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NeuromuscularZoom

Genes:
See test page

Myopathy

Genes: ACTA1, ADSS1, AGL, AGRN, ALG14, ALG2, AMPD1, ANO5, ASAH1, ATP2A1, B3GALNT2, B4GAT1, BAG3, BIN1, BVES, CACNA1S, CAPN1, CAPN3, CASQ1, CAV3, CAVIN1, CCDC78, CFL2, CHAT, CHKB, CHRNA1, CHRNB1, CHRND, CHRNE, CLCN1, CNTN1, COL12A1, COL13A1, COL6A1, COL6A2, COL6A3, COLQ, CPT2, CRPPA, CRYAB, DAG1, DCTN1, DES, DMD, DNAJB6, DNM2, DOK7, DPAGT1, DPM1, DPM2, DPM3, DYSF, EMD, FBXO38, FHL1, FKBP14, FKRP, FKTN, FLNC, GAA, GARS1, GBE1, GFPT1, GLE1, GMPPB, GNE, GYS1, HNRNPA1, HNRNPA2B1, HNRNPDL, ISCU, ITGA7, KBTBD13, KCNJ2, KLHL40, KLHL41, KY, LAMA2, LAMP2, LARGE1, LDB3, LIMS2, LMNA, LMOD3, LRP4, MATR3, MEGF10, MICU1, MTM1, MUSK, MYH2, MYH3, MYH7, MYO18B, MYOT, MYPN, NALCN, NEB, ORAI1, PAX7, PFKM, PLEC, PMM2, PNPLA2, POMGNT1, POMGNT2, POMK, POMT1, POMT2, PREPL, PYGM, PYROXD1, RAPSN, RXYLT1, RYR1, SCN4A, SELENON, SETX, SGCA, SGCB, SGCD, SGCE, SGCG, SIL1, SLC18A3, SLC52A2, SLC5A7, SNAP25, SPEG, SQSTM1, STAC3, STIM1, SYNE1, SYNE2, SYT2, TAZ, TCAP, TIA1, TMEM43, TNNI2, TNNT1, TNPO3, TOR1AIP1, TPM2, TPM3, TRAPPC11, TRIM32, TRIP4, TTN, UBA1, VCP, VMA21, VRK1

Charcot-Marie-Tooth disease

Genes: AARS1, AIFM1, ATL1, ATP7A, BICD2, BSCL2, DNAJB2, DNM2, DNMT1, DYNC1H1, EGR2, ELP1, FGD4, FIG4, GAN, GARS1, GDAP1, GJB1, GLA, GNB4, HARS1, HINT1, HSPB1, HSPB8, IGHMBP2, INF2, KIF1A, KIF5A, LITAF, LMNA, LRSAM1, MFN2, MME, MORC2, MPZ, MTMR2, NDRG1, NEFL, NGF, NTRK1, PHKA1, PLEKHG5, PMP22, PRDM12, PRPS1, PRX, RAB7A, REEP1, RETREG1, SBF1, SBF2, SCN11A, SCN9A, SEPTIN9, SH3TC2, SLC12A6, SLC52A2, SLC52A3, SPTLC1, SPTLC2, TFG, TRIM2, TRPV4, TTR, WNK1, YARS1

Hereditary spastic paraplegia

Genes: ABCD1, ALDH18A1, ALS2, AP4B1, AP4E1, AP4M1, AP4S1, AP5Z1, ATL1, ATP13A2, B4GALNT1, BSCL2, C12ORF65, CYP2U1, CYP7B1, DDHD1, DDHD2, ERLIN2, FA2H, GBA2, GJC2, HSPD1, KIF1A, KIF1C, KIF5A, L1CAM, NIPA1, NT5C2, PLP1, PNPLA6, REEP1, RTN2, SACS, SLC16A2, SLC33A1, SPART, SPAST, SPG11, SPG21, SPG7, TECPR2, TFG, VPS37A, WASHC5, ZFYVE26

Test Information

Test Method

DNA extraction (if applicable) and ultrasonic fragmentation; targeted capture of the coding regions and intron/exon boundaries of protein coding RefSeq genes using the Agilent Clinical Research Exome kit; next generation sequencing (NGS) on an Illumina HiSeq 2500 instrument; alignment to the human reference genome (GRCh37/hg19) using the Burrows-Wheeler Aligner (bwa); variant calling using GATK and detection of exonic deletions and duplications using ExomeDepth; Sanger sequencing to confirm low quality and/or complex indel variants related to the specified phenotype(s); Review of sequence and dosage data for the specified genes by multiple staff members; Variant classification following ACMG criteria (if applicable). Bioinformatic analysis was performed using DDL pipeline DDL.CRExome.v1.2019_07_15 and DDL.CRExome.Dosage.v1.2019_08_20.

Clinical Utility

Discrimination between multiple heritable disorders involving the neuromuscular system; identification of causative mutations in complex cases that span multiple phenotypes; facilitation of targeted carrier or presymptomatic testing of relatives of proband and/or predictive prenatal testing.

Clinical Sensitivity

The detection rate for the NeuromuscularZoom panel is undetermined at this point, due to ongoing research in the field.

Analytic Sensitivity

> 99% for single nucleotide and >92% for small insertion/deletion variants for the nucleotides evaluated. Lower limit of detection: Single nucleotide variants: 25% allele frequency (>96% sensitivity), Small insertion/deletion variants: 50% allele frequency (>94% sensitivity). This test is not validated to identify deletions/insertions of greater than 20bp, copy number changes, nucleotide repeat expansions, mitochondrial DNA variants or mosaicism. Disease-associated variants in regions that are not captured and/or sufficiently sequenced will not be detected by this assay.

Sample Requirements

3-6ml whole blood in EDTA (purple topped) tubes
Saliva collected in an appropriate collection device (Oragene®-DNA 500 or 600 device)
DNA extracted from fibroblast or lymphocyte cell line (must be extracted in a CLIA-certified laboratory)

Turn Around Time

6-8 weeks

Fee and CPT Codes

Exome Panel: $2915
CPT Code: 81479
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