CardiopulmonaryCheck+

_Methodology

The Cardiopulmonary Panel is designed to detect single nucleotide variants (SNVs) and small insertions and deletions in 63genes associated with neurological 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}

ACTA2, ACTC1, AGL, APOB, APOE, BMPR2, CACNB2, CAV3, CFTR, COL3A1, DES,DSC2, DSG2, DSP, ENG, F9, FBN1, FHL1, FKRP, FKTN, KCNH2, KCNQ1, LDLR, MECP2,MYBPC3, MYH11, MYH6, MYH7, MYLK, NF1, PCSK9, PHOX2B, PKP2, PLN, PRKAG2, PTPN11,RAF1, RET, RYR1, RYR2, SCN4A, SCNN1A, SCNN1B, SERPINA1, SGCD, SLC22A5, SMAD3,SMAD4, SOS1, STAT3, TAZ, TGFBR1, TGFBR2, TINF2, TMEM43, TNNC1, TNNT2, TPM1,TSC1, TSC2, TTN, TTR, ZEB2

_{Test Limitations}

This test aims to detect all clinically relevant variants within the coding regions of the genes evaluated. Pathogenic and likely pathogenic variants detected in these genes should be confirmed by orthogonal methods. Detected genetic variants classified as benign, likely benign, or of uncertain significance are not included in this report. Homopolymer regions and regions outside of the coding regions cannot be captured by the standard NGS target enrichment protocols. At this time, the assay does not detect large deletions 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 mosaicism and is not designed to detect complex gene rearrangements or genomic aneuploidy events. It is important to understand that there may be variants in these genes undetectable using current technology. Additionally, there may be genes associated with specified disease pathology whose clinical association has not yet been definitively established. The test may therefore not detect all variants associated with specified disease pathology. The interpretation of variants is based on our current understanding of the genes in 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 care providers should be aware that future reclassifications of genetic variants can occur as ACMG guidelines are updated.  Factors influencing the quantity and quality of extracted DNA include, but are not limited to, collection technique, the amount of buccal epithelial cells obtained, the patient’s oral hygiene, and the presence of dietary or microbial sources of nucleic acids and nucleases, as well other interfering substances and matrix-dependent influences. PCR inhibitors, extraneous DNA, and nucleic acid degrading enzymes 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. Vankeerberghen A,Wei L, Jaspers M, Cassiman JJ, et al. Human molecular genetics. 1998, Oct.Characterization of 19 disease-associated missense mutations in the regulatory domain of the cystic fibrosis transmembrane conductance regulator. (PMID: 9736778)

2.Billet A, Melin P,Jollivet M, Mornon JP, et al. The Journal of Biological Chemistry. 2010, Jul16. C terminus of nucleotide binding domain 1 contains critical features for cystic fibrosis transmembrane conductance regulator trafficking and activation. (PMID: 20435887)

3. Marion H, NatachaG, Brigitte M, François C, et al. Journal of cystic fibrosis: official journal of the European Cystic Fibrosis Society. 2015, May. The p.Gly622Asp (G622D)mutation, frequently found in Reunion Island and in black populations, is associated with a wide spectrum of CF and CFTR-RD phenotypes. (PMID: 25443471)

4. Raraigh KS, HanST, Davis E, Evans TA, et al. American journal of human genetics. 2018, Jun 07.Functional Assays Are Essential for Interpretation of Missense Variants Associated with Variable Expressivity. (PMID: 29805046)

^{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 exon in each of these genes.}

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