Clinical Bioinformatics in Precise Diagnosis of Mitochondrial Disease.

[1]  Larry N. Singh,et al.  Regulation of nuclear epigenome by mitochondrial DNA heteroplasmy , 2019, Proceedings of the National Academy of Sciences.

[2]  John Reynders,et al.  Diagnosis of genetic diseases in seriously ill children by rapid whole-genome sequencing and automated phenotyping and interpretation , 2019, Science Translational Medicine.

[3]  Marni J. Falk,et al.  Landscape of Germline and Somatic Mitochondrial DNA Mutations in Pediatric Malignancies. , 2019, Cancer research.

[4]  Ryan L. Collins,et al.  Variation across 141,456 human exomes and genomes reveals the spectrum of loss-of-function intolerance across human protein-coding genes , 2019, bioRxiv.

[5]  K. Kinoshita,et al.  3.5KJPNv2: an allele frequency panel of 3552 Japanese individuals including the X chromosome , 2019, Human Genome Variation.

[6]  C. Bris,et al.  Bioinformatics Tools and Databases to Assess the Pathogenicity of Mitochondrial DNA Variants in the Field of Next Generation Sequencing , 2018, Front. Genet..

[7]  Marni J. Falk,et al.  Mitochondrial disease genetics update: recent insights into the molecular diagnosis and expanding phenotype of primary mitochondrial disease , 2018, Current opinion in pediatrics.

[8]  Tudor Groza,et al.  Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources , 2018, Nucleic Acids Res..

[9]  Marcella Attimonelli,et al.  HmtVar: a new resource for human mitochondrial variations and pathogenicity data , 2018, Nucleic Acids Res..

[10]  D. Wallace.  Mitochondrial genetic medicine , 2018, Nature Genetics.

[11]  Marni J. Falk,et al.  MSeqDR mvTool: A mitochondrial DNA Web and API resource for comprehensive variant annotation, universal nomenclature collation, and reference genome conversion , 2018, Human mutation.

[12]  Robert W. Taylor,et al.  mtDNA heteroplasmy level and copy number indicate disease burden in m.3243A>G mitochondrial disease , 2018, EMBO molecular medicine.

[13]  Vincent Procaccio,et al.  Predicting the pathogenicity of novel variants in mitochondrial tRNA with MitoTIP , 2017, PLoS Comput. Biol..

[14]  P. Chinnery,et al.  Background sequence characteristics influence the occurrence and severity of disease-causing mtDNA mutations , 2017, PLoS genetics.

[15]  S. Plon,et al.  Evaluation of in silico algorithms for use with ACMG/AMP clinical variant interpretation guidelines , 2017, bioRxiv.

[16]  Angelo L. Vescovi,et al.  High-confidence assessment of functional impact of human mitochondrial non-synonymous genome variations by APOGEE , 2017, PLoS Comput. Biol..

[17]  Koji Ishiya,et al.  MitoSuite: a graphical tool for human mitochondrial genome profiling in massive parallel sequencing , 2017, PeerJ.

[18]  Funded Statistical Methods groups-AWG,et al.  Improving genetic diagnosis in Mendelian disease with transcriptome sequencing , 2017 .

[19]  Elvira Mayordomo,et al.  Machine learning classifier for identification of damaging missense mutations exclusive to human mitochondrial DNA-encoded polypeptides , 2017, BMC Bioinformatics.

[20]  Thomas Meitinger,et al.  Genetic diagnosis of Mendelian disorders via RNA sequencing , 2017, Nature Communications.

[21]  Marcella Attimonelli,et al.  HmtDB 2016: data update, a better performing query system and human mitochondrial DNA haplogroup predictor , 2016, Nucleic Acids Res..

[22]  Tudor Groza,et al.  The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species , 2016, bioRxiv.

[23]  Núria Queralt-Rosinach,et al.  DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants , 2016, Nucleic Acids Res..

[24]  Francesco Muntoni,et al.  Improving genetic diagnosis in Mendelian disease with transcriptome sequencing , 2016, Science Translational Medicine.

[25]  R. Płoski,et al.  New perspective in diagnostics of mitochondrial disorders: two years’ experience with whole-exome sequencing at a national paediatric centre , 2016, Journal of Translational Medicine.

[26]  Marcella Attimonelli,et al.  MSeqDR: A Centralized Knowledge Repository and Bioinformatics Web Resource to Facilitate Genomic Investigations in Mitochondrial Disease , 2016, Human mutation.

[27]  Hans-Jürgen Bandelt,et al.  HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing , 2016, Nucleic Acids Res..

[28]  Günther Specht,et al.  mtDNA-Server: next-generation sequencing data analysis of human mitochondrial DNA in the cloud , 2016, Nucleic Acids Res..

[29]  E. Boerwinkle,et al.  dbNSFP v3.0: A One‐Stop Database of Functional Predictions and Annotations for Human Nonsynonymous and Splice‐Site SNVs , 2016, Human mutation.

[30]  Abhishek Niroula,et al.  PON-mt-tRNA: a multifactorial probability-based method for classification of mitochondrial tRNA variations , 2016, Nucleic acids research.

[31]  Damian Smedley,et al.  Next-generation diagnostics and disease-gene discovery with the Exomiser , 2015, Nature Protocols.

[32]  Laura C. Greaves,et al.  The presence of highly disruptive 16S rRNA mutations in clinical samples indicates a wider role for mutations of the mitochondrial ribosome in human disease , 2015, Mitochondrion.

[33]  D. Wallace.  Mitochondrial DNA Variation in Human Radiation and Disease , 2015, Cell.

[34]  Brendan F. Kohrn,et al.  Detection of Ultra-Rare Mitochondrial Mutations in Breast Stem Cells by Duplex Sequencing , 2015, PloS one.

[35]  Patrick F. Chinnery,et al.  The dynamics of mitochondrial DNA heteroplasmy: implications for human health and disease , 2015, Nature Reviews Genetics.

[36]  Gonçalo R. Abecasis,et al.  Assessing Mitochondrial DNA Variation and Copy Number in Lymphocytes of ~2,000 Sardinians Using Tailored Sequencing Analysis Tools , 2015, PLoS genetics.

[37]  Shashikant Kulkarni,et al.  Good laboratory practice for clinical next-generation sequencing informatics pipelines , 2015, Nature Biotechnology.

[38]  Janey L. Wiggs,et al.  Phy-Mer: a novel alignment-free and reference-independent mitochondrial haplogroup classifier , 2015, Bioinform..

[39]  Bale,et al.  Standards and Guidelines for the Interpretation of Sequence Variants: A Joint Consensus Recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology , 2015, Genetics in Medicine.

[40]  Richard J. Rodenburg,et al.  Whole exome sequencing of suspected mitochondrial patients in clinical practice , 2015, Journal of Inherited Metabolic Disease.

[41]  Tommaso Mazza,et al.  MitImpact: an Exhaustive Collection of Pre‐computed Pathogenicity Predictions of Human Mitochondrial Non‐synonymous Variants , 2015, Human mutation.

[42]  Thomas C. Wiegers,et al.  The Comparative Toxicogenomics Database's 10th year anniversary: update 2015 , 2014, Nucleic Acids Res..

[43]  Vincent Procaccio,et al.  Progressive increase in mtDNA 3243A>G heteroplasmy causes abrupt transcriptional reprogramming , 2014, Proceedings of the National Academy of Sciences.

[44]  Ernesto Picardi,et al.  MToolBox: a highly automated pipeline for heteroplasmy annotation and prioritization analysis of human mitochondrial variants in high-throughput sequencing , 2014, Bioinform..

[45]  Y. Okazaki,et al.  Diagnosis and molecular basis of mitochondrial respiratory chain disorders: exome sequencing for disease gene identification. , 2014, Biochimica et biophysica acta.

[46]  Q. Cai,et al.  Very low-level heteroplasmy mtDNA variations are inherited in humans. , 2013, Journal of genetics and genomics = Yi chuan xue bao.

[47]  Christian Gilissen,et al.  A Post‐Hoc Comparison of the Utility of Sanger Sequencing and Exome Sequencing for the Diagnosis of Heterogeneous Diseases , 2013, Human mutation.

[48]  Deanna M. Church,et al.  ClinVar: public archive of relationships among sequence variation and human phenotype , 2013, Nucleic Acids Res..

[49]  Laura C. Greaves,et al.  The role of the mitochondrial ribosome in human disease: searching for mutations in 12S mitochondrial rRNA with high disruptive potential , 2013, Human molecular genetics.

[50]  D. Wallace,et al.  Mitochondrial DNA genetics and the heteroplasmy conundrum in evolution and disease. , 2013, Cold Spring Harbor perspectives in biology.

[51]  M. Nalls,et al.  Two-stage association study and meta-analysis of mitochondrial DNA variants in Parkinson disease , 2013, Neurology.

[52]  V. Mootha,et al.  Targeted exome sequencing of suspected mitochondrial disorders , 2013, Neurology.

[53]  Marni J. Falk,et al.  Molecular Genetic Testing for Mitochondrial Disease: From One Generation to the Next , 2013, Neurotherapeutics.

[54]  Jesse J. Salk,et al.  Detection of ultra-rare mutations by next-generation sequencing , 2012, Proceedings of the National Academy of Sciences.

[55]  S. Dimauro,et al.  Mitochondrial Diseases , 2012, Journal of epilepsy research.

[56]  D. Jaffe,et al.  Molecular Diagnosis of Infantile Mitochondrial Disease with Targeted Next-Generation Sequencing , 2012, Science Translational Medicine.

[57]  Jared C. Roach,et al.  Kaviar: an accessible system for testing SNV novelty , 2011, Bioinform..

[58]  Yong-Gang Yao,et al.  MitoTool: a web server for the analysis and retrieval of human mitochondrial DNA sequence variations. , 2011, Mitochondrion.

[59]  Thomas Meitinger,et al.  Exome sequencing identifies ACAD9 mutations as a cause of complex I deficiency , 2010, Nature Genetics.

[60]  Manfred Kayser,et al.  Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation , 2009, Human mutation.

[61]  D. Vigetti,et al.  Assessing heteroplasmic load in Leber's hereditary optic neuropathy mutation 3460G->A/MT-ND1 with a real-time PCR quantitative approach. , 2007, The Journal of molecular diagnostics : JMD.

[62]  Pierre Baldi,et al.  An enhanced MITOMAP with a global mtDNA mutational phylogeny , 2006, Nucleic Acids Res..

[63]  Alan F. Scott,et al.  Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders , 2002, Nucleic Acids Res..

[64]  A. Torroni,et al.  Phylogenetic analysis of Leber's hereditary optic neuropathy mitochondrial DNA's indicates multiple independent occurrences of the common mutations , 1995, Human mutation.