The following exons are not sequenced due to technical limitations of the assay:
      • CXCR4 (NM_001348056, NM_001348059) exon(s) 2
      • DCLRE1C (NM_001350965) exon(s) 15
      • DCLRE1C (NM_001350966) exon(s) 13
      • DCLRE1C (NM_001350967) exon(s) 16
      • PRKCD (NM_001354676, NM_001354678) exon(s) 1
      • XIAP (NM_001167, NM_001204401, NM_001378590, NM_001378591, NM_001378592) exon(s) 4
  • The following may not be detected:
    • Deletions/duplications/insertions of any size by massively parallel sequencing
    • Large duplications less than 3 exons in size
    • Noncoding transcripts
    • Some variants due to technical limitations in the presence of pseudogenes, repetitive, or homologous regions
    • Low-level somatic variants
    • Single exon deletions/duplications in the following exons: 
      • ADA (NM_000022, NM_001322051) 1; CXCR4 (NM_001348056) 2; CXCR4 (NM_001348059) 2; DCLRE1C (NM_001033855) 4-9; DCLRE1C (NM_001033857, NM_001289077) 6-10; DCLRE1C (NM_001033858, NM_001289079) 7-11; DCLRE1C (NM_001289076, NM_001289078) 3-7; DCLRE1C (NM_001350965) 4-9,15; DCLRE1C (NM_001350966) 3-7,13; DCLRE1C (NM_001350967) 6-10,16; DCLRE1C (NM_022487) 4-8; HELLS (NM_018063, NM_001289067, NM_001289068, NM_001289069, NM_001289070, NM_001289072) 7; HELLS (NM_001289071) 8; HELLS (NM_001289073) 6; IGLL (NM_152855) 2; IKZF1 (NM_001291846, NM_001291847) 4; MOGS (NM_001146158) 2; PRKCD (NM_001354676, NM_001354678) 1; XIAP (NM_001167, NM_001204401, NM_001378590, NM_001378592) 4; XIAP (NM_001378591) 5

Genes Tested

Gene MIM Number Disorder Inheritance

ADA

608958

Adenosine deaminase deficiency, partial

Severe combined immunodeficiency due to ADA deficiency

AR

ADA2

607575

Sneddon syndrome

Vasculitis, autoinflammation, immunodeficiency, and hematologic defects syndrome

AR

AICDA

605257

Immunodeficiency with hyper-IgM, type 2

AR

ATM

607585

Ataxia-telangiectasia

AR

ATP6AP1

300197

Immunodeficiency 47

XL

BLNK

604515

Agammaglobulinemia

AR

BTK

300300

Agammaglobulinemia, X-linked 1

Isolated growth hormone deficiency, type III, with agammaglobulinemia

XL

CARD11

607210

Immunodeficiency 11

AR

B-cell expansion with NFKB and T-cell energy

Immunodeficiency 11B with atopic dermatitis

 AD

CD19

107265

CVID 3

AR

CD27

186711

Lymphoproliferative syndrome 2

AR

CD40

109535

Immunodeficiency with hyper-IgM, type 3

AR

CD40LG

300386

Immunodeficiency, X-linked, with hyper-IgM

XL

CD70

602840

Lymphoproliferative syndrome 3

AR

CD79A

112205

Agammaglobulinemia 3

AR

CD79B

147245

Agammaglobulinemia 6

AR

CDCA7

609937

Immunodeficiency-centromeric instability-facial anomalies syndrome 3

AR

CR2

120650

CVID 7

AR

CTLA4

123890

Immune dysregulation with autoimmunity, immunodeficiency, and lymphoproliferation

AD

CXCR4

162643

Whim syndrome

Myelokathexis, isolated

AD

DCLRE1C

605988

SCID, Athabascan type

Omenn syndrome

AR

DNMT3B

602900

Immunodeficiency-centromeric instability-facial anomalies syndrome 1

AR

GATA2

137295

Immunodeficiency 21

Emberger syndrome

AD

HELLS

603946

Immunodeficiency-centromeric instability-facial anomalies syndrome 4

AR

ICOS

604558

CVID 1

AR

IGHM

147020

Agammaglobulinemia 1

AR

IGLL1

146770

Agammaglobulinemia 2

AR

IKZF1

603023

CVID 13

AD

IL21R

605383

IgE, elevated level of

AD
Immunodeficiency 56 AR

KDM6A

300128

Kabuki syndrome 2

XL

KMT2D

602113

Kabuki syndrome 1

AD

LRBA

606453

CVID 8 with autoimmunity

AR

MOGS

601336

Congenital disorder of glycosylation, type IIB

AR

MS4A1

112210

CVID 5

AR

NBN

602667

Nijmegen breakage syndrome

Aplastic anemia

Leukemia, acute lymphoblastic

AR

NFKB1

164011

CVID 12 

AD

NFKB2

164012

CVID 10

AD

NFKBIA

164008

Ectodermal dysplasia and immunodeficiency 2

AD

PIK3CD

602839

Immunodeficiency 14A, autosomal dominant

AD
Immunodeficiency 14B, autosomal recessive AR

PIK3CG

601232

Hyper-IgM

AD

PIK3R1

171833

Immunodeficiency 36

SHORT syndrome

AD

PLCG2

600220

Autoinflammation, antibody deficiency, and immune dysregulation

Familial cold autoinflammatory syndrome 3

AD

PRKCD

176977

Autoimmune lymphoproliferative syndrome, type III

AR

RAC2

602049

Immunodeficiency 73A and 73B with defective neutrophil chemotaxis and leukocytosis

AD

RAG1

179615

Combined cellular and humoral immune defects with granulomas

SCID, B-cell negative

Omenn syndrome

Alpha/beta T-cell lymphopenia with gamma/delta T-cell expansion, severe cytomegalovirus infection, and autoimmunity

AR

RAG2

179616

Combined cellular and humoral immune defects with granulomas

SCID, B-cell negative

Omenn syndrome

AR

RNF168

612688

RIDDLE syndrome

AR

SH2D1A

300490

Lymphoproliferative syndrome, X-linked, 1

XL

STAT3

102582

Hyper-IgE recurrent infection syndrome

Autoimmune disease, multisystem, infantile-onset 1

AD

TCF3

147141

Agammaglobulinemia 8A, autosomal dominant

AD
Agammaglobulinemia 8B, autosomal recessive AR

TNFRSF13B

604907

CVID 2

Immunoglobulin A deficiency

AR, AD

TRNT1

612907

Sideroblastic anemia with B-cell immunodeficiency, periodic fevers, and developmental delay

Retinitis pigmentosa and erythrocytic microcytosis

AR

TTC37

614589

Trichohepatoenteric syndrome 1

AR

UNG

191525

Immunodeficiency with hyper-IgM syndrome, type 5

AR

XIAP

300079

X-linked lymphoproliferative syndrome 2

XL

ZBTB24

614064

Immunodeficiency-centromeric instability-facial anomalies syndrome 2

AR

AD, autosomal dominant; AR, autosomal recessive; SCID, severe combined immunodeficiency; XL, X-linked

References

Related Information
Common Variable Immunodeficiency
Primary Immunodeficiency Diseases - Immunoglobulin Disorders