NeuroCheck+

Test Methodology

The Comprehensive Neurology 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

ACADM, APOE, BCKDHA, BCKDHB, COQ2, COX10, FANCC, FUS, GBA, GBE1 , GJB1, HBB, IKBKAP, MCOLN1, PLCG2, ARDBP, TBP, APP, ASPA, BCS1L, BLM,  BSCL2,     C10orf2, DGUOK,  DHCR7,  ERBB4, G6PC, GAA, GALT, HEXA, LRRK2, MPV17, PRNP, PSEN1, PSEN2, REEP1, SCO1, SCO2, SOD1, SPAST, SUCLA2, ARSA, ATM, ATXN2,    GRN, MFN2, MPZ, NPC1, OPA1, OPTN, PAH, PDSS2, POLG, POLG2, RRM2B, SETX, SLC9A6, SPG11, SPTLC1, SUCLG1, TAZ, TK2, TYMP, ANG, ARX, ATP7B, EHMT1, EZH2, FOXG1, GABRG2, GAMT, KDM5C, MED12, MTHFR, NLGN3, PIK3CA, PTEN, SLC2A1, SLC6A8, THAP1, ADNP, APTX, ATP1A2, CC2D1A, CHD2, COL4A3BP, CSTB, DPYD, EN2, FMR1, FOXP1, FXN, GCH1, L1CAM, MAPT, NDP, NDUFA1, NLGN4X, NTRK1, NTRK2, PINK1, PMP22, SCN1B, SLC16A2, SLC25A4, STXBP1, TCF4, TH, TOR1A, TPP1, TSC2, TTR, ALDH7A1, BCL11A, C12orf4, CACNA1A, CACNA1C, CDKL5, CNTN6, COL4A1, CSNK2A1, CTNND2, FBXO11, GATM, GRIN2A, KCNQ2, MBOAT7,  MECP2, NOTCH3, NSD1, PCDH19, PDHA1, PRRT2, SCN1A, SCN2A, SCN8A, SYNGAP1, TSC1, ZEB2, ASXL1, ATN1, EGR2, HSPB1, PDGFB, UBA1, FTSJ1, SGCE, CNOT3, GARS, PNKD,

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 with neurologicalpathology whose clinical association has not yet been definitively established. The test may therefore not detect all variantsassociated with neurological pathology. The interpretation of variants is based on our current understanding of the genes in this paneland is based on current ACMG professional guidelines for the interpretation of germline sequence variants. Interpretations maychange over time as more information about the genes in this panel becomes available. Qualified health care providers should beaware that future reclassifications of genetic variants can occur as ACMG guidelines are updated. Factors influencing the quantityand quality of extracted DNA include, but are not limited to, collection technique, the amount of buccal epithelial cells obtained, thepatient’s oral hygiene, and the presence of dietary or microbial sources of nucleic acids and nucleases, as well as other interferingsubstances and matrix-dependent influences. PCR inhibitors, extraneous DNA, and nucleic acid degrading enzymes may adverselyaffect 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.

^{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.}