Method Description

Next-generation sequencing (NGS) and/or Sanger sequencing are 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 to be over 99% for single nucleotide variants, over 94% for deletions-insertions (delins) less than 40 base pairs (bp), and over 95% for deletions up to 75 bp and insertions up to 47 bp. NGS and/or a polymerase chain reaction-based quantitative method is performed to test for the presence of deletions and duplications in the genes analyzed.

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. See Targeted Genes and Methodology Details for Nuclear Mitochondrial Gene Panel, Next-Generation Sequencing, Varies for details regarding the targeted genes analyzed for each test and specific gene regions not routinely covered.(Unpublished Mayo method)

Confirmation of select reportable variants may be performed by alternate methodologies based on internal laboratory criteria.

Genes analyzed: AARS2, ABAT, ABCB7, ACACA, ACAD9, ACO2, AFG3L2, AGK, AIFM1, ALDH3A2, APOPT1 (COA8), APTX, ATP5F1A, ATP5F1E, ATPAF2, AUH, BCS1L, BOLA3, C12orf65 (MTRFR), CA5A, CARS2, CHAT, CHCHD10, CLPP, COA5, COA6, COA8 (APOPT1), COASY, COQ2, COQ4, COQ6, COQ7, COQ8A, COQ8B, COQ9, COX10, COX14, COX15, COX20, COX4I1, COX4I2, COX6A1, COX6A2, COX6B1, COX7B, COX8A, CPT1C, CYC1, D2HGDH, DARS2, DGUOK, DLAT, DLD, DNA2, DNAJC19, DNM1L, EARS2, ELAC2, ETFA, ETFB, ETFDH, ETHE1, FARS2, FASTKD2, FBXL4, FDX2, FDXR, FH, FOXRED1, FXN, GAMT, GARS1, GCDH, GDAP1, GFER, GFM1, GFM2, GLYCTK, GPT2, GTPBP3, HARS2, HIBCH, HK1, HSPD1, IARS2, IBA57, IDH2, INF2, ISCU, L2HGDH, LARS2, LIAS, LRPPRC, LYRM4, LYRM7, MARS2, MFF, MGME1, MICU1, MPC1, MPV17, MRPL3, MRPL44, MRPS16, MRPS2, MRPS22, MRPS7, MSTO1, MTFMT, MTO1, MTPAP, MTRFR (C12orf65), NARS2, NBAS, NDUFA1, NDUFA10, NDUFA11, NDUFA12, NDUFA13, NDUFA2, NDUFA4, NDUFA9, NDUFAF1, NDUFAF2, NDUFAF3, NDUFAF4, NDUFAF5, NDUFAF6, NDUFB3, NDUFB9, NDUFS1, NDUFS2, NDUFS3, NDUFS4, NDUFS6, NDUFS7, NDUFS8, NDUFV1, NDUFV2, NFU1, NR2F1, NUBPL, OGDH, OPA1, OPA3, OXCT1, PANK2, PARS2, PC, PCK2, PDHA1, PDHB, PDHX, PDP1, PDSS1, PDSS2, PET100, PNKD, PNPT1, POLG, POLG2, PTRH2, PUS1, QARS1, RARS1, RARS2, RMND1, RNASEH1, RRM2B, RTN4IP1, SACS, SARS2, SCO1, SCO2, SDHAF1, SERAC1, SFXN4, SLC19A3, SLC25A1, SLC25A12, SLC25A19, SLC25A22, SLC25A26, SLC25A3, SLC25A4, SLC25A42, SLC25A46, SLC52A2, SLC9A6, SOD1, SPG7, SUCLA2, SUCLG1, SUGCT, SURF1, TACO1, TAFAZZIN (TAZ), TARS2, TAZ (TAFAZZIN), TFAM, TIMM8A, TK2, TMEM126A, TMEM126B, TMEM70, TOP3A, TPK1, TRIT1, TRMT10C, TRMU, TRNT1, TSFM, TTC19, TUFM, TWNK, TYMP, UQCC2, UQCRB, UQCRC2, UQCRQ, VARS2, WDR45, XPNPEP3, and YARS2