Prevalence of rare mitochondrial DNA mutations in mitochondrial disorders

Abstract

Background: Mitochondrial DNA (mtDNA) diseases are rare disorders whose prevalence is estimated around 1 in 5000. Patients are usually tested only for deletions and for common mutations of mtDNA which account for 5-40% of cases, depending on the study. However, the prevalence of rare mtDNA mutations is not known.

Methods: We analysed the whole mtDNA in a cohort of 743 patients suspected of manifesting a mitochondrial disease, after excluding deletions and common mutations. Both heteroplasmic and homoplasmic variants were identified using two complementary strategies (Surveyor and MitoChip). Multiple correspondence analyses followed by hierarchical ascendant cluster process were used to explore relationships between clinical spectrum, age at onset and localisation of mutations.

Results: 7.4% of deleterious mutations and 22.4% of novel putative mutations were identified. Pathogenic heteroplasmic mutations were more frequent than homoplasmic mutations (4.6% vs 2.8%). Patients carrying deleterious mutations showed symptoms before 16 years of age in 67% of cases. Early onset disease (<1 year) was significantly associated with mutations in protein coding genes (mainly in complex I) while late onset disorders (>16 years) were associated with mutations in tRNA genes. MTND5 and MTND6 genes were identified as 'hotspots' of mutations, with Leigh syndrome accounting for the large majority of associated phenotypes.

Conclusions: Rare mitochondrial DNA mutations probably account for more than 7.4% of patients with respiratory chain deficiency. This study shows that a comprehensive analysis of mtDNA is essential, and should include young children, for an accurate diagnosis that is now accessible with the development of next generation sequencing technology.

Keywords: Mitochondrial DNA; Mitochondrial disease; Patient cohort; Rare mutations.

Figure 1

Analysis of the population harbouring heteroplasmic pathogenic mitochondrial DNA (mtDNA) mutations according to age at onset. n, number of patients. (A) Age at onset (in years). (B) Clinical characteristics. CNS, central nervous system; D, deafness; DM, diabetes mellitus. GR, growth retardation (intrauterine or postnatal); HCM, hypertrophic cardiomyopathy; L, liver involvement; Mu, muscle; OC, ocular involvement (optic atrophy or pigmentary retinopathy); PN, peripheral neuropathy; Re, renal involvement. (C) Respiratory chain analysis by spectrophotometry. CI, CV, respiratory chain deficiency in complex I, in complex V; mul, multiple respiratory chain deficiency; N, normal. (D) Localisation of mtDNA mutations. CI, CIII, CV, genes encoding subunits of complexes I, III, V; tRNA, genes encoding tRNA. (E) Statistical analyses with hierarchical ascendant classification of pathogenic heteroplasmic mutations found in the 34 patients. The upper right quadrant is complementary to the bottom left quadrant. The numbers on the axes are the scores that represent the contribution of each feature to the overall inertia. Our model (axes 1–3) explains 48% of total inertia. The circles represent the variables. Their size is proportional to the quality of representation of the variables on the plane (axes 1 and 3). Patients with disease onset <1 year are clustered with mutations in protein coding genes, psychomotor retardation, hypotonia, optic atrophy, postnatal growth retardation and Leigh syndrome. Patients with disease onset >16 years are clustered with mutations in tRNA genes and affected maternal relatives.

Figure 2

Analysis of the population harbouring homoplasmic pathogenic mitochondrial DNA (mtDNA) mutations according to age at onset. n, number of patients. (A) Age at onset (in years). (B) Clinical characteristics. CNS, central nervous system; D, deafness; DM, diabetes mellitus; GR, growth retardation (intrauterine or postnatal); HCM, hypertrophic cardiomyopathy; L, liver involvement; Mu, muscle; OC, ocular involvement (optic atrophy or pigmentary retinopathy); PN, peripheral neuropathy; Re, renal involvement. (C) Respiratory chain analysis by spectrophotometry. CI, CIII, CIV, respiratory chain deficiency in complex I, complex III, complex IV; mul, multiple respiratory chain deficiency; N, normal. (D) Localisation of mtDNA mutations. CI, CIII, CV, genes encoding subunits of complexes I, III, V; rRNA, genes encoding rRNA; tRNA, genes encoding tRNA.

Figure 3

Analysis of the pooled populations harbouring heteroplasmic or homoplasmic pathogenic mitochondrial DNA (mtDNA) mutations according to age at onset. n, number of patients. (A). Age at onset (in years). (B) Clinical characteristics. CNS, central nervous system; D, deafness; DM, diabetes mellitus; GR, growth retardation (intrauterine or postnatal); HCM, hypertrophic cardiomyopathy; L, liver involvement; Mu, muscle; OC, ocular involvement (optic atrophy or pigmentary retinopathy); PN, peripheral neuropathy; Re, renal involvement. (C) Respiratory chain analysis by spectrophotometry. CI, CIII, CIV, CV, respiratory chain deficiency in complex I, complex III, complex IV, complex V; mul, multiple respiratory chain deficiency; N, normal. (D) Localisation of mtDNA mutations. CI, CIII, CV, genes encoding subunits of complexes I, III, V; rRNA, genes encoding rRNA; tRNA, genes encoding tRNA. (E). Statistical analyses with hierarchical ascendant classification of pathogenic mutations found in the 55 patients. Our model (axes 1–3) explains 45% of total inertia. The circles represent the variables. Their size is proportional to the quality of representation of the variables on the plane (axes 1 and 2). Patients with disease onset <1 year are clustered with protein coding gene mutations, psychomotor retardation, stroke-like episodes, regression, movement disorders, Leigh syndrome and white matter involvement. Patients with late onset are clustered with tRNA gene mutations and affected maternal relatives.