scholarly journals Oxygraphy Versus Enzymology for the Biochemical Diagnosis of Primary Mitochondrial Disease

Metabolites ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. 220
Author(s):  
Matthew J Bird ◽  
Isabelle Adant ◽  
Petra Windmolders ◽  
Ingrid Vander Elst ◽  
Catarina Felgueira ◽  
...  
Keyword(s):  
Mitochondrial Disease ◽  
Genetic Disorders ◽  
Genetic Diagnosis ◽  
Fibroblast Cell ◽  
Specific Information ◽  
Mitochondrial Oxidative Phosphorylation ◽  
Biochemical Tests ◽  
Sequencing Technologies ◽  
Generation Sequencing ◽  
Fibroblast Cell Lines

Primary mitochondrial disease (PMD) is a large group of genetic disorders directly affecting mitochondrial function. Although next generation sequencing technologies have revolutionized the diagnosis of these disorders, biochemical tests remain essential and functional confirmation of the critical genetic diagnosis. While enzymological testing of the mitochondrial oxidative phosphorylation (OXPHOS) complexes remains the gold standard, oxygraphy could offer several advantages. To this end, we compared the diagnostic performance of both techniques in a cohort of 34 genetically defined PMD patient fibroblast cell lines. We observed that oxygraphy slightly outperformed enzymology for sensitivity (79 ± 17% versus 68 ± 15%, mean and 95% CI), and had a better discriminatory power, identifying 58 ± 17% versus 35 ± 17% as “very likely” for oxygraphy and enzymology, respectively. The techniques did, however, offer synergistic diagnostic prediction, as the sensitivity rose to 88 ± 11% when considered together. Similarly, the techniques offered varying defect specific information, such as the ability of enzymology to identify isolated OXPHOS deficiencies, while oxygraphy pinpointed PDHC mutations and captured POLG mutations that were otherwise missed by enzymology. In summary, oxygraphy provides useful information for the diagnosis of PMD, and should be considered in conjunction with enzymology for the diagnosis of PMD.

Validation of next-generation sequencing technologies in genetic diagnosis of dementia

2014 ◽  
Vol 35 (1) ◽  
pp. 261-265 ◽  
Author(s):  
John Beck ◽  
Alan Pittman ◽  
Gary Adamson ◽  
Tracy Campbell ◽  
Joanna Kenny ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Genetic Diagnosis ◽  
Next Generation ◽  
Sequencing Technologies ◽  
Diagnosis Of Dementia ◽  
Generation Sequencing

scholarly journals Diagnosing Mitochondrial Disorders Remains Challenging in the Omics Era

2021 ◽  
Vol 7 (3) ◽  
pp. e597
Author(s):  
Patrick Forny ◽  
Emma Footitt ◽  
James E. Davison ◽  
Amanda Lam ◽  
Cathy E. Woodward ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Muscle Biopsy ◽  
Mitochondrial Disease ◽  
Biochemical Markers ◽  
Genetic Diagnosis ◽  
Mitochondrial Disorders ◽  
Biochemical Tests ◽  
Respiratory Chain Enzyme ◽  
Clinical Exome Sequencing ◽  
Respiratory Chain Enzyme Activity

ObjectiveWe hypothesized that novel investigative pathways are needed to decrease diagnostic odysseys in pediatric mitochondrial disease and sought to determine the utility of clinical exome sequencing in a large cohort with suspected mitochondrial disease and to explore whether any of the traditional indicators of mitochondrial disease predict a confirmed genetic diagnosis.MethodsWe investigated a cohort of 85 pediatric patients using clinical exome sequencing and compared the results with the outcome of traditional diagnostic tests, including biochemical testing of routine parameters (lactate, alanine, and proline), neuroimaging, and muscle biopsy with histology and respiratory chain enzyme activity studies.ResultsWe established a genetic diagnosis in 36.5% of the cohort and report 20 novel disease-causing variants (1 mitochondrial DNA). Counterintuitively, routine biochemical markers were more predictive of mitochondrial disease than more invasive and elaborate muscle studies.ConclusionsWe propose using biochemical markers to support the clinical suspicion of mitochondrial disease and then apply first-line clinical exome sequencing to identify a definite diagnosis. Muscle biopsy studies should only be used in clinically urgent situations or to confirm an inconclusive genetic result.Classification of EvidenceThis is a Class II diagnostic accuracy study showing that the combination of CSF and plasma biochemical tests plus neuroimaging could predict the presence or absence of exome sequencing confirmed mitochondrial disorders.

P1-182: Validation of next-generation sequencing technologies to radically change dementia genetic diagnosis

2013 ◽  
Vol 9 ◽  
pp. P215-P215
Author(s):  
Jon Beck ◽  
Gary Adamson ◽  
Tracy Campbell ◽  
Janna Kenny ◽  
Henry Houlden ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Genetic Diagnosis ◽  
Next Generation ◽  
Sequencing Technologies ◽  
Generation Sequencing

scholarly journals Detection of pathogenic splicing events from RNA-sequencing data using dasper

2021 ◽  
Author(s):  
David Zhang ◽  
Regina H. Reynolds ◽  
Sonia Garcia-Ruiz ◽  
Emil K Gustavsson ◽  
Sid Sethi ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Diagnostic Yield ◽  
Genetic Diagnosis ◽  
Fibroblast Cell ◽  
Sequencing Data ◽  
Sequencing Technologies ◽  
Pathogenic Variants ◽  
Splicing Variants ◽  
Gene Filter ◽  
Disease Associations

AbstractAlthough next-generation sequencing technologies have accelerated the discovery of novel gene-to-disease associations, many patients with suspected Mendelian diseases still leave the clinic without a genetic diagnosis. An estimated one third of these patients will have disorders caused by mutations impacting splicing. RNA-sequencing has been shown to be a promising diagnostic tool, however few methods have been developed to integrate RNA-sequencing data into the diagnostic pipeline. Here, we introduce dasper, an R/Bioconductor package that improves upon existing tools for detecting aberrant splicing by using machine learning to incorporate disruptions in exon-exon junction counts as well as coverage. dasper is designed for diagnostics, providing a rank-based report of how aberrant each splicing event looks, as well as including visualization functionality to facilitate interpretation. We validate dasper using 16 patient-derived fibroblast cell lines harbouring pathogenic variants known to impact splicing. We find that dasper is able to detect pathogenic splicing events with greater accuracy than existing LeafCutterMD or z-score approaches. Furthermore, by only applying a broad OMIM gene filter (without any variant-level filters), dasper is able to detect pathogenic splicing events within the top 10 most aberrant identified for each patient. Since using publicly available control data minimises costs associated with incorporating RNA-sequencing into diagnostic pipelines, we also investigate the use of 504 GTEx fibroblast samples as controls. We find that dasper leverages publicly available data effectively, ranking pathogenic splicing events in the top 25. Thus, we believe dasper can increase diagnostic yield for a pathogenic splicing variants and enable the efficient implementation of RNA-sequencing for diagnostics in clinical laboratories.

scholarly journals The Application of Whole−Exome Sequencing in Patients With FUO

2022 ◽  
Vol 11 ◽  
Author(s):  
Wanru Guo ◽  
Xuewen Feng ◽  
Ming Hu ◽  
Yanwan Shangguan ◽  
Jiafeng Xia ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Fever Of Unknown Origin ◽  
Genetic Diagnosis ◽  
Clinical Information ◽  
Unknown Origin ◽  
Sequencing Technologies ◽  
Whole Exome ◽  
Positive Results ◽  
Generation Sequencing

BackgroundFever of unknown origin (FUO) is still a challenge for clinicians. Next-generation sequencing technologies, such as whole exome sequencing (WES), can be used to identify genetic defects in patients and assist in diagnosis. In this study, we investigated the application of WES in individuals with FUO.MethodsWe performed whole-exome sequencing on 15 FUO patients. Clinical information was extracted from the hospital information system.ResultsIn 7/15 samples, we found positive results, including potentially causative mutations across eight different genes: CFTR, CD209, IRF2BP2, ADGRV 1, TYK2, MEFV, THBD and GATA2.ConclusionsOur results show that whole-exome sequencing can promote the genetic diagnosis and treatment of patients with FUO.

scholarly journals Diagnosis of ‘possible’ mitochondrial disease: an existential crisis

2019 ◽  
Vol 56 (3) ◽  
pp. 123-130 ◽  
Author(s):  
Sumit Parikh ◽  
Amel Karaa ◽  
Amy Goldstein ◽  
Enrico Silvio Bertini ◽  
Patrick F Chinnery ◽  
...  
Keyword(s):  
Mitochondrial Disease ◽  
Clinical Phenotype ◽  
Genetic Disorders ◽  
Genetic Diagnosis ◽  
Mitochondrial Diseases ◽  
Genomic Testing ◽  
Existential Crisis ◽  
Specific Description ◽  
Genetic Abnormalities ◽  
Biochemical Abnormalities

Primary genetic mitochondrial diseases are often difficult to diagnose, and the term ‘possible’ mitochondrial disease is used frequently by clinicians when such a diagnosis is suspected. There are now many known phenocopies of mitochondrial disease. Advances in genomic testing have shown that some patients with a clinical phenotype and biochemical abnormalities suggesting mitochondrial disease may have other genetic disorders. In instances when a genetic diagnosis cannot be confirmed, a diagnosis of ‘possible’ mitochondrial disease may result in harm to patients and their families, creating anxiety, delaying appropriate diagnosis and leading to inappropriate management or care. A categorisation of ‘diagnosis uncertain’, together with a specific description of the metabolic or genetic abnormalities identified, is preferred when a mitochondrial disease cannot be genetically confirmed.

Approaches to Finding the Molecular Basis of Mitochondrial Oxidative Phosphorylation Disorders

2008 ◽  
Vol 11 (4) ◽  
pp. 395-411 ◽  
Author(s):  
Denise M. Kirby ◽  
David R. Thorburn
Keyword(s):  
Mitochondrial Dna ◽  
Oxidative Phosphorylation ◽  
Mitochondrial Disease ◽  
De Novo ◽  
Genetic Diagnosis ◽  
Nuclear Genes ◽  
Mitochondrial Oxidative Phosphorylation ◽  
Inherited Disorders ◽  
Protein Subunits ◽  
Wide Range

AbstractInherited disorders of mitochondrial oxidative phosphorylation are the most common group of inborn errors of metabolism and cause a wide range of clinical presentations. Mitochondrial DNA encodes 13 protein subunits required for oxidative phosphorylation plus 22 transfer RNAs and two ribosomal RNAs, and mutations in most of these genes cause human disease. Nuclear genes encode most of the protein subunits and all other proteins required for mitochondrial biogenesis and mitochondrial DNA replication and expression. Mutations in 64 nuclear genes and 34 mitochondrial genes are now known to cause mitochondrial disease and many novel mitochondrial disease genes await discovery. The genetic complexity of oxidative phosphorylation means that maternal, autosomal recessive, autosomal dominant and X-linked modes of inheritance can occur, along with de novo mutations. This complexity presents a challenge in planning efficient molecular genetic diagnosis of patients with suspected mitochondrial disease. In some situations, clinical phenotype can be strongly predictive of the underlying genotype. However, more often this is not the case and it is usually helpful, particularly with pediatric patients, to determine whether the activity of one or more of the individual oxidative phosphorylation enzymes is deficient before proceeding with mutation analysis. In this review we will summarize the genetic bases of mitochondrial disease and discuss some approaches to integrate information from clinical presentation, laboratory findings, family history, and imaging to guide molecular investigation.

scholarly journals Rapid Exome Sequencing for Critically Ill Children: Implementation and Challenges in the Asian Context

2021 ◽  
Author(s):  
Nikki Fong ◽  
Jiin Ying Lim ◽  
Breana Cham ◽  
Sylvia Kam ◽  
Chew Yin Goh ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Critically Ill ◽  
Diagnostic Yield ◽  
Genetic Disorders ◽  
Genetic Diagnosis ◽  
Critically Ill Children ◽  
Diagnostic Study ◽  
Next Generation ◽  
Paediatric Patients ◽  
Generation Sequencing

Abstract Objective: Use rapid next-generation sequencing (NGS) to improve our diagnostic yield in critically ill paediatric patients with suspected genetic disorders in the Asian setting.Design: A diagnostic study conducted between April 2018 and January 2019.Methods: Next-generation sequencing was performed with the TruSight One gene panel (targeting 4813 genes) followed by MiSeq sequencing on 10 patients who presented with suspected genetic disorders as assessed by their attending physicians. Results: In 4 of the 10 cases (40%), a genetic diagnosis was achieved, with one further case diagnosed on re-analysis of data 2 years later. The median turn-around time (TAT) for results was 9.5 working days (range 5-19 days). Challenges faced during implementation included sample availability, managing parental and primary physician expectations, cost of testing, and bioinformatic resources.Conclusion: RapidSeq is an effective method for diagnosing patients with rare diseases, which aids in shortening the diagnostic odyssey, while allowing clinicians to appropriately tailor management for the underlying disorder, and provide accurate genetic counselling for families. However, challenges such as cost and insurance implications still remain a barrier to more widespread use of genomic testing in the local setting, and continued efforts will be required to optimise RapidSeq for use in paediatric patients in the ICU.

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