MSeqDR: A Centralized Knowledge Repository and Bioinformatics Web Resource to Facilitate Genomic Investigations in Mitochondrial Disease

Human Mutation

Volumn 37, Issue 6, 2016, Pages 540-548

  Shen, Lishuang ^a,b   Diroma, Maria Angela ^c,d   Gonzalez, Michael ^e,f   Navarro Gomez, Daniel ^b   Leipzig, Jeremy ^g   Lott, Marie T ^g   van Oven, Mannis ^h   Wallace, Douglas C ^g,i   Muraresku, Colleen Clarke ^g   Zolkipli Cunningham, Zarazuela ^g   Chinnery, Patrick F ^j   Attimonelli, Marcella ^c   Zuchner, Stephan ^e,f   Falk, Marni J ^g,i   Gai, Xiaowu ^a,b  

^a CHILDREN S HOSPITAL LOS ANGELES   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

^c UNIVERSITY OF BARI   (Italy)

^d CEINGE BIOTECNOLOGIE AVANZATE   (Italy)

^e UNIVERSITY OF MIAMI MILLER SCHOOL OF MEDICINE   (United States)

^f The Genesis Project Inc   (United States)

^g CHILDREN S HOSPITAL OF PHILADELPHIA   (United States)

^h ERASMUS MEDICAL CENTER   (Netherlands)

ⁱ UNIVERSITY OF PENNSYLVANIA   (United States)

^j UNIVERSITY OF CAMBRIDGE   (United Kingdom)

more..

Author keywords

Database; Genetics; Informatics; Mitochondria

Indexed keywords

MITOCHONDRIAL DNA;

ACCESS TO INFORMATION; ARTICLE; BIOINFORMATICS; DATABASE MANAGEMENT SYSTEM; DISORDERS OF MITOCHONDRIAL FUNCTIONS; DNA SEQUENCE; EXOME; GENETIC DATABASE; GENETIC VARIATION; GENOME; HUMAN; KNOWLEDGE BASE; MEDICAL TERMINOLOGY; ONTOLOGY; PATHOGENICITY; PHENOTYPE; PRIORITY JOURNAL; BIOLOGY; COMPUTER INTERFACE; GENETICS; GENOMICS; INFORMATION DISSEMINATION; MITOCHONDRIAL GENOME; PROCEDURES; WEB BROWSER;

COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENETIC VARIATION; GENOME, MITOCHONDRIAL; GENOMICS; HUMANS; INFORMATION DISSEMINATION; MITOCHONDRIAL DISEASES; USER-COMPUTER INTERFACE; WEB BROWSER;

EID: 84961876861     PISSN: 10597794     EISSN: 10981004     Source Type: Journal    
DOI: 10.1002/humu.22974     Document Type: Article

References (38)

1. 1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA. 2012. An integrated map of genetic variation from 1, 092 human genomes. Nature 491:56-65.
2. Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR. 2010. A method and server for predicting damaging missense mutations. Nat Methods 7:248-249.
3. Behar DM, van Oven M, Rosset S, Metspalu M, Loogväli EL, Silva NM, Kivisild T, Torroni A, Villems R. 2012. A "Copernican" reassessment of the human mitochondrial DNA tree from its root. Am J Hum Genet 90:675-684.
4. Calabrese C, Simone D, Diroma MA, Santorsola M, Guttà C, Gasparre G, Picardi E, Pesole G, Attimonelli M. 2014. MToolBox: a highly automated pipeline for heteroplasmy annotation and prioritization analysis of human mitochondrial variants in high-throughput sequencing. Bioinformatics 30:3115-3117.
5. Consugar MB, Navarro-Gomez D, Place EM, Bujakowska KM, Sousa ME, Fonseca-Kelly ZD, Taub DG, Janessian M, Wang DY, Au ED, Sims KB, Sweetser DA et al. 2015. Panel-based genetic diagnostic testing for inherited eye diseases is highly accurate and reproducible, and more sensitive for variant detection, than exome sequencing. Genet Med 17:253-261.
6. Cooper GM, Stone EA, Asimenos G; NISC Comparative Sequencing Program, Green ED, Batzoglou S, Sidow A. 2005. Distribution and intensity of constraint in mammalian genomic sequence. Genome Res. 15:901-913.
7. Cunningham F, Ridwan Amode M, Barrell D, Beal K, Billis K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fitzgerald S, Gil L, Garcín Girón C et al. 2015. Ensembl 2015. Nucleic Acids Res 43(Database issue):D662-D669.
8. Damas J, Carneiro J, Amorim A, Pereira F. 2014. MitoBreak: the mitochondrial DNA breakpoints database Nucleic Acids Res 42:D1261-D1268.
9. Davis AP, Wiegers TC, Rosenstein MC, Mattingly CJ. 2012. MEDIC: a practical disease vocabulary used at the Comparative Toxicogenomics Database. Database (Oxford). 2012:bar065.
10. Davis AP, Grondin CJ, Lennon-Hopkins K, Saraceni-Richards C, Sciaky D, King BL, Wiegers TC, Mattingly CJ. 2015. The Comparative Toxicogenomics Database's 10th year anniversary: update 2015. Nucleic Acids Res 43(Database issue):D914-D920.
11. Diroma MA, Calabrese C, Simone D, Santorsola M, Calabrese FM, Gasparre G, Attimonelli M. 2014. Extraction and annotation of human mitochondrial genomes from 1000 Genomes Whole Exome Sequencing data. BMC Genomics 15(Suppl 3):S2.
12. Exome Aggregation Consortium, Lek M, Karczewski K, Minikel E, Samocha K, Banks E, Fennell F, O'Donnell-Luria A, Ware J, Hill A, Cummings B, Tukiainen T et al. 2015. Analysis of protein-coding genetic variation in 60, 706 humans. bioRxiv 030338. doi:10.1101/030338.
13. Falk MJ, Shen L, Gonzalez M, Leipzig J, Lott MT, Stassen AP, Diroma MA, Navarro-Gomez D, Yeske P, Bai R, Boles RG, Brilhante V et al. 2015. Mitochondrial Disease Sequence Data Resource (MSeqDR): a global grass-roots consortium to facilitate deposition, curation, annotation, and integrated analysis of genomic data for the mitochondrial disease clinical and research communities. Mol Genet Metab 114:388-396.
14. Falk MJ, Zhang Q, Nakamaru-Ogiso E, Kannabiran C, Fonseca-Kelly Z, Chakarova C, Audo I, Mackay DS, Zeitz C, Borman AD, Staniszewska M, Shukla R et al. 2012. NMNAT1 mutations cause Leber congenital amaurosis. Nat Genet 44:1040-1045.
15. Finsterer J, Harbo HF, Baets J, Van Broeckhoven C, Di Donato S, Fontaine B, De Jonghe P, Lossos A, Lynch T, Mariotti C, Schöls L et al. 2009. EFNS guidelines on the molecular diagnosis of mitochondrial disorders. Eur J Neurol 16:1255-1264.
16. Fokkema IF, Taschner PE, Schaafsma GC, Celli J, Laros JF, den Dunnen JT. 2011. LOVD v.2.0: the next generation in gene variant databases. Hum Mutat 32:557-563.
17. Gai X, Ghezzi D, Johnson MA, Biagosch CA, Shamseldin HE, Haack TB, Reyes A, Tsukikawa M, Sheldon CA, Srinivasan S, Gorza M, Kremer LS et al. 2013. Mutations in FBXL4, encoding a mitochondrial protein, cause early-onset mitochondrial encephalomyopathy. Am J Hum Genet 93:482-495.
18. Girdea M, Dumitriu S, Fiume M, Bowdin S, Boycott KM, Chénier S, Chitayat D, Faghfoury H, Meyn MS, Ray PN, So J, Stavropoulos DJ et al. 2013. PhenoTips: patient phenotyping software for clinical and research use. Hum Mutat 34:1057-1065.
19. Gonzalez M, Falk MJ, Gai X, Postrel R, Schüle R, Zuchner S. 2005. Innovative genomic collaboration using the GENESIS (GEM.app) platform. Hum Mutat 36:950-956.
20. Hamosh A, Scott AF, Amberger JS, Bocchini CA, McKusick VA. 2005. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res 33:D514-D517.
21. Kircher M, Witten DM, Jain P, O'Roak BJ, Cooper GM, Shendure J. 2014. A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet 46:310-315.
22. Köhler S, Doelken SC, Mungall CJ, Bauer S, Firth HV, Bailleul-Forestier I, Black GC, Brown DL, Brudno M, Campbell J, FitzPatrick DR, Eppig JT et al. 2014. The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. Nucleic Acids Res 42(DI):D966-D974.
23. Landrum MJ, Lee JM, Riley GR, Jang W, Rubinstein WS, Church DM, Maglott DR. 2014.ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Res 42(DI):D980-D985.
24. Liu X, Jian X, Boerwinkle E. 2013. dbNSFP v2.0: a database of human non-synonymous SNVs and their functional predictions and annotations. Hum Mutat 34:E2393-E2402.
25. Longley MJ, Graziewicz MA, Bienstock RJ, Copeland WC. 2005. Consequences of mutations in human DNA polymerase gamma. Gene 354:125-131.
26. Lott MT, Leipzig JN, Derbeneva O, Xie HM, Chalkia D, Sarmady M, Procaccio V, Wallace DC. 2013. mtDNA variation and analysis using MITOMAP and MITOMASTER. Curr Protoc Bioinformatics 1:1.23.1-1.23.26.
27. McLaren W, Pritchard B, Rios D, Chen Y, Flicek P, Cunningham F. 2010. Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics 26:2069-2070.
28. Navarro-Gomez D, Leipzig J, Shen L, Lott M, Stassen AP, Wallace DC, Wiggs JL, Falk MJ, van Oven M, Gai X. 2015. Phy-Mer: a novel alignment-free and reference-independent mitochondrial haplogroup classifier. Bioinformatics 31:1310-1312.
29. Ng PC, Henikoff S. 2001. Predicting deleterious amino acid substitutions. Genome Res. 11:863-874.
30. Pagliarini DJ, Calvo SE, Chang B, Sheth SA, Vafai SB, Ong SE, Walford GA, Sugiana C, Boneh A, Chen WK, Hill DE, Vidal M, et al. 2008. A mitochondrial protein compendium elucidates complex I disease biology. Cell 134:112-123.
31. Rubino F, Piredda R, Calabrese FM, Simone D, Lang M, Calabrese C, Petruzzella V, Tommaseo-Ponzetta M, Gasparre G, Attimonelli M. 2012. HmtDB, a genomic resource for mitochondrion-based human variability studies. Nucleic Acids Res 40:D1150-D1159.
32. Scharfe C, Lu HH, Neuenburg JK, Allen EA, Li GC, Klopstock T, Cowan TM, Enns GM, Davis RW. 2009. Mapping gene associations in human mitochondria using clinical disease phenotypes. PLoS Comput Biol 5:e1000374.
33. Shabani M, Dyke SO, Joly Y, Borry P. 2015. Controlled access under review: improving the governance of genomic data access. PLoS Biol 13:e1002339.
34. Smedley D, Jacobsen JO, Jager M, Kohler S, Holtgrewe M, Schubach M, Siragusa E, Zemojtel T, Buske OJ, Washington NL, Bone WP, Haendel MA, Robinson PN. 2015. Next-generation diagnostics and disease-gene discovery with the Exomiser. Nat Protoc 10:2004-15.
35. Stein LD, Mungall C, Shu S, Caudy M, Mangone M, Day A, Nickerson E, Stajich JE, Harris TW, Arva A, Lewis S. 2002. The generic genome browser: a building block for a model organism system database. Genome Res. 12:1599-1610.
36. Thorogood A, Zawati MH. 2015. International guidelines for privacy in genomic biobanking (or the unexpected virtue of pluralism). J Law Med Ethics 43:690-702.
37. van Oven M, Kayser M. 2009. Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Hum Mutat 30:E386-E394.
38. Wildeman M, van Ophuizen E, den Dunnen JT, Taschner PE. 2008. Improving sequence variant descriptions in mutation databases and literature using the Mutalyzer sequence variation nomenclature checker. Hum Mutat. 29:6-13.