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NGS Targeted Gene Panels for Testing of Inherited Mitochondrial Disorders


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The mitochondrion is an organell that is found in most eukaryotic cells. Besides providing energy by the oxidative phosphorylation the mitochondria are components of calcium signalling, regulation of metabolism, heam and steroid synthesis, and for programmed cell death (van der Giezen and Tovar 2005).

Mitochondria contain a double stranded DNA molecule denoted as mtDNA with a size of about 17000 bp containing 37 genes. The complex interaction of the mtDNA with the cellular DNA makes the diagnosis of mitochondrial genetic diseases difficult. The mtDNA is exposed to higher oxidative stress compared with the cellular DNA due to the generation of mitochondrial reactive oxygen
species (ROS) during the oxidative phosphorylation. Disorders can result from mtDNA point mutations and deletions as well as from mutations in cellular genes that interact with mitochondrial gene products (Chinnery and Hudson 2013).

A number of inherited mtDNA diseases are described, some of the most common known are Leber’s hereditary optic neuropathy (LHON), mitochondrial encephalomyopathy, lactic acidosis and stroke-like episodes (MELAS), myoclonus epilepsy with ragged red fibres (MERRF), kearns–sayre syndrome (KSS), sporadic progressive external ophthalmoplegia (PEO), and Pearson’s syndrome.

This website introduces a number of targeted NGS gene panels for the screening and diagnosis of different mtDNA genetic disorders including anemia, deafness, encephalopathy, myopathy, ophthalmoplegia and others.

For more information about the targeted genes please contact the NGS gene panel provider. For general information on mtDNA and genetics we recommend the Genetics Home Reference website.


Mitochondrial Defects - NGS Panels

Combined Mito Genome Plus Mito Nuclear Gene Panel

The Combined Mito Genome Plus Mito Nuclear Gene Panel includes sequencing and deletion testing of the mitochondrial genome and sequence analysis and exon-level deletion/duplication testing of 319 nuclear genes important for normal mitochondrial function.


Targeted genes: AARS, AARS2, ABCB11, ABCB4, ABCB7, ABCD4, ACAD9, ACADM, ACADVL, ACO2, ACSF3, ADCK3 (CABC1; COQ8), ADCK4, AFG3L2, AGK, AGL, AIFM1, ALAS2, ALDOA, ALDOB, ALG1, ALG11, ALG13, ALG2, ALG3, ALG6, ALG9, AMACR, APOPT1, APTX, ARG1, ASL, ASS1, ATP5A1, ATP5E, ATP7B, ATP8B1, ATPAF2 (ATP12), AUH, B4GALT1, BCKDHA, BCKDHB, BCS1L, BOLA3, C10ORF2, C12ORF65, C19orf12, CA5A, CARS2, CHKB, CISD2, CLPB, COA5 (C2ORF64), COA6, COASY, COG4, COG5, COG6, COG7, COG8, COQ2, COQ4, COQ6, COQ9, COX10, COX14 (C12ORF62), COX15, COX20 (FAM36A), COX4I2, COX6A1, COX6B1, COX7B, CPS1, CPT1A, CPT2, CYC1, DARS, DARS2, DBT, DDHD1, DDHD2, DDOST, DGUOK, DLAT, DLD, DMGDH, DNA2, DNAJC19, DNM1L, DNM2 , DOLK, DPAGT1, DPM1, DPM3, EARS2, ECHS1, ELAC2, ENO3, ETFA, ETFB, ETFDH, ETHE1, FAH, FARS2, FASTKD2, FBP1, FBXL4, FDX1L, FH, FLAD1, FOXRED1, G6PC, GAA, GAMT, GARS, GATM, GBE1, GCDH, GFER, GFM1 (EFG1), GFM2, GLRX5, GMPPA, GSS, GTPBP3, GYG1, GYG2, GYS1, GYS2, HADHA, HADHB, HARS2, HCFC1, HIBCH, HLCS, HMGCL, HMGCS2, HSD17B10, HSPD1, IARS2, IBA57, ISCA2, ISCU, IVD, LAMP2, LARS, LARS2, LDHA, LIAS, LIPT1, LMBRD1, LRPPRC, LYRM4, LYRM7, MARS, MARS2, MCCC1, MCCC2, MCEE, MFF, MFN2, MGAT2, MGME1, MICU1, MLYCD, MMAA, MMAB, MMACHC, MMADHC (C2ORF25) , MOGS, MPC1 (BRP44L), MPDU1, MPI, MPV17, MRPL12, MRPL3, MRPL44, MRPS16, MRPS22, MRPS7, MTFMT, MTO1, MTPAP, MTR, MTRR, MUT, NADK2, NAGS, NARS2, NDUFA1, NDUFA10, NDUFA11, NDUFA12, NDUFA2, NDUFA4, NDUFA9, NDUFAF1, NDUFAF2, NDUFAF3 (C3ORF60), NDUFAF4 (C6ORF66), NDUFAF5, NDUFAF6, NDUFAF7 (C2ORF56), NDUFB3, NDUFB9, NDUFS1, NDUFS2, NDUFS3, NDUFS4, NDUFS6, NDUFS7, NDUFS8, NDUFV1, NDUFV2, NFS1, NFU1, NGLY1, NR2F1, NUBPL, OPA1, OPA3, OTC, PARS2, PC, PCCA, PCCB, PDHA1, PDHB, PDHX, PDP1, PDSS1, PDSS2, PET100, PFKM, PGAM2, PGM1, PHKA1, PHKA2, PHKB, PHKG2, PMM2, PNPT1, POLG, POLG2, PRKAG2, PRPS1, PTRH2, PUS1, PYGM, QARS, RANBP2, RARS, RARS2, REEP1 (C2ORF23), RFT1, RMND1, RRM2B, SARS2, SCO1, SCO2, SDHA, SDHAF1, SERAC1, SFXN4, SLC19A2, SLC19A3, SLC22A5, SLC25A1, SLC25A13, SLC25A15, SLC25A19, SLC25A20, SLC25A22, SLC25A3 (PHC), SLC25A38, SLC25A4, SLC2A2, SLC35A1, SLC35A2, SLC35C1, SLC37A4, SLC6A8, SLC7A7, SPAST, SPG7, SPTLC1, SRD5A3, SSR4, STT3A, STT3B, STXBP1, SUCLA2, SUCLG1, SURF1, TACO1, TARS2, TAZ, TIMM8A, TK2, TMEM126A, TMEM165, TMEM70, TPK1, TRIT1, TRMU, TRNT1, TSFM, TTC19, TUFM, TYMP, UQCC2 , UQCC3, UQCRB, UQCRC2, UQCRQ, VARS2, WDR45, WFS1, YARS2

Disorders:
2,4-Dienoyl-CoA Reductase Deficiency (DECRD)
3-Hydroxyisobutryl-CoA Hydrolase Deficiency (HIBCH)
3-Methylglutaconic Aciduria Type VII (MGCA7)
Alacrima, Achalasia, and Mental Retardation Syndrome (AAMR)
Alpha-Methylacyl-CoA Racemase Deficiency
Axonal Charcot-Marie-Tooth Disease Type 2 (CMT2N)
Benign Recurrent Intrahepatic Cholestasis-2 (BRIC2)
Bosch-Boonstra-Schaaf Optic Atrophy Syndrome
Cerebral Creatine Deficiency Syndrome-1 (CCDS1)
Combined D-2- and L-2-Hydroxyglutaric Aciduria
Congenital Disorder of Glycosylation
Congenital Sideroblastic Anemia with B-cell Immunodeficiency, Periodic fevers, and Developmental delay (SIFD)
Fanconi-Bickel Syndrome
Glutathione Synthetase Deficiency (GSSD)
Glycogen Storage Disease 0, Muscle (GSD0B)
Glycogen Storage Disease IIIa; Glycogen Storage Disease IIIb
Glycogen Storage Disease IV
Glycogen Storage Disease IXc (GSD9C)
Glycogen Storage Disease IXd (GDS9D)
Glycogen Storage Disease Type IXa
Glycogen Storage Disease Type IXb (GSD9B)
Glycogen Storage Disease VII (GSD7)
Glycogen Storage Disease X (GSD10)
Glycogen Storage Disease XI (GSD11)
Glycogen Storage Disease XII (GSD12)
Glycogen Storage Disease XIII (GSD13)
Glycogen Storage Disease XV (GSD15)
Hereditary Fructose Intolerance
Hyperammonemia Due to Carbonic Anhydrase VA Deficiency (CA5AD)
Intrahepatic Cholestasis of Pregnancy
Lipoyltransferase 1 Deficiency (LIPT1)
Methylmalonic Acidemia and Hyperhomocysteinemia, cblX Type
Methylmalonic Aciduria and Homocystinuria, cblJ Type
Mitochondrial DNA Depletion Syndrome
Mitochondrial DNA Multiple Deletions
Mitochondrial Short-Chain Enoyl-CoA Hydratase-1 Deficiency (ECHS1D)
Multiple Mitochondrial Dysfunctions Syndrome
Nephrotic Syndrome Type 9 (NPHS9)
Oxidative Phosphorylation (OXPHOS) Deficiency
Perrault Syndrome 4 (PRLTS4)
Primary Coenzyme Q10 Deficiency
Progressive Familial Intrahepatic Cholestasis
Progressive Familial Intrahepatic Cholestasis-2 (PFIC2)
Pyridoxine-Refractory Sideroblastic Anemia
Pyridoxine-Refractory Sideroblastic Anemia, Autosomal Recessive
Spastic Paraplegia 28 (SPG28)
Spastic Paraplegia 4 (SPG4)
Spastic Paraplegia 43 (SPG43)
Spastic Paraplegia 54 (SPG54)
Spastic Paraplegia 74 (SPG74)
Thiamine-Responsive Megaloblastic Anemia Syndrome (TRMA)
Wilson Disease

Source: GeneDx

Complex I Defect

Multi Gene Panel (26 Genes)
Targeted genes: ACAD9 FOXRED1 NDUFA1 NDUFA10 NDUFA11 NDUFA12 NDUFA2 NDUFA9 NDUFAF1 NDUFAF2 NDUFAF3 NDUFAF4 NDUFAF5 NDUFAF6 NDUFB3 NDUFB9 NDUFS1 NDUFS2 NDUFS3 NDUFS4 NDUFS6 NDUFS7 NDUFS8 NDUFV1 NDUFV2 NUBPL
Source: Medical Genetics Center

Complex II Defect

Multi Gene Panel (7 Genes)
Targeted genes: ISCU SDHA SDHAF1 SDHAF2 SDHB SDHC SDHD
Source: Medical Genetics Center

Complex III Defect

Multi Gene Panel (5 Genes)
Targeted genes: BCS1L TTC19 UQCRB UQCRC2 UQCRQ
Source: Medical Genetics Center

Complex IV Defect

Multi Gene Panel (10 Genes)
Targeted genes: C12orf65 COX10 COX14 COX4I2 COX6B1 ETHE1 FASTKD2 LRPPRC SURF1 TACO1
Source: Medical Genetics Center

Complex V Defect

Multi Gene Panel (4 Genes)
Targeted genes: ATP5A1 ATP5E ATPAF2 TMEM70
Source: Medical Genetics Center

Coenzyme Q10 deficiency

Targeted genes: ADCK3, APTX, COQ2, COQ6, COQ9, ETFDH, PDSS1, PDSS2

Source: CGC Genetics

CoQ10 Deficiency

Multi Gene Panel (11 Genes)
Targeted genes: ADCK3 ANO10 APTX COQ2 COQ6 COQ9 ETFA ETFB ETFDH PDSS1 PDSS2
Source: Medical Genetics Center

Leigh syndrome and mitochondrial encephalopathy panel

Targeted genes: ACAD9, ADCK3, AIFM1, APTX, ATPAF2, BCS1L, C10orf2, NDUFAF6, COQ2, COQ9, COX10, COX15, COX6B1, DARS2, DGUOK, DLAT, DLD, DNM1L, ETFDH, ETHE1, FASTKD2, FH, FOXRED1, GFER, GFM1, LRPPRC, MPV17, NDUFA1, NDUFA10, NDUFA11, NDUFA2, NDUFA13, NDUFAF1, NDUFAF2, NDUFAF4, NDUFS1, NDUFS2, NDUFS3, NDUFS4, NDUFS6, NDUFS7, NDUFS8, NDUFV1, NDUFV2, NUBPL, NDUFA12, NDUFA9, NDUFAF5, SDHA, PC, PDHA1, PDHB, PDHX, PDP1, PDSS1, PDSS2, RARS2, SCO1, SCO2, SDHAF1, SUCLA2, SUCLG1, SURF1, TACO1, TK2, TMEM70, TSFM, TTC19, TUFM, TYMP

Source: Centogene

Mitochondrial Anemia

Multi Gene Panel (4 Genes)
Targeted genes: PUS1 SLC19A2 SLC25A38 YARS2
Source: Medical Genetics Center

Mitochondrial Deafness

Multi Gene Panel (8 Genes)
Targeted genes: HARS2 PNPT1 RMND1 SLC33A1 SUCLA2 SUCLG1 TIMM8A WFS1
Source: Medical Genetics Center

Mitochondrial Diseases

Multi Gene Panel (168 Genes)
Targeted genes: AARS2 ABCB7 ABHD5 ACAD9 ACADM ACADS ACADVL ACTG2 ADCK3 AFG3L2 AGK AGL AIFM1 ANO10 APTX ATP5A1 ATP5E ATPAF2 AUH BCS1L BOLA3 C10orf2 C12orf65 CHKB CLPP COQ2 COQ6 COQ9 COX10 COX14 COX15 COX4I2 COX6B1 CPT1A CPT2 DARS2 DGUOK DLAT DLD DNA2 DNAJC19 DPAGT1 EARS2 EIF2AK3 ETFA ETFB ETFDH ETHE1 FARS2 FASTKD2 FBXL4 FDX1L FLAD1 FOXRED1 GARS GBE1 GDAP1 GFAP GFER GFM1 HARS2 IBA57 ISCU KARS KIF5A LAMP2 LARS2 LRPPRC LYRM7 MARS2 MFN2 MGME1 MICU1 MPV17 MRPS16 MRPS22 MTFMT MTO1 MTPAP NDUFA1 NDUFA10 NDUFA11 NDUFA12 NDUFA2 NDUFA9 NDUFAF1 NDUFAF2 NDUFAF3 NDUFAF4 NDUFAF5 NDUFAF6 NDUFB3 NDUFB9 NDUFS1 NDUFS2 NDUFS3 NDUFS4 NDUFS6 NDUFS7 NDUFS8 NDUFV1 NDUFV2 NFU1 NUBPL OPA1 OPA3 PANK2 PC PDHA1 PDHB PDHX PDP1 PDSS1 PDSS2 PNPLA2 PNPT1 POLG POLG2 PTCD1 PUS1 RARS2 RMND1 RRM2B SARS2 SCO1 SCO2 SDHA SDHAF1 SDHAF2 SDHB SDHC SDHD SERAC1 SLC19A2 SLC19A3 SLC22A5 SLC25A12 SLC25A19 SLC25A20 SLC25A3 SLC25A38 SLC25A4 SLC33A1 SLC6A8 SPG7 SUCLA2 SUCLG1 SURF1 TACO1 TARS2 TAZ TIMM8A TK2 TMEM126A TMEM70 TPK1 TRIT1 TRMU TSFM TTC19 TUFM TYMP UQCRB UQCRC2 UQCRQ VARS2 WFS1 YARS2
Source: Medical Genetics Center

Mitochondrial Disorders

Mitochondrial Disorders (121 Nuclear Genes by Sequencing, 119 Nuclear Genes by Deletion/Duplication)
Genes tested by Sequencing: ABCB7, ACAD9, ACADL, ACADM, ACADS, ACADVL, ACAT1, ADCK3, APTX, ASS1, ATPAF2, BCKDHA, BCKDHB, BCS1L, C10orf2, COQ2, COQ9, COX10, COX15, COX4I2, COX6B1, CPT1A, CPT2, CYCS, DARS2, DBT, DGUOK, DLAT, DLD, DNAJC19, DNM1L, ETFA, ETFB, ETFDH, ETHE1, FASTKD2, FH, FXN, GFER, GFM1, HADH, HADHA, HADHB, HMGCL, HMGCS2, HSPD1, ISCU, LARS2, LRPPRC, MCCC2, MFN2, MPV17, MRPS16, MRPS22, NDUFA1, NDUFA11, NDUFA2, NDUFAF1, NDUFAF2, NDUFAF3, NDUFAF4, NDUFAF5, NDUFS1, NDUFS2, NDUFS3, NDUFS4, NDUFS6, NDUFS7, NDUFS8, NDUFV1, NDUFV2, OPA1, OXCT1, PC, PCK2, PDHA1, PDHB, PDHX, PDP1, PDSS1, PDSS2, PINK1, POLG, POLG2, PPM1B, PREPL, PUS1, RARS2, RRM2B, SCO1, SCO2, SDHAF1, SDHB, SDHC, SDHD, SLC22A5, SLC25A13, SLC25A15, SLC25A19, SLC25A20, SLC25A22, SLC25A3, SLC25A4, SLC3A1, SPG7, SUCLA2, SUCLG1, SUOX, SURF1, TAZ, TIMM8A, TK2, TMEM70, TMPO, TRMU, TSFM, TUFM, TYMP, UQCRB, UQCRQ, WFS1
Source: Arup Laboratories

Mitochondrial Encephalopathy

Multi Gene Panel (131 Genes)
Targeted genes: AARS2 ACAD9 ADCK3 AGK AIFM1 ATP5A1 ATP5E ATPAF2 AUH BCS1L BOLA3 C10orf2 COQ2 COQ6 COQ9 COX10 COX14 COX15 COX4I2 COX6B1 DARS2 DGUOK DLAT DLD DNAJC19 DPAGT1 EARS2 EIF2AK3 ETFA ETFB ETFDH ETHE1 FARS2 FASTKD2 FBXL4 FLAD1 FOXRED1 GFAP GFER GFM1 IBA57 LRPPRC LYRM7 MARS2 MICU1 MPV17 MRPS16 MRPS22 MTFMT MTO1 MTPAP NDUFA1 NDUFA12 NDUFA2 NDUFA9 NDUFAF2 NDUFAF3 NDUFAF4 NDUFAF5 NDUFAF6 NDUFB3 NDUFB9 NDUFS1 NDUFS2 NDUFS3 NDUFS4 NDUFS6 NDUFS7 NDUFS8 NDUFV1 NDUFV2 NFU1 NUBPL OPA1 PANK2 PC PDHA1 PDHB PDHX PDP1 PDSS1 PDSS2 PNPT1 POLG PTCD1 PUS1 RARS2 RMND1 RRM2B SARS2 SCO1 SCO2 SDHA SDHAF1 SDHAF2 SDHB SDHC SDHD SERAC1 SLC19A2 SLC19A3 SLC25A12 SLC25A19 SLC25A20 SLC25A3 SLC25A4 SLC33A1 SLC6A8 SPG7 SUCLA2 SUCLG1 SURF1 TACO1 TARS2 TAZ TIMM8A TK2 TMEM70 TPK1 TRIT1 TRMU TSFM TTC19 TUFM TYMP UQCRB UQCRC2 UQCRQ VARS2 WFS1 YARS2
Source: Medical Genetics Center

Mitochondrial Encephalopathy/ Leigh Syndrome Nuclear Gene Panel

Targeted genes: AARS2, ACAD9, ACO2, ADCK3 (CABC1; COQ8), AFG3L2, AIFM1, APOPT1, APTX, ATP5A1, ATP5E, ATPAF2 (ATP12), AUH, BCS1L, BOLA3, C10ORF2, C12ORF65, CA5A, COG8, COQ2, COQ4, COQ6, COQ9, COX10, COX14 (C12ORF62), COX15, COX20 (FAM36A), COX6B1, CPT1A, CPT2, CYC1, DARS, DARS2, DGUOK, DLAT, DLD, DNM1L, EARS2, ECHS1, ETFDH, ETHE1, FARS2, FASTKD2, FBP1, FBXL4, FH, FOXRED1, GCDH, GFER, GFM1 (EFG1), GFM2, GTPBP3, GYG2, HIBCH, HLCS, HSPD1, IARS2, IBA57, ISCA2, LARS2, LIAS, LIPT1, LRPPRC, LYRM7, MARS2, MFF, MFN2, MPC1 (BRP44L), MPV17, MRPL44, MRPS22, MTFMT, MTPAP, NADK2, NARS2, NDUFA1, NDUFA10, NDUFA11, NDUFA12, NDUFA2, NDUFA4, NDUFA9, NDUFAF1, NDUFAF2, NDUFAF3 (C3ORF60), NDUFAF4 (C6ORF66), NDUFAF5, NDUFAF6, NDUFAF7 (C2ORF56), NDUFB3, NDUFS1, NDUFS2, NDUFS3, NDUFS4, NDUFS6, NDUFS7, NDUFS8, NDUFV1, NDUFV2, NFU1, NUBPL, PC, PCCA, PCCB, PDHA1, PDHB, PDHX, PDP1, PDSS1, PDSS2, PET100, PNPT1, POLG, RANBP2, RARS2, RMND1, RRM2B, SCO1, SCO2, SDHA, SDHAF1, SERAC1, SLC19A3, SLC22A5, SLC25A1, SLC25A15, SLC25A19, SLC25A22, SLC35A2, STXBP1, SUCLA2, SUCLG1, SURF1, TACO1, TARS2, TK2, TMEM70, TPK1, TRMU, TSFM, TTC19, TUFM, TYMP, UQCC2 , UQCC3, UQCRQ, VARS2

Disorders:
2,4-Dienoyl-CoA Reductase Deficiency (DECRD)
3-Hydroxyisobutryl-CoA Hydrolase Deficiency (HIBCH)
Hyperammonemia Due to Carbonic Anhydrase VA Deficiency (CA5AD)
Lipoyltransferase 1 Deficiency (LIPT1)
Mitochondrial Short-Chain Enoyl-CoA Hydratase-1 Deficiency (ECHS1D)
Multiple Mitochondrial Dysfunctions Syndrome
Perrault Syndrome 4 (PRLTS4)
Spastic Paraplegia 74 (SPG74)

Source: GeneDx

Mitochondrial Myopathy

Multi Gene Panel (15 Genes)
Targeted genes: ACADVL C10orf2 CHKB CPT2 ETFA ETFB ETFDH FDX1L ISCU LAMP2 POLG PUS1 RRM2B SLC22A5 TK2
Source: Medical Genetics Center

Mitochondriopathy – Chronic Progressive External Ophthalmoplegia (CPEO)

Multi Gene Panel (9 Genes)
Targeted genes: C10orf2 MGME1 POLG POLG2 RRM2B SLC25A4 SPG7 TK2 TYMP
Source: Medical Genetisc Center

mtDNA Depletion Syndrome NGS Panel

Targeted Genes: C10orf2, DGUOK, MPV17, POLG, POLG2, RRM2B, SLC25A4, SUCLA2, SUCLG1, TK2, TYMP
Source: Fulgent Diagnostics


Mitochondrial Exome & Genome - NGS Panels

mtSEEK® test

Courtagen’s mtSEEK® test uses Next Generation Sequencing to sequence the 16,569 nucleotide bases that make up the 37 genes of the mitochondrial genome.
The analysis and interpretation of a patient’s nuclear mitochondrial exome is valuable for obtaining a definitive diagnosis, estimating prognosis, guiding treatment choices, and determining recurrence risks.
Source: Courtagen

Website

Nuclear-Mito NGS Panel

Number of Targeted Genes: 504
Source: Fulgent Diagnostics

nucSEEK® test

Courtagen’s nucSEEK® test uses Next Generation Sequencing to detect variants in these nuclear genes. The analysis and interpretation of a patient’s nuclear mitochondrial exome is valuable for obtaining a definitive diagnosis, estimating prognosis, guiding treatment choices, and determining recurrence risks.
Source: Courtagen

Website


Van der Giezen and Tovar (2005) Degenerate mitochondria |PubMed|

Chinnery and Hudson (2013) Mitochondrial genetics | PubMed |


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