ImmunoCheck+

Learn about how genetic diagnostics can benefit individuals with hereditary immunodeficiencies.

Accurate genetic diagnosis of immunodeficiency, combined with a detailed disease phenotype, is crucial in characterizing these rare diseases. It also improves treatment and follow-up strategies for affected patients and their family members. Identifying family members at risk makes it possible to begin preventive treatments and make lifestyle recommendations. It also justifies routine follow-ups by healthcare professionals. A genetic diagnosis can also help in family planning.

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Test Methodology

The Comprehensive Immunology Panel is designed to detect single nucleotide variants (SNVs) and small insertions and deletions in 97 genes associated with immunological risk. Targeted regions for this panel include the coding exons and 10 bp intronic sequencesimmediate to the exon-intron boundary of each coding exon in each of these genes. Extracted patient DNA is prepared using targetedhybrid capture, assignment of a unique index, and sequencing via Illumina sequencing by synthesis (SBS) technology. Data is alignedusing human genome build GRCh37. Variant interpretation is performed according to current American College of Medical Geneticsand Genomics (ACMG) professional guidelines for the interpretation of germline sequence variants using Fabric EnterpriseTM Pipeline6.6.15. Variant interpretation and reporting is performed by Fabric Clinical (CLIA ID: 45D2281059 and CAP ID: 9619501). The followingquality filters are applied to all variants: quality <500, allelic balance <0.3, coverage <10x.

Genes Evaluated

ADA, AIRE, ARX, ATM, ATRX, BLM, BRCA1, BRCA2, BTK, C1QBP, CASP10, CD40, CD70, CDKL5, CEBPA, CFTR, CHD7, COPA, CR2, CTLA4,DNASE2, EPCAM, FAS, FASLG, FCHO1, FGD1, FMR1, FOXP3, G6PD, GP1BB, HUWE1, HYOU1, IL1RAPL1, IL23R, IL2RB, IL2RG, IL6R,IL6ST, IL7R, ITCH, JAK1, JAK2, JAK3, KDM5C, KRAS, L1CAM, LIG1, LIG4, LRBA, MAP3K14, MECP2, MED12, MID1, MKL1, MLH1, MSH2,MSH6, MTHFD1, NF1, NFKB1, NFKB2, NHEJ1, OCRL, PALB2, PMS2, POLE2, PRKCD, PTEN, PTPRC, RASGRP1, RELA, RIPK1, RLTPR,RPS6KA3, SLC16A2, SPPL2A, STAT3, TNFRSF13B, TP53, ATM, CYBA, CYBB, F13B, F5, F7, F9 ,FANCC, FGB, G6PC, MEFV, MPL, MYD88, NRAS   PLCG2, RUNX1, TERT, VPS13B

Test Limitations

This test aims to detect all clinically relevant variants within the coding regions of the genes evaluated. Pathogenic and likelypathogenic variants detected in these genes should be confirmed by orthogonal methods. Detected genetic variants classified asbenign, likely benign, or of uncertain significance are not included in this report. Homopolymer regions and regions outside of thecoding regions cannot be captured by the standard NGS target enrichment protocols. At this time, the assay does not detect largedeletions and duplications. This analysis also cannot detect pathogenic variants within regions which were not analyzed (e.g., introns,promoter and enhancer regions, long repeat regions, and mitochondrial sequence). This assay is not designed to detect mosaicismand is not designed to detect complex gene rearrangements or genomic aneuploidy events. It is important to understand that theremay be variants in these genes undetectable using current technology. Additionally, there may be genes associated withimmunological pathology whose clinical association has not yet been definitively established. The test may therefore not detect allvariants associated with immunological pathology. The interpretation of variants is based on our current understanding of the genesin this panel and is based on current ACMG professional guidelines for the interpretation of germline sequence variants.Interpretations may change over time as more information about the genes in this panel becomes available. Qualified health careproviders should be aware that future reclassifications of genetic variants can occur as ACMG guidelines are updated. Factorsinfluencing the quantity and quality of extracted DNA include, but are not limited to, collection technique, the amount of buccalepithelial cells obtained, the patient’s oral hygiene, and the presence of dietary or microbial sources of nucleic acids and nucleases, aswell as other interfering substances and matrix-dependent influences. PCR inhibitors, extraneous DNA, and nucleic acid degradingenzymes may adversely affect assay results.

Regulatory Disclosures

This laboratory developed test (LDT) was developed and its performance characteristics were determined by PreCheck HealthServices, Inc. This test was performed at PreCheck Health Services, Inc. (CLIA ID: 10D2210020 and CAP ID: 9101993) that is certifiedunder the Clinical Laboratory Improvement Amendments of 1988 (CLIA) as qualified to perform high complexity testing. This assayhas not been cleared or approved by the U.S. Food and Drug Administration (FDA). Clearance or approval by the FDA is not requiredfor the clinical use of this analytically and clinically validated laboratory developed test. This assay has been developed for clinicalpurposes and it should not be regarded as investigational or for research.

References

1.Town M, Bautista JM, Mason PJ, Luzzatto L. Human molecular genetics. 1992, Jun. Both mutations in G6PD A- are necessary toproduce the G6PD deficient phenotype. (PMID: 1303173)

2.Beutler E, Kuhl W, Vives-Corrons JL, Prchal JT. Blood. 1989, Nov 15. Molecular heterogeneity of glucose-6-phosphate dehydrogenaseA-. (PMID: 2572288)

3.Hirono A, Beutler E. Proceedings of the National Academy of Sciences of the United States of America. 1988, Jun. Molecular cloningand nucleotide sequence of cDNA for human glucose-6-phosphate dehydrogenase variant A(-). (PMID: 2836867)

4.Yoshida A, Stamatoyannopoulos G, Motulsky AG. Science (New York, N.Y.). 1967, Jan 06. Negro variant of glucose-6-phosphatedehydrogenase deficiency (A-) in man. (PMID: 6015571)

5.Gómez-Gallego F, Garrido-Pertierra A, Bautista JM. The Journal of biological chemistry. 2000, Mar 31. Structural defects underlyingprotein dysfunction in human glucose-6-phosphate dehydrogenase A(-) deficiency. (PMID: 10734064)

6.Hirono A, Kawate K, Honda A, Fujii H, et al. Blood. 2002, Feb 15. A single mutation 202G>A in the human glucose-6-phosphatedehydrogenase gene (G6PD) can cause acute hemolysis by itself. (PMID: 11852882)

7.Dallol A, Banni H, Gari MA, Al-Qahtani MH, et al. Journal of translational medicine. 2012, Sep 24. Five novel glucose-6-phosphatedehydrogenase deficiency haplotypes correlating with disease severity. (PMID: 23006493) Shahjahani M, Mortazavi Y, Heli B, Dehghanifard A. International journal of hematology-oncology and stem cell research. 2013.Prevalence of G6PD Deficiency in Iran. (PMID: 24505519)

8.Shah SS, Macharia A, Makale J, Uyoga S, et al. BMC medical genetics. 2014, Sep 09. Genetic determinants of glucose-6-phosphatedehydrogenase activity in Kenya. (PMID: 25201310)

^{All NGS panels have a turnaround time of 10-14 days for results.}

^{Each panel is designed to detect single nucleotide variants (SNVs) and small insertions and deletions with gene specific limitations.Targeted regions include the coding exons and 10 bp intronic sequences immediate to the exon-intron boundary of each coding exonin each of these genes.}