New perspective in diagnostics of mitochondrial disorders: two years’ experience with whole-exome sequencing at a national paediatric centre

Abstract

BackgroundWhole-exome sequencing (WES) has led to an exponential increase in identification of causative variants in mitochondrial disorders (MD).MethodsWe performed WES in 113 MD suspected patients from Polish paediatric reference centre, in whom routine testing failed to identify a molecular defect. WES was performed using TruSeqExome enrichment, followed by variant prioritization, validation by Sanger sequencing, and segregation with the disease phenotype in the family.ResultsLikely causative mutations were identified in 67 (59.3 %) patients; these included variants in mtDNA (6 patients) and nDNA: X-linked (9 patients), autosomal dominant (5 patients), and autosomal recessive (47 patients, 11 homozygotes). Novel variants accounted for 50.5 % (50/99) of all detected changes. In 47 patients, changes in 31 MD-related genes (ACAD9, ADCK3, AIFM1, CLPB, COX10, DLD, EARS2, FBXL4, MTATP6, MTFMT, MTND1, MTND3, MTND5, NAXE, NDUFS6, NDUFS7, NDUFV1, OPA1, PARS2, PC, PDHA1, POLG, RARS2, RRM2B, SCO2, SERAC1, SLC19A3, SLC25A12, TAZ, TMEM126B, VARS2) were identified. The ACAD9, CLPB, FBXL4, PDHA1 genes recurred more than twice suggesting higher general/ethnic prevalence. In 19 cases, variants in 18 non-MD related genes (ADAR, CACNA1A, CDKL5, CLN3, CPS1, DMD, DYSF, GBE1, GFAP, HSD17B4, MECP2, MYBPC3, PEX5, PGAP2, PIGN, PRF1, SBDS, SCN2A) were found. The percentage of positive WES results rose gradually with increasing probability of MD according to the Mitochondrial Disease Criteria (MDC) scale (from 36 to 90 % for low and high probability, respectively). The percentage of detected MD-related genes compared with non MD-related genes also grew with the increasing MD likelihood (from 20 to 97 %). Molecular diagnosis was established in 30/47 (63.8 %) neonates and in 17/28 (60.7 %) patients with basal ganglia involvement. Mutations in CLPB, SERAC1, TAZ genes were identified in neonates with 3-methylglutaconic aciduria (3-MGA) as a discriminative feature. New MD-related candidate gene (NDUFB8) is under verification.ConclusionsWe suggest WES rather than targeted NGS as the method of choice in diagnostics of MD in children, including neonates with 3-MGA aciduria, who died without determination of disease cause and with limited availability of laboratory data. There is a strong correlation between the degree of MD diagnosis by WES and MD likelihood expressed by the MDC scale.Electronic supplementary materialThe online version of this article (doi:10.1186/s12967-016-0930-9) contains supplementary material, which is available to authorized users.

Lethal Neonatal LTBL Associated with Biallelic EARS2 Variants: Case Report and Review of the Reported Neuroradiological Features

“…To date, 26 patients are reported with LTBL (12 by Steenweg et al (2012), one by Talim et al (2013), two by Taylor et al (2014), one by Biancheri et al (2015), one by Kohda et al (2016), one by Kevelam et al (2016), one by Danhauser et al (2016), one by Taskin et al (2016), one by G€ ung€ or et al (2016), two by Şahin et al (2016) and two by Pronicka et al (2016)), with our patient being the 26th reported patient. The phenotype of our patient fits the severe group of LTBL patients, mostly due to signs of perinatal presentation of the disease and rapid decline of her clinical status.…”

“…Although liver respiratory chain activity was normal, there was evident liver dysfunction. Liver involvement was also described in six additional EARS2 patients, which included one or more of neonatal transient icterus, hepatomegaly, fatty liver and steatosis (Steenweg et al 2012;Talim et al 2013;Taylor et al 2014;Pronicka et al 2016). Post-mortem examination of the liver from the patient reported by Talim et al (2013) also found COXdeficiency.…”

“…The fifth patient from Taskin et al (2016) had a homozygous c.322C>T (p.Arg108Trp) missense change and presented a mild phenotype. Compound heterozygous changes were identified in three additional patients as part of large-scale WES studies but without specific details of phenotypes for comparison (Kohda et al 2016;Pronicka et al 2016). Regarding the two heterozygous variants in our patient, the start-loss p.Met1?…”

Neuropathological characteristics of the brain in two patients with SLC19A3 mutations related to the biotin-thiamine-responsive basal ganglia disease

“…Recently, whole exome sequencing has revealed homozygous SLC19A3 c.74dupT (p.Ser26Leufs*19) mutation. Molecular analysis performed in his family confirmed parental inheritance of the identified variant [13].…”

“…Two Polish patients with the SLC19A3 mutations identified out of 113 mitochondrial patients studied in The Children's Memorial Health Institute (CMHI) in the period of 1995-2016 [13] were included.…”