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FeedbackMassively Parallel Sequencing/Sequencing
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
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
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9545398
Conley ME, Mathias D, Treadaway J, et al. Mutations in btk in patients with presumed X-linked agammaglobulinemia. Am J Hum Genet. 1998;62(5):1034-1043.
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19302039
Conley ME, Dobbs AK, Farmer DM, et al. Primary B cell immunodeficiencies: comparisons and contrasts. Annu Rev Immunol. 2009;27:199-227.
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29867916
de Valles-Ibáńez G, Esteve-Solé A, Piquer M, et al. Evaluating the genetics of common variable immunodeficiency: monogenetic model and beyond. Front Immunol. 2018;9:636.
Determine the genetic etiology of a primary antibody deficiency in affected individuals.