Why pharmacogenomics? Why now?

Typing SNP based on the near-infrared spectroscopy and artificial neural network

Based on the near-infrared spectra (NIRS) of the measured samples as the discriminant variables of their genotypes, the genotype discriminant model of SNP has been established by using back-propagation artificial neural network (BP-ANN). Taking a SNP (857G>A) of N-acetyltransferase 2 (NAT2) as an example, DNA fragments containing the SNP site were amplified by the PCR method based on a pair of primers to obtain the three-genotype (GG, AA, and GA) modeling samples. The NIRS-s of the amplified samples were directly measured in transmission by using quartz cell. Based on the sample spectra measured, the two BP-ANN-s were combined to obtain the stronger ability of the three-genotype classification. One of them was established to compress the measured NIRS variables by using the resilient back-propagation algorithm, and another network established by Levenberg-Marquardt algorithm according to the compressed NIRS-s was used as the discriminant model of the three-genotype classification. For the established model, the root mean square error for the training and the prediction sample sets were 0.0135 and 0.0132, respectively. Certainly, this model could rightly predict the three genotypes (i.e. the accuracy of prediction samples was up to 100%) and had a good robust for the prediction of unknown samples. Since the three genotypes of SNP could be directly determined by using the NIRS-s without any preprocessing for the analyzed samples after PCR, this method is simple, rapid and low-cost.

The use of experimental murine models to assess novel agents of hematopoietic stem and progenitor cell mobilization

The recent explosion in the understanding of the cellular and molecular mechanisms underlying hematopoietic stem and progenitor cell (HSPC) mobilization has facilitated development of novel therapeutic agents, targeted at improving mobilization kinetics as well as HSPC yield. With the development of new agents comes the challenge of choosing efficient and relevant preclinical studies for the testing of the HSPC mobilization efficacy of these agents. This article reviews the use of the mouse as a convenient small animal model of HSPC mobilization and transplantation, and outlines the range of murine assays that can be applied to assess novel HSPC mobilizing agents. Techniques to demonstrate murine HSPC mobilization are discussed, as well as the role of murine assays to confirm human HSPC mobilization, and techniques to investigate the biologic phenotype of HSPC mobilized by these novel agents. Technical aspects regarding mobilization regimens and control arms, and choice of experimental animals are also discussed.

Databases and the future of clinical trials in bladder cancer

As clinical trials continue to expand and evolve to include a wider range of collected information, the amount and variety of information available to clinical researchers has concurrently grown. This article describes a range of means to address this complexity and to accommodate the collection, storage, and integration of this information based on current approaches in biomedical informatics. By reviewing these current approaches, and drawing examples from actual practice within the clinical informatics community, a range of potential solutions and their potential impacts are discussed.

Various pharmacogenetic aspects of antiepileptic drug therapy: a review

Pharmacogenetics concerns the influence of an individual's genetic background on the pharmacokinetics and pharmacodynamics of xenobiotics. Much of the pharmacogenetic data in the field of epilepsy deals with the pharmacokinetics of antiepileptic drugs (AEDs). In particular, two polymorphisms of cytochrome P450 2C9 are known to slow down the metabolism of phenytoin to a degree that increases the risk of the neurotoxic adverse effects of this drug among carriers of these polymorphisms. A significant number of patients with epilepsy do not respond to AEDs and such pharmacoresistance is a major, largely unsolved, problem that is likely to be multifactorial in nature. In this regard, genetic factors may influence transmembrane drug transporter proteins, thereby modifying the intracerebral penetration of AEDs. Monogenic idiopathic epilepsies are rare and frequently associated with ion channel mutations; however, to date, a consistent relationship between changes in channel properties and clinical phenotype has not been established nor has any association between genotype and response to specific treatment options. Polymorphisms of drug targets may represent another genetic facet in epilepsy: a recent study demonstrated for the first time a polymorphism of a drug target (the alpha-subunit of a voltage-gated sodium channel) associated in clinical practice with differing response to two classic AEDs. Adverse drug reactions and teratogenicity of AEDs remain a major concern. Whole-genome single nucleotide polymorphism profiling might in the future help to determine genetic predisposing factors for adverse drug reactions. Recently, in Han Chinese treated with carbamazepine and presenting with Stevens-Johnson syndrome, a strong association was found with HLA B*1502. If genetically targeted drug development becomes more affordable/cost efficient in the near future, the development of new drugs for relatively rare diseases could become economically viable for the pharmaceutical industry. The synergy of lower trial costs and efficacy-based prescribing may reduce the cost of medical treatment for a particular disease. This hypothetical advantage of the practical use of pharmacogenetics is, however, counterbalanced by several possible dangers, including illicit data mining and the development of a human 'genetic underclass' with the risk of exclusion from, for example employment or health insurance, because of an 'unfavourable' genetic profile.

DNA attachment chemistry at the flexible silicone elastomer surface: toward disposable microarrays

This paper describes the preparation and surface characterization of maleimide-activated silicone elastomer (PDMS(MCC)) followed by covalent functionalization using thiol-terminated DNA sequences (primary oligo). The stability of this attachment chemistry was demonstrated by the retention of the primary oligo through the process of hybridization with a labeled complementary DNA sequence. In these studies, the hybridized labeled DNA oligomers were detected using confocal fluorescence microscopy. We have employed a vapor deposition technique in which a plasma-treated silicone elastomer (PDMS(OH)) was exposed to vapors of 3-(aminopropyl)triethoxysilane (APTS) under vacuum, to yield the amine-functionalized silicone elastomer (PDMS(NH)(2)). PDMS(NH)(2) was further coupled with a heterofunctional cross-linker, sulfosuccinimidyl-4-(N-maleimidomethyl)cyclohexane-1-carboxylate to obtain PDMS(MCC). The surface functionalities of the elastomers were characterized using contact angle measurements and X-ray photoelectron spectroscopy. Surface-modified silicone elastomers appear to be promising substrates for use as substrates for disposable microarrays.

Hypertensive patients from two rural Chinese counties respond differently to benazepril: the Anhui Hypertension Health Care Study

PURPOSE

Essential hypertension, as a complex disorder with unknown etiology cause, is a major public health problem worldwide. Patients need constant drug therapy to maintain their blood pressure in a normal range. However, the current facts suggest that the treatment is not optimized in a large number of patients, and as a result they are at risk for compliance resulting in uncontrolled blood pressure. Genetic and environmental factors associated with individual variation in response to anti-hypertensive drug remain largely unknown.

METHODS

In order to illustrate the existence and to attempt to identify the factors modifying drug effect, we conducted a large-scale follow-up study in two Chinese rural counties differing in both genetic background and residential environment. Hypertensive patients were treated with benazepril, a commonly used angiotensin converting enzyme inhibitor, for 15 days, and the end-point effect was evaluated.

RESULTS

We found that there were large and significant differences in drug response between subjects from two counties, even after adjustment for known factors. The responses to benazepril, measured in diastolic blood pressure drop, in male patients from Yuexi was twice as effective as their counterparts from Huoqiu.

CONCLUSIONS

These results suggest that adjustment of treatment regimen is necessary to improve efficacy, and it could be done at the population level to make it more feasible and affordable.

New genetics, new ethics? Globalisation and its discontents

The paper discusses the rapid and significant development of new genetic technologies (in health, food and agriculture) in the theoretical context of the globalisation debate. We show how the studies on the ethical, legal and social implications of biotechnological innovation have themselves emerged as an important factor in the technological innovation and product development process. Ethical considerations are becoming integral to attempts to understand techno-scientific developments in late modernity. However, ethical studies have so far been more focused on the medical rather than the overall commercial application of genomics. Their relevance to this wider context of the globalised commodification of new genetics needs to be explored. Of special significance is the introduction of ethical considerations into the debates on globalised risk, which we will explore in relation to increasing disparities between the global North and South.

Pharmacogenomic profiling in postmarketing surveillance: prospects and challenges

Adverse drug reactions (ADRs) represent a major public health and economic global problem. Growing evidence suggests that pharmacogenomics may potentially play a role in reducing drug-induced adverse events. Research efforts are increasingly directed towards this goal. However, knowledge about whether or not pharmacogenomics may be useful as a novel approach in postmarketing surveillance programs is at present rather limited. A critical analysis of some of the methodological design and ethical issues generated by the potential incorporation of pharmacogenomic profiling into pharmacosurveillance programs is presented.

DNA probe attachment on plastic surfaces and microfluidic hybridization array channel devices with sample oscillation

DNA probe immobilization on plastic surfaces and device assembly are both critical to the fabrication of microfluidic hybridization array channel (MHAC) devices. Three oligonucleotide (oligo) probe immobilization procedures were investigated for attaching oligo probes on four different types of plastic surfaces (polystyrene, polycarbonate, poly(methylmethacrylate), and polypropylene). These procedures are the Surmodics procedure, the cetyltrimethylammonium bromide (CTAB) procedure, and the Reacti-Bind procedure. To determine the optimal plastic substrate and attachment chemistry for array fabrication, we investigated plastic hydrophobicity, intrinsic fluorescence, and oligo attachment efficiency. The Reacti-Bind procedure is least effective for attaching oligo probes in the microarray format. The CTAB procedure performs well enough to use in array fabrication, and the concentration of CTAB has a significant effect on oligo immobilization efficiency. We also found that use of amine-modified oligo probes resulted in better immobilization efficiency than use of unmodified oligos with the CTAB procedure. The oligo probe immobilization on plastic surfaces by the Surmodics procedure is the most effective with regard to probe spot quality and hybridization sensitivity. A DNA hybridization assay on such a device results in a limit of detection of 12pM. Utilizing a CO(2) IR laser machining and adhesive layer approach, we have developed an improved procedure for realizing a DNA microarray inside a microfluidic channel. This device fabrication procedure allows for more feasible spot placement in the channel and reduced sample adsorption by adhesive tapes used in the fabrication procedure. We also demonstrated improved hybridization kinetics and increased detection sensitivity in MHAC devices by implementing sample oscillation inside the channel. A limit of detection of 5pM has been achieved in MHAC devices with sample oscillation.

The drugs don't work: expectations and the shaping of pharmacogenetics

This article examines one particular set of technologies arising from developments in human genetics, those aimed at improving the targeting, design and use of conventional small molecule drugs-pharmacogenetics. Much of the debate about the applications and consequences of pharmacogenetics has been highly speculative, since little or no working technology is yet on the market. This article provides a novel analysis of the development of pharmacogenetics, and the social and ethical issues it raises, based on the sociology of technological expectations. In particular, it outlines how two alternative visions for the development of the technology are being articulated and embedded in a range of heterogeneous discourses, artefacts, actor strategies and practices, including: competing scientific research agendas, experimental technologies, emerging industrial structures and new ethical discourses. Expectations of how pharmacogenetics might emerge in each of these arenas are actively shaping the trajectory of this nascent technology and its potential socio-economic consequences.

Emerging ethical issues in pharmacogenomics: from research to clinical practice

Pharmacogenomics holds much promise for the application of genetic information to the improvement of clinical care. Ethical issues for pharmacogenomics arise at the intersection of the spheres of drug development and genetic testing. Clinical drug trial designs which use subject selection based on genotype must consider the features of scientific validity, social value and risk-benefit ratio, and later, the impact of this strategy on post-market studies and clinical use of drugs. Although the testing context for pharmacogenomic tests is different from other genetic tests, decisions to use any new clinical tests in medical practice will require evaluation of not only the benefit linked to improved drug use but also the risks arising in part from the scale of testing, predictive value and collateral potential of the genetic test. Integration of pharmacogenomic information into clinical practice will require clinical trials to assess their clinical usefulness, including the impact of tests on therapeutic outcomes. Trials will also be needed to demonstrate the effectiveness of education, informed consent and counseling.

Pharmacogenetics of schizophrenia

Patients display significant differences in response to therapeutic agents which may be caused by a variety of factors. Among them, genetic components presumably play a major role. Pharmacogenetics is the field of research that attempts to unravel the relationship between genetic variation affecting drug metabolism (pharmacokinetic level) or drug targets (pharmacodynamic level) and interindividual differences in pharmacoresponse. In schizophrenia, pharmacokinetic studies have shown the role of genetic variants of the cytochrome P450 enzymes CYP2D6, CYP2C19, and CYP2C9 in the metabolism of neuroleptic drugs. At the level of the drug target, variants of the dopamine D3 and D4, and 5-HT2A and 5-HT2C receptors have been examined. A general problem of pharmacogenetic studies in schizophrenia is the high number of controversial findings which may be related to the lack of standardized phenotype definition. Recently, guidelines for an exact and comparable phenotype characterization have been proposed and will aid in designing and evaluating pharmacogenetic studies in the future. The final goal of pharmacogenetic studies-making a prediction of drug response at the level of the individual patient-will require a simultaneous look at a large number of response-determining genetic variants by applying the tools of pharmacogenomics, e.g. large-scale Single Nucleotide Polymorphism (SNP) detection and genotyping.

A novel method for SNP detection using a new duplex-specific nuclease from crab hepatopancreas

We have characterized a novel nuclease from the Kamchatka crab, designated duplex-specific nuclease (DSN). DSN displays a strong preference for cleaving double-stranded DNA and DNA in DNA-RNA hybrid duplexes, compared to single-stranded DNA. Moreover, the cleavage rate of short, perfectly matched DNA duplexes by this enzyme is essentially higher than that for nonperfectly matched duplexes of the same length. Thus, DSN differentiates between one-nucleotide variations in DNA. We developed a novel assay for single nucleotide polymorphism (SNP) detection based on this unique property, termed "duplex-specific nuclease preference" (DSNP). In this innovative assay, the DNA region containing the SNP site is amplified and the PCR product mixed with signal probes (FRET-labeled short sequence-specific oligonucleotides) and DSN. During incubation, only perfectly matched duplexes between the DNA template and signal probe are cleaved by DSN to generate sequence-specific fluorescence. The use of FRET-labeled signal probes coupled with the specificity of DSN presents a simple and efficient method for detecting SNPs. We have employed the DSNP assay for the typing of SNPs in methyltetrahydrofolate reductase, prothrombin and p53 genes on homozygous and heterozygous genomic DNA.

A genotyping strategy based on incorporation and cleavage of chemically modified nucleotides

Aiming to facilitate the analysis of human genetic variations in the context of disease susceptibility and varied drug response, we have developed a genotyping method that entails incorporation of a chemically labile nucleotide by PCR followed by specific chemical cleavage of the resulting amplicon at the modified bases. The identity of the cleaved fragments determines the genotype of the DNA. This method, termed Incorporation and Complete Chemical Cleavage, utilizes modified nucleotides 7-deaza-7-nitro-dATP, 7-deaza-7-nitro-dGTP, 5-hydroxy-dCTP, and 5-hydroxy-dUTP, which have increased chemical reactivity but are able to form standard Watson-Crick base pairs. Thus one analog is substituted for the corresponding nucleotide during PCR, generating amplicons that contain nucleotide analogs at each occurrence of the selected base throughout the target DNA except for the primer sequences. Subsequent treatment with an oxidant followed by an organic base results in chemical cleavage at each site of modification, which produces fragments of different lengths and/or molecular weights that reflect the genotype of the original DNA sample at the site of interest. This incorporation and cleavage chemistry are widely applicable to many existing nucleic acid analysis platforms, including gel electrophoresis and mass spectrometry. By combining DNA amplification and analog incorporation into one step, this strategy eliminates preamplification, DNA-strand separation, primer extension, and purification procedures associated with traditional chain-termination chemistry and therefore presents significant advantages in terms of speed, cost, and simplicity of genotyping.

Pharmacogenetics: the therapeutic drug monitoring of the future?

Genetic variability in drug response occurs as a result of molecular alterations at the level of drug-metabolising enzymes, drug targets/receptors, and drug transport proteins. In this paper, we discuss the possibility that therapeutic drug monitoring (TDM) in the future will involve not the mere measurement and interpretation of drug concentrations but will include both traditional TDM and pharmacogenetics-oriented TDM. In contrast to traditional TDM, which cannot be performed until after a drug is administered to the patient. pharmacogenetics-oriented TDM can be conducted even before treatment begins. Other advantages of genotyping over traditional TDM include, but are not limited to, the following: (i) it does not require the assumption of steady-state conditions (or patient compliance) for the interpretation of results; (ii) it can often be performed less invasively (with saliva, hair root or buccal swab samples); (iii) it can provide predictive value for multiple drugs [e.g. a number of cytochrome P450 (CYP) 2D6, CYP2C 19 or CYP2C9 substrates] rather than a single drug; (iv) it provides mechanistic, instead of merely descriptive, information; and (v) it is constant over an individual's lifetime (and not influenced by concurrent drug administration, alteration in hormonal levels or disease states). Pharmacogenetic information can be applied a priori for initial dose stratification and identification of cases where certain drugs are simply not effective. However, traditional TDM will still be required for all of the reasons that we use it now. In current clinical practice, pharmacogenetic testing is performed for only a few drugs (e.g. mercaptopurine, thioguanine, azathioprine, trastuzumab and tacrine) and in a limited number of teaching hospitals and specialist academic centres. We propose that other drugs (e.g. warfarin, phenytoin, codeine, oral hypoglycaemics, tricyclic antidepressants, aminoglycosides, digoxin, cyclosporin, cyclophosphamide, ifosfamide, theophylline and clozapine) are potential candidates for pharmacogenetics-oriented TDM. However, prospective studies of phaymacogenetics-oriented TDM must be performed to determine its efficacy and cost effectiveness in optimising therapeutic effects while minimising toxicity. In the future, in addition to targeting a patient's drug concentrations within a therapeutic range, pharmacists are likely to be making dosage recommendations for individual drugs on the basis of the individual patient's genotype. As we enter the era of personalised drug therapy, we will be able to identify not only the best drug to be administered to a particular patient, but also the most effective and safest dosage from the outset of therapy.

Clinical pharmacogenetics and future prospects in drug therapy

The human genome project has a large impact on various drug-related fields including drug discovery and clinical medication. Although clinical pharmacogenetics introduced the importance of studying genetic factors determining inter-individual variation on drug response for establishing a personalized medicine, which will be achieved in this century, recent strategies for exploring the genetic factors drastically differ from those of classical pharmacogenetics. The usefulness of an application of findings obtained from basic researches to a medication is uncertain at present because of limited in vivo evidence on the significance of genetic polymorphism to ensure an efficacy or to avoid adverse reactions of the drugs. In this review, a brief history of pharmacogenetics and the current status of the research are summarized. A number of problems that make it difficult to do clinical trials to clarify the significance of genetic polymorphism are discussed. Finally, it is expected in the near future that information on genetic variation with in silico technologies may predict the response toward drugs in each patient with various physiological and therapeutic conditions.

Allelic frequencies and patterns of single-nucleotide polymorphisms in candidate genes for asthma and atopy in Iceland

Numerous asthma and atopy loci have been reported in studies demonstrating associations of the asthma-related phenotypes atopy, elevated IgE levels, and bronchial hyperresponsiveness with alleles of microsatellite markers and single-nucleotide polymorphisms (SNPs) within specific cytokine/chemokine and IgE-regulating genes. Although the studies reporting these observations are compelling, most of them lack statistical power. We assessed the nature, pattern, and frequency of SNPs in 24 candidate genes in Iceland and looked for associations with asthma and atopy. We identified 42 SNPs with an average minor allele frequency of 20.3% (asthma) and 20.7% (control). Twenty SNPs (48%) were within coding sequences and 90% of those led to a predicted change in protein sequence. No differences were detected in the allelic frequencies of SNPs in any of these candidate genes between control subjects and the patients with atopic asthma. Moreover, linkage analysis that included 269 patients with atopic asthma uncovered no evidence of linkage to markers associated with these genes. We conclude that this study has failed to produce evidence in support of the notion that variations within these 24 candidate atopy and asthma genes significantly influence the expression of the atopic asthmatic phenotype or contribute to the susceptibility of atopic asthma.

Validation of a single nucleotide polymorphism genotyping assay for the human serum paraoxonase gene using electronically active customized microarrays

OBJECTIVES

Develop a microarray based genotyping assay to detect SNPs in human paraoxonase (PON I) and compare its accuracy with DNA sequencing and RFLP based assays.

DESIGN AND METHODS

Amplicons spanning the polymorphic regions of interest were genotyped by sequencing, RFLP, and microarray technology. Validation parameters included precision, linearity of signal response, and carryover between adjacent sites on the microarray.

RESULTS

A 100% correlation in results obtained using DNA sequencing, RFLP and microarray technology was observed.

CONCLUSIONS

The microarray technology provides an accurate and reliable assay platform with applicability in high throughput genotyping studies.

High-throughput biopolymer desalting by solid-phase extraction prior to mass spectrometric analysis

In the last 10 years mass spectrometry (MS) has become an important method for analysis of peptides, proteins and DNA. It was recently utilized for accurate high-throughput protein identification, sequencing and DNA genotyping. The presence of non-volatile buffers compromises sensitivity and accuracy of MS biopolymer analysis; it is essential to remove sample contaminants prior to analysis. We have developed a fast and efficient method for desalting of DNA oligonucleotides and peptides using 96-well solid-phase extraction plates packed with 5 mg of Waters Oasis HLB sorbent (Waters, Milford, MA, USA). This reversed-phase sorbent retains the biopolymer analytes, while non-retained inorganic ions are washed out with pure deionized water. DNA oligonucleotides or peptides are eluted using a small amount (20-100 microl) of acetonitrile-water (70:30, v/v) solution. The SPE desalting performance meets the requirements for MS applications such as protein digest analysis and DNA genotyping.

Microchips, microarrays, biochips and nanochips: personal laboratories for the 21st century

Micro miniaturization of analytical procedures is having significant impact on diagnostic testing, and will enable highly complex clinical testing to be miniaturized and permit testing to move from the central laboratory into non-laboratory settings. The diverse range of micro analytical devices includes microchips, gene chips, bioelectronic chips. They have been applied to several clinically important assays (e.g., PCR, immunoassay). The main advantages of the new devices are integration of multiple steps in complex analytical procedures, diversity of application, sub-microliter consumption of reagents and sample, and portability. These devices form the basis of new and smaller analyzers (e.g., capillary electrophoresis) and may ultimately be used in even smaller devices useful in decentralized testing (lab-on-a-chip, personal laboratories). The impact of microchips on healthcare costs could be significant via timely intervention and monitoring, combined with improved treatments (e.g., microchip-based pharmacogenomic tests). Empowerment of health consumers to perform self-testing is limited, but microchips could accelerate this process and so produce a level of self-awareness of biochemical and genetic information hitherto unimaginable. The next level of miniaturization is the nanochip (nanometer-sized features) and the technological foundation for these futuristic devices is discernable in nanotubes and self-assembling molecular structures.

Detection of mitochondrial single nucleotide polymorphisms using a primer elongation reaction on oligonucleotide microarrays

We have developed a novel allele-specific primer elongation protocol using a DNA polymerase on oligonucleotide chips. Oligonucleotide primers carrying polymorphic sites at their free 3'end were covalently bound to glass slides. The generation of single-stranded targets of genomic DNA containing single nuclotide polymorphisms (SNPs) to be typed was achieved by an asymmetric PCR reaction or exonuclease treatment of phosphothioate (PTO)-modified PCR products. In the presence of DNA polymerase and all four dNTPs, with Cy3-dUTP replacing dTTP, allele-specific extension of the immobilized primers took place along a stretch of target DNA sequence. The yield of elongated products was increased by repeated reaction cycles. We performed multiplexed assays with many small DNA targets, or used single targets of up to 4.4 kb mitochondrial DNA (mtDNA) sequence to detect multiple SNPs in one reaction. The latter approach greatly simplifies preamplification of SNP-containing regions, thereby providing a framework for typing hundreds of mtDNA polymorphisms.

Predicting the functional consequences of non-synonymous single nucleotide polymorphisms: structure-based assessment of amino acid variation

We have developed a formalism and a computational method for analyzing the potential functional consequences of non-synonymous single nucleotide polymorphisms. Our approach uses a structural model and phylogenetic information to derive a selection of structure and sequence-based features serving as indicators of an amino acid polymorphim's effect on function. The feature values can be integrated into a probabilistic assessment of whether an amino acid polymorphism will affect the function or stability of a target protein. The method has been validated with data sets of unbiased mutations in the lac repressor and lysoyzyme. Applying our methodology to recent surveys of genetic variation in the coding regions of clinically important genes, we estimate that approximately 26-32 % of the natural non-synonymous single nucleotide polymorphisms have effects on function. This estimate suggests that a typical person will have about 6240-12,800 heterozygous loci that encode proteins with functional variation due to natural amino acid polymorphism.

Identification of novel, functional genetic variants in the human matrix metalloproteinase-2 gene: role of Sp1 in allele-specific transcriptional regulation

Matrix metalloproteinase-2 (MMP-2) is an enzyme with proteolytic activity against matrix and nonmatrix proteins, particularly basement membrane constituents. Thus, any naturally occurring genetic variants that directly affect gene expression and/or protein function would be expected to impact on progression of pathological processes involving tissue remodeling. We scanned a 2-kilobase pair promoter region and all 13 exons of the human MMP-2 gene, from a panel of 32 individuals, and we identified the position, nature, and relative allele frequencies of 15 variant loci as follows: 6 in the promoter, 1 in the 5'-untranslated region, 6 in the coding region, 1 in intronic sequence, and 1 in the 3'-untranslated region. The majority of coding region polymorphisms resulted in synonymous substitutions, whereas three promoter variants (at -1306, -790, and +220) mapped onto cis-acting elements. We functionally characterized all promoter variants by transient transfection experiments with 293, RAW264.7, and A10 cells. The common C --> T transition at -1306 (allele frequency 0.26), which disrupts an Sp1-type promoter site (CCACC box), displayed a strikingly lower promoter activity with the T allele. Electrophoretic mobility shift assays confirmed that these differences in allelic expression were attributable to abolition of Sp1 binding. These data suggest that this common functional genetic variant influences MMP-2 gene transcription in an allele-specific manner and is therefore an important candidate to test for association in a wide spectrum of pathologies for which a role for MMP-2 is implicated, including atherogenesis and tumor invasion and metastasis.

A SNP resource for human chromosome 22: extracting dense clusters of SNPs from the genomic sequence

The recent publication of the complete sequence of human chromosome 22 provides a platform from which to investigate genomic sequence variation. We report the identification and characterization of 12,267 potential variants (SNPs and other small insertions/deletions) of human chromosome 22, discovered in the overlaps of 460 clones used for the chromosome sequencing. We found, on average, 1 potential variant every 1.07 kb and approximately 18% of the potential variants involve insertions/deletions. The SNPs have been positioned both relative to each other, and to genes, predicted genes, repeat sequences, other genetic markers, and the 2730 SNPs previously identified on the chromosome. A subset of the SNPs were verified experimentally using either PCR-RFLP or genomic Invader assays. These experiments confirmed 92% of the potential variants in a panel of 92 individuals. [Details of the SNPs and RFLP assays can be found at http://www.sanger.ac.uk and in dbSNP.]

Efficient mobilization of haematopoietic progenitors after a single injection of pegylated recombinant human granulocyte colony-stimulating factor in mouse strains with distinct marrow-cell pool sizes

We have compared the efficacy of a single injection of SD/01, a newly engineered, pegylated form of recombinant human granulocyte colony stimulating factor (rhG-CSF), with a single injection of glycosylated rhG-CSF (Filgrastim). SD/01 was administered to regular and recombinant inbred strains of mice (AKR, C57L/J, DBA/2, C57BL/6, AKXL) known to have widely distinct marrow-cell pool sizes and proliferation kinetics. A single injection of G-CSF was unable to mobilize granulocyte-macrophage colony-forming units (CFU-GM). In sharp contrast, a single dose of SD/01 resulted in massive mobilization of progenitors and stem cells. Although all mice strains showed qualitatively similar mobilization responses, large interstrain differences remained. C57L and C57BL/6 mice mobilized relatively poorly, whereas AKR and DBA/2 mice showed threefold to tenfold superior responses. In order to explain these different phenotypes, we studied the effects of SD/01 in nine AKXL recombinant inbred strains, derived from well-responding AKR and poorly responding C57L parental strains. The best predictor for SD/01 responsiveness in these strains was marrow cellularity prior to mobilization. Comparison of the AKXL strain distribution pattern for marrow cellularity with loci previously mapped in these strains showed complete concordance with Aat, a serine protease inhibitor mapping to chromosome 12.

Distinct functional properties of highly purified hematopoietic stem cells from mouse strains differing in stem cell numbers

We have previously demonstrated that young adult DBA/2 (DBA) mice have more stem cells than C57BL/6 (B6) mice, as measured in a cobblestone area-forming cell (CAFC) assay using unfractionated marrow. To study the nature of this difference, we have now compared the proliferative fate of single, highly enriched Sca-1+c-kit+Lin−stem cells from these strains. Although equal in frequency, functional comparison revealed that Sca-1+c-kit+Lin−cells from DBA mice contained twice as many cells with CAFC activity. DBA clones persisted much longer in vitro, and developed later in time. To assess whether these differences were of any functional relevance in vivo, we compared engraftment of lethally irradiated mice transplanted with 1000 B6 or DBA Sca-1+c-kit+Lin−cells. Recipients of enriched DBA cells recovered much faster than animals transplanted with B6 cells. We also studied endogenous hematopoietic recovery after 5-fluorouracil (5-FU) treatment in vivo. Progenitors and peripheral blood cells recovered twice as fast in DBA mice. Thus, DBA stem cells have superior proliferative potential compared with phenotypically identical stem cells obtained from B6 mice. Such genetically determined quantitative and qualitative differences in stem cell behavior likely contribute to the dramatically different hematopoietic recovery rates observed in human transplant patients.

Distinct functional properties of highly purified hematopoietic stem cells from mouse strains differing in stem cell numbers

We have previously demonstrated that young adult DBA/2 (DBA) mice have more stem cells than C57BL/6 (B6) mice, as measured in a cobblestone area-forming cell (CAFC) assay using unfractionated marrow. To study the nature of this difference, we have now compared the proliferative fate of single, highly enriched Sca-1+c-kit+Lin−stem cells from these strains. Although equal in frequency, functional comparison revealed that Sca-1+c-kit+Lin−cells from DBA mice contained twice as many cells with CAFC activity. DBA clones persisted much longer in vitro, and developed later in time. To assess whether these differences were of any functional relevance in vivo, we compared engraftment of lethally irradiated mice transplanted with 1000 B6 or DBA Sca-1+c-kit+Lin−cells. Recipients of enriched DBA cells recovered much faster than animals transplanted with B6 cells. We also studied endogenous hematopoietic recovery after 5-fluorouracil (5-FU) treatment in vivo. Progenitors and peripheral blood cells recovered twice as fast in DBA mice. Thus, DBA stem cells have superior proliferative potential compared with phenotypically identical stem cells obtained from B6 mice. Such genetically determined quantitative and qualitative differences in stem cell behavior likely contribute to the dramatically different hematopoietic recovery rates observed in human transplant patients.

Combining structure-based design with phage display to create new Cys(2)His(2) zinc finger dimers

BACKGROUND

Several strategies have been reported for the design and selection of novel DNA-binding proteins. Most of these studies have used Cys(2)His(2) zinc finger proteins as a framework, and have focused on constructs that bind DNA in a manner similar to Zif268, with neighboring fingers connected by a canonical (Krüppel-type) linker. This linker does not seem ideal for larger constructs because only modest improvements in affinity are observed when more than three fingers are connected in this manner. Two strategies have been described that allow the productive assembly of more than three canonically linked fingers on a DNA site: connecting sets of fingers using linkers (covalent), or assembling sets of fingers using dimerization domains (non-covalent).

RESULTS

Using a combination of structure-based design and phage display, we have developed a new dimerization system for Cys(2)His(2) zinc fingers that allows the assembly of more than three fingers on a desired target site. Zinc finger constructs employing this new dimerization system have high affinity and good specificity for their target sites both in vitro and in vivo. Constructs that recognize an asymmetric binding site as heterodimers can be obtained through substitutions in the zinc finger and dimerization regions.

CONCLUSIONS

Our modular zinc finger dimerization system allows more than three Cys(2)His(2) zinc fingers to be productively assembled on a DNA-binding site. Dimerization may offer certain advantages over covalent linkage for the recognition of large DNA sequences. Our results also illustrate the power of combining structure-based design with phage display in a strategy that assimilates the best features of each method.

The Human Genome Project--an overview

The human genome sequence will underpin human biology and medicine in the next century, providing a single, essential reference to all genetic information. The international program to determine the complete DNA sequence (3,000 million bases) is well underway. As of January 2000, 50% of the sequence is available in the public domain. A comprehensive working draft is expected this year, and the entire sequence is projected to be finished in 2003. DNA sequencing is carried out on mapped, overlapping bacterial clones of 150-200 kb. The working draft comprises assembled unfinished sequence and is released immediately in the public domain. The draft sequence of each clone is then completed, by closing any remaining gaps and resolving any ambiguities, before the entire sequence is checked, annotated, and submitted to the public databases. The sequence of each clone is finished to an accuracy of >99.99%. The availability of a reference sequence of the genome provides the basis for studying the nature of sequence variation, particularly single nucleotide polymorphisms (SNPs), in human populations. SNP typing is a powerful tool for genetic analysis, and will enable us to uncover the association of loci at specific sites in the genome with many disease traits. SNPs occur at a frequency of approximately 1 SNP/kb throughout the genome when the sequence of any two individuals is compared. Programs to detect and map SNPs in the human genome are underway with the aim of establishing a SNP map of the genome during the next two years. The human genome sequence will provide a complete description of all the genes. Annotation of the sequence with the gene structures is achieved by a combination of computational analysis (predictive and homology-based) and experimental confirmation by cDNA sequencing. Detecting homologies between newly defined gene products and proteins of known function helps to postulate biochemical functions for them, which can then be tested. Establishing the association of specific genes with disease phenotypes by mutation screening, particularly for monogenic disorders, provides further assistance in defining the functions of some gene products, as well as helping to establish the cause of the disease. As our knowledge of gene sequences and sequence variation in populations increases, we will pinpoint more and more of the genes and proteins that are important in common, complex diseases. A more detailed understanding of the function of the human genome will be achieved as we identify sequences that control gene expression. Given the availability of gene sequences, the expression status of genes in particular tissues can be monitored in parallel. By comparing corresponding genomic sequences in different species (for example: man, mouse, chicken, and zebrafish), regions that have been highly conserved during evolution can be identified, many of which reflect conserved functions such as gene regulation. These approaches promise to greatly accelerate our interpretation of the human genome sequence.

Preparing for the revolution--pharmacogenomics and the clinical lab

Pharmacogenomics seeks to apply the field of genomics to improve the efficacy and safety of therapeutics. Sinmply put, pharmacogenomics is genetic-based testing to determine patient therapy. Interestingly, the clinical lab has rarely been discussed within the context of pharmacogenomics. Since clinical labs fill a key role in drug development it is important that they are included in pharmacogenomic discussions. Currently, clinical labs assist pharmaceutical sponsors in preclinical pharmacogenetic testing. In the future, clinical labs will be looked to for genetic test development and validation, and high-throughput genotyping of patients in clinical trials and routine testing. Clinical labs are an essential link in the chain of pharmacogenomic drug development, a fact which must be recognised by both the labs themselves and the industry as a whole.

Pharmacogenetics of antipsychotic treatment: lessons learned from clozapine

The reintroduction of clozapine, the prototype of atypical antipsychotics, in the late 1980s has led to significant advances in the pharmacological management of schizophrenia. Since then, there has been a rapid development of novel "atypical" antipsychotic agents that have been pharmacologically modeled, to a certain extent, after their predecessor clozapine. As with all antipsychotics, there is variability among individuals in their response to these "atypical" drugs. Pharmacogenetics can provide a foundation for understanding this interindividual variability in antipsychotic response. This review first provides a rationale for the pharmacogenetic investigation of this variable trait. Studies of pharmacokinetic and pharmacodynamic factors of antipsychotic therapy are considered in the development of this rationale. Next, the molecular genetic techniques used to study this interindividual variation in response are described. This is followed by a review and discussion of the published studies examining genetic factors involved in clozapine response. From this, several recommendations for future pharmacogenetic investigations of antipsychotic response are proposed. Although still in its early stages, psychiatric pharmacogenetics should provide a basis for individualized pharmacotherapy of schizophrenia, and may also lead to the development of newer, more efficacious antipsychotic agents.

Pharmacogenomics: the genomics of drug response

Pharmacogenomics is defined as the study of the association between genetics and drug response. This is a rapidly expanding field with the hope that, within a few years, prospective genotyping will lead to patients being prescribed drugs which are both safer and more effective ('the right drug for the right patient', or personalized medicine). There are many existing examples in the literature of strong associations between genetic variation and drug response, and some of these even form the basis of accepted clinical tests. The molecular basis for some of these associations is described, and includes examples of variation in genes responsible for absorption and metabolism of the drug, and in target and disease genes. However, there are many issues surrounding the legal, regulatory and ethical framework to these studies that remain unanswered, and a huge amount of education both for the public and healthcare professionals will be needed before the results of this new medicine can be widely accepted.

5′ Nuclease Assays for the Loci CCR5-+/Δ32, CCR2-V64I, and SDF1-G801A Related to Pathogenesis of AIDS

Background: Variations within the human genome play important roles in human disease. To study variations related to susceptibility to AIDS, we have developed 5′ nuclease assays that eliminate post-PCR molecular biology steps.

Methods: TaqMan assays based on the 5′ nuclease activity of Taq polymerase and fluorescent resonance energy transfer were developed to score alleles at the biallelic loci CCR5-+/Δ32, CCR2-V64I and SDF1-G801A. For each assay, 72 samples were analyzed. Data collection and analysis were performed on the Prism 7700 Sequence Detection System. For comparison with gel electrophoresis methods, each locus was also scored on a subset of 24 samples, using restriction enzymes or single-strand conformational polymorphism (SSCP).

Results: Clear allelic discrimination was obtained on each of the 72 samples for all three TaqMan assays. The TaqMan scores for the subset of 24 samples were concordant with the restriction enzyme and SSCP scores.

Conclusions: Because of its simplicity, speed, and potential for automation and miniaturization, TaqMan is an excellent candidate for investigation of genetic variation in clinical, research, and forensic settings.

The promise of comparative genomics in mammals

Dense genetic maps of human, mouse, and rat genomes that are based on coding genes and on microsatellite and single-nucleotide polymorphism markers have been complemented by precise gene homolog alignment with moderate-resolution maps of livestock, companion animals, and additional mammal species. Comparative genetic assessment expands the utility of these maps in gene discovery, in functional genomics, and in tracking the evolutionary forces that sculpted the genome organization of modern mammalian species.

Patterns of single-nucleotide polymorphisms in candidate genes for blood-pressure homeostasis

Sequence variation in human genes is largely confined to single-nucleotide polymorphisms (SNPs) and is valuable in tests of association with common diseases and pharmacogenetic traits. We performed a systematic and comprehensive survey of molecular variation to assess the nature, pattern and frequency of SNPs in 75 candidate human genes for blood-pressure homeostasis and hypertension. We assayed 28 Mb (190 kb in 148 alleles) of genomic sequence, comprising the 5' and 3' untranslated regions (UTRs), introns and coding sequence of these genes, for sequence differences in individuals of African and Northern European descent using high-density variant detection arrays (VDAs). We identified 874 candidate human SNPs, of which 22% were confirmed by DNA sequencing to reveal a discordancy rate of 21% for VDA detection. The SNPs detected have an average minor allele frequency of 11%, and 387 are within the coding sequence (cSNPs). Of all cSNPs, 54% lead to a predicted change in the protein sequence, implying a high level of human protein diversity. These protein-altering SNPs are 38% of the total number of such SNPs expected, are more likely to be population-specific and are rarer in the human population, directly demonstrating the effects of natural selection on human genes. Overall, the degree of nucleotide polymorphism across these human genes, and orthologous great ape sequences, is highly variable and is correlated with the effects of functional conservation on gene sequences.

The Future of Molecular Genetic Testing

The potential applications for genetic testing are immense, with most diseases having some aspect influenced by, if not directly caused by, changes in the genome of the patient. The translation of genetic information into medical applications will be influenced by our understanding of the human genome, technological advances, and social, ethical, and legal issues surrounding genetic testing. With time, new genetic information will be translated into clinical tests for the diagnosis of current illness and prediction of future disease risk, and will be used for the development of genetically directed therapies and preventive interventions. Most genetic testing will be highly automated, with only rare genetic disease tests performed manually. The challenge for the clinical genetic laboratory is to keep pace with this information explosion to provide state-of-the-art genetic testing and to ensure that the genetic test results are used in a morally, ethically, and socially responsible way.

Genomes and proteomes: towards a multidimensional view of biology

The third Siena proteomics conference held August 31-September 4, 1998, heralded a change in emphasis from technology development to using proteomics to assist in resolving biological questions. In this review, proteomics is placed in context with other major influences in the way discovery research is conducted in biology. The current status of genomics is examined in its broadest sense, including how such studies may influence the development of proteomics. It is suggested that we are entering a new phase in biology where information is no longer limiting and integration of different technologies is required to attack the big problems of biology. While much of the focus of funding bodies, both in the public and private sector, is on practical outcomes (new drugs, etc.), the new technologies are equally amenable to attacking long-standing fundamental challenges, such as cell division, cell patterning and morphogenesis.