Primary Immunodeficiency Region of Interest - Trio or Proband Only

Test Background

The Primary Immunodeficiency Region of Interest Analysis is designed to facilitate genetic diagnosis of patients with Primary Immunodeficiency. Such patients may have a condition that would benefit from immediate treatment and customized clinical management.

Developed in collaboration with experts in the field, this Region of Interest (ROI) study evaluates 283 immune-related genes. The Primary Immunodeficiency Region of Interest Report includes orthogonally-confirmed sequence variants identified by Next Generation Sequencing and the results of the companion deletion/duplication analysis, if ordered. This study can be ordered for the proband alone by submitting a sample from the affected individual or as a trio with parental samples included in the analysis.

In the case of a non-diagnostic finding, ordering providers have the option to go beyond the Region of Interest Analysis by ordering an expansion to the Claritas Clinical Exome (Test Code: N0527). A new sample will not need to be submitted. Interpretation will be provided in a new report that will be available in 12-14 weeks.

Clinical Phenotypes Evaluated

  • Defects in Innate Immunity with Invasive Bacterial Infections
  • Mendelian Susceptibility to Mycobacterial Diseases
  • Predisposition to Severe Viral Infections
  • EBV Disease
  • Candidiasis
  • Combined Immunodeficiency
  • B Cell Defects and Antibody Deficiencies
  • Hyper-IgE
  • Autoimmune Lymphoproliferative Disease
  • Immune Dysregulation Disease
  • Early-Onset Colitis
  • Hemophagocytic Lymphohistiocytosis
  • Defects in Major Histocompatibility Complexes

Test Characteristics

  • Assesses 283 genes related to Primary Immunodeficiency. This gene list is updated based on input from Claritas scientists and partners.
  • Orthogonally-confirmed variants demonstrate high specificity (PPV~99.998%)
  • Orthogonal approach using Illumina NextSeq™ with simultaneous confirmation of 95% of variants on the ThermoFisher Ion Proton™
  • Remaining phenotypically-relevant variants are Sanger sequenced so that all reported variants are confirmed
  • Mean coverage of >100x for both the Illumina NextSeq™ and LIFE Ion Proton™
  • Protein coding sequences and 10 bp of adjacent intronic sequences are analyzed
  • This assay detects SNVs, insertions, and deletions less than 10 bp
  • Adding the companion deletion/duplication analysis (Test Code C0892) increases detection rate for copy number variants and larger indels. If not otherwise indicated, genes in this region of interest are partially or fully covered. Genes with no deletion/duplication coverage are indicated by an asterisk (see below).

Increase the Power of the Assay

  • Add companion deletion/duplication testing (Test Code C0892)
  • If no diagnostic findings are reported in the ROI, providers can order an expanded interpretation of the whole clinical exome (Test Code N0527)

Special Notes

  • If a patient has had a bone marrow transplant or recent blood transfusion, please note this on the requisition form and contact Client Services for the most updated specimen submission guidance.

Additional Service Highlights

  1. Providers may request a review of variant classification at any time.
  2. Providers may access the Interpretative Genomics Service at Boston Children’s Hospital, which provides consultation with experts in genes and/or phenotypes. Please contact MedicalDirector@claritasgenomics.com for more information.
  3. Claritas Genomics will release raw data file or provide access to exome data via NextCODE to authorized health care providers. Review Data Return Program details here.

Genes:

ACD, ACP5, ACTB*, ADA, ADAM17, ADAR, AICDA, AIRE, AK2, AP3B1, APOL1, ATM, B2M*, BCL10, BLM, BLNK, BLOC1S6, BTK, C1QA, C1QB, C1QC, C1R*, C1S, C2, C3, C4A*, C4B, C5, C6*, C7, C8A*, C8B, C8G*, C9*, CARD11, CARD14, CARD9, CASP10, CASP8, CCBE1, CD19, CD247, CD27*, CD3D, CD3E, CD3G, CD40, CD40LG, CD46, CD59*, CD79A, CD79B, CD81, CD8A*, CEBPE, CECR1, CFB, CFD*, CFH, CFHR1, CFHR2, CFHR3, CFHR4, CFHR5, CFI, CFP, CHD7, CIITA, CLPB, COLEC11, COPA*, CORO1A, CR2*, CSF2RA*, CSF3R, CTLA4*, CTPS1*, CTSC, CXCR4, CYBA*, CYBB, DCLRE1B*, DCLRE1C, DKC1, DNMT3B, DOCK2*, DOCK8, ELANE*, EPG5, FADD*, FAS, FASLG, FCAMR*, FCGR3A*, FCGR3B*, FCN3*, FERMT3, FOXN1, FOXP3, FPR1*, G6PC3, GATA2, GFI1*, HAX1, ICOS, IFIH1, IFNAR2*, IFNG, IFNGR1, IFNGR2, IGLL1, IKBKB, IKBKG*, IKZF1*, IL10, IL10RA, IL10RB, IL12A*, IL12B, IL12RB1, IL17A*, IL17F*, IL17RA*, IL17RC*, IL1RN, IL21*, IL21R, IL23R*, IL2RA, IL2RG, IL36RN, IL7R, INO80, IRAK4, IRF7*, IRF8, ISG15*, ITCH, ITGAM*, ITGB2, ITK, JAGN1*, JAK3, KRAS, LAMTOR2, LCK, LIG4, LPIN2, LRBA, LYST, MAGT1, MALT1*, MAP3K14*, MASP1, MASP2, MCM4, MEFV, MOGS, MRE11A, MS4A1, MSH6, MTHFD1, MVK, MYD88, NCF1*, NCF2, NCF4, NFAT5*, NFKB1, NFKB2*, NFKBIA, NFKBIB*, NHEJ1, NHP2*, NLRC4*, NLRP12, NLRP2*, NLRP3, NOD2, NOP10, NRAS*, ORAI1, PARN*, PGM1, PGM3, PIK3CD*, PIK3R1, PLCG2, PMS2, PNP, POLE, PRF1, PRKCD, PRKDC, PSMB8*, PSTPIP1, PTPRC, RAB27A*, RAC2*, RAG1, RAG2, RBCK1, RELB*, RFX5, RFXANK, RFXAP, RHOH*, RMRP*, RNASEH2A, RNASEH2B, RNASEH2C, RNF168, RNF31*, RNU4ATAC*, RORC*, RPSA, RTEL1, SAMHD1, SBDS, SEMA3E, SERPING1, SH2D1A, SH3BP2, SLC29A3, SLC35C1, SLC37A4, SLC46A1, SMARCAL1, SP110, SPINK5, STAT1, STAT2*, STAT3, STAT5B, STIM1, STK4, STX11, STXBP2, TAP1, TAP2, TAPBP, TAZ, TBK1*, TBX1, TCF3, TCN2, TERC*, TERT, TFRC, THBD, TICAM1*, TINF2, TLR3, TMC6, TMC8, TMEM173*, TNFAIP3*, TNFRSF13B, TNFRSF13C*, TNFRSF1A, TNFRSF1B*, TNFRSF4*, TNFSF12*, TPP2, TRAF3*, TRAF3IP2*, TREX1, TRNT1, TTC37, TTC7A, TYK2, UNC119, UNC13D, UNC93B1, UNG, USB1, VPS13B, VPS45, WAS, WIPF1, XIAP, ZAP70, ZBTB24

*Companion deletion/duplication analysis is not available for this gene

About Claritas

Claritas Genomics serves children affected with complex genetic disorders by providing timely and accurate results, resolving families’ long search for answers. By combining clinical expertise of the world’s best pediatric specialists with innovative platform solutions, Claritas is working to improve patient care and enable new discoveries. We are committed to the highest quality and accessibility of information and our interpretive services and unique approach to reporting set the standard for reliably and clearly communicating genetic information.

Now is the time to integrate genomics into clinical practice to inform, guide and improve medical treatment for kids around the world.