Abstract
Summary: What next? The Human Genome Project signifies complexity rather than simplification in the relationship between genotype and phenotype. Genotypes are embedded in genomes. Individuality in phenotypes is embedded in components of the phenome (transcriptome, metabolome, proteome, etc.). The phenome, its layers, and its nodes, links and networks, require elucidation; there is a need for a Human Phenome Project (Freimer and Sabatti 2003). Biology has largely been a reductive science in the recent past; integrative biology lies ahead. Clinician-scientists (including human biochemical geneticists) will be recognized as key participants in the ‘medical’ Phenome Project as it reveals components of individuality, and their contributions, in simple or combinatorial fashion, to Mendelian and complex traits; better ways to treat ‘genetic disease’ will be by-products of the project.
Although the Word is common to all, most men live as if each had a private wisdom of his own.
Herakleitos
Similar content being viewed by others
REFERENCES
Avise JC (2001) Evolving genomic metaphors: a new look at the language of DNA. Science 294: 86–87.
Badano JL, Katsanis N (2002) Beyond Mendel: an evolving view of human genetic disease transmission. Nat Rev Genet 3: 779–789.
Bearn AG (ed.) (1993) Archibald Garrod and the Individuality of Man. Oxford: Clarendon Press.
Bell JI (2003) The double helix in clinical practice. Nature 421: 414–416.
Bray D (2003) Molecular prodigality. Science 299: 1189–1190.
Caspi A, Sugden K, Moffitt TE, et al (2003) Influence of life stress on depression: Moderation by a polymorphism in the 5-HTT gene. Science 301: 386–389.
Cavalli-Sforza LL, Menozzi P, Piazza A (1993) Demic expansions and human evolution. Science 259: 639–646.
Chakravarti A, Little P (2003) Nature, nurture and human disease. Nature 421: 412–414.
Chesney RW, Friedman A, Kanto WP Jr, Stanton BF, Stull TL (2002) Pediatric practice and education in the genomic/postgenomic era. J Pediatr 141: 453–458.
Cheung VG, Conlin LK, Weber TM, et al (2003) Natural variation in human gene expression assessed in lymphoblastoid cells. Nature Genetics 33: 422–425.
Childs B (1999) Genetic Medicine. A Logic of Disease. Baltimore, MD: The Johns Hopkins University Press.
Collins FS, Green ED, Guttmacher AE, Guyer MS, USNHGRI (2003) A vision for the future of genomics research. Nature 422: 835–847.
Cowles CR, Hirshorn JN, Altshuler D, Lander ES (2002) Detection of regulatory variation in mouse genes. Nature Genetics 32: 432–437.
Dennis C and Campbell P (2003) The eternal molecule. Nature 421: 396.
Dobzhansky T (1973) Nothing in biology makes sense except in the light of evolution. Am Biol Teacher 35: 125–129.
Evans WE, Relling MV (1999) Pharmacogenomics: translating functional genomics into rational therapeutics. Science 286: 487–491.
Freimer N, Sabatti C (2003) The Human Phenome Project. Nature Genetics 34: 15–21.
Gavin A-C, Bosche M, Krause R, et al (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415: 141–147.
Glazier AM, Nadeau JH, Altman TJ (2002) Finding genes that underlie complex traits. Science 298: 2345–2349.
Goldstein JL, Brown MS (1997) The clinical investigator: bewitched, bothered and bewildered-but still beloved. J Clin Invest 99: 2803–2812.
Hall JG (2003) A clinician's plea. Nature Genetics 33: 440–442.
Hariharan IK, Haber DA (2003) Yeast, flies, worms, and fish in the study of human disease. N Engl J Med 348: 2457–2463.
Harris H, Hopkinson DA, Edwards YH (1977) Polymorphism and the subunit structure of enzymes: a contribution to the neutralist selectionist controversy. Proc Natl Acad Sci USA 74: 697–701.
Hartman JL, Garvik B, Hartwell L (2001) Principles for the buffering of genetic variation. Science 291 (Feb. 9): 1001–1004.
Ho Y, Gruhler A, Heilbut A, et al (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415: 180–183.
Hudson TJ (2003) Wanted: regulatory SNPs. Nature Genetics 33: 439–440.
Ideker T, Thorsson V, Ranish JA, et al (2001) Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 292: 929–934.
International Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nature 409: 860–921.
Jacob F (1977) Evolution and tinkering. Science 196: 1161–1166.
Jeong H, Tombor B, Albert R, Otlval ZN, Barabasi AL (2000) The large-scale organization of metabolic networks. Nature 407 (Oct. 5): 651–654.
Jimenez-Sanchez G, Childs B, Valle D (2001) Human disease genes. Nature 409: 853–855.
Kacser H, Porteous JW (1987) Control of metabolism: What do we have to measure? Trends Biochem Sci 12: 5–14.
Kauffman SA (1993) The Origins of Order. New York: Oxford University Press.
Kumar A, Snyder M (2002) Protein complexes take the bait. Nature 415: 123–124.
Lau NC, Bartel DP (2003) Censors of the genome. Sci Am August: 34–41.
Legrain P, Wojcik J, Gauthier J-M (2001) Protein-protein interaction maps: a lead towards cellular functions. Trends Genet 17: 346–352.
Maddox B (2003) The double helix and the 'wronged heroine'. Nature 421: 407–408.
Maurer SM, Firestone RB, Scriver CR (2000) Science's neglected legacy. Nature 405: 117–120.
McManus MT, Sharp PA (2002) Gene silencing in mammals by small interfering RNAs. Nat Rev Genet 3: 737–747.
Muntau AC, Roschinger W, Habich M et al (2002) Tetrahydrobiopterin as an alternative treatment for mild phenylketonuria. N Engl J Med 347: 2122–2132.
Nadeau JH (2001) Modifier genes in mice and humans. Nature Genetics 2: 165–174.
Oltvai ZN, Barabasi AL (2002) Life's complexity pyramid. Science 298: 763–764.
Ouzounis CA, Coulson RMR, Enright AJ, Kunin V, Pereira-Leal JB (2003) Classification schemes for protein structure and function. Nat Rev Genet 4: 508–519.
Prigogine I (1980) From Being to Becoming. Time and Complexity in the Physical Sciences. New York: WH Freeman.
Rees J (2002) Complex disease and the new clinical sciences. Science 296: 698–701.
Rose S (2001) The biology of the future and the future of biology. Perspect Biol Med 44(Autumn): 473–484.
Rosenberg LE (1999) The physician-scientist: an essential-and fragile-link in the medical research chain. J Clin Invest 103: 1621–1626.
Scriver CR (1993) Genetics and society: what society expects of geneticists-overview. Trans R Soc Canada IV: 3–10.
Scriver CR (2001) Garrod's foresight; our hindsight. J Inherit Metab Dis 24: 93–116.
Scriver CR (2002a) Does hereditary metabolic disease modulate senescence and ageing? J Inherit Metab Dis 25: 235–251.
Scriver CR (2002b) Why mutation analysis does not always predict clinical consequences: explanations in the era of genomics. J Pediatr 140: 502–506.
Scriver CR (2003) Tinkered masterpieces or master tinker. American Society for Human Genetics. http://www.faseb.org/ashg/educ/evo-00.shtml (website).
Scriver CR, Gregory DM, Sovetts D, Tissenbaum G (1985) Normal plasma free amino acid values in adults: the influence of some common physiological variables. Metabolism 34: 868–873.
Scriver CR, Nowacki PM (1999) Genomics, mutations and the internet: the naming and use of parts. J Inherit Metab Dis 22: 519–530.
Sober E (1984) The Nature of Selection. Evolutionary Theory in Philosophical Focus. Cambridge, MA: MIT Press.
Strohman R (2003) ThermodynamicsDold laws in medicine and complex diseases. Nature Biotechnology 21: 477–479.
Tong AHY, Evangelista M, Parsons AB, et al (2001) Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science: 2364–2368.
Venter JC, Adams MD, Myers EW, et al (2001) The sequence of the human genome. Science 291(Feb. 16): 1304–1351.
Waters PJ Parniak MA, Akerman BR, et al (1999) Missense mutations in the phenylalanine hydroxylase gene (PAH) can cause accelerated proteolytic turnover of PAH enzyme: a mechanism underlying phenylketonuria. J Inherit Metab Dis 22: 208–212.
Watson JD, Crick FHC (1953) Molecular structure of nucleic acids: a structure for deoxyribose nucleic acid. Nature 171: 737–738.
Weiss KM, Buchanan AV (2003) Evolution by phenotype: a biomedical perspective. Perspect Biol Med 46(2): 159–182.
Willett WC (2002) Balancing life-style and genomics research for disease prevention. Science 296: 695–698.
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Scriver, C.R. After the genome—the phenome?. J Inherit Metab Dis 27, 305–317 (2004). https://doi.org/10.1023/B:BOLI.0000031100.26546.6e
Issue Date:
DOI: https://doi.org/10.1023/B:BOLI.0000031100.26546.6e