Inter-Species Comparative Sequence Analysis: A Tool for Genomic Medicine

Genomic and Personalized Medicine: V1-2

Volumn , Issue , 2008, Pages 120-130

  Antonellis, Anthony ^a   Green, Eric D ^a  

^a NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84996605002     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1016/B978-0-12-369420-1.00010-X     Document Type: Chapter

References (50)

1. Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. J Mol Biol 1990, 215:403-410.
2. Altshuler D., Clark A.G. Harvesting medical information from the human family tree. Science 2005, 307:1052-1053.
3. Anderson M.P., Welsh M.J. Regulation by ATP and ADP of CFTR chloride channels that contain mutant nucleotide-binding domains. Science 1992, 257:1701-1704.
4. Antonellis A., Bennett W.R., Menheniott T.R., Prasad A.B., Lee-Lin S.Q., Green E.D., Paisley D., Kelsh R.N., Pavan W.J., Ward A. Deletion of long-range sequences at Sox10 compromises developmental expression in a mouse model of Waardenburg-Shah (WS4) syndrome. Hum Mol Genet 2006, 15:259-271.
5. Aparicio S., Chapman J., Stupka E., Putnam N., Chia J.M., Dehal P., Christoffels A., Rash S., Hoon S., Smit A., et al. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 2002, 297:1301-1310.
6. Bailey T.L., Elkan C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 1994, 2:28-36.
7. Batourina E., Gim S., Bello N., Shy M., Clagett-Dame M., Srinivas S., Costantini F., Mendelsohn C. Vitamin A controls epithelial/mesenchymal interactions through Ret expression. Nat Genet 2001, 27:74-78.
8. Bondurand N., Girard M., Pingault V., Lemort N., Dubourg O., Goossens M. Human Connexin 32, a gap junction protein altered in the X-linked form of Charcot-Marie-Tooth disease, is directly regulated by the transcription factor SOX10. Hum Mol Genet 2001, 10:2783-2795.
9. Carrasquillo M.M., McCallion A.S., Puffenberger E.G., Kashuk C.S., Nouri N., Chakravarti A. Genome-wide association study and mouse model identify interaction between RET and EDNRB pathways in Hirschsprung disease. Nat Genet 2002, 32:237-244.
10. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 2005, 437:69-87. Chimpanzee Sequencing and Analysis Consortium.
11. Collins F.S., Green E.D., Guttmacher A.E., Guyer M.S. A vision for the future of genomics research. Nature 2003, 422:835-847.
12. Edery P., Lyonnet S., Mulligan L.M., Pelet A., Dow E., Abel L., Holder S., Nihoul-Fekete C., Ponder B.A., Munnich A. Mutations of the RET proto-oncogene in Hirschsprung's disease. Nature 1994, 367:378-380.
13. Emison E.S., McCallion A.S., Kashuk C.S., Bush R.T., Grice E., Lin S., Portnoy M.E., Cutler D.J., Green E.D., Chakravarti A. A common sex-dependent mutation in a RET enhancer underlies Hirschsprung disease risk. Nature 2005, 434:857-863.
14. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. nature 2007, 447:799-816. ENCODE Project Consortium.
15. Frazer K.A., Elnitski L., Church D.M., Dubchak I., Hardison R.C. Cross-species sequence comparisons: A review of methods and available resources. Genome Res 2003, 13:1-12.
16. Frazer K.A., Pachter L., Poliakov A., Rubin E.M., Dubchak I. VISTA: Computational tools for comparative genomics. Nucleic Acids Res 2004, 32:W273-W279.
17. Goldstein D.B., Tate S.K., Sisodiya S.M. Pharmacogenetics goes genomic. Nat. Rev. Genet. 2003, 4:937-947.
18. Houlden H., Girard M., Cockerell C., Ingram D., Wood N.W., Goossens M., Walker R.W., Reilly M.M. Connexin 32 promoter P2 mutations: A mechanism of peripheral nerve dysfunction. Ann Neurol 2004, 56:730-734.
19. Hull J., Shackleton S., Harris A. Abnormal mRNA splicing resulting from three different mutations in the CFTR gene. Hum Mol Genet 1993, 2:689-692.
20. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 2004, 432:695-716. International Chicken Genome Sequencing Consortium.
21. Initial sequencing and analysis of the human genome. Nature 2001, 409:860-921. International Human Genome Sequencing Consortium.
22. Finishing the euchromatic sequence of the human genome. Nature 2004, 431:931-945. International Human Genome Sequencing Consortium.
23. Ionasescu V., Searby C., Ionasescu R. Point mutations of the connexin32 (GJB1) gene in X-linked dominant Charcot-Marie-Tooth neuropathy. Hum Mol Genet 1994, 3:355-358.
24. Kamal M., Xie X., Lander E.S. A large family of ancient repeat elements in the human genome is under strong selection. Proc Natl Acad Sci U S A 2006, 103:2740-2745.
25. Kent W.J. BLAT--the BLAST-like alignment tool. Genome Res 2002, 12:656-664.
26. Kent W.J., Sugnet C.W., Furey T.S., Roskin K.M., Pringle T.H., Zahler A.M., Haussler D. The human genome browser at UCSC. Genome Res 2002, 12:996-1006.
27. Kerem B., Rommens J.M., Buchanan J.A., Markiewicz D., Cox T.K., Chakravarti A., Buchwald M., Tsui L.C. Identifica-tion of the cystic fibrosis gene: Genetic analysis. Science 1989, 245:1073-1080.
28. Lindblad-Toh K., Wade C.M., Mikkelsen T.S., Karlsson E.K., Jaffe D.B., Kamal M., Clamp M., Chang J.L., Kulbokas E.J., Zody M.C., et al. Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature 2005, 438:803-819.
29. Logan J., Hiestand D., Daram P., Huang Z., Muccio D.D., Hartman J., Haley B., Cook W.J., Sorscher E.J. Cystic fibrosis transmembrane conductance regulator mutations that disrupt nucleotide binding. J Clin Invest 1994, 94:228-236.
30. Loots G.G., Locksley R.M., Blankespoor C.M., Wang Z.E., Miller W., Rubin E.M., Frazer K.A. Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons. Science 2000, 288:136-140.
31. Margulies E.H., Blanchette M., Haussler D., Green E.D. Identification and characterization of multi-species conserved sequences. Genome Res 2003, 13:2507-2518.
32. Matys V., Kel-Margoulis O.V., Fricke E., Liebich I., Land S., Barre-Dirrie A., Reuter I., Chekmenev D., Krull M., Hornischer K., et al. TRANSFAC and its module TRANSCompel: Trans-criptional gene regulation in eukaryotes. Nucleic Acids Res 2006, 34:D108-D110.
33. Initial sequencing and comparative analysis of the mouse genome. Nature 2002, 420:520-562. Mouse Genome Sequencing Consortium.
34. Nadeau J.H. Modifier genes in mice and humans. Nat Rev Genet 2001, 2:165-174.
35. Nishihara H., Smit A.F., Okada N. Functional noncoding sequences derived from SINEs in the mammalian genome. Genome Res 2006, 16:864-874.
36. Plessy C., Dickmeis T., Chalmel F., Strahle U. Enhancer sequence conservation between vertebrates is favoured in developmental regulator genes. Trends Genet 2005, 21:207-210.
37. Pollard K.S., Salama S.R., Lambert N., Lambot M.A., Coppens S., Pedersen J.S., Katzman S., King B., Onodera C., Siepel A., et al. An RNA gene expressed during cortical development evolved rapidly in humans. Nature 2006, 443:149-150.
38. Prabhakar S., Poulin F., Shoukry M., Afzal V., Rubin E.M., Couronne O., Pennacchio L.A. Close sequence comparisons are sufficient to identify human cis-regulatory elements. Genome Res 2006, 16:855-862.
39. Prabhakar S., Noonan J.P., Paabo S., Rubin E.M. Accelerated evolution of conserved noncoding sequences in humans. Science 2006, 314:786.
40. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 2004, 428:493-521. Rat Genome Sequencing Project Consortium.
41. Riordan J.R., Rommens J.M., Kerem B., Alon N., Rozmahel R., Grzelczak Z., Zielenski J., Lok S., Plavsic N., Chou J.L., et al. Identification of the cystic fibrosis gene: Cloning and characterization of complementary DNA. Science 1989, 245:1066-1073.
42. Rommens J.M., Iannuzzi M.C., Kerem B., Drumm M.L., Melmer G., Dean M., Rozmahel R., Cole J.L., Kennedy D., Hidaka N., et al. Identification of the cystic fibrosis gene: Chromosome walking and jumping. Science 1989, 245:1059-1065.
43. Schwartz S., Zhang Z., Frazer K.A., Smit A., Riemer C., Bouck J., Gibbs R., Hardison R., Miller W. PipMaker - a web server for aligning two genomic DNA sequences. Genome Res 2000, 10:577-586.
44. Schwartz S., Elnitski L., Li M., Weirauch M., Riemer C., Smit A., Green E.D., Hardison R.C., Miller W. MultiPipMaker and supporting tools: Alignments and analysis of multiple genomic DNA sequences. Nucleic Acids Res 2003, 31:3518-3524.
45. Scott L.J., Mohlke K.L., Bonnycastle L.L., Willer C.J., Li Y., Duren W.L., Erdos M.R., Stringham H.M., Chines P.S., Jackson A.U., Prokunina-Olsson L., et al. A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants. Science 2007, 316:1341-1345.
46. Shoba T., Dheen S.T., Tay S.S. Retinoic acid influences Phox2 expression of cardiac ganglionic cells in the developing rat heart. Neurosci Lett 2002, 321:41-44.
47. Stalker J., Gibbins B., Meidl P., Smith J., Spooner W., Hotz H.R., Cox A.V. The Ensembl Web site: Mechanics of a genome browser. Genome Res 2004, 14:951-955.
48. Thompson J.D., Higgins D.G., Gibson T.J. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22:4673-4680.
49. Tzetis M., Efthymiadou A., Doudounakis S., Kanavakis E. Qualitative and quantitative analysis of mRNA associated with four putative splicing mutations (621+3A?G, 2751+2T?A, 296+1G?C, 1717-9T?C-D565G) and one nonsense mutation (E822X) in the CFTR gene. Hum Genet 2001, 109:592-601.
50. Zeggini E., Weedon M.N., Lindgren C.M., Frayling T.M., Elliott K.S., Lango H., Timpson N.J., Perry J.R., Rayner N.W., Freathy R.M., et al. Replication of genome-wide association signals in UK samples reveals risk loci for type 2 diabetes. Science 2007, 316:1336-1341.