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  • Test code: 08130
  • Turnaround time:
    10–21 calendar days (14 days on average)
  • Preferred specimen:
    3mL whole blood in a purple-top EDTA tube (K2EDTA or K3EDTA)
  • Alternate specimens:
    Saliva, assisted saliva, buccal swab and gDNA
  • Sample requirements
  • Request a sample kit
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Invitae Comprehensive Severe Combined Immunodeficiency (SCID) and Combined Immunodeficiency (CID) Panel

Test description

The Invitae Comprehensive Severe Combined Immunodeficiency (SCID) and Combined Immunodeficiency (CID) Panel analyzes genes that are associated with SCID and CID. These conditions are characterized by the dysfunction of T-lymphocytes and B-lymphocytes, and in some sub-types, natural killer cells. Children with SCID often present with severe, recurrent, and often life-threatening infections. Combined immunodeficiency syndrome (CID) is generally less severe than SCID.

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Primary panel (127 genes)

ACD ADA AK2 ARPC1B ATM B2M BCL10 BCL11B BLM CARD11 CARMIL2 CCBE1 CD247 CD27 CD3D CD3E CD3G CD40 CD40LG CD8A CDCA7 CHD7 CIITA CORO1A CTC1 CTPS1 CXCR4 DCLRE1C DKC1 DNMT3B DOCK2 DOCK8 EPG5 ERBIN ERCC6L2 EXTL3 FAT4 FCHO1 FOXI3 FOXN1 HELLS ICOS ICOSLG IKBKB IL21 IL21R IL2RG IL6R IL6ST IL7R ITK JAK3 KDM6A KMT2D LAT LCK LIG1 LIG4 LRBA MAGT1 MALT1 MAP3K14 MCM4 MSN MTHFD1 MYSM1 NBN NFE2L2 NFKBIA NHEJ1 NHP2 NOP10 NSMCE3 ORAI1 PARN PAX1 PGM3 PNP POLD1 POLE POLE2 PRKDC PTPRC RAC2 RAG1 RAG2 RELA RELB RFX5 RFXANK RFXAP RHOH RMRP RNF168 RNF31 RNU4ATAC RTEL1 SEMA3E SH2D1A SKIV2L SLC46A1 SMARCAL1 SP110 SPINK5 STAT3 STAT5B STIM1 STK4 STN1 TAP1 TAP2 TAPBP TBX1 TCN2 TERC TERT TFRC TINF2 TNFRSF4 TP63 TTC37 TTC7A WAS WIPF1 ZAP70 ZBTB24 ZNF341

Add-on Combined Immunodeficiency (CID) with Syndromic Features Genes (36 genes)

Combined immunodeficiencies (CID) with syndromic features have significant overlap of immunological findings compared to patients with non-syndromic CID. Especially at very early ages, some syndromic features may be difficult to identify or have not yet manifested. Given the significant overlap between syndromic and non-syndromic CID and the difficulty in differentiating between the syndromic and non-syndromic forms early in life, analyzing the genes associated with syndromic CID may be appropriate. These genes can be included at no additional charge.

ACD ATM CHD7 CTC1 DCLRE1B DKC1 DNMT3B EPG5 FOXN1 NBN NFKBIA NHP2 NOP10 ORAI1 PARN PGM3 PMS2 POLE RMRP RTEL1 SEMA3E SMARCAL1 SP110 SPINK5 STAT3 STAT5B STIM1 TBX1 TCN2 TERC TERT TINF2 TTC7A WAS WIPF1 ZBTB24

Alternative tests to consider

  • severe combined immunodeficiency
  • combined immunodeficiency
  • combined immunodeficiency with syndromic features
  • major histocompatibility complex class I and II deficiencies

To view the complete clinical description of this panel, click here.

Conditions on this panel can occur in several inheritance patterns, including autosomal dominant, autosomal recessive, and X-linked.

Assay and technical information

Invitae is a College of American Pathologists (CAP)-accredited and Clinical Laboratory Improvement Amendments (CLIA)-certified clinical diagnostic laboratory performing full-gene sequencing and deletion/duplication analysis using next-generation sequencing technology (NGS).

Our sequence analysis covers clinically important regions of each gene, including coding exons and 10 to 20 base pairs of adjacent intronic sequence on either side of the coding exons in the transcript listed below, depending on the specific gene or test. In addition, the analysis covers select non-coding variants. Any variants that fall outside these regions are not analyzed. Any limitations in the analysis of these genes will be listed on the report. Contact client services with any questions.

Based on validation study results, this assay achieves >99% analytical sensitivity and specificity for single nucleotide variants, insertions and deletions <15bp in length, and exon-level deletions and duplications. Invitae's methods also detect insertions and deletions larger than 15bp but smaller than a full exon but sensitivity for these may be marginally reduced. Invitae’s deletion/duplication analysis determines copy number at a single exon resolution at virtually all targeted exons. However, in rare situations, single-exon copy number events may not be analyzed due to inherent sequence properties or isolated reduction in data quality. Certain types of variants, such as structural rearrangements (e.g. inversions, gene conversion events, translocations, etc.) or variants embedded in sequence with complex architecture (e.g. short tandem repeats or segmental duplications), may not be detected. Additionally, it may not be possible to fully resolve certain details about variants, such as mosaicism, phasing, or mapping ambiguity. Unless explicitly guaranteed, sequence changes in the promoter, non-coding exons, and other non-coding regions are not covered by this assay. Please consult the test definition on our website for details regarding regions or types of variants that are covered or excluded for this test. This report reflects the analysis of an extracted genomic DNA sample. In very rare cases, (circulating hematolymphoid neoplasm, bone marrow transplant, recent blood transfusion) the analyzed DNA may not represent the patient's constitutional genome.

Gene Transcript reference Sequencing analysis Deletion/Duplication analysis
ACD NM_001082486.1
ADA NM_000022.2
AK2 NM_001625.3
ARPC1B NM_005720.3
ATM* NM_000051.3
B2M NM_004048.2
BCL10 NM_003921.4
BCL11B NM_138576.3
BLM NM_000057.3
CARD11 NM_032415.5
CARMIL2 NM_001013838.1
CCBE1 NM_133459.3
CD247 NM_198053.2
CD27 NM_001242.4
CD3D NM_000732.4
CD3E NM_000733.3
CD3G NM_000073.2
CD40 NM_001250.5
CD40LG NM_000074.2
CD8A NM_001768.6
CDCA7 NM_031942.4
CHD7 NM_017780.3
CIITA NM_000246.3
CORO1A* NM_007074.3
CTC1 NM_025099.5
CTPS1 NM_001905.3
CXCR4 NM_003467.2
DCLRE1B NM_022836.3
DCLRE1C NM_001033855.2
DKC1 NM_001363.4
DNMT3B NM_006892.3
DOCK2 NM_004946.2
DOCK8 NM_203447.3
EPG5 NM_020964.2
ERBIN NM_001253697.1
ERCC6L2 NM_020207.4
EXTL3 NM_001440.3
FAT4 NM_024582.4
FCHO1 NM_001161357.1
FOXI3 NM_001135649.2
FOXN1 NM_003593.2
HELLS NM_018063.4
ICOS NM_012092.3
ICOSLG NM_015259.5
IKBKB NM_001556.2
IL21 NM_021803.3
IL21R NM_021798.3
IL2RG NM_000206.2
IL6R NM_000565.3
IL6ST NM_002184.3
IL7R NM_002185.3
ITK NM_005546.3
JAK3 NM_000215.3
KDM6A NM_021140.3
KMT2D NM_003482.3
LAT NM_001014987.1
LCK NM_001042771.2
LIG1 NM_000234.2
LIG4 NM_002312.3
LRBA NM_006726.4
MAGT1 NM_032121.5
MALT1 NM_006785.3
MAP3K14 NM_003954.4
MCM4 NM_005914.3
MSN NM_002444.2
MTHFD1 NM_005956.3
MYSM1 NM_001085487.2
NBN NM_002485.4
NFE2L2 NM_006164.4
NFKBIA NM_020529.2
NHEJ1 NM_024782.2
NHP2 NM_017838.3
NOP10 NM_018648.3
NSMCE3 NM_138704.3
ORAI1 NM_032790.3
PARN NM_002582.3
PAX1 NM_006192.4
PGM3 NM_001199917.1
PMS2* NM_000535.5
PNP NM_000270.3
POLD1* NM_002691.3
POLE NM_006231.3
POLE2 NM_002692.3
PRKDC NM_006904.6
PTPRC* NM_002838.4
RAC2 NM_002872.4
RAG1 NM_000448.2
RAG2 NM_000536.3
RELA NM_021975.3
RELB NM_006509.3
RFX5 NM_000449.3
RFXANK NM_003721.3
RFXAP NM_000538.3
RHOH NM_004310.4
RMRP NR_003051.3
RNF168 NM_152617.3
RNF31 NM_017999.4
RNU4ATAC NR_023343.1
RTEL1 NM_001283009.1
SEMA3E NM_012431.2
SH2D1A NM_002351.4
SKIV2L NM_006929.4
SLC46A1 NM_080669.5
SMARCAL1 NM_014140.3
SP110 NM_004509.3
SPINK5 NM_006846.3
STAT3 NM_139276.2
STAT5B* NM_012448.3
STIM1 NM_003156.3
STK4 NM_006282.3
STN1 NM_024928.4
TAP1 NM_000593.5
TAP2 NM_000544.3
TAPBP NM_003190.4
TBX1 NM_080647.1
TCN2 NM_000355.3
TERC NR_001566.1
TERT NM_198253.2
TFRC NM_003234.3
TINF2 NM_001099274.1
TNFRSF4 NM_003327.3
TP63 NM_003722.4
TTC37 NM_014639.3
TTC7A NM_020458.3
WAS NM_000377.2
WIPF1 NM_001077269.1
ZAP70 NM_001079.3
ZBTB24 NM_014797.2
ZNF341 NM_032819.4

ATM: Sequencing analysis for exons 6, 24, 43 includes only cds +/- 10 bp.
CORO1A: Deletion/duplication and sequencing analysis is not offered for exon 11.
PMS2: Sequencing analysis for exons 7 includes only cds +/- 10 bp.
POLD1: Sequencing analysis for exons 22 includes only cds +/- 10 bp.
PTPRC: Sequencing analysis is not offered for exons 3, 15.
STAT5B: Deletion/duplication and sequencing analysis is not offered for exons 6-8.