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Mitochondria sequence mapping strategies and practicability of mitochondria variant detection from exome and RNA sequencing data
2015
Briefings in Bioinformatics
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We designed a study to evaluate the practicability of mtDNA variant detection using exome and RNA sequencing data. ...
Mitochondrial targeted sequencing was used as the gold standard to compute the validation and false discovery rates of SNP and heteroplasmy detection in exome and RNAseq data. ...
for Clinical and Translational Research (VR7875 towards sequencing of the two total RNA library samples). ...
doi:10.1093/bib/bbv057
pmid:26249222
pmcid:PMC5974936
fatcat:pwzfbvlw2vdebclt7btbywu4f4
The genetics of mitochondrial disease: dissecting mitochondrial pathology using multi-omic pipelines
2021
Journal of Pathology
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Next-generation sequencing strategies, particularly exome and whole-genome sequencing, have revolutionised mitochondrial diagnostics such that the traditional muscle biopsy has largely been replaced with ...
The application of supplementary 'omics' technologies, including transcriptomics, proteomics, and metabolomics, has the potential to greatly improve diagnostic strategies. ...
for Mitochondrial Research (203105/Z/16/Z), the German Bundesministerium für Bildung und Forschung (BMBF) through the German network for mitochondrial disorders (mitoNET; 01GM1906D), the German BMBF and ...
doi:10.1002/path.5641
pmid:33586140
pmcid:PMC8600955
fatcat:c3nc665fszd5xjs6ph7tw6doju
High-throughput sequencing in mitochondrial DNA research
2014
Mitochondrion (Amsterdam. Print)
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Based on previous studies conducted by various groups, we provide strategies for processing mitochondrial DNA sequencing data, including assembly, variant calling, and quality control. ...
Mitochondrial research has also benefitted greatly from high-throughput sequencing; sequencing technology now allows for screening of all 16569 base pairs of the mitochondrial genome simultaneously for ...
Yan Guo, and ...
doi:10.1016/j.mito.2014.05.004
pmid:24859348
pmcid:PMC4149223
fatcat:oyygad2lz5bwja5pusosojftbq
Signal transducer and activator of transcription 2 deficiency is a novel disorder of mitochondrial fission
2015
Brain
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In muscle and fibroblasts from these patients, and a third unrelated STAT2-deficient patient, we observed extremely elongated mitochondria. ...
In two children presenting with severe neurological deterioration following viral infection we identified a novel homozygous STAT2 mutation, c.1836 C4A (p.Cys612Ter), using whole exome sequencing. ...
and Joshua Paulin for technical assistance. ...
doi:10.1093/brain/awv182
pmid:26122121
pmcid:PMC5808733
fatcat:5qh3omrvkrhofbgdy44li4oo6u
Next-generation sequencing for mitochondrial disorders
2014
British Journal of Pharmacology
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Here we review the strategies and findings from studies applying next-generation sequencing methods for the genetic diagnosis of mitochondrial disorders. ...
A great deal of our understanding of mitochondrial function has come from studies of inherited mitochondrial diseases, but still majority of the patients lack molecular diagnosis. ...
C. is supported by a postdoctoral research fellowship from the Academy of Finland. ...
doi:10.1111/bph.12469
pmid:24138576
pmcid:PMC3976608
fatcat:h36jgwai3vevrb6sasgj3tb34q
Candidate Modifier Genes for the Penetrance of Leber's Hereditary Optic Neuropathy
2022
International Journal of Molecular Sciences
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Whole exome sequencing (WES) is a new molecular technique for sequencing the protein-coding region of all genes in a whole genome. We performed WES from five families with 17 members. ...
Through whole exome analysis, we found that many mitochondria related (MT-related) nuclear genes have high percentage of variants in either the proband group or control group. ...
Acknowledgments: We thank Shao-Min Wu (Compassbioinfo Inc.) for the assistance and consultation of the WES data analysis.
Conflicts of Interest: The authors declare no conflict of interest. ...
doi:10.3390/ijms231911891
pmid:36233195
pmcid:PMC9569928
fatcat:yyugjyh4xbamfltdej5si5db3a
TNNI3K mutation in familial syndrome of conduction system disease, atrial tachyarrhythmia and dilated cardiomyopathy
2014
Human Molecular Genetics
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Whole-exome sequencing (WES) provides a powerful new tool for familial disease gene discovery. ...
Variants from WES of two affected cousins were filtered for rare, predicted-deleterious, positional variants, revealing an unreported heterozygous missense mutation disrupting the highly conserved kinase ...
ACKNOWLEDGEMENTS We thank the family and patients who participated in this study and the physicians who referred them. ...
doi:10.1093/hmg/ddu297
pmid:24925317
pmcid:PMC4189907
fatcat:pl4mksqf5vhy3isu47nnbipt7q
Evaluation of Allele Frequency Estimation Using Pooled Sequencing Data Simulation
2013
The Scientific World Journal
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In this study, we designed a rigorous simulation model to test the practicability of estimating allele frequency from pooled sequencing data. ...
We found that pooled sequencing data can introduce high levels of relative error rate (defined as error rate divided by targeted allele frequency) and that the error rate is more severe for low minor allele ...
Acknowledgments The authors would like to thank Peggy Schuyler and Margot Bjoring for their editorial support. ...
doi:10.1155/2013/895496
pmid:23476151
pmcid:PMC3582166
fatcat:3jesnzo4b5f7rdo7pj4uimymzy
Next-Generation Sequencing in Genetic Hearing Loss
2013
Genetic Testing and Molecular Biomarkers
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The recent technological advances in target-enrichment methods and next generation sequencing offer a unique opportunity to break through the barriers of limitations imposed by gene arrays. ...
The advent of the $1000 genome has the potential to revolutionize the identification of genes and their mutations underlying genetic disorders. ...
Acknowledgments This work was supported by the National Institutes of Health grants R01DC05575, 1 R01 DC012546-01, translational R01DC012115, and the Hurong Scholar award at the Central-South University ...
doi:10.1089/gtmb.2012.0464
pmid:23738631
pmcid:PMC3732417
fatcat:ysrmhfxvrjd63hx3b5qvi6rw2i
Detection of canonical A-to-G editing events at 3' UTRs and microRNA target sites in human lungs using next-generation sequencing
2015
OncoTarget
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In this study, we sequenced DNA and RNA from human lungs and identified RNA editing sites with high confidence via a computational pipeline utilizing stringent analysis thresholds. ...
The majority of these changes result from adenosine deaminase acting on RNA (ADARs) catalyzing the conversion of adenosine residues to inosine in double-stranded RNAs (dsRNAs). ...
Secondly, we have adopted a strict two-pass alignment strategy adopted as the GATK best practice for calling sequencing variants from RNA (https://www.broadinstitute.org/gatk/guide/ article?id=3891). ...
doi:10.18632/oncotarget.6132
pmid:26486088
pmcid:PMC4742137
fatcat:6k2zledabvgqzhtvjh24hgnwdu
Systematic comparative analysis of single-nucleotide variant detection methods from single-cell RNA sequencing data
2019
Genome Biology
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While SNV detection from abundant single-cell RNA sequencing (scRNA-seq) data is applicable and cost-effective in identifying expressed variants, inferring sub-clones, and deciphering genotype-phenotype ...
Although variant callers for bulk RNA-seq have been sporadically used in scRNA-seq, the performances of different tools have not been assessed. ...
We also thank Iain Bruce for the English editing, and the Computing Platform of the CLS (Peking University). ...
doi:10.1186/s13059-019-1863-4
pmid:31744515
pmcid:PMC6862814
fatcat:opwccwv5i5g5df7srym2bx4jq4
Precision mitochondrial medicine
2022
Cambridge Prisms: Precision Medicine
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Mitochondria play a key role in cell homeostasis as a major source of intracellular energy (adenosine triphosphate), and as metabolic hubs regulating many canonical cell processes. ...
diseases, opening to door for the incorporation of mitochondrial genetic variant analysis in population disease risk stratification. ...
Acknowledgements PFC is a Wellcome Trust Principal Research Fellow (212219/Z/18/Z), and a UK NIHR Senior Investigator, who receives support from the Medical Research Council Mitochondrial Biology ...
doi:10.1017/pcm.2022.8
pmid:38550943
pmcid:PMC10953752
fatcat:dkc2paj66bd45pwgr2yadhb6dm
Next-generation sequencing data analysis Xinkun Wan
2017
Briefings in Bioinformatics
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My sincere thanks also goes to my colleagues at the Institute of Human Genetics for a great working atmosphere and for helping me with all the big and small problems that are an unavoidable part of each ...
I want to especially thank Alice and Thomas for correcting this thesis. And last but not least I want to thank my friends and family, without whom I couldn't have done this whole project. ...
First of all I want to thank my supervisor Tim Strom for all his advice and guidance over the last couple of years and for giving me the freedom to work on many interesting topics. ...
doi:10.1093/bib/bbx038
fatcat:b7kevx76vjbuld6wdd6u2vnlay
New genes and pathomechanisms in mitochondrial disorders unraveled by NGS technologies
2016
Biochimica et Biophysica Acta - Bioenergetics
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We have been using a combined, two-step strategy, based on targeted genes panel as a first NGS screening, followed by whole exome sequencing (WES) in still unsolved cases, to analyze a large cohort of ...
subjects, that failed to show mutations in mtDNA and in ad hoc sets of specific nuclear genes, sequenced by the Sanger's method. ...
Sequencing of the cDNA obtained from patient's fibroblast RNA showed only the presence of the allele with the missense mutation. ...
doi:10.1016/j.bbabio.2016.02.022
pmid:26968897
fatcat:qcbpucggpnbzfg7z4aqadjt36y
Genetic basis of mitochondrial diseases
2021
FEBS Letters
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The implementation of whole exome sequencing has led to a revolution in their diagnosis, duplicated the number of associated disease genes, and significantly increased the diagnosed fraction. ...
However, the genetic etiology of a substantial fraction of patients exhibiting mitochondrial disorders remains unknown, highlighting limitations in variant detection and interpretation, which calls for ...
Acknowledgements The authors acknowledge the support by a German Federal Ministry of Education and Research (BMBF) Grant to the German Network for Mitochondrial Disorders (mitoNET, 01GM1906B), and by the ...
doi:10.1002/1873-3468.14068
pmid:33655490
fatcat:a7aa23alwzhrrfkebdmqgh6lty
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