Sequencing the entire genomes of free-living organisms: the foundation of pharmacology in the new millennium.

The power and effectiveness of clinical pharmacology are about to be transformed with a speed that earlier in this decade could not have been foreseen even by the most astute visionaries. In the very near future, we will have at our disposal the reference DNA sequence for the entire human genome, estimated to contain approximately 3.5 billion bp. At the same time, the science of whole genome sequencing is fostering the computational science of bioinformatics needed to develop practical applications for pharmacology and toxicology. Indeed, it is likely that pharmacology, toxicology, bioinformatics, and genomics will merge into a new branch of medical science for studying and developing pharmaceuticals from molecule to bedside.

[1]  M. Sanak,et al.  Leukotriene C4 synthase polymorphism and aspirin-induced asthma. , 2001, The Journal of allergy and clinical immunology.

[2]  N. Shen,et al.  Patterns of single-nucleotide polymorphisms in candidate genes for blood-pressure homeostasis , 1999, Nature Genetics.

[3]  G. Aithal,et al.  Warfarin dose requirement and CYP2C9 polymorphisms , 1999, The Lancet.

[4]  M. Wahlgren Creating deaths from malaria , 1999, Nature Genetics.

[5]  L. Kruglyak Prospects for whole-genome linkage disequilibrium mapping of common disease genes , 1999, Nature Genetics.

[6]  A. Clark,et al.  Chips for chimps , 1999, Nature Genetics.

[7]  Kevin Marsh,et al.  A polymorphism that affects OCT-1 binding to the TNF promoter region is associated with severe malaria , 1999, Nature Genetics.

[8]  Nicholas Schork,et al.  Pharmacogenetic association between ALOX5 promoter genotype and the response to anti-asthma treatment , 1999, Nature Genetics.

[9]  S. P. Fodor,et al.  Determination of ancestral alleles for human single-nucleotide polymorphisms using high-density oligonucleotide arrays , 1999, Nature Genetics.

[10]  S. Salzberg,et al.  Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima , 1999, Nature.

[11]  N. Holtzman Promoting safe and effective genetic tests in the United States: work of the task force on genetic testing. , 1999, Clinical chemistry.

[12]  M B Daly,et al.  Modification of BRCA1-associated breast cancer risk by the polymorphic androgen-receptor CAG repeat. , 1999, American journal of human genetics.

[13]  S. Gutman The role of Food and Drug Administration regulation of in vitro diagnostic devices--applications to genetics testing. , 1999, Clinical chemistry.

[14]  M. Goodman,et al.  Model for the fetal recruitment of simian gamma-globin genes based on findings from two New World monkeys Cebus apella and Callithrix jacchus (Platyrrhini, Primates). , 1999, The Journal of experimental zoology.

[15]  T. Fukuda,et al.  Deficiency of platelet-activating factor acetylhydrolase is a severity factor for asthma. , 1999, The Journal of clinical investigation.

[16]  A. Cravchik,et al.  Functional analysis of the human D5 dopamine receptor missense and nonsense variants: differences in dopamine binding affinities. , 1999, Pharmacogenetics.

[17]  Jeannie T. Lee,et al.  Tsix, a gene antisense to Xist at the X-inactivation centre , 1999, Nature Genetics.

[18]  Ronald W. Davis,et al.  Comparative genomes of Chlamydia pneumoniae and C. trachomatis , 1999, Nature Genetics.

[19]  J. Long,et al.  Cladistic association analysis of Y chromosome effects on alcohol dependence and related personality traits. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[20]  J. Hey,et al.  X chromosome evidence for ancient human histories. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[21]  J. Goedert,et al.  HLA and HIV-1: heterozygote advantage and B*35-Cw*04 disadvantage. , 1999, Science.

[22]  G. Aithal,et al.  Association of polymorphisms in the cytochrome P450 CYP2C9 with warfarin dose requirement and risk of bleeding complications , 1999, The Lancet.

[23]  D. Sibley,et al.  Analysis of neuroleptic binding affinities and potencies for the different human D2 dopamine receptor missense variants. , 1999, Pharmacogenetics.

[24]  D. R. Lawrenz Sickle cell disease: a review and update of current therapy. , 1999, Journal of oral and maxillofacial surgery : official journal of the American Association of Oral and Maxillofacial Surgeons.

[25]  Benjamin L. King,et al.  Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori , 1999, Nature.

[26]  Andrew Smith Genome sequence of the nematode C-elegans: A platform for investigating biology , 1998 .

[27]  D. Collier,et al.  Lack of association between a polymorphism in the promoter region of the dopamine-2 receptor gene and clozapine response. , 1998, Pharmacogenetics.

[28]  R. Gornall,et al.  p53 polymorphism and risk of cervical cancer , 1998, The Lancet.

[29]  T. Sicheritz-Pontén,et al.  The genome sequence of Rickettsia prowazekii and the origin of mitochondria , 1998, Nature.

[30]  E V Koonin,et al.  Chromosome 2 sequence of the human malaria parasite Plasmodium falciparum. , 1998, Science.

[31]  H. McLeod,et al.  Thiopurine Methyltransferase Genotype Predicts Therapy-Limiting Severe Toxicity from Azathioprine , 1998, Annals of Internal Medicine.

[32]  P. D'Athis,et al.  Pharmacokinetics:6‐Mercaptopurine Pharmacokinetics After Use of Azathioprine in Renal Transplant Recipients with Intermediate or High Thiopurine Methyl Transferase Activity Phenotype , 1998, The Journal of pharmacy and pharmacology.

[33]  J. Dewar,et al.  Polymorphisms of the Beta Chain of the High-Affinity Immunoglobulin E Receptor (Fc ɛ RI- β ) in South African Black and White Asthmatic and Nonasthmatic Individuals , 1998 .

[34]  R. W. Davis,et al.  Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis. , 1998, Science.

[35]  R. Koup,et al.  A 32-bp deletion within the CCR5 locus protects against transmission of parenterally acquired human immunodeficiency virus but does not affect progression to AIDS-defining illness. , 1998, The Journal of infectious diseases.

[36]  P. Hartge,et al.  The APC I1307K allele and cancer risk in a community-based study of Ashkenazi Jews , 1998, Nature Genetics.

[37]  D. Shih,et al.  Genetically determined susceptibility to organophosphorus insecticides and nerve agents: developing a mouse model for the human PON1 polymorphism. , 1998, Neurotoxicology.

[38]  E. Boerwinkle,et al.  Haplotype structure and population genetic inferences from nucleotide-sequence variation in human lipoprotein lipase. , 1998, American journal of human genetics.

[39]  P. Kwok,et al.  Reading bits of genetic information: methods for single-nucleotide polymorphism analysis. , 1998, Genome research.

[40]  M. J. Arranz,et al.  Meta-analysis of studies on genetic variation in 5-HT2A receptors and clozapine response , 1998, Schizophrenia Research.

[41]  M. Margaglione,et al.  Increased Risk for Venous Thrombosis in Carriers of the Prothrombin GA20210 Gene Variant , 1998, Annals of Internal Medicine.

[42]  E. Boerwinkle,et al.  DNA sequence diversity in a 9.7-kb region of the human lipoprotein lipase gene , 1998, Nature Genetics.

[43]  W. Evans,et al.  Pharmacogenetics of cancer therapy: getting personal. , 1998, American journal of human genetics.

[44]  P. McKeigue,et al.  Mapping genes that underlie ethnic differences in disease risk: methods for detecting linkage in admixed populations, by conditioning on parental admixture. , 1998, American journal of human genetics.

[45]  K M Weiss,et al.  In search of human variation. , 1998, Genome research.

[46]  C R Woese,et al.  Erratum: The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus , 1998, Nature.

[47]  B. Nordestgaard,et al.  ΔF508 heterozygosity in cystic fibrosis and susceptibility to asthma , 1998, The Lancet.

[48]  B. Barrell,et al.  Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence , 1998, Nature.

[49]  M. Adams,et al.  Shotgun Sequencing of the Human Genome , 1998, Science.

[50]  Irene M. Leigh,et al.  Role of a p53 polymorphism in the development of human papilloma-virus-associated cancer , 1998, Nature.

[51]  L. Peltonen,et al.  Dual origins of Finns revealed by Y chromosome haplotype variation. , 1998, American journal of human genetics.

[52]  D. Kwiatkowski,et al.  Absence of an association between intercellular adhesion molecule 1, complement receptor 1 and interleukin 1 receptor antagonist gene polymorphisms and severe malaria in a West African population. , 1998, Transactions of the Royal Society of Tropical Medicine and Hygiene.

[53]  M. Adams,et al.  The malaria genome sequencing project. , 1998, Protist.

[54]  P. Bray,et al.  PlA2 polymorphism and efficacy of aspirin , 1998, The Lancet.

[55]  R. Huber,et al.  The complete genome of the hyperthermophilic bacterium Aquifex aeolicus , 1998, Nature.

[56]  H. Whittle,et al.  Variations in the NRAMP1 gene and susceptibility to tuberculosis in West Africans. , 1998, The New England journal of medicine.

[57]  R. Minchin,et al.  Functional polymorphism of the human arylamine N-acetyltransferase type 1 gene caused by C190T and G560A mutations. , 1998, Pharmacogenetics.

[58]  A Chakravarti,et al.  Allele frequency distributions in pooled DNA samples: applications to mapping complex disease genes. , 1998, Genome research.

[59]  Z. Hijazi,et al.  High frequency of IgE receptor FcεRIß variant (Leu181/Leu183) in Kuwaiti Arabs and its association with asthma , 1998 .

[60]  R. Argueta,et al.  Coccidioidal infection of the thyroid. , 1998, Archives of internal medicine.

[61]  R. Erickson,et al.  Association between genetic polymorphisms of the beta2-adrenoceptor and response to albuterol in children with and without a history of wheezing. , 1997, The Journal of clinical investigation.

[62]  S. Salzberg,et al.  Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi , 1997, Nature.

[63]  R. Fleischmann,et al.  The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus , 1997, Nature.

[64]  A. Goffeau,et al.  The complete genome sequence of the Gram-positive bacterium Bacillus subtilis , 1997, Nature.

[65]  G. Church,et al.  Complete genome sequence of Methanobacterium thermoautotrophicum deltaH: functional analysis and comparative genomics , 1997, Journal of bacteriology.

[66]  L. Siever,et al.  D4 dopamine-receptor (DRD4) alleles and novelty seeking in substance-dependent, personality-disorder, and control subjects. , 1997, American journal of human genetics.

[67]  N. W. Davis,et al.  The complete genome sequence of Escherichia coli K-12. , 1997, Science.

[68]  E. McConkey,et al.  A Human Genome Evolution Project is needed. , 1997, Trends in genetics : TIG.

[69]  Edward M. Rubin,et al.  Functional screening and complex traits: human 21q22.2 sequences affecting learning in mice. , 1997, Human molecular genetics.

[70]  Leonid Kruglyak,et al.  The use of a genetic map of biallelic markers in linkage studies , 1997, Nature Genetics.

[71]  F. Ntoumi,et al.  Plasmodium falciparum: sickle-cell trait is associated with higher prevalence of multiple infections in Gabonese children with asymptomatic infections. , 1997, Experimental parasitology.

[72]  J J Goedert,et al.  Contrasting genetic influence of CCR2 and CCR5 variants on HIV-1 infection and disease progression. Hemophilia Growth and Development Study (HGDS), Multicenter AIDS Cohort Study (MACS), Multicenter Hemophilia Cohort Study (MHCS), San Francisco City Cohort (SFCC), ALIVE Study. , 1997, Science.

[73]  Mark Borodovsky,et al.  The complete genome sequence of the gastric pathogen Helicobacter pylori , 1997, Nature.

[74]  R. Snow,et al.  A high frequency African coding polymorphism in the N-terminal domain of ICAM-1 predisposing to cerebral malaria in Kenya. , 1997, Human molecular genetics.

[75]  C. Naspitz,et al.  HLA antigens in asthmatic children , 1997, Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology.

[76]  R. Weinshilboum,et al.  Human thiopurine methyltransferase pharmacogenetics: Gene sequence polymorphisms , 1997, Clinical pharmacology and therapeutics.

[77]  J. Lafitte,et al.  Polymorphism of the cytochrome P450 CYP2D6 gene in a European population: characterization of 48 mutations and 53 alleles, their frequencies and evolution. , 1997, Pharmacogenetics.

[78]  A. Thiel,et al.  Ischaemic brain tissue salvaged from infarction with alteplase , 1997, The Lancet.

[79]  P. Hartge,et al.  The risk of cancer associated with specific mutations of BRCA1 and BRCA2 among Ashkenazi Jews. , 1997, The New England journal of medicine.

[80]  D. Grant,et al.  Human acetyltransferase polymorphisms. , 1997, Mutation research.

[81]  André Goffeau,et al.  The yeast genome directory. , 1997, Nature.

[82]  H. Okkels,et al.  Arylamine N-acetyltransferase 1 (NAT1) and 2 (NAT2) polymorphisms in susceptibility to bladder cancer: the influence of smoking. , 1997, Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology.

[83]  Jan-Fang Cheng,et al.  Functional screening of 2 Mb of human chromosome 21q22.2 in transgenic mice implicates minibrain in learning defects associated with Down syndrome , 1997, Nature Genetics.

[84]  W. Willett,et al.  Methylenetetrahydrofolate reductase polymorphism, dietary interactions, and risk of colorectal cancer. , 1997, Cancer research.

[85]  J. Beijnen,et al.  Limited oral bioavailability and active epithelial excretion of paclitaxel (Taxol) caused by P-glycoprotein in the intestine. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[86]  R. Prough,et al.  Pharmacogenetics: a laboratory tool for optimizing therapeutic efficiency. , 1997, Clinical chemistry.

[87]  J. Spring,et al.  Vertebrate evolution by interspecific hybridisation – are we polyploid? , 1997, FEBS letters.

[88]  K. Lesch,et al.  Association of Anxiety-Related Traits with a Polymorphism in the Serotonin Transporter Gene Regulatory Region , 1996, Science.

[89]  M. Keifer,et al.  The effect of the human serum paraoxonase polymorphism is reversed with diazoxon, soman and sarin , 1996, Nature Genetics.

[90]  E. Rimm,et al.  A methylenetetrahydrofolate reductase polymorphism and the risk of colorectal cancer. , 1996, Cancer research.

[91]  H. Hilbert,et al.  Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae. , 1996, Nucleic acids research.

[92]  J. Goldstein,et al.  Human CYP2C19 is a major omeprazole 5-hydroxylase, as demonstrated with recombinant cytochrome P450 enzymes. , 1996, Drug metabolism and disposition: the biological fate of chemicals.

[93]  P. Yarowsky,et al.  Consequences of Trisomy 16 for Mouse Brain Development: Corticogenesis in a Model of Down Syndrome , 1996, The Journal of Neuroscience.

[94]  M H Tarbit,et al.  Genetic analysis of the human cytochrome P450 CYP2C9 locus. , 1996, Pharmacogenetics.

[95]  N Risch,et al.  The Future of Genetic Studies of Complex Human Diseases , 1996, Science.

[96]  J. Brockmöller,et al.  Homozygous rapid arylamine N-acetyltransferase (NAT2) genotype as a susceptibility factor for lung cancer. , 1996, Cancer research.

[97]  X. Estivill,et al.  A human homologue of Drosophila minibrain (MNB) is expressed in the neuronal regions affected in Down syndrome and maps to the critical region. , 1996, Human molecular genetics.

[98]  R. Fleischmann,et al.  Complete Genome Sequence of the Methanogenic Archaeon, Methanococcus jannaschii , 1996, Science.

[99]  Marc Parmentier,et al.  Resistance to HIV-1 infection in Caucasian individuals bearing mutant alleles of the CCR-5 chemokine receptor gene , 1996, Nature.

[100]  M. Takano,et al.  Effect of CYP2C polymorphisms on the pharmacokinetics of phenytoin in Japanese patients with epilepsy. , 1996, Biological & pharmaceutical bulletin.

[101]  W. Cookson,et al.  A new variant of the beta subunit of the high-affinity receptor for immunoglobulin E (Fc epsilon RI-beta E237G): associations with measures of atopy and bronchial hyper-responsiveness. , 1996, Human molecular genetics.

[102]  V. Georgoulias,et al.  HLA antigens and asthma in Greeks. , 1996, Respiratory medicine.

[103]  D W Nebert,et al.  Human drug-metabolizing enzyme polymorphisms: effects on risk of toxicity and cancer. , 1996, DNA and cell biology.

[104]  R. Ebstein,et al.  Excess dopamine D4 receptor (D4DR) exon III seven repeat allele in opioid dependent subjects , 1996 .

[105]  R. Fleischmann,et al.  The Minimal Gene Complement of Mycoplasma genitalium , 1995, Science.

[106]  R. Fleischmann,et al.  Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. , 1995, Science.

[107]  P. Keck,et al.  Structural change in dopamine D2 receptor gene in a patient with neuroleptic malignant syndrome. , 1995, American journal of medical genetics.

[108]  N J Cox,et al.  Association of attention-deficit disorder and the dopamine transporter gene. , 1995, American journal of human genetics.

[109]  Kamboh Mi Apolipoprotein E polymorphism and susceptibility to Alzheimer's disease. , 1995 .

[110]  S. Cichon,et al.  Human dopamine D4 receptor gene: frequent occurrence of a null allele and observation of homozygosity. , 1994, Human molecular genetics.

[111]  D. May Genetic Differences in Drug Disposition , 1994, Journal of clinical pharmacology.

[112]  W. Gehring,et al.  Homology of the eyeless gene of Drosophila to the Small eye gene in mice and Aniridia in humans. , 1994, Science.

[113]  Jack A. Taylor,et al.  Genetic risk and carcinogen exposure: a common inherited defect of the carcinogen-metabolism gene glutathione S-transferase M1 (GSTM1) that increases susceptibility to bladder cancer. , 1993, Journal of the National Cancer Institute.

[114]  Eric Lander,et al.  Linkage disequilibrium mapping in isolated founder populations: diastrophic dysplasia in Finland , 1992, Nature Genetics.

[115]  R. Maas,et al.  Genomic structure, evolutionary conservation and aniridia mutations in the human PAX6 gene , 1992, Nature Genetics.

[116]  M. Goodman,et al.  Fetal recruitment of anthropoid γ-globin genes: Findings from phylogenetic analyses involving the 5′-flanking sequences of the ψγ1 globin gene of spider monkey Ateles geoffroyi , 1992 .

[117]  J. Gearhart,et al.  Genetic basis for a mouse model of down syndrome , 1986, Brain Research Bulletin.

[118]  Morris Goodman,et al.  Phylogenetic origins and adaptive evolution of avian and mammalian haemoglobin genes , 1982, Nature.

[119]  J. Yunis,et al.  The origin of man: a chromosomal pictorial legacy. , 1982, Science.

[120]  村田 万里子 Cytochrome P4501A1 and glutathione S-transferase M1 genotypes as risk factors for prostate cancer in Japan , 2000 .

[121]  M. Goodman,et al.  The genomic record of Humankind's evolutionary roots. , 1999, American journal of human genetics.

[122]  Y. Kawarabayasi,et al.  Complete genome sequence of an aerobic hyper-thermophilic crenarchaeon, Aeropyrum pernix K1. , 1999, DNA research : an international journal for rapid publication of reports on genes and genomes.

[123]  H. Joost,et al.  Structural and functional characteristics of Dyrk, a novel subfamily of protein kinases with dual specificity. , 1999, Progress in nucleic acid research and molecular biology.

[124]  E. Lander,et al.  Characterization of single-nucleotide polymorphisms in coding regions of human genes , 1999 .

[125]  H. Yamazaki,et al.  Linkage between the distribution of mutations in the CYP2C18 and CYP2C19 genes in the Japanese and Caucasian. , 1998, Xenobiotica; the fate of foreign compounds in biological systems.

[126]  F. Robb,et al.  Complete sequence and gene organization of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3. , 1998, DNA research : an international journal for rapid publication of reports on genes and genomes.

[127]  S. Salzberg,et al.  Complete genome sequence of Treponema pallidum, the syphilis spirochete. , 1998, Science.

[128]  Z. Hijazi,et al.  High frequency of IgE receptor Fc epsilonRIbeta variant (Leu181/Leu183) in Kuwaiti Arabs and its association with asthma. , 1998, Clinical Genetics.

[129]  N. Nomura,et al.  Gene identification in 1.6-Mb region of the Down syndrome region on chromosome 21. , 1997, Genome research.

[130]  M. Goodman,et al.  Dynamics of regulatory evolution in primate beta-globin gene clusters: cis-mediated acquisition of simian gamma fetal expression patterns. , 1997, Gene.

[131]  A D Roses,et al.  Apolipoprotein E alleles as risk factors in Alzheimer's disease. , 1996, Annual review of medicine.

[132]  Sayaka,et al.  Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions. , 1996, DNA research : an international journal for rapid publication of reports on genes and genomes.

[133]  Y. Nakamura,et al.  Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions (supplement). , 1996, DNA research : an international journal for rapid publication of reports on genes and genomes.

[134]  M. Kamboh,et al.  Apolipoprotein E polymorphism and susceptibility to Alzheimer's disease. , 1995, Human biology.

[135]  W. Gehring,et al.  Homeodomain proteins. , 1994, Annual review of biochemistry.

[136]  M. Goodman,et al.  Fetal recruitment of anthropoid gamma-globin genes. Findings from phylogenetic analyses involving the 5'-flanking sequences of the psi gamma 1 globin gene of spider monkey Ateles geoffroyi. , 1992, Journal of Molecular Biology.