Analysis of human mRNAs with the reference genome sequence reveals potential errors, polymorphisms, and RNA editing

Genome Research

Volumn 14, Issue 10 B, 2004, Pages 2034-2040

  Furey, Terrence S ^a   Diekhans, Mark ^a   Lu, Yontao ^a   Graves, Tina A ^b   Oddy, Lachlan ^b   Randall Maher, Jennifer ^b   Hillier, LaDeana W ^b   Wilson, Richard K ^b   Haussler, David ^c  

^a University of California Santa Cruz   (United States)

^b WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; GENOMIC RNA; MESSENGER RNA;

ACCURACY; ANALYTICAL ERROR; ARTICLE; CLINICAL OBSERVATION; CONTROLLED STUDY; EXPRESSED SEQUENCE TAG; FRAMESHIFT MUTATION; GENE DELETION; GENE INSERTION; GENE LOCUS; GENETIC CODE; GENETIC IDENTIFICATION; GENETIC POLYMORPHISM; GENETIC SCREENING; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; HUMAN; HUMAN CELL; HUMAN GENOME; MAMMAL; NUCLEOTIDE SEQUENCE; POPULATION GENETICS; PRIORITY JOURNAL; RNA ANALYSIS; RNA EDITING; RNA SEQUENCE; SEQUENCE DATABASE; SINGLE NUCLEOTIDE POLYMORPHISM; SOMATIC MUTATION; STATISTICAL SIGNIFICANCE;

MAMMALIA;

EID: 7444258530     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.2467904     Document Type: Article

References (28)

1. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. 1990. Basic local alignment search tool. J. Mol. Biol. 215: 403-410.
2. Bailey, J., Gu, Z., Clark, R., Reinert, K., Samonte, R., Schwartz, S., Adams, M., Li, E.M.P., and Eichler, E. 2002. Recent segmental duplications in the human genome. Science 297: 1003-1007.
3. Bass, B. 2002. RNA editing by adenosine deaminases that act on RNA. Ann. Rev. Biochem. 71: 817-846.
4. Benson, D., Karsch-Mizrachi, I., Lipman, D., Ostell, J., Rapp, B., and Wheeler, D. 2002. GenBank. Nucleic Acids Res. 30: 17-20.
5. Broman, K.W., Murray, J.C., Sheffield, V.C., White, R.L., and Weber, J.L. 1998. Comprehensive human genetic maps: Individual and sex-specific variation in recombination. Am. J. Hum. Genet. 63: 861-869.
6. Dib, C., Faure, S., Fizames, C., Samson, D., Drouot, N., Vignal, A., Millasseau, P., Marc, S., Hazan, J., Seboun, E. et al. 1996. A comprehensive genetic map of the human genome based on 5265 microsatellites. Nature 380: 152-154.
7. Diehn, M., Sherlock, G., Binkley, G., Jin, H., Matese, J., Hernandez-Boussard, T., Rees, C., Cherry, J., Botstein, D., Brown, P. et al. 2003. SOURCE: A unified genomic resource of functional annotations, ontologies, and gene expression data. Nucleic Acids Res. 31: 219-223.
8. Gerber, A.P. and Keller, W. 2001. RNA editing by base deamination: More enzymes, more targets, new mysteries. Trends Biochem. Sci. 26: 376-384.
9. Gunaratne, P., Wu, J., Garcia, A., Hulyk, S., Worley, K., Margolin, J., and Gibbs, R. 2003. Concatenation cDNA sequencing for transcriptome analysis. C. R. Biol. 326: 971-977.
10. International Human Genome Sequencing Consortium 2001. Initial sequencing and analysis of the human genome. Nature 409: 860-921.
11. Kawahara, Y., Ito, K., Sun, H., Kanazawa, I., and Kwak, S. 2003. Low editing efficiency of GluR2 mRNA is associated with a low relative abundance of ADAR2 mRNA in white matter of normal human brain. Eur. J. Neurosci. 18: 23-33.
12. Kent, W.J. 2002. BLAT: The BLAST-like alignment tool. Genome Res. 11: 1541-1548.
13. Kong, A., Gudbjartsson, D.F., Sainz, J., Jonsdottir, G.M., Gudjonsson, S.A., Richardsson, B., Sigurdardottir, S., Barnard, J., Hallbeck, B., Masson, G. et al. 2002. A high-resolution recombination map of the human genome. Nat. Genet. 31: 241-247.
14. Kulikova, T., Aldebert, P., Althorpe, N., Baker, W., Bates, K., Browne, P., van den Broek, A., Cochrane, G., Duggan, K., Eberhart, R. et al. 2004. The EMBL mucleotide sequence database. Nucleic Acids Res. 32: D27-D30.
15. MGC Program Team. 2002. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proc. Natl. Acad. Sci. 99: 16899-16903.
16. MGC Project Team. 2004. The status, quality, and expansion of the NIH full-length cDNA project: The mammalian gene collection (MGC). Genome Res. (this issue).
17. Miyazaki, S., Sugawara, H., Ikeo, K., Gojobori, T., and Tateno, Y. 2004. DDBJ in the stream of various biological data. Nucleic Acids Res. 32: D32-D34.
18. Mouse Genome Sequencing Consortium 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520-562.
19. Okazaki, Y., Furuno, M., Kasukawa, T., Adachi, J., Bono, H., Kondo, S., Nikaido, I., Osato, N., Saito, R., Suzuki, H. et al. 2002. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 420: 563-573.
20. Paschen, W., Hedreen, J., and Ross, C. 1994. RNA editing of the glutamate receptor subunits GluR2 and GluR6 in human brain tissue. J. Neurochem. 63: 1596-1602.
21. Pruitt, K.D. and Maglott, D.R. 2001. RefSeq and LocusLink: NCBI gene-centered resources. Nucleic Acids Res. 29: 137-140.
22. Pruitt, K.D., Tatusova, T., and Maglott, D.R. 2003. NCBI Reference sequence project: Update and current status. Nucleic Acids Res. 31: 34-37.
23. Schmutz, J., Wheeler, J., Grimwood, J., Dickson, M., Yang, J., Caoile, C., Bajorek, E., Black, S., Chan Y.M., Denys, M., et al. 2004. Quality assessment of the human genome sequence. Nature 429: 365-368
24. Sommer, B., Kohler, M., Sprengel, R., and Seeburg, P., 1991. RNA editing in brain controls a determinant of ion flow in glutamate-gated channels. Cell 67: 11-19.
25. Stapelton, M., Carlson, J., Brokstein, P., Yu, C., Champe, M., George, R., Guarin, H., Kronmiller, B., Pacleb, J., Park, S. et al. 2002. A Drosophila full-length cDNA resource. Genome Biol. 3: RESEARCH0080.1-0080.8.
26. Strausberg, R.L., Feingold, E.A., and Collins, F.S. 1999. The mammalian gene collection. Science 286: 455-457.
27. Wheelan, S.J., Church, D.M., and Ostell, J.M. 2001. Spidey: A tool for mRNA-to-genomic alignments. Genome Res. 11: 1952-1957.
28. Yu, W., Andersson, B., Worley, K., Muzny, D., Ding, Y., Liu, W., Ricafrente, J., Wentland, M., Lennon, G., and Gibbs, R. 1997. Large-scale concatenation cDNA sequencing. Genome Res. 7: 353-358.