Severe Combined Immunodeficiency Panel

Last modified: Jun 12, 2018

Summary

  • Is a 79 gene panel that includes assessment of non-coding variants
  • Is ideal for patients with a clinical suspicion of combined immunodeficiencies. The genes on this panel are included in the Primary Immunodeficiency Panel.

Analysis methods

  • PLUS
  • SEQ
  • DEL/DUP

Availability

3-4 weeks

Number of genes

79

Test code

IM0101

CPT codes

SEQ 81400
SEQ 81406
SEQ 81408
DEL/DUP 81479

Summary

The Blueprint Genetics Severe Combined Immunodeficiency Panel (test code IM0101):

  • Is a 79 gene panel that includes assessment of selected non-coding disease-causing variants
  • Is available as PLUS analysis (sequencing analysis and deletion/duplication analysis), sequencing analysis only or deletion/duplication analysis only

ICD codes

Commonly used ICD-10 code(s) when ordering the Severe Combined Immunodeficiency Panel

ICD-10 Disease
D81.9 Combined immunodeficiencies

Sample Requirements

  • EDTA blood, min. 1 ml
  • Purified DNA, min. 3μg
  • Saliva (Oragene DNA OG-500 kit)

Label the sample tube with your patient’s name, date of birth and the date of sample collection.

Note that we do not accept DNA samples isolated from formalin-fixed paraffin-embedded (FFPE) tissue.

Severe combined immunedeficiencies (SCIDs) are a group of primary immunodeficiencies characterized by specific mutations in genes of T and B-lymphocyte systems and leading to little or no immune response. Different subtypes of SCIDs are characterized and subdivided by the presence of circulating T and B cells. T cells are absent or markedly decreased in the most types, but levels of B cells vary. In addition, both of these disease subgroups (T-B+ and T-B-) can occur with or without NK cells. Patients with SCID are susceptible to recurrent infections that can be fatal. The worldwide prevalence of SCID is estimated to be at least 1:100,000 births, while some genetically more homogenous populations may show markedly increased numbers. Mutations in IL2RG are the most common reason for SCIDs, explaining approximately 50% of all cases and close to 100% of X-linked cases.

Genes in the Severe Combined Immunodeficiency Panel and their clinical significance

Gene Associated phenotypes Inheritance ClinVar HGMD
ADA Severe combined immunodeficiency due to adenosine deaminase deficiency AR 39 88
AK2 Reticular dysgenesis AR 14 17
ATM Breast cancer, Ataxia-Telangiectasia AD/AR 860 1026
BCL11B Immunodeficiency 49 AD 3 1
BLM Bloom syndrome AR 91 107
CARD11 B-cell expansion with NFKB and T-cell anergy, Immunodeficiency AD/AR 11 8
CD3D Immunodeficiency AR 3 5
CD3E Immunodeficiency AR 3 7
CD3G Immunodeficiency AR 3 3
CD8A CD8 deficiency AR 1 1
CD27 Lymphoproliferative syndrome AR 2 8
CD40 Immunodeficiency with Hyper-IgM AR 5 9
CD40LG Immunodeficiency, with hyper-IgM XL 31 227
CD247 Immunodeficiency AR 7 4
CIITA Bare lymphocyte syndrome AR 8 14
CORO1A* Immunodeficiency AR 39 6
DCLRE1C* Omenn syndrome, Severe combined immunodeficiency with sensitivity to ionizing radiation AR 17 83
DNMT3B Immunodeficiency-centromeric instability-facial anomalies syndrome AR 14 50
DOCK8 Hyper-IgE recurrent infection syndrome, Mental retardation, autosomal dominant 2 AR 38 162
EPG5 Vici syndrome AR 29 50
FOXN1 T-cell immunodeficiency, congenital alopecia, and nail dystrophy AR 4 6
IFNGR1 Immunodeficiency AD/AR 16 40
IKBKB Immunodeficiency 15 AR 2 6
IL2RA Interleukin 2 receptor, alpha, deficiency AR 6 6
IL2RG Combined immunodeficiency XL 52 220
IL7R Severe combined immunodeficiency, , T-cell negative, B-cell positive, NK cell positive AR 20 47
IL12RB1 Immunodeficiency AR 10 82
IRF8 Immunodeficiency 32A (CD11C-positive/CD1C-positive dendritic cell deficiency), Immunodeficiency 32B (monocyte and dendritic cell deficiency) AD 3 6
ITGB2 Leukocyte adhesion deficiency AR 33 114
ITK Lymphoproliferative syndrome AR 4 10
JAK3 Severe combined immunodeficiency, , T cell-negative, B cell-positive, natural killer cell-negative AR 27 63
LAT Immunodeficiency 52 AR 2 18
LCK Immunodeficiency AR 2 3
LIG4 Severe combined immunodeficiency with sensitivity to ionizing radiation, LIG4 syndrome AR 16 35
LRBA Common variable immunodeficiency AR 19 60
MAGT1 Immunodeficiency, with magnesium defect, Epstein-Barr virus infection and neoplasia, Mental retardation, X-linked 95 XL 5 14
MALT1 Immunodeficiency AR 3 5
MAP3K14 Primary immunodeficiency with multifaceted aberrant lymphoid immunity AR 1 1
MSN* Immunodeficiency 50 XL 2 2
NHEJ1 Severe combined immunodeficiency with microcephaly, growth retardation, and sensitivity to ionizing radiation AR 14 15
NSMCE3 Lung disease, immunodeficiency, and chromosome breakage syndrome (LICS) AR 2 2
ORAI1 Immunodeficiency, Myopathy, tubular aggregate, 2 AR 9 13
PARN* Pulmonary fibrosis and/or bone marrow failure, Dyskeratosis congenita AD/AR 15 24
PGM3 Immunodeficiency 23 AR 13 14
PIK3CD* Immunodeficiency AD 5 11
PMS2* Mismatch repair cancer syndrome, Colorectal cancer, hereditary nonpolyposis AD/AR 259 324
PNP Purine nucleoside phosphorylase deficiency AR 11 33
POLE Colorectal cancer, Facial dysmorphism, immunodeficiency, livedo, and short stature syndrome (FILS syndrome) AD/AR 7 50
POLE2 Combined immunodeficiency AR 3
PRKDC Immunodeficiency AR 6 7
PTPRC Severe combined immunodeficiency, , T-cell negative, B-cell positive, NK cell positive AR 4 5
RAG1 Omenn syndrome, Alpha/beta T-cell lymphopenia with gamma/delta T-cell expansion, severe cytomegalovirus infection, and autoimmunity, T cell-negative, B cell-negative, natural killer cell-positive severe combined immunodeficiency, Combined cellular and humoral immune defects with granulomas AR 48 182
RAG2 Omenn syndrome, Combined cellular and humoral immune defects with granulomas AR 26 79
RFX5 Bare lymphocyte syndrome AR 5 6
RFXANK MHC class II deficiency AR 6 14
RFXAP Bare lymphocyte syndrome AR 5 7
RHOH T-cell immunodeficiency with epidermodysplasia verruciformis AD/AR 1
RMRP Cartilage-hair hypoplasia, Metaphyseal dysplasia without hypotrichosis, Anauxetic dysplasia AR 34 123
RTEL1 Pulmonary fibrosis and/or bone marrow failure, Dyskeratosis congenita AD/AR 33 45
SH2D1A Lymphoproliferative syndrome XL 15 126
SMARCAL1 Schimke immunoosseous dysplasia AR 17 88
SP110 Hepatic venoocclusive disease with immunodeficiency AR 7 7
SPINK5 Netherton syndrome AR 23 83
STAT1 Immunodeficiency AD/AR 34 117
STAT2 Immunodeficiency AR 2 6
STAT3 Hyper-IgE recurrent infection syndrome, Autoimmune disease, multisystem, infantile onset AD 44 147
STAT5B* Growth hormone insensitivity with immunodeficiency AR 8 10
STIM1 Stormorken syndrome, Immunodeficiency, Myopathy, tubular aggregate 1 AD/AR 12 22
STK4 T-cell immunodeficiency syndrome, recurrent infections, autoimmunity, AR 3 7
TAP1 Bare lymphocyte syndrome AR 1 7
TAP2 Bare lymphocyte syndrome AR 2 8
TAPBP Bare lymphocyte syndrome AR 1 2
TBX1 Conotruncal anomaly face syndrome AD 15 65
TFRC Immunodeficiency 46 AR 8 1
TNFRSF4 Immunodeficiency AR 1 1
TYK2 Immunodeficiency AR 8 8
UNC119 Immunodeficiency, Cone-rod dystrophy 2 AR 1 5
WAS Neutropenia, severe congenital, Thrombocytopenia, Wiskott-Aldrich syndrome XL 53 435
ZAP70 Selective T-cell defect AR 14 26

* Some, or all, of the gene is duplicated in the genome. Read more.

# The gene has suboptimal coverage (means <90% of the gene’s target nucleotides are covered at >20x with mapping quality score (MQ>20) reads).

The sensitivity to detect variants may be limited in genes marked with an asterisk (*) or number sign (#)

Gene refers to the HGNC approved gene symbol; Inheritance refers to inheritance patterns such as autosomal dominant (AD), autosomal recessive (AR), X-linked (XL), X-linked dominant (XLD) and X-linked recessive (XLR); ClinVar refers to the number of variants in the gene classified as pathogenic or likely pathogenic in this database (ClinVar); HGMD refers to the number of variants with possible disease association in the gene listed in Human Gene Mutation Database (HGMD). The list of associated, gene specific phenotypes are generated from CGD or Orphanet databases.

Non-coding variants covered by the panel

Gene Genomic location HG19 HGVS RefSeq RS-number
ADA Chr20:43248503 c.1079-15T>A NM_000022.2 rs387906268
ADA Chr20:43249076 c.976-34G>A NM_000022.2
ATM Chr11:108093770 c.-174A>G NM_000051.3
ATM Chr11:108098321 c.-30-1G>T NM_000051.3 rs869312754
ATM Chr11:108094508 c.-31+595G>A NM_000051.3
ATM Chr11:108121024 c.1236-404C>T NM_000051.3
ATM Chr11:108138753 c.2639-384A>G NM_000051.3
ATM Chr11:108141209 c.2839-579_2839-576delAAGT NM_000051.3
ATM Chr11:108151710 c.3403-12T>A NM_000051.3 rs201370733
ATM Chr11:108158168 c.3994-159A>G NM_000051.3 rs864622543
ATM Chr11:108179837 c.5763-1050A>G NM_000051.3 rs774925473
CD40LG ChrX:135736517 c.289-15T>A NM_000074.2
CD40LG ChrX:135737600 c.347-915A>T NM_000074.2
DCLRE1C Chr10:14966845 c.973-1777G>C NM_001033855.1
DNMT3B Chr20:31395557 c.2421-11G>A NM_006892.3 rs547940069
DOCK8 Chr9:368196 c.1797+61A>C NM_203447.3 rs786205596
DOCK8 Chr9:271626 c.54-1G>T NM_203447.3 rs192864327
DOCK8 Chr9:317028 c.742-15T>G NM_203447.3 rs111627162
DOCK8 Chr9:317025 c.742-18C>G NM_203447.3 rs112373444
IL2RG ChrX:70327278 c.*308A>G NM_000206.2
IL2RG ChrX:70331494 c.-105C>T NM_000206.2
IL2RG ChrX:70330553 c.270-15A>G NM_000206.2
IL7R Chr5:35867853 c.379+288G>A NM_002185.3
ITGB2 Chr21:46321660 c.500-12T>G NM_000211.3
ITGB2 Chr21:46320404 c.742-14C>A NM_000211.3 rs183204825
JAK3 Chr19:17946035 c.1915-11G>A NM_000215.3
JAK3 Chr19:17943239 c.2680+89G>A NM_000215.3
PARN Chr16:14724045 c.-165+2C>T NM_001134477.2
PNP Chr14:20942914 c.286-18G>A NM_000270.3
PRKDC Chr8:48844056 c.1777-710dupA NM_006904.6 rs760771518
RAG2 Chr11:36619652 c.-28G>C NM_000536.3
RMRP Chr9:35657745 NR_003051.3 rs377349293
RMRP Chr9:35657746 NR_003051.3 rs551655682
SPINK5 Chr5:147484503 c.1431-12G>A NM_006846.3 rs368134354
SPINK5 Chr5:147491511 c.1820+53G>A NM_006846.3 rs754599628
SPINK5 Chr5:147465956 c.283-12T>A NM_006846.3
TBX1 Chr22:19743735 c.-620A>C NM_080647.1 rs536892777
TBX1 Chr22:19743578 c.-777C>T NM_080647.1
ZAP70 Chr2:98354447 c.1624-11G>A NM_001079.3 rs730880318
ZAP70 Chr2:98349927 c.838-80G>A NM_001079.3 rs113994173

Added and removed genes from the panel

Genes added Genes removed
BCL11B
EPG5
FOXN1
IKBKB
IRF8
LAT
MAP3K14
MSN
NSMCE3
PARN
PGM3
POLE
POLE2
TFRC
IKBKG
STAT4
TRAC

Test strength

The strengths of this test include:
  • CAP and ISO-15189 accreditations covering all operations at Blueprint Genetics including all Whole Exome Sequencing, NGS panels and confirmatory testing
  • CLIA-certified personnel performing clinical testing in a CLIA-certified laboratory
  • Powerful sequencing technologies, advanced target enrichment methods and precision bioinformatics pipelines ensure superior analytical performance
  • Careful construction of clinically effective and scientifically justified gene panels
  • Our Nucleus online portal providing transparent and easy access to quality and performance data at the patient level
  • Our publically available analytic validation demonstrating complete details of test performance
  • ~1,500 non-coding disease causing variants in Blueprint WES assay (please see below ‘Non-coding disease causing variants covered by this panel’)
  • Our rigorous variant classification based on modified ACMG variant classification scheme
  • Our systematic clinical interpretation workflow using proprietary software enabling accurate and traceable processing of NGS data
  • Our comprehensive clinical statements

Test limitations

The following exons are not included in the panel as they are not sufficiently covered with high quality sequence reads: CORO1A (11), PMS2 (15). Genes with partial, or whole gene, segmental duplications in the human genome are marked with an asterisk (*) if they overlap with the UCSC pseudogene regions. The technology may have limited sensitivity to detect variants in genes marked with these symbols (please see the Panel content table above).

This test does not detect the following:
  • Complex inversions
  • Gene conversions
  • Balanced translocations
  • Mitochondrial DNA variants
  • Repeat expansion disorders unless specifically mentioned
  • Non-coding variants deeper than ±20 base pairs from exon-intron boundary unless otherwise indicated (please see above Panel Content / non-coding variants covered by the panel).

This test may not reliably detect the following:

  • Low level mosaicism
  • Stretches of mononucleotide repeats
  • Indels larger than 50bp
  • Single exon deletions or duplications
  • Variants within pseudogene regions/duplicated segments

The sensitivity of this test may be reduced if DNA is extracted by a laboratory other than Blueprint Genetics.

For additional information, please refer to the Test performance section and see our Analytic Validation.

The Blueprint Genetics severe combined immunodeficiency panel covers classical genes associated with Wiskott-Aldrich syndrome, combined immunodeficiencies, Omenn syndrome, CD40 ligand deficiency, DOCK8 deficiency, complement receptor 3 deficiency, purine nucleoside phosphorylase PNP deficiency, STAT deficiencies and Job's syndrome. The genes on the panel have been carefully selected based on scientific literature, mutation databases and our experience.

Our panels are sliced from our high-quality whole exome sequencing data. Please see our sequencing and detection performance table for different types of alterations at the whole exome level (Table).

Assays have been validated for different starting materials including EDTA-blood, isolated DNA (no FFPE), saliva and dry blood spots (filter card) and all provide high-quality results. The diagnostic yield varies substantially depending on the assay used, referring healthcare professional, hospital and country. Blueprint Genetics' Plus Analysis (Seq+Del/Dup) maximizes the chance to find a molecular genetic diagnosis for your patient although Sequence Analysis or Del/Dup Analysis may be a cost-effective first line test if your patient's phenotype is suggestive of a specific mutation type.

Performance of Blueprint Genetics Whole Exome Sequencing (WES) assay. All individual panels are sliced from WES data.

Sensitivity % (TP/(TP+FN) Specificity %
Single nucleotide variants 99.65% (412,456/413,893) >99.99%
Insertions, deletions and indels by sequence analysis
1-10 bps 96.94% (17,070/17,608) >99.99%
11-50 bps 99.07% (957/966) >99.99%
Copy number variants (exon level dels/dups)
Clinical samples (small CNVs, n=52)
1 exon level deletion 92.3% (24/26) NA
2 exons level deletion/duplication 100.0% (11/11) NA
3-7 exons level deletion/duplication 93.3% (14/15) NA
Microdeletion/-duplication sdrs (large CNVs, n=37))
Size range (0.1-47 Mb) 100% (37/37)
Simulated CNV detection
2 exons level deletion/duplication 90.98% (7,357/8,086) 99.96%
5 exons level deletion/duplication 98.63% (7,975/8,086) 99.98%
     
The performance presented above reached by WES with the following coverage metrics
     
Mean sequencing depth at exome level 174x
Nucleotides with >20x sequencing coverage (%) 99.4%

Bioinformatics

The target region for each gene includes coding exons and ±20 base pairs from the exon-intron boundary. In addition, the panel includes non-coding variants if listed above (Non-coding variants covered by the panel). Some regions of the gene(s) may be removed from the panel if specifically mentioned in the ‘Test limitations” section above. The sequencing data generated in our laboratory is analyzed with our proprietary data analysis and annotation pipeline, integrating state-of-the art algorithms and industry-standard software solutions. Incorporation of rigorous quality control steps throughout the workflow of the pipeline ensures the consistency, validity and accuracy of results. Our pipeline is streamlined to maximize sensitivity without sacrificing specificity. We have incorporated a number of reference population databases and mutation databases such as, but not limited, to 1000 Genomes Project, gnomAD, ClinVar and HGMD into our clinical interpretation software to make the process effective and efficient. For missense variants, in silico variant prediction tools such as SIFT, PolyPhen, MutationTaster are used to assist with variant classification. Through our online ordering and statement reporting system, Nucleus, the customer has an access to details of the analysis, including patient specific sequencing metrics, a gene level coverage plot and a list of regions with inadequate coverage if present. This reflects our mission to build fully transparent diagnostics where customers have easy access to crucial details of the analysis process.

Clinical interpretation

We provide customers with the most comprehensive clinical report available on the market. Clinical interpretation requires a fundamental understanding of clinical genetics and genetic principles. At Blueprint Genetics, our PhD molecular geneticists, medical geneticists and clinical consultants prepare the clinical statement together by evaluating the identified variants in the context of the phenotypic information provided in the requisition form. Our goal is to provide clinically meaningful statements that are understandable for all medical professionals regardless of whether they have formal training in genetics.

Variant classification is the corner stone of clinical interpretation and resulting patient management decisions. Our classifications follow the Blueprint Genetics Variant Classification Schemes based on the ACMG guideline 2015. Minor modifications were made to increase reproducibility of the variant classification and improve the clinical validity of the report. Our experience with tens of thousands of clinical cases analyzed at our laboratory allowed us to further develop the industry standard.

The final step in the analysis of sequence variants is confirmation of variants classified as pathogenic or likely pathogenic using bi-directional Sanger sequencing. Variant(s) fulfilling all of the following criteria are not Sanger confirmed: 1) the variant quality score is above the internal threshold for a true positive call, 2) an unambiguous IGV in-line with the variant call and 3) previous Sanger confirmation of the same variant at least three times at Blueprint Genetics. Reported variants of uncertain significance are confirmed with bi-directional Sanger sequencing only if the quality score is below our internally defined quality score for true positive call. Reported copy number variations with a size <10 exons are confirmed by orthogonal methods such as qPCR if the specific CNV has been seen less than three times at Blueprint Genetics.

Our clinical statement includes tables for sequencing and copy number variants that include basic variant information (genomic coordinates, HGVS nomenclature, zygosity, allele frequencies, in silico predictions, OMIM phenotypes and classification of the variant). In addition, the statement includes detailed descriptions of the variant, gene and phenotype(s) including the role of the specific gene in human disease, the mutation profile, information about the gene’s variation in population cohorts and detailed information about related phenotypes. We also provide links to the references used, congress abstracts and mutation databases to help our customers further evaluate the reported findings if desired. The conclusion summarizes all of the existing information and provides our rationale for the classification of the variant.

Identification of pathogenic or likely pathogenic variants in dominant disorders or their combinations in different alleles in recessive disorders are considered molecular confirmation of the clinical diagnosis. In these cases, family member testing can be used for risk stratification within the family. In the case of variants of uncertain significance (VUS), we do not recommend family member risk stratification based on the VUS result. Furthermore, in the case of VUS, we do not recommend the use of genetic information in patient management or genetic counseling. For eligible cases, Blueprint Genetics offers a no charge service to investigate the role of reported VUS (VUS Clarification Service).

Our interpretation team analyzes millions of variants from thousands of individuals with rare diseases. Thus, our database, and our understanding of variants and related phenotypes, is growing by leaps and bounds. Our laboratory is therefore well positioned to re-classify previously reported variants as new information becomes available. If a variant previously reported by Blueprint Genetics is re-classified, our laboratory will issue a follow-up statement to the original ordering health care provider at no additional cost.