The utility of next-generation sequencing technologies in diagnosis of Mendelian mitochondrial diseases and reflections on clinical spectrum

Abstract

Objectives Diagnostic process of mitochondrial disorders (MD) is challenging because of the clinical variability and genetic heterogeneity of these conditions. Next-Generation Sequencing (NGS) technology offers a high-throughput platform for nuclear MD. Methods We included 59 of 72 patients that undergone WES and targeted exome sequencing panel suspected to have potential PMDs. Patients who were included in the analysis considering the possible PMD were reviewed retrospectively and scored according to the Mitochondrial Disease Criteria Scale. Results Sixty-one percent of the patients were diagnosed with whole-exome sequencing (WES) (36/59) and 15% with targeted exome sequencing (TES) (9/59). Patients with MD-related gene defects were included in the mito group, patients without MD-related gene defects were included in the nonmito group, and patients in whom no etiological cause could be identified were included in the unknown etiology group. In 11 out of 36 patients diagnosed with WES, a TES panel was applied prior to WES. In 47 probands in 39 genes (SURF1, SDHAF1, MTO1, FBXL4, SLC25A12, GLRX5, C19oRF12, NDUFAF6, DARS2, BOLA3, SLC19A3, SCO1, HIBCH, PDHA1, PDHAX, PC, ETFA, TRMU, TUFM, NDUFS6, WWOX, UBCD TREX1, ATL1, VAC14, GFAP, PLA2G6, TPRKB, ATP8A2, PEX13, IGHMBP2, LAMB2, LPIN1, GFPT1, CLN5, DOLK) (20 mito group, 19 nonmito group) 59 variants (31 mito group, 18 nonmito group) were detected. Seven novel variants in the mito group (SLC25A12, GLRX5, DARS2, SCO1, PC, ETFA, NDUFS6), nine novel variants in the nonmito group (IVD, GCDH, COG4, VAC14, GFAP, PLA2G6, ATP8A2, PEX13, LPIN1) were detected. Conclusions We explored the feasibility of identifying pathogenic alleles using WES and TES in MD. Our results show that WES is the primary method of choice in the diagnosis of MD until at least all genes responsible for PMD are found and are highly effective in facilitating the diagnosis process.

Genotypic and phenotypic spectrum of infantile liver failure due to pathogenic TRMU variants

“…2 In that original patient cohort of 13 individuals, 4 died of ALF, but the other 9 patients survived and showed no further hepatological or neurologic issues over the next 14 years of follow up. A further 23 cases have since been reported in the literature, [3][4][5][6][7][8][9][10][11][12][13][14][15][16] with TRMU deficiency now termed as transient, infantile liver failure (OMIM 613070).…”

AGC1 Deficiency: Pathology and Molecular and Cellular Mechanisms of the Disease

“…Several AGC1/Aralar mutations have been reported to produce AGC1 deficiency in humans [ 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 ]. AGC1 deficiency, named “early infantile epileptic encephalopathy 39” (EIEE39; OMIM ID # 612949; DEE39, “Developmental and Epileptic Encephalopathy 39”), is an inborn error of metabolism affecting AGC1-MAS activity and producing symptoms that include neurodevelopmental delay, hypomyelination, refractory epilepsy, and severe hypotonia.…”

“…Subsequently, whole-exome sequencing (WES) analysis of undiagnosed pediatric patients allowed for the identification of more cases of AGC1 deficiency, such as those reported by Pronicka et al (2016) [ 13 ], Nashabat et al (2019) [ 15 ] and Kose et al (2021) [ 18 ] showing different homozygous missense pathogenic variants in SLC25A12 (c.1335C > A, p.Asn445Lys; c.1385C > T, p.Thr462Met; and, c.125G > C, p.Arg42Pro, respectively), presenting epileptic encephalopathy and global developmental delay. Surprisingly, a recent case reported by Pfeiffer et al (2020) [ 16 ] describing a homozygous missense variant in the same region (c.1331C > T; p.Thr444Ile) suffered refractory seizures and developmental arrest but did not have evidence of cerebral hypomyelination on MRI demonstrated at 10 months of age.…”

“…These findings support that the striatum is a preferential target of Aralar-MAS deficiency which leads to a reduction and/or mishandling of DA and that oxidative stress caused by AGC1/Aralar deficiency might be at the origin of DA mishandling in striatum. Interestingly, fluctuating changes in the basal ganglia by MRI were reported in AGC1-deficient patients associated with motor disturbances, spasticity [ 10 , 11 , 18 ] and dystonia with a discrete response to levodopa treatment [ 12 ].…”

“…Aralar-MAS deficiency in mice has been shown to produce severe neurological deficits with motor coordination defects and refractory epilepsy along with an impairment in myelination in the central nervous system [ 4 ]. The first human patient with AGC1/aralar deficiency presented with neurodevelopmental arrest, epilepsy and severe hypomyelination was described more than ten years ago [ 10 ]; and, more recently, other AGC1 deficient patients with early infantile epileptic encephalopathy were reported [ 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 ]. Most of these patients have homozygous or compound heterozygous mutations in aralar with low or no activity of the protein as a glutamate-aspartate carrier.…”