Method Description

Capture-based or amplicon-based next-generation sequencing (NGS) is performed to test for the presence of variants in coding regions and intron/exon boundaries of the genes analyzed, as well as some other regions that have known disease-causing variants. The human genome reference GRCh37/hg19 build was used for sequence read alignment. At least 99% of the bases are covered at a read depth over 30X. Sensitivity is estimated at above 99% for single nucleotide variants, above 94% for deletions-insertions (delins) less than 40 base pairs (bp), above 95% for deletions up to 75 bp and insertions up to 47 bp. NGS and/or multiplex ligation-dependent probe amplification is performed to test for the presence of deletions and duplications in the genes analyzed. Digital droplet polymerase chain reaction is performed to test for 3 mitochondrial variants.

There may be regions of genes that cannot be effectively evaluated by sequencing or deletion and duplication analysis as a result of technical limitations of the assay, including regions of homology, high guanine-cytosine (GC) content, and repetitive sequences.(Unpublished Mayo method)

See Targeted Genes and Methodology Details for AudioloGene Hearing Loss Panel the for details regarding the targeted genes analyzed for each test and specific gene regions not routinely covered.

Reference transcript numbers may be updated due to transcript re-versioning. Always refer to the final patient report for gene transcript information referenced at the time of testing. Confirmation of select reportable variants may be performed by alternate methodologies based on internal laboratory criteria.

Genes analyzed: ABHD12, ACTG1, ADCY1, ADGRV1 (GPR98), AIFM1, ALMS1, ARSG, ATP2B2, ATP6V1B1, ATP6V1B2, BCS1L, BSND, BTD, CABP2, CACNA1D, CATSPER2, CCDC50, CD164, CDC14A, CDH23, CEACAM16, CEP250, CEP78, CHD7, CIB2, CISD2, CLDN14, CLIC5, CLPP, CLRN1, COCH, COL11A1, COL11A2, COL2A1, COL4A3, COL4A4, COL4A5, COL4A6, COL9A1, COL9A2, COL9A3, CRYL1, CRYM, DCDC2, DIABLO, DIAPH1, DIAPH3, DMXL2, DNMT1, DSPP, EDN3, EDNRB, ELMOD3, EPS8, EPS8L2, ESPN, ESRRB, EYA1, EYA4, FDXR, FGF3, FGFR2, FGFR3, FITM2, FLNA, FOXC1, FOXI1, GATA3, GIPC3, GJB2 (DFNB1), GJB6, GPSM2, GREB1L, GRHL2, GRXCR1, GRXCR2, GSDME, HARS2, HGF, HOMER2, HOXA2, HSD17B4, ILDR1, KARS1, KCNE1, KCNJ10, KCNQ1, KCNQ4, KITLG, LARS2, LHFPL5, LMX1A, LOXHD1, LRP2, LRTOMT, MAN2B1, MANBA, MARVELD2, MCM2, MET, MIR96, MITF, MPZL2, MSRB3, MT-RNR1, MT-TS1, MYH14, MYH9, MYO15A, MYO3A, MYO6, MYO7A, NARS2, NDRG1, NF2, NLRP3, OPA1, OSBPL2, OTOA, OTOF, OTOG, OTOGL, P2RX2, PAX3, PCDH15, PDZD7, PEX1, PEX10, PEX11B, PEX12, PEX13, PEX14, PEX16, PEX19, PEX2, PEX26, PEX3, PEX5, PEX6, PEX7, PHYH, PJVK, PLS1, PNPT1, POLR1B, POLR1C, POLR1D, POU3F4, POU4F3, PRPS1, PTPN11, PTPRQ, RAI1, RDX, RIPOR2, RMND1, S1PR2, SALL1, SERAC1, SERPINB6, SIX1, SLC12A2, SLC17A8, SLC19A2, SLC22A4, SLC26A4, SLC26A5, SLC29A3, SLC4A11, SLC52A2, SLC52A3, SLITRK6, SMPX, SNAI2, SOX10, SPATA5, STRC, SUCLA2, SYNE4, TBC1D24, TCOF1, TECTA, TFAP2A, TIMM8A, TJP2, TMC1, TMEM132E, TMIE, TMPRSS3, TNC, TPRN, TRIOBP, TUBB4B, TWNK, USH1C, USH1G, USH2A, WBP2, WFS1, and WHRN