A phylogenetic approach to assessing the significance of missense mutations in disease genes

Human Mutation

Volumn 22, Issue 1, 2003, Pages 51-58

  Santibanez Koref M F ^a   Gangeswaran, R ^e   Santibanez Koref I P ^b   Shanahan, N ^c   Hancock, J M ^c,d  

^a MAX DELBRÜCK CENTER FOR MOLECULAR MEDICINE   (Germany)

^b TECHNISCHE UNIVERSITÄT BERLIN   (Germany)

^c UNIVERSITY OF LONDON   (United Kingdom)

^d MRC MAMMALIAN GENETICS UNIT   (United Kingdom)

^e NONE

Author keywords

Evolution; Inherited disease; Mutation analysis; p53; TP53

Indexed keywords

PROTEIN P53;

ARTICLE; EVOLUTION; GENE FREQUENCY; GENE IDENTIFICATION; GENETIC CONSERVATION; GENETIC DISORDER; GENETIC MODEL; HUMAN; MISSENSE MUTATION; MUTATION RATE; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; TUMOR SUPPRESSOR GENE;

COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DNA MUTATIONAL ANALYSIS; EVOLUTION, MOLECULAR; GENE FREQUENCY; GENES; GENES, P53; GENETIC DISEASES, INBORN; HUMANS; MODELS, GENETIC; MUTATION, MISSENSE; PHYLOGENY; TUMOR SUPPRESSOR PROTEIN P53; VARIATION (GENETICS);

EID: 17144461605     PISSN: 10597794     EISSN: None     Source Type: Journal    
DOI: 10.1002/humu.10235     Document Type: Article

References (21)

1. Beroud C, Soussi T. 1998. p53 gene mutation: software and database. Nucleic Acids Res 26:200-204.
2. Fleming MA, Potter JD, Ramirez CJ, Ostrander GK, Ostrander EA. 2003. Understanding missense mutations in the BRCA1 gene: an evolutionary approach. Proc Natl Acad Sci USA 100:1151-1156.
3. Hainaut P, Hollstein M. 2000. p53 and human cancer: the first ten thousand mutations. Adv Cancer Res 77:81-137.
4. Kondrashov AS, Sunyaev S, Kondrashov FA. 2002. Dobzhansky-Muller incompatibilities in protein evolution. Proc Natl Acad Sci USA 99:14878-14883.
5. Kumar S, Hedges SB. 1998. A molecular timescale for vertebrate evolution. Nature 392:917-920.
6. Kyte J, Doolittle RF. 1982. A simple method for displaying the hydropathic character of a protein. J Mol Biol 157:105-132.
7. Levine AJ. 1997. p53, the cellular gatekeeper for growth and division. Cell 88:323-331.
8. Li WH. 1993. Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J Mol Evol 36:96-99.
9. Maddison WP, Maddison DR. 1992. Mac Clade: analysis of phylogeny and character evolution. Version 3.04. Sunderland, Massachusetts: Sinauer Associates.
10. Malkin D, Li FP, Strong LC, Fraumeni JF Jr, Nelson CE, Kim DH, Kassel J, Gryka MA, Bischoff FZ, Tainsky MA, Friend SH. 1990. Germ line p53 mutations in a familial syndrome of breast cancer, sarcomas, and other neoplasms. Science 250:1233-1238.
11. Martin AC, Facchiano AM, Cuff AL, Hemandez-Boussard T, Olivier M, Hainaut P, Thornton JM. 2002. Integrating mutation data and structural analysis of the TP53 tumor, suppressor protein. Hum Mutat 19:149-164.
12. Ng PC, Henikoff S. 2001. Predicting deleterious amino acid substitutions. Genome Res 11:863-874.
13. Sambrook J, Fritsch EF, Maniatis T. 1989. Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press. p. 9.16-9.19.
14. Sneath PH. 1966. Relations between chemical structure and biological activity in peptides. J Theor Biol 12:157-195.
15. Sourvinos G, Rizos E, Spandidos DA. 2001. p53 codon 72 polymorphism is linked to the development and not the progression of benign and malignant laryngeal tumours. Oral Oncol 37:572-578.
16. Storey A, Thomas M, Kalita A, Harwood C, Gardiol D, Mantovani F, Breuer J, Leigh IM, Matlashewski G, Banks L. 1998. Role of a p53 polymorphism in the development of human papilloma-virus-associated cancer. Nature 393:229-234.
17. Sunyaev S, Ramensky V, Koch I, Lathe W III, Kondrashov AS, Bork P. 2001. Prediction of deleterious human alleles. Hum Mol Genet 10:591-597.
18. Swofford DL. 1998. Paup 4.0 Beta Version for Windows: Phylogenetic analysis using parsimony. Sunderland, Massachusetts: Sinauer Associates.
19. Thompson JD, Higgins DG, Gibson TJ. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673-4680.
20. Varley JM, McGown G, Thorncroft M, James LA, Margison GP, Forster G, Evans DG, Harris M, Kelsey AM, Birch JM. 1999. Are there low-penetrance TP53 Alleles? Evidence from childhood adrenocortical tumors. Am J Hum Genet 65:995-1006.
21. Wang Z, Moult J. 2001. SNPs, protein structure, and disease. Hum Mutat 17:263-270.