Targeted next generation sequencing in patients with inborn errors of metabolism

BACKGROUND: Next-generation sequencing (NGS) technology has allowed the promotion of genetic diagnosis and are becoming increasingly inexpensive and faster. To evaluate the utility of NGS in the clinical field, a targeted genetic panel approach was designed for the diagnosis of a set of inborn errors of metabolism (IEM). The final aim of the study was to compare the findings for the diagnostic yield of NGS in patients who presented with consistent clinical and biochemical suspicion of IEM with those obtained for patients who did not have specific biomarkers. METHODS: The subjects studied (n = 146) were classified into two categories: Group 1 (n = 81), which consisted of patients with clinical and biochemical suspicion of IEM, and Group 2 (n = 65), which consisted of IEM cases with clinical suspicion and unspecific biomarkers. A total of 171 genes were analyzed using a custom targeted panel of genes followed by Sanger validation. RESULTS: Genetic diagnosis was achieved in 50% of patients (73/146). In addition, the diagnostic yield obtained for Group 1 was 78% (63/81), and this rate decreased to 15.4% (10/65) in Group 2 (X2 = 76.171; p < 0.0001). CONCLUSIONS: A rapid and effective genetic diagnosis was achieved in our cohort, particularly the group that had both clinical and biochemical indications for the diagnosis

GDF-15 is elevated in children with mitochondrial diseases and is induced by mitochondrial dysfunction

Background We previously described increased levels of growth and differentiation factor 15 (GDF-15) in skeletal muscle and serum of patients with mitochondrial diseases. Here we evaluated GDF-15 as a biomarker for mitochondrial diseases affecting children and compared it to fibroblast-growth factor 21 (FGF-21). To investigate the mechanism of GDF-15 induction in these pathologies we measured its expression and secretion in response to mitochondrial dysfunction. Methods We analysed 59 serum samples from 48 children with mitochondrial disease, 19 samples from children with other neuromuscular diseases and 33 samples from aged-matched healthy children. GDF-15 and FGF-21 circulating levels were determined by ELISA. Results Our results showed that in children with mitochondrial diseases GDF-15 levels were on average increased by 11-fold (mean 4046pg/ml, 1492 SEM) relative to healthy (350, 21) and myopathic (350, 32) controls. The area under the curve for the receiver-operating-characteristic curve for GDF-15 was 0.82 indicating that it has a good discriminatory power. The overall sensitivity and specificity of GDF-15 for a cut-off value of 550pg/mL was 67.8% (54.4%-79.4%) and 92.3% (81.5%-97.9%), respectively. We found that elevated levels of GDF-15 and or FGF-21 correctly identified a larger proportion of patients than elevated lev- els of GDF-15 or FGF-21 alone. GDF-15, as well as FGF-21, mRNA expression and protein secretion, were significantly induced after treatment of myotubes with oligomycin and that levels of expression of both factors significantly correlated. Conclusions Our data indicate that GDF-15 is a valuable serum quantitative biomarker for the diagnosis of mitochondrial diseases in children and that measurement of both GDF-15 and FGF-21 improves the disease detection ability of either factor separately. Finally, we demonstrate for the first time that GDF-15 is produced by skeletal muscle cells in response to mitochon- drial dysfunction and that its levels correlate in vitro with FGF-21 level

Estudi del coenzim Q10 en pacients neuropediàtrics: avenços diagnòstics i identificació de noves causes d'alteracions secundàries

[cat] L’àrea de treball de la present tesi doctoral se situa en el context de les malalties genètiques del metabolisme energètic mitocondrial. Són malalties rares i hereditàries que afecten al conjunt de sistemes que fa servir l’organisme per incorporar i transformar els substrats en energia utilitzable per al correcte funcionament cel·lular. El coenzim Q10 és un component lipídic de totes les membranes cel·lulars que realitza un paper essencial a la cadena respiratòria mitocondrial, però també participa en moltes altres funcions cel·lulars, tan dins dels mitocondris com fora. En l’àmbit pediàtric, la deficiència de coenzim Q10 s’associa a estats de malaltia amb expressions fenotípiques heterogènies, i les causes que la expliquen poden ser primàries o bé secundàries (és a dir, per alteració dels gens implicats en la via de síntesi d’aquesta molècula –deficiència primària–, o per alteració d’altres gens no directament relacionats en la via biosintètica del coenzim Q10 –deficiència secundària). Aquesta deficiència bioquímica implica una disfunció del sistema de la fosforilació oxidativa mitocondrial, i normalment es manifesta de forma multiorgànica, alterant en major o menor grau els diferents òrgans, segons els nivells energètics que requereixen els teixits i d’altres factors no massa coneguts. L’objectiu principal d’aquesta tesi ha estat la millora del diagnòstic de pacients amb deficiències de coenzim Q10, a través de l’estudi sistemàtic d’aquest en diverses espècimens biològics i en associació amb dades clíniques, bioquímiques, histoquímiques, enzimàtiques i moleculars. A través de l’estudi i valoració de grans grups de pacients, s’ha pogut intuir la dinàmica d’aquesta molècula en certs tipus de malalties. Hem pogut descriure tres malalties que s’associen a una deficiència de coenzim Q10 de forma secundària, permetent que pacients afectats puguin beneficiar-se de la suplementació oral amb coenzim Q10, la qual ha demostrat millores clíniques de l’estat de pacients afectats amb patologies mitocondrials. També, hem realitzat avenços metodològics i tècnics, a nivell bioquímic i d’anàlisi de dades, que permetran abordar les classificacions actuals dels pacients amb malalties mitocondrials, en les quals és complicat assolir un diagnòstic molecular definitiu degut a la seva immensa complexitat.[eng] Mitochondrial diseases are genetic rare diseases which affect the energetic cellular system to obtain the required energy for basic survival. Coenzyme Q10 is a lipidic antioxidant located in all eukaryotic cellular membranes that is essential for mitochondrial respiratory chain activity, amongst other important roles not strictly related to mitochondrial function. Coenzyme Q10 deficiency is a biochemical trait defined by low coenzyme Q10 levels in tissues, which can manifest in five main classical phenotypes (from isolated nephropathies to fatal infantile multisystemic disease). The ethiology can be primary (when the genetic defect is in a gene affecting the coenzyme Q10 biosynthetic pathway) or secondary (when the altered gene is not directly related to the coenzyme Q10 biosynthesis), and this partially explains the high heterogeneity observed in these patients. The patophysiology is explained because there is a mitochondrial respiratory chain malfunction that affects the oxidative phosphorylation system and unbalances the antioxidant protection, consequently changing normal cellular behaviour. The main objective of this work has been to improve the diagnosis of patients with coenzyme Q10 deficiency, through the systematic analysis of various biological samples in association with clinical, biochemical, histochemical, enzymatic and molecular data. Through the study and evaluation of big cohorts of patients, we could establish that secondary coenzyme Q10 deficiencies are commoner than primary. Furthermore, we have reported an association of three different diseases with secondary coenzyme Q10 deficient states (GLUT-1 deficiency syndrome, pyrivate dehydrogenase deficiency, mucopolysaccharidosis type III), diseases that could benefit from coenzyme Q10 supplementation, which has demonstrated to produce clinical amelioration in mitochondrial patients. Finally, methodological improvements for coenzyme Q10 deficiency diagnosis were done through two different approaches. One is the analysis of coenzyme Q10 in urinary sediment to assess coenzyme Q10 levels of renal system cells, and the other one is the development of a statistical algorithm which shows the potential of coenzyme Q10 as a mitochondrial activity biomarker

Molecular Modelling Hurdle in the Next-Generation Sequencing Era

There are challenges in the genetic diagnosis of rare diseases, and pursuing an optimal strategy to identify the cause of the disease is one of the main objectives of any clinical genomics unit. A range of techniques are currently used to characterize the genomic variability within the human genome to detect causative variants of specific disorders. With the introduction of next-generation sequencing (NGS) in the clinical setting, geneticists can study single-nucleotide variants (SNVs) throughout the entire exome/genome. In turn, the number of variants to be evaluated per patient has increased significantly, and more information has to be processed and analyzed to determine a proper diagnosis. Roughly 50% of patients with a Mendelian genetic disorder are diagnosed using NGS, but a fair number of patients still suffer a diagnostic odyssey. Due to the inherent diversity of the human population, as more exomes or genomes are sequenced, variants of uncertain significance (VUSs) will increase exponentially. Thus, assigning relevance to a VUS (non-synonymous as well as synonymous) in an undiagnosed patient becomes crucial to assess the proper diagnosis. Multiple algorithms have been used to predict how a specific mutation might affect the protein&rsquo;s function, but they are far from accurate enough to be conclusive. In this work, we highlight the difficulties of genomic variability determined by NGS that have arisen in diagnosing rare genetic diseases, and how molecular modelling has to be a key component to elucidate the relevance of a specific mutation in the protein&rsquo;s loss of function or malfunction. We suggest that the creation of a multi-omics data model should improve the classification of pathogenicity for a significant amount of the detected genomic variability. Moreover, we argue how it should be incorporated systematically in the process of variant evaluation to be useful in the clinical setting and the diagnostic pipeline

The Increasing Impact of Translational Research in the Molecular Diagnostics of Neuromuscular Diseases

The diagnosis of neuromuscular diseases (NMDs) has been progressively evolving from the grouping of clinical symptoms and signs towards the molecular definition. Optimal clinical, biochemical, electrophysiological, electrophysiological, and histopathological characterization is very helpful to achieve molecular diagnosis, which is essential for establishing prognosis, treatment and genetic counselling. Currently, the genetic approach includes both the gene-targeted analysis in specific clinically recognizable diseases, as well as genomic analysis based on next-generation sequencing, analyzing either the clinical exome/genome or the whole exome or genome. However, as of today, there are still many patients in whom the causative genetic variant cannot be definitely established and variants of uncertain significance are often found. In this review, we address these drawbacks by incorporating two additional biological omics approaches into the molecular diagnostic process of NMDs. First, functional genomics by introducing experimental cell and molecular biology to analyze and validate the variant for its biological effect in an in-house translational diagnostic program, and second, incorporating a multi-omics approach including RNA-seq, metabolomics, and proteomics in the molecular diagnosis of neuromuscular disease. Both translational diagnostics programs and omics are being implemented as part of the diagnostic process in academic centers and referral hospitals and, therefore, an increase in the proportion of neuromuscular patients with a molecular diagnosis is expected. This improvement in the process and diagnostic performance of patients will allow solving aspects of their health problems in a precise way and will allow them and their families to take a step forward in their lives

Targeted Next Generation Sequencing in Patients with Inborn Errors of Metabolism

<div><p>Background</p><p>Next-generation sequencing (NGS) technology has allowed the promotion of genetic diagnosis and are becoming increasingly inexpensive and faster. To evaluate the utility of NGS in the clinical field, a targeted genetic panel approach was designed for the diagnosis of a set of inborn errors of metabolism (IEM). The final aim of the study was to compare the findings for the diagnostic yield of NGS in patients who presented with consistent clinical and biochemical suspicion of IEM with those obtained for patients who did not have specific biomarkers.</p><p>Methods</p><p>The subjects studied (n = 146) were classified into two categories: Group 1 (n = 81), which consisted of patients with clinical and biochemical suspicion of IEM, and Group 2 (n = 65), which consisted of IEM cases with clinical suspicion and unspecific biomarkers. A total of 171 genes were analyzed using a custom targeted panel of genes followed by Sanger validation.</p><p>Results</p><p>Genetic diagnosis was achieved in 50% of patients (73/146). In addition, the diagnostic yield obtained for Group 1 was 78% (63/81), and this rate decreased to 15.4% (10/65) in Group 2 (<i>X</i>² = 76.171; p < 0.0001).</p><p>Conclusions</p><p>A rapid and effective genetic diagnosis was achieved in our cohort, particularly the group that had both clinical and biochemical indications for the diagnosis.</p></div

Targeted next generation sequencing in patients with inborn errors of metabolism

BACKGROUND: Next-generation sequencing (NGS) technology has allowed the promotion of genetic diagnosis and are becoming increasingly inexpensive and faster. To evaluate the utility of NGS in the clinical field, a targeted genetic panel approach was designed for the diagnosis of a set of inborn errors of metabolism (IEM). The final aim of the study was to compare the findings for the diagnostic yield of NGS in patients who presented with consistent clinical and biochemical suspicion of IEM with those obtained for patients who did not have specific biomarkers. METHODS: The subjects studied (n = 146) were classified into two categories: Group 1 (n = 81), which consisted of patients with clinical and biochemical suspicion of IEM, and Group 2 (n = 65), which consisted of IEM cases with clinical suspicion and unspecific biomarkers. A total of 171 genes were analyzed using a custom targeted panel of genes followed by Sanger validation. RESULTS: Genetic diagnosis was achieved in 50% of patients (73/146). In addition, the diagnostic yield obtained for Group 1 was 78% (63/81), and this rate decreased to 15.4% (10/65) in Group 2 (X2 = 76.171; p < 0.0001). CONCLUSIONS: A rapid and effective genetic diagnosis was achieved in our cohort, particularly the group that had both clinical and biochemical indications for the diagnosis

Global genetic results.

<p>Genetic results (positive, under-study, and negative cases) shown as a percentages for each nosological group (aminoacidopathies (AA); organic acidurias (OA); free fatty acid oxidation defects (FFA); and neurometabolic (NM) and complex molecules (CM) defects) and for both diagnostic groups (Groups 1 and 2).</p

Severe encephalopathy associated to pyruvate dehydrogenase mutations and unbalanced coenzyme Q10 content

none16sinoneAsencio, Claudio*; Rodríguez-Hernandez, María A; Briones, Paz; Montoya, Julio; Cortés, Ana; Emperador, Sonia; Gavilán, Angela; Ruiz-Pesini, Eduardo; Yubero, Dèlia; Montero, Raquel; Pineda, Mercedes; O'Callaghan, María M; Alcázar-Fabra, María; Salviati, Leonardo; Artuch, Rafael; Navas, PlácidoAsencio, Claudio; Rodríguez-Hernandez, María A; Briones, Paz; Montoya, Julio; Cortés, Ana; Emperador, Sonia; Gavilán, Angela; Ruiz-Pesini, Eduardo; Yubero, Dèlia; Montero, Raquel; Pineda, Mercedes; O'Callaghan, María M; Alcázar-Fabra, María; Salviati, Leonardo; Artuch, Rafael; Navas, Plácid

GDF-15 is elevated in children with mitochondrial diseases and is induced by mitochondrial dysfunction

Background We previously described increased levels of growth and differentiation factor 15 (GDF-15) in skeletal muscle and serum of patients with mitochondrial diseases. Here we evaluated GDF-15 as a biomarker for mitochondrial diseases affecting children and compared it to fibroblast-growth factor 21 (FGF-21). To investigate the mechanism of GDF-15 induction in these pathologies we measured its expression and secretion in response to mitochondrial dysfunction. Methods We analysed 59 serum samples from 48 children with mitochondrial disease, 19 samples from children with other neuromuscular diseases and 33 samples from aged-matched healthy children. GDF-15 and FGF-21 circulating levels were determined by ELISA. Results Our results showed that in children with mitochondrial diseases GDF-15 levels were on average increased by 11-fold (mean 4046pg/ml, 1492 SEM) relative to healthy (350, 21) and myopathic (350, 32) controls. The area under the curve for the receiver-operating-characteristic curve for GDF-15 was 0.82 indicating that it has a good discriminatory power. The overall sensitivity and specificity of GDF-15 for a cut-off value of 550pg/mL was 67.8% (54.4%-79.4%) and 92.3% (81.5%-97.9%), respectively. We found that elevated levels of GDF-15 and or FGF-21 correctly identified a larger proportion of patients than elevated lev- els of GDF-15 or FGF-21 alone. GDF-15, as well as FGF-21, mRNA expression and protein secretion, were significantly induced after treatment of myotubes with oligomycin and that levels of expression of both factors significantly correlated. Conclusions Our data indicate that GDF-15 is a valuable serum quantitative biomarker for the diagnosis of mitochondrial diseases in children and that measurement of both GDF-15 and FGF-21 improves the disease detection ability of either factor separately. Finally, we demonstrate for the first time that GDF-15 is produced by skeletal muscle cells in response to mitochon- drial dysfunction and that its levels correlate in vitro with FGF-21 level