Genetic diagnosis of Mendelian disorders via RNA sequencing

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

[2]  Gao Wang,et al.  The impact of rare variation on gene expression across tissues , 2016, Nature.

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

[4]  David A. Knowles,et al.  LeafCutter: annotation-free quantification of RNA splicing , 2016, bioRxiv.

[5]  R. Wiesner,et al.  CLPP coordinates mitoribosomal assembly through the regulation of ERAL1 levels , 2016, The EMBO journal.

[6]  Michaela Frye,et al.  Deficient methylation and formylation of mt-tRNAMet wobble cytosine in a patient carrying mutations in NSUN3 , 2016, Nature Communications.

[7]  Christopher R. Sibley,et al.  Lessons from non-canonical splicing , 2016, Nature Reviews Genetics.

[8]  David A. Knowles,et al.  RNA splicing is a primary link between genetic variation and disease , 2016, Science.

[9]  David T. Miller,et al.  A Clinician’s perspective on clinical exome sequencing , 2016, Human Genetics.

[10]  R. Aebersold,et al.  On the Dependency of Cellular Protein Levels on mRNA Abundance , 2016, Cell.

[11]  Guoli Ji,et al.  Exploiting aberrant mRNA expression in autism for gene discovery and diagnosis , 2015, Human Genetics.

[12]  Jing Zhao,et al.  A Burden of Rare Variants Associated with Extremes of Gene Expression in Human Peripheral Blood. , 2016, American journal of human genetics.

[13]  T. Meitinger,et al.  Human thioredoxin 2 deficiency impairs mitochondrial redox homeostasis and causes early-onset neurodegeneration. , 2016, Brain : a journal of neurology.

[14]  Michael D. Wilson,et al.  RNAseq analysis for the diagnosis of muscular dystrophy , 2015, Annals of clinical and translational neurology.

[15]  M. Swanson,et al.  RNA mis-splicing in disease , 2015, Nature Reviews Genetics.

[16]  James Y. Zou.  Analysis of protein-coding genetic variation in 60,706 humans , 2015, Nature.

[17]  Y. Qu,et al.  A rare variant (c.863G>T) in exon 7 of SMN1 disrupts mRNA splicing and is responsible for spinal muscular atrophy , 2015, European Journal of Human Genetics.

[18]  Hiromi W L Koh,et al.  Differential dynamics of the mammalian mRNA and protein expression response to misfolding stress , 2015, bioRxiv.

[19]  R. Sandberg,et al.  Random monoallelic expression of autosomal genes: stochastic transcription and allele-level regulation , 2015, Nature Reviews Genetics.

[20]  Gabor T. Marth,et al.  A global reference for human genetic variation , 2015, Nature.

[21]  Gabor T. Marth,et al.  An integrated map of structural variation in 2,504 human genomes , 2015, Nature.

[22]  J. Ganesh,et al.  Recurrent De Novo Mutations Affecting Residue Arg138 of Pyrroline-5-Carboxylate Synthase Cause a Progeroid Form of Autosomal-Dominant Cutis Laxa. , 2015, American journal of human genetics.

[23]  Karynne E. Patterson,et al.  The Genetic Basis of Mendelian Phenotypes: Discoveries, Challenges, and Opportunities. , 2015, American journal of human genetics.

[24]  A. Durr,et al.  Alteration of ornithine metabolism leads to dominant and recessive hereditary spastic paraplegia. , 2015, Brain : a journal of neurology.

[25]  Davis J. McCarthy,et al.  Factors influencing success of clinical genome sequencing across a broad spectrum of disorders , 2015, Nature Genetics.

[26]  G. Gibson.  GTEx detects genetic effects , 2015, Science.

[27]  Georgia Drakakaki,et al.  Beyond Glycolysis: GAPDHs Are Multi-functional Enzymes Involved in Regulation of ROS, Autophagy, and Plant Immune Responses , 2015, PLoS genetics.

[28]  T. Meitinger,et al.  Spectrum of combined respiratory chain defects , 2015, Journal of Inherited Metabolic Disease.

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

[30]  X. Bian,et al.  Systemic Delivery of MicroRNA-101 Potently Inhibits Hepatocellular Carcinoma In Vivo by Repressing Multiple Targets , 2015, PLoS genetics.

[31]  Lora J. H. Bean,et al.  A comprehensive genomic approach for neuromuscular diseases gives a high diagnostic yield , 2015, Annals of neurology.

[32]  Matthew E. Ritchie,et al.  limma powers differential expression analyses for RNA-sequencing and microarray studies , 2015, Nucleic acids research.

[33]  B. Frey,et al.  The human splicing code reveals new insights into the genetic determinants of disease , 2015, Science.

[34]  Guoli Ji,et al.  Aberrant Gene Expression in Humans , 2015, PLoS genetics.

[35]  S. Subramanian,et al.  Europeans have a higher proportion of high-frequency deleterious variants than Africans , 2015, Human Genetics.

[36]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[37]  Matthias Mann,et al.  The Q Exactive HF, a Benchtop Mass Spectrometer with a Pre-filter, High-performance Quadrupole and an Ultra-high-field Orbitrap Analyzer* , 2014, Molecular & Cellular Proteomics.

[38]  Beril Talim,et al.  Use of whole-exome sequencing to determine the genetic basis of multiple mitochondrial respiratory chain complex deficiencies. , 2014, JAMA.

[39]  Jeffrey R. Whiteaker,et al.  Proteogenomic characterization of human colon and rectal cancer , 2014, Nature.

[40]  Marco Y. Hein,et al.  Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ * , 2014, Molecular & Cellular Proteomics.

[41]  David L. Spector,et al.  Random monoallelic expression: regulating gene expression one allele at a time. , 2014, Trends in genetics : TIG.

[42]  John P. Overington,et al.  An atlas of genetic influences on human blood metabolites , 2014, Nature Genetics.

[43]  M. Mann,et al.  Minimal, encapsulated proteomic-sample processing applied to copy-number estimation in eukaryotic cells , 2014, Nature Methods.

[44]  Allyn McConkie-Rosell,et al.  The utility of the traditional medical genetics diagnostic evaluation in the context of next-generation sequencing for undiagnosed genetic disorders , 2013, Genetics in Medicine.

[45]  Edward L. Huttlin,et al.  TIMMDC1/C3orf1 Functions as a Membrane-Embedded Mitochondrial Complex I Assembly Factor through Association with the MCIA Complex , 2013, Molecular and Cellular Biology.

[46]  I. Fearnley,et al.  Assembly factors for the membrane arm of human complex I , 2013, Proceedings of the National Academy of Sciences.

[47]  Julien Gagneur,et al.  Genotype-Environment Interactions Reveal Causal Pathways That Mediate Genetic Effects on Phenotype , 2013, PLoS genetics.

[48]  Robert W. Taylor,et al.  ELAC2 mutations cause a mitochondrial RNA processing defect associated with hypertrophic cardiomyopathy. , 2013, American journal of human genetics.

[49]  Robert Gentleman,et al.  Software for Computing and Annotating Genomic Ranges , 2013, PLoS Comput. Biol..

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

[51]  Julian R. E. Davis,et al.  Perrault syndrome is caused by recessive mutations in CLPP, encoding a mitochondrial ATP-dependent chambered protease. , 2013, American journal of human genetics.

[52]  Heng Li.  Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM , 2013, 1303.3997.

[53]  Roderic Guigó,et al.  Intron-centric estimation of alternative splicing from RNA-seq data , 2012, Bioinform..

[54]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[55]  Vamsi K. Mootha,et al.  Mitochondrial disorders as windows into an ancient organelle , 2012, Nature.

[56]  Bronwen L. Aken,et al.  GENCODE: The reference human genome annotation for The ENCODE Project , 2012, Genome research.

[57]  T. Cooper,et al.  Pre-mRNA splicing in disease and therapeutics. , 2012, Trends in molecular medicine.

[58]  Matthias Mann,et al.  SprayQc: a real-time LC-MS/MS quality monitoring system to maximize uptime using off the shelf components. , 2012, Journal of proteome research.

[59]  C. Kratz,et al.  Faculty Opinions recommendation of Compound inheritance of a low-frequency regulatory SNP and a rare null mutation in exon-junction complex subunit RBM8A causes TAR syndrome. , 2012 .

[60]  M. Baumgartner,et al.  Lack of the mitochondrial protein acylglycerol kinase causes Sengers syndrome. , 2012, American journal of human genetics.

[61]  F. Piva,et al.  SpliceAid 2: A database of human splicing factors expression data and RNA target motifs , 2012, Human mutation.

[62]  Julian R. E. Davis,et al.  Perrault syndrome: further evidence for genetic heterogeneity , 2012, Journal of Neurology.

[63]  Heng Li,et al.  A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data , 2011, Bioinform..

[64]  T. Tatusova,et al.  Cryptic splice sites and split genes , 2011, Nucleic acids research.

[65]  M. Mann,et al.  Andromeda: a peptide search engine integrated into the MaxQuant environment. , 2011, Journal of proteome research.

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

[67]  Anne M. Evans,et al.  Organization of GC/MS and LC/MS metabolomics data into chemical libraries , 2010, J. Cheminformatics.

[68]  A. Vogler,et al.  Why barcode? High-throughput multiplex sequencing of mitochondrial genomes for molecular systematics , 2010, Nucleic acids research.

[69]  M. DePristo,et al.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.

[70]  Daniel Rios,et al.  Bioinformatics Applications Note Databases and Ontologies Deriving the Consequences of Genomic Variants with the Ensembl Api and Snp Effect Predictor , 2022 .

[71]  J. Smeitink,et al.  Detection and manipulation of mitochondrial reactive oxygen species in mammalian cells. , 2010, Biochimica et biophysica acta.

[72]  W. Huber,et al.  which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets , 2011 .

[73]  Corey D. DeHaven,et al.  Integrated, nontargeted ultrahigh performance liquid chromatography/electrospray ionization tandem mass spectrometry platform for the identification and relative quantification of the small-molecule complement of biological systems. , 2009, Analytical chemistry.

[74]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[75]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[76]  C. Béroud,et al.  Human Splicing Finder: an online bioinformatics tool to predict splicing signals , 2009, Nucleic acids research.

[77]  M. Mann,et al.  MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification , 2008, Nature Biotechnology.

[78]  Y. Aniya,et al.  Novel function of glutathione transferase in rat liver mitochondrial membrane: role for cytochrome c release from mitochondria. , 2008, Toxicology and applied pharmacology.

[79]  I. Tetko,et al.  MitoP2: An Integrative Tool for the Analysis of the Mitochondrial Proteome , 2008, Molecular biotechnology.

[80]  Gil Ast,et al.  Alternative splicing and disease , 2008, RNA biology.

[81]  Lise Getoor,et al.  SplicePort—An interactive splice-site analysis tool , 2007, Nucleic Acids Res..

[82]  Robert A Hegele,et al.  0021-972X/06/$15.00/0 The Journal of Clinical Endocrinology & Metabolism 91(7):2689–2695 Printed in U.S.A. Copyright © 2006 by The Endocrine Society doi: 10.1210/jc.2005-2746 A LMNA Splicing Mutation in Two Sisters with Severe Dunnigan-Type Familial Parti , 2022 .

[83]  David Haussler,et al.  The UCSC Known Genes , 2006, Bioinform..

[84]  R. Durbin,et al.  The Sequence Ontology: a tool for the unification of genome annotations , 2005, Genome Biology.

[85]  Gene W. Yeo,et al.  Variation in sequence and organization of splicing regulatory elements in vertebrate genes. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[86]  A. Clarke,et al.  Plant mitochondria contain proteolytic and regulatory subunits of the ATP-dependent Clp protease , 2001, Plant Molecular Biology.

[87]  Francesco Muntoni,et al.  Dystrophin and mutations: one gene, several proteins, multiple phenotypes , 2003, The Lancet Neurology.

[88]  D. Thorburn,et al.  Minimum birth prevalence of mitochondrial respiratory chain disorders in children. , 2003, Brain : a journal of neurology.

[89]  M. Baumgartner,et al.  Hyperammonemia with reduced ornithine, citrulline, arginine and proline: a new inborn error caused by a mutation in the gene encoding delta(1)-pyrroline-5-carboxylate synthase. , 2000, Human molecular genetics.

[90]  Gustavo Glusman,et al.  Identification of the gene causing mucolipidosis type IV , 2000, Nature Genetics.

[91]  S. Karlin,et al.  Prediction of complete gene structures in human genomic DNA. , 1997, Journal of molecular biology.

[92]  S. Dimauro,et al.  Mitochondrial diseases. , 1989, Neurologic clinics.

[93]  Y. Hochberg.  A sharper Bonferroni procedure for multiple tests of significance , 1988 .

[94]  E. Adams,et al.  Metabolism of proline and the hydroxyprolines. , 1980, Annual review of biochemistry.

[95]  E. Lewis.  A gene complex controlling segmentation in Drosophila , 1978, Nature.