The non-obese diabetic mouse sequence, annotation and variation resource: An aid for investigating type 1 diabetes

Database

Volumn 2013, Issue , 2013, Pages

  Steward, Charles A ^a   Gonzalez, Jose M ^a   Trevanion, Steve ^a   Sheppard, Dan ^a   Kerry, Giselle ^a   Gilbert, James G R ^a   Wicker, Linda S ^b   Rogers, Jane ^c   Harrow, Jennifer L ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^c EARLHAM INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL; ARTICLE; BASE PAIRING; C57BL MOUSE; DNA SEQUENCE; GENE LOCUS; GENETIC VARIABILITY; GENETICS; GENOME; HUMAN; INSULIN DEPENDENT DIABETES MELLITUS; MOLECULAR GENETICS; MOUSE; NONOBESE DIABETIC MOUSE; NUCLEOTIDE SEQUENCE; SEQUENCE ALIGNMENT; SINGLE NUCLEOTIDE POLYMORPHISM;

ANIMALS; BASE PAIRING; BASE SEQUENCE; DIABETES MELLITUS, TYPE 1; GENETIC LOCI; GENETIC VARIATION; GENOME; HUMANS; MICE; MICE, INBRED C57BL; MICE, INBRED NOD; MOLECULAR SEQUENCE ANNOTATION; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

EID: 84885940703     PISSN: 17580463     EISSN: None     Source Type: Journal    
DOI: 10.1093/database/bat032     Document Type: Article

References (65)

1. Bluestone,J.A., Herold,K. and Eisenbarth,G. (2010) Genetics, pathogenesis and clinical interventions in type 1 diabetes. Nature, 464, 1293-1300.
2. Pociot,F., Akolkar,B., Concannon,P. et al. (2010) Genetics of type 1 diabetes: what's next? Diabetes, 59, 1561-1571.
3. Todd,J.A. (1999) From genome to aetiology in a multifactorial disease, type 1 diabetes. Bioessays, 21, 164-174.
4. Wen,L., Ley,R.E., Volchkov,P.Y. et al. (2008) Innate immunity and intestinal microbiota in the development of Type 1 diabetes. Nature, 455, 1109-1113.
5. Todd,J.A. and Wicker,L.S. (2001) Genetic protection from the inflammatory disease type 1 diabetes in humans and animal models. Immunity, 15, 387-395.
6. Wicker,L.S., Clark,J., Fraser,H.I. et al. (2005) Type 1 diabetes genes and pathways shared by humans and NOD mice. J. Autoimmun., 25 (Suppl.), 29-33.
7. Makino,S., Kunimoto,K., Muraoka,Y. et al. (1980) Breeding of a non-obese, diabetic strain of mice. Jikken Dobutsu, 29, 1-13.
8. Wicker,L.S., Todd,J.A. and Peterson,L.B. (1995) Genetic control of autoimmune diabetes in the NOD mouse. Annu. Rev. Immunol., 13, 179-200.
9. Gan,M.J., Albanese-O'Neill,A. and Haller,M.J. (2012) Type 1 diabetes: current concepts in epidemiology, pathophysiology, clinical care, and research. Curr. Probl Pediatr Adolesc Health Care, 42, 269-291.
10. Chaparro,R.J. and Dilorenzo,T.P. (2010) An update on the use of NOD mice to study autoimmune (Type 1) diabetes. Expert Rev. Clin. Immunol., 6, 939-955.
11. Rainbow,D.B., Moule,C., Fraser,H.I. et al. (2011) Evidence that Cd101 is an autoimmune diabetes gene in nonobese diabetic mice. J. Immunol., 187, 325-336.
12. Fraser,H.I., Dendrou,C.A., Healy,B. et al. (2010) Nonobese diabetic congenic strain analysis of autoimmune diabetes reveals genetic complexity of the Idd18 locus and identifies Vav3 as a candidate gene. J. Immunol., 184, 5075-5084.
13. Ridgway,W.M., Peterson,L.B., Todd,J.A. et al. (2008) Gene-gene interactions in the NOD mouse model of type 1 diabetes. Adv. Immunol., 100, 151-175.
14. Rogner,U.C. and Avner,P. (2003) Congenic mice: cutting tools for complex immune disorders. Nat. Rev. Immunol., 3, 243-252.
15. Steward,C.A., Humphray,S., Plumb,B. et al. (2010) Genome-wide end-sequenced BAC resources for the NOD/MrkTac() and NOD/ShiLtJ() mouse genomes. Genomics, 95, 105-110.
16. Flicek,P., Amode,M.R., Barrell,D. et al. (2012) Ensembl 2012. Nucleic Acids Res., 40, D84-D90.
17. National Institutes of Health (2013) http://www.nih.gov/.
18. Lyons,P.A., Hancock,W.W., Denny,P. et al. (2000) The NOD Idd9 genetic interval influences the pathogenicity of insulitis and contains molecular variants of Cd30, Tnfr2, and Cd137. Immunity, 13, 107-115.
19. Onengut-Gumuscu,S., Ewens,K.G., Spielman,R.S. et al. (2004) A functional polymorphism (1858C/T) in the PTPN22 gene is linked and associated with type I diabetes in multiplex families. Genes Immun., 5, 678-680.
20. Human and Vertebrate Analysis and Annotation team (2013) http://www.sanger.ac.uk/research/projects/vertebrategenome/havana/.
21. Shiraki,T., Kondo,S., Katayama,S. et al. (2003) Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. Proc. Natl Acad. Sci. USA, 100, 15776-15781.
22. Church,D.M., Schneider,V.A., Graves,T. et al. (2011) Modernizing reference genome assemblies. PLoS Biol., 9, e1001091.
23. NOD mouse ftp site (2013) ftp://ftp.sanger.ac.uk/pub/NODmouse/NOD- resource-paper-data/.
24. Wendl,M.C., Dear,S., Hodgson,D. et al. (1998) Automated sequence preprocessing in a large-scale sequencing environment. Genome Res., 8, 975-984.
25. European Nucleotide Archive (2013) http://www.ebi.ac.uk/ena/.
26. Nakamura,Y., Cochrane,G. and Karsch-Mizrachi,I. (2012) The International Nucleotide Sequence Database Collaboration. Nucleic Acids Res., 40, D33-D37.
27. NOD mouse webpage (2013) http://www.sanger.ac.uk/resources/mouse/nod/.
28. NOD mouse sequences (2013) http://www.sanger.ac.uk/cgi-bin/Projects/M- musculus/mouse-NOD-clones-TPF.
29. Genome Reference Consortium (GRC) (2013) http://www.ncbi.nlm.nih.gov/ projects/genome/assembly/grc/mouse/.
30. Wilming,L.G., Gilbert,J.G., Howe,K. et al. (2008) The vertebrate genome annotation (Vega) database. Nucleic Acids Res., 36, D753-D760.
31. Vega Idd regions (2012) http://vega.sanger.ac.uk/info/data/mouse-regions. html.
32. Burren,O.S., Adlem,E.C., Achuthan,P. et al. (2011) T1DBase: update 2011, organization and presentation of large-scale data sets for type 1 diabetes research. Nucleic Acids Res., 39, D997-D1001.
33. Keane,T.M., Goodstadt,L., Danecek,P. et al. (2011) Mouse genomic variation and its effect on phenotypes and gene regulation. Nature, 477, 289-294.
34. Mouse-Genomes (2012) http://www.sanger.ac.uk/resources/mouse/genomes/.
35. Belanger,S., Tai,L.H., Anderson,S.K. et al. (2008) Ly49 cluster sequence analysis in a mouse model of diabetes: an expanded repertoire of activating receptors in the NOD genome. Genes Immun., 9, 509-521.
36. Ivakine,E.A., Gulban,O.M., Mortin-Toth,S.M. et al. (2006) Molecular genetic analysis of the Idd4 locus implicates the IFN response in type 1 diabetes susceptibility in nonobese diabetic mice. J. Immunol., 176, 2976-2990.
37. Bentley,D.R., Balasubramanian,S., Swerdlow,H.P. et al. (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature, 456, 53-59.
38. Sonnhammer,E.L. and Durbin,R. (1995) A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis. Gene, 167, GC1-GC10.
39. Manske,H.M. and Kwiatkowski,D.P. (2009) LookSeq: a browser-based viewer for deep sequencing data. Genome Res., 19, 2125-2132.
40. Waterston,R.H., Lindblad-Toh,K., Birney,E. et al. (2002) Initial sequencing and comparative analysis of the mouse genome. Nature, 420, 520-562.
41. Wade,C.M., Kulbokas,E.J. III, Kirby,A.W. et al. (2002) The mosaic structure of variation in the laboratory mouse genome. Nature, 420, 574-578.
42. Grimm,C.H., Rogner,U.C. and Avner,P. (2003) Lrmp and Bcat1 are candidates for the type I diabetes susceptibility locus Idd6. Autoimmunity, 36, 241-246.
43. Wicker,L.S., Chamberlain,G., Hunter,K. et al. (2004) Fine mapping, gene content, comparative sequencing, and expression analyses support Ctla4 and Nramp1 as candidates for Idd5.1 and Idd5.2 in the nonobese diabetic mouse. J. Immunol., 173, 164-173.
44. Kachapati,K., Adams,D.E., Wu,Y. et al. (2012) The B10 Idd9.3 locus mediates accumulation of functionally superior CD137+ regulatory T cells in the nonobese diabetic type 1 diabetes model. J. Immunol., 189, 5001-5015.
45. Penha-Goncalves,C., Moule,C., Smink,L.J. et al. (2003) Identification of a structurally distinct CD101 molecule encoded in the 950-kb Idd10 region of NOD mice. Diabetes, 52, 1551-1556.
46. Mattick,J.S. (2012) RNA driving the epigenetic bus. EMBO J., 31, 515-516.
47. Skarnes,W.C., Rosen,B., West,A.P. et al. (2011) A conditional knockout resource for the genome-wide study of mouse gene function. Nature, 474, 337-342.
48. Saleh,N.M., Raj,S.M., Smyth,D.J. et al. (2011) Genetic association analyses of atopic illness and proinflammatory cytokine genes with type 1 diabetes. Diabetes Metab. Res. Rev., 27, 838-843.
49. Soderlund,C., Humphray,S., Dunham,A. et al. (2000) Contigs built with fingerprints, markers, and FPC V4.7. Genome Res., 10, 1772-1787.
50. Bird,C. and Grafham,D. (2004) BAC finishing strategies. Methods Mol. Biol., 255, 255-277.
51. European Bioinformatics Institute (2013) http://www.ebi.ac.uk/embl.
52. Potter,S.C., Clarke,L., Curwen,V. et al. (2004) The ensembl analysis pipeline. Genome Res., 14, 934-941.
53. RepeatMasker (2012) http://repeatmasker.genome.washington.edu.
54. Benson,G. (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res., 27, 573-580.
55. HAVANA-software-manual (2013) http://www.sanger.ac.uk/research/projects/ vertebrategenome/havana/assets/otterlace-user-manual.pdf.
56. HAVANA annotation guidelines (2013) http://www.sanger.ac.uk/research/ projects/vertebrategenome/havana/assets/guidelines.pdf.
57. Harrow,J., Frankish,A., Gonzalez,J.M. et al. (2012) GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res., 22, 1760-1774.
58. Bult,C.J., Eppig,J.T., Blake,J.A. et al. (2013) The mouse genome database: genotypes, phenotypes, and models of human disease. Nucleic Acids Res., 41, D885-D891.
59. Maglott,D., Ostell,J., Pruitt,K.D. et al. (2011) Entrez gene: gene-centered information at NCBI. Nucleic Acids Res., 39, D52-D57.
60. UniProt (2013) http://www.uniprot.org/.
61. Vega biotypes (2013) http://vega.sanger.ac.uk/info/about/gene-and- transcript-types.html.
62. Slater,G.S. and Birney,E. (2005) Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics, 6, 31.
63. Cingolani,P., Platts,A., Wang le,L. et al. (2012) A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin), 6, 80-92.
64. Li,H., Handsaker,B., Wysoker,A. et al. (2009) The sequence alignment/map format and SAMtools. Bioinformatics, 25, 2078-2079.
65. Trapnell,C., Pachter,L. and Salzberg,S.L. (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics, 25, 1105-1111.