Individual variation in protein-coding sequences of human genome

Advances in Protein Chemistry

Volumn 54, Issue , 2000, Pages 409-437

  Sunyaev, Shamil ^a,b   Hanke, Jens ^a,b   Brett, David ^a,b   Aydin, Atakan ^a,b   Zastrow, Inga ^a,b   Lathe, Warren ^a,b   Bork, Peer ^a,b   Reich, Jens ^a,b  

^a MAX DELBRÜCK CENTER FOR MOLECULAR MEDICINE   (Germany)

^b EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ALTERNATIVE RNA SPLICING; AMINO ACID SEQUENCE; GENETIC DRIFT; GENETIC POLYMORPHISM; GENETIC SELECTION; GENOME; HUMAN; MUTATION; POPULATION DYNAMICS; PRIORITY JOURNAL; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM; SPECIES DIFFERENCE;

EID: 0033939604     PISSN: 00653233     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0065-3233(00)54012-1     Document Type: Review

References (72)

1. Altschul, S., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D. J. (1997). Gapped BLAST anmd PSI-BLAST: a new generation of protein database search programs. Nucl. Acids Res. 25, 3389-3402.
2. Bairoch, A., and Apweiler, R. (1999). The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999. Nucl. Acids. Res. 27, 49-54.
3. Benson, D. A., Boguski, M. S., Lipman, D. J., Ostell, J., Ouellette, B. F., Rapp, B. A., and Wheeler, D. L. (1999). Genbank. Nucl. Acids Res. 27, 12-17.
4. Bergstrom, T. F., Josefsson, A., Ehrlich, H. A., and Gyllensten, U. (1998). Recent origin of HLA-DRB 1 alleles and implications for human evolution. Nat. Genet. 18, 237-242.
5. BLAST server (1999): http://www.ncbi.nlm.nih.gov/blast.
6. Boguski, M. S. (1995). The turning point of the history of human ESTs in genome research. Trends Biochem. Sci. 20, 295-296.
7. Boguski, M. S., Lowe, T. M. J., and Tolstoshev, C. M. (1993) dbEST - data base for expressed sequence tags. Nat. Genet. 4, 332-333.
8. Buetow, K. H., Edmonson, M. N., and Cassidy, A. B. (1999). Reliable identification of large numbers of candidate SNPs from public EST data. Nat. Genet. 21, 323-325.
9. Cargill, M., Altschuler, D., Ireland, J., Sklar, P., Ardlie, K., Patil, N., Lane, C. R., Lim, E. P., Kalyanaraman, N., Nemesh, J., Ziaugra, L., Friedland, L., Rolfe, A., Warrington, J., Lipshutz, R., Daley, G. O., and Lander, E. S. (1999). Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nat. Genet. 22, 231-238.
10. Chakravarti, A. (1998). It's raining SNPs, hallelujah? Nat. Genet. 19, 216-217.
11. Chakravarti, A. (1999). Population genetics - making sense out of sequence. Nat. Genet. 21, 56-60.
12. Chee, M., Yang, R., Hubbell, E., Berno, A., Huang, X. C., Stern, D., Winkler, J., Lockhart, D. J., Morris, M. S., and Fodor, S. P. A. (1996). Accessing genetic information with high-density DNA arrays. Science 274, 610-614.
13. Clark, A. G., Weiss, K. M., Nickerson, D. A., Taylor, S. L., Buchanan, A., Stengard, J., Salomaa, V., Virtianen, E., Perola, M., Boerwinkle, E., and Sing, C. F. (1998). Haplotype structure and population genetic inferences from Nucleotide-sequence variation in human lipoprotein lipase. Am. J. Hum. Genet. 63, 595-612.
14. Collins, F. S., Guyer, M. S., and Chakravarti, A. (1997). Variations on a theme: cataloging human DNA sequence variation. Science 278, 1580-1581.
15. Cooper, D. N., Smith, B. A., Cooke, H., Niemann, S., and Schmidtke, J. (1985). An estimate of unique sequence heterozygosity in the human genome. Hum. Genet. 69, 201-205.
16. Ewing, B., Hillier, L., Wendl, M. C., and Green, P. (1998). Base-calling of automated sequencer traces using Phred. I. Accuracy assessment. Genome Res. 8, 175-185.
17. Ewing, B., and Green, P. (1998). Base-calling of automated sequencer traces using Phred. II. Error probabilities. Genome Res. 8, 186-194.
18. Gillespie, J. H. (1994). Alternatives to the neutral theory. In "Non-Neutral Evolution: Theories and Molecular Data." (B. Golding, ed.) pp. 1-17. Chapman & Hall, New York.
19. Gordon, D., Abajian, C., and Green, P. (1998). Consed: a graphical tool for sequence finishing. Genome Res. 8, 195-202.
20. Green, P. (1998). Phrap, sequence alignment and contig assembly program, http:// genome.washington.edu.
21. Hacia, J. G. (1999). Resequencing and mutational analysis using oligonucleotide arrays. Nat. Genet. 21, 42-47.
22. Hacia, J. G., Fan, J. B., Ryder, O., Jin, L., Edgemon, K., Ghandour, G., Mayer, R. A., Sun, B., Hsie, L., Robbins, C. M., Brody, L. C., Wang, D., Lander, E. S., Lipshutz, R., Fodor, S. P. A., and Collins, F. S. (1999). Determination of ancestral alleles for human single-nucleotide polymorphisms using high-density oligonucleotide arrays. Nat. Genet. 22, 164-167.
23. Halushka, M. K., Fan, J. B., Bentley, K., Hsie, L., Shen, N., Weder, A., Cooper, R., Lipshutz, R., and Chakravarti, A., (1999). Patterns of single-nucleotide polymorphisms in candidate genes for blood-pressure homeostasis. Nat. Genet. 22, 239-247.
24. Hanke, J., Brett, D., Zastrow, I., Aydin, A., Delbrück, S., Lehmann, G., Luft, F., Reich, J., and Bork, P. (1999). Trends Genet. 15, 389-390.
25. Harding, R. M., Fullerton, S. M., Griffiths, R. C., Bond, J., Cox, M. J., Schneider, J. A., Moulin, D. S., and Clegg, J. B. (1997) Archaic African and Asian lineages in the genetic ancestry of modern humans. Am. J. Hum. Genet. 60, 772-789.
26. Harpending, H. C., Batzer, M. A., Gurvens, M., Jorde, L. B., Rogers, A. R., and Sherry, S. T. (1998). Genetic traces of ancient demography. Proc. Natl. Acad. Sci. U.S.A. 95, 1961-1967.
27. Harris, H. (1966). Enzyme polymorphisms in man. Proc. Roy. Soc. London [B] 164, 298-310.
28. Harris, H., and Hopkinson, D. A. (1972). Average heterozygosity per locus in man: an estimate on the incidence of enzyme polymorphisms. Ann. Hum. Genet. 36, 9-20.
29. Hartl. D. L., and Clark, A. G. (1989). "Principles of Population Genetics." Sinauer Ass., Sunderland, MA.
30. Housman, D., and Ledley, F. D. (1998). Why pharmacogenetics? Why now? Nat. Biotechnol. 16, 492-493.
31. Hudson, R. R. (1993). Levels of DNA polymorphism and divergence yield important insights into evolutionary processes. Proc. Natl. Acad. Sci. U.S.A. 90, 7425-7426.
32. Ingram, V. M. (1956). A specific chemical difference between the globins of normal human and sickle cell anaemia haemoglobin. Nature 178, 792-794.
33. Karlin, S., and Altschul, S. (1990). Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc. Natl. Acad. Sci. U.S.A. 87, 2264-2268.
34. Karlin, S., and Altschul, S. (1993). Applications and statistics for multiple high-scoring schemes in molecular sequences. Proc. Natl. Acad. Sci. U.S.A. 90, 5873-5877.
35. Kimura, M. (1962). On the probability of fixation of mutant genes in populations. Genetics 47, 713-719.
36. Kimura, M. (1983). "The Neutral Theory of Molecular Evolution." Cambridge University Press, Cambridge, UK.
37. Kimura, M., and Otha, T. (1969). Average number of generations until fixation of a mutant gene in a finite population. Genetics 61, 763-771.
38. Klamt, B., Koziell, A., Poulat, F., Wieacker, P., Scambler, P., Berta, P., and Gessler, M. (1998). Fraier syndrome is caused by defective alternative splicing of WT1 leading to an altered ratio of WT1 +/- KTS splice isoforms. Hum. Mol. Genet. 4, 709-714.
39. Koyama, S., Maruyama, T., and Adachi, S. (1999). Expression of epidermal growth factor receptor and CD44 splicing variant sharing exons 6 and 9 on gastric and esophageal carcinomas: a two flow-cytometric analysis. J. Cancer Res. Clin. Oncol. 125, 47-54.
40. Li, W. H. and Sadler, L. A. (1991). Low nucleotide diversity in man. Genetics 129, 513-523.
41. Li, W. H. (1997). "Molecular Evolution." Sinauer Ass., Sunderland, MA.
42. Lipshutz, R. J., Fodor, S. P., Gingeras, T. R., and Lockhart, D. J. (1999) High density synthetic oligonucleotide arrays. Nat. Genet. 21, 20-24.
43. McDonald, J., and Kreitman, M. (1991). Adaptive protein evolution at adh locus in Drosophila. Nature 351, 652-654.
44. McKusick, V. (1999). Available as "NCBI-distributed Online Mendelian Inheritance in Man", http://www.ncbi.nlm.nih.gov/omim.
45. Moriyama, E. N., and Powell, J. R. (1996). Intraspecific nuclear DNA variation in Drosophila. Mol. Biol. Evol. 13, 261-277.
46. Nei, M. (1975). "Molecular Population Genetics and Evolution." North Holland, Amsterdam.
47. Nickerson, D. A., Taylor, S. L., Weiss, K. M., Clark, A. G., Hutchinson, R. G., Stengard, J., Salomaa, V., Vartiainen, E., Boerwinkle, E., and Sing, C. F. (1998). DNA sequence diversity in a 9.7 kb region of the human lipoprotein lipase gene. Nat. Genet. 19, 233-240.
48. Ozon, S., Byk, T., and Sobel, A. (1998). SCLIP: anovel SCG10-like protein of the stathmin family expressed in the nervous system. J. Neurochem. 70, 2386-2396.
49. Pauling, L., Itano, H. A., Singer, S. J., and Wells, I. C. (1949). Sickle cell anemia: a molecular disease. Science 110, 543-546.
50. Picoult-Newberg, L., Ideker, T. E., Pohl, M. G., Taylor, S. L., Donaldson, M. A., Nickerson, D. A., and Boyce-Jacino, M. (1999). Mining SNPs from EST databases. Genome Res. 9, 167-174.
51. Qi, M., Byers, P. H. (1998). Constitutive skipping of alternatively spliced exon 10 in the ATP7A gene abolishes Golgi localization of the the Menkes protein and produces the occipital horn syndrome. Hum. Mol. Genet. 7, 465-469.
52. Race, R. R., and Sanger, R. (1975). "Blood groups in man, " 6th ed. Blackwell, Oxford, UK.
53. Ramsay, G. (1998). DNA chips: state of the art. Nat. Biotechnol. 16, 40-44.
54. Risch, N., and Merikangas, K. (1996). The future of genetic studies of complex human diseases. Science 273, 1516-1517.
55. Sachse, G., Brockmöller, J., Bauer, S., and Roots, I. (1997). Cytochrome P450 2D6 variants in a Caucasian population: allele frequencies and phenotypic consequences. Am. J. Hum. Genet. 60, 284-295.
56. Sadoulet-Puccio, H. M., Khurana, T. S., Cohen, J. B., and Kundel, L. M. (1996). Cloning and characterization of the human homologue of a dystrophin related phosphoprotein found at the Torpedo electric organ post-synaptic membrane. Hum. Mol. Genet. 4, 44489-44496.
57. Sato, N., Hori, O., Yamaguchi, A., Lambert, J. C., Chartier-Harlin, M. C., Robinson, P. A., Delacourte, A., Schmidt, A. M., Furuyama, T., Tohyama, M., and Takagi, T. (1999). A novel presenilin-2 splice variant in the human Alzheimer's disease brain tissue. J. Neurochem. 72, 2498-2505.
58. Schuler, G. D. (1996). A gene map of the human gene. Science 274, 540-546.
59. Schuler, G. D. (1997). Pieces of the puzzle: expressed sequence tags and the catalog of human genes. J. Mol. Med. 75, 694-698.
60. Sharp, P. A. (1994). Split genes and RNA splicing. Cell 77, 805-815.
61. Siffert, W., Rosskopf, D., Siffert, G., Busch, S., Moritz, A., Erbel, R., Sharma, A. M., Ritz, E., Wichmann, H. E., Jakobs, K. H., and Horsthemke, B. (1998). Association of a human G-protein beta3 subunit variant with hypertension. Nat. Genet. 18, 45-48.
62. Sigalas, I., Calvert, A. H., Anderson, J. J., Neal, D. E., and Lunec, J. (1996). Alternatively spliced mdm2 transcript with loss of p53 binding domain sequences: transforming ability and frequent detection in human cancer. Nat. Med. 8, 912-917.
63. Smit, A. F. A., and Green, P. (1997). Repeat Masker: http//ftp.genome.washington.edu/ RM/RepeatMasker.html.
64. Smithies, O. (1955). Zone electrophoresis in starch gels: group variations in the serum proteins of normal human adults. Biochem. J. 61, 629-641.
65. Taillon-Miller, P., Gu, Y., Li, Q., Hillier, L., and Kwok, P. Y. (1998). Overlapping genomic sequences: a treasure trove of single-nucleotide polymorphisms. Genome Res. 8, 748-784.
66. UNIGENE web server (1999): http://www.ncbi.nlm.nih.gov/UniGene/index.html.
67. Wang, D. G., Fan, J. B., Siao, C. J., Berno, A., Young, P., Sapolsky, R., Ghandour, G., Perkins, N., Winchester, E., Spence, J., Kruglyak, L., Stein, L., Hsie, L., Topaloglou, T., Hubell, E., Robinson, E., Mittmann, M., Morris, M. S., Shen, N., Kilburn, D., Rioux, J., Nusbaum, C., Rozen, S., Hudson, T. J., Lipshutz, R., Chee, M., and Lander, E. S. (1998). Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science 280, 1077-1082.
68. Winzeler, E. A., Richards, D. R., Conway, A. R., Goldstein, A. L., Kalman, S., McCullough, M. J., McCusker, J. H., Stevens, D. A., Wodlicka L., Lockhart, D. J., and Davis, R. W. (1998). Direct allelic vaiation scanning of the yeast genome. Science 281, 1994-1197.
69. Wolfsberg, T. G., and Landsman, D. (1997). A comparison of expressed sequence tags (ESTs) two human genomic sequences. Nucl. Acids Res. 25, 1626-1632.
70. Yamakawa, H., and Ohara, O. (1997). A DNA cycle sequencing reaction that minimizes compressions on automated fluorescent sequencers. Nucleic Acid Res. 25(6), 1311-1312.
71. Zietkiewicz, E., Yotova, V., Jarnik, M., Korab-Laskowska, M., Kidd, KK., Modiano, D., Scozzari, R., Stoneking, M., Tishkoff, S., Batzer, M., and Labuda, D. (1997). Nuclear DNA diversity in world-wide distributed human populations. Gene 205, 161-171.
72. ZuckerKandl, E., and Pauling, L. (1965). Evolutionary divergence and convergence in proteins, In "Evolving Genes and Proteins." (V. Bryson, and H. J. Vogel, eds.) pp. 189-225. Academic Press, New York.