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Andrew Collins

Publications and source records attributed to Andrew Collins.

At least 37 records · Page 2Linked to original sources
PubMed2004

Establishing the background level of base oxidation in human lymphocyte DNA: results of an interlaboratory validation study.

Accurate measurement of low levels of 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodGuo) in DNA is hampered by the ease with which guanine is oxidized during preparation of DNA for analysis. ESCODD, a consortium of mainly European laboratories, has attempted to minimize this artifact and to provide standard, reliable protocols for sample preparation and analysis. ESCODD has now analyzed 8-oxodGuo in the DNA of lymphocytes isolated from venous blood from healthy young male volunteers in several European countries. Two approaches were used. Analysis of 8-oxodGuo by HPLC with electrochemical detection was performed on lymphocytes from 10 groups of volunteers, in eight countries. The alternative enzymic approach was based on digestion of DNA with formamidopyrimidine DNA glycosylase (FPG) to convert 8-oxo-7,8-dihydroguanine (8-oxoGua) to apurinic sites, subsequently measured as DNA breaks using the comet assay (7 groups of volunteers, in six countries). The median concentration of 8-oxodGuo in lymphocyte DNA, calculated from the mean values of each group of subjects as determined by HPLC, was 4.24 per 10(6) guanines. The median concentration of FPG-sensitive sites, measured with the comet assay, was 0.34 per 10(6) guanines. Identical samples of HeLa cells were supplied to all participants as a reference standard. The median values for 8-oxodGuo in HeLa cells were 2.78 per 10(6) guanines (by HPLC) and 0.50 per 10(6) guanines (by enzymic methods). The discrepancy between chromatographic and FPG-based approaches may reflect overestimation by HPLC (if spurious oxidation is still not completely controlled) or underestimation by the enzymic method. Meanwhile, it is clear that the true background level of base oxidation in DNA is orders of magnitude lower than has often been claimed in the past.

8-Hydroxy-2'-Deoxyguanosine↗
PubMed2004

Genotoxic effects of asbestos in humans.

Risks of carcinogenic and non-carcinogenic effects from asbestos continue owing to the persistence of the fibres in building materials and other products. For this reason, epidemiological and mechanistic research on the toxic effects of asbestos and mineral fibres is still needed. The present molecular epidemiological study was conducted in a former asbestos cement plant in Slovakia. Altogether 82 subjects were investigated, 61 exposed subjects (24 smokers and 37 non-smokers), and 21 factory controls (8 smokers and 13 non-smokers). Workers were exposed to asbestos for between 5 and 40 years. Though the exposure to asbestos during past 40 years was relatively high, at the time of sampling the concentrations of asbestos in the production hall exceeded the Slovak occupational limit (0.001 fibre/cm3) by a factor of only 3-5. The office area levels were below this limit. Biomarkers of exposure, effect and individual susceptibility were measured, including DNA damage (strand breaks [SBs], base oxidation and alkylation, using the comet assay); cytogenetic parameters; and individual DNA repair capacity (incision at 8-oxoguanine measured using a modified comet assay). Oxidised pyrimidines were significantly higher in exposed men compared with non-exposed (P = 0.04). There was also a positive association between SBs (P = 0.04) and age, and alkylation damage to DNA (P = 0.04) and age. Moreover, oxidised pyrimidines (P = 0.01) and alkylated bases (P = 0.001) strongly correlated with years of occupational exposure. Micronucleus frequency did not differ between exposed and control subjects. Repair capacity overall did not show any effect of exposure, though female controls had higher incision rates than did female exposed subjects. However, exposed asbestos workers had significantly higher numbers of chromosomal aberrations (P = 0.01) compared with control group. This finding is consistent with the known association of chromosome aberrations with cancer-risk.

Asbestos↗
PubMed2004

Does occupational exposure to mineral fibres cause DNA or chromosome damage?

Markers of genetic stability were monitored in lymphocytes from 98 workers employed in rockwool manufacture in a factory in the Slovak Republic, and 43 controls (administrative employees in the same factory). Strand breaks in lymphocyte DNA were higher in exposed compared to control non-smokers, but there was no effect of exposure on specific damage to bases in DNA, nor on chromosome aberrations. The frequency of micronuclei was higher in women in the control group than in rockwool-exposed women. DNA repair (8-oxoguanine DNA glycosylase activity) was unaffected by exposure, but was negatively correlated with micronucleus frequency, implying that unrepaired 8-oxoguanine contributes to micronucleus formation. The conclusion from this study is that, overall, rockwool exposure has no deleterious effect on genetic stability in humans.

DNA↗
PubMed2004

Immunomodulatory effects of mineral fibres in occupationally exposed workers.

In the context of a large-scale molecular epidemiology study, the possible immunomodulatory effects of mineral fibres, in workers occupationally exposed to asbestos, rockwool and glass fibres, were examined. In each plant, 61, 98 and 80 exposed workers and 21, 43 or 36 control clerical subjects, respectively, were recruited. In the case of the asbestos-exposed subjects, an additional town-control group of 49 people was included. Evidence of pulmonary fibrosis was found in 42% of the asbestos-exposed workers, while evidence of pleural fibrosis was found in 24%. The asbestos-exposed cohort had significantly decreased forced vital capacity of lungs as well as forced expiratory volume per first second. Our findings indicate that exposure to all three types of fibres examined modulates to different degrees the immune response. Suppression of T-cell immunity and to a lesser extent, B-cell immunity was found in the case of workers from a former asbestos cement plant, while stimulation of T-cell response was observed in rockwool workers, and stimulation of T- and B-cell response was seen in glass fibre workers. Depression of the percentage of lymphocyte subpopulation of CD 16+56 (natural killer cells) in peripheral blood was found in glass fibre workers. Statistical analysis showed increased levels of proinflammatory cytokines (IL-6 asbestos; IL-8 all three fibres), expression of adhesion molecule L-selectin on granulocytes and monocytes (asbestos), levels of soluble adhesion molecules (SAMs) in sera (ICAM-1 all three fibres; E-selectin glass fibres), increased levels of immunoglobulin E (asbestos and rockwool) and elevated expression of activation markers on eosinophils (CD66b asbestos, glass fibres; CD69 asbestos). Significant correlations were observed between lymphocyte proliferation and markers of DNA damage and repair. Increased levels of proinflammatory cytokines, SAMs, immunoglobulin E and elevated expression of activation markers on eosinophils was found in people with symptoms of hypersensitivity and an elevated inflammatory status.

B-Lymphocytes↗
PubMed2004

Seasonal changes in markers of oxidative damage to lipids and DNA; correlations with seasonal variation in diet.

We have addressed the question whether the relatively high incidence of cardiovascular disease and certain cancers in countries of central/eastern Europe might be associated with nutritional imbalance, in particular a lack of fresh fruit and vegetables in the diet in winter months. Nutritional parameters and markers of oxidative stress were studied in three Slovak population groups: 46 survivors of myocardial infarction (MI group) and 48 healthy, normolipidemic subjects (NL), living in or near Bratislava; and 70 rural controls (RC group) living a more traditional life style in a country town. Data were collected in February/March and September/October of two consecutive years, representing times of minimum and maximum local availability of fresh fruits and vegetables. Oxidative stress was monitored using two biomarkers; plasma malondialdehyde (MDA, a product of lipid peroxidation), and oxidation of lymphocyte DNA. Dietary antioxidants, folic acid, homocysteine, total antioxidant status (FRAP) and uric acid were measured in plasma. Food frequency questionnaires were administered. Vegetable consumption in summer/autumn was twice as high as in winter/spring. DNA damage did not vary consistently across the seasons. Mean plasma MDA levels for the MI and NL groups showed a clear pattern, with high levels in winter/spring and low levels in summer/autumn. Folic acid showed a reciprocal pattern, similar to the pattern of vegetable consumption. The RC group had the smallest seasonal variations in vegetable consumption, folic acid levels, and MDA. High winter MDA levels are seen in those individuals with relatively low folic acid; they never occur in subjects with high plasma folic acid, implying that folic acid might directly protect against lipid oxidation. This study illustrates the value of the molecular epidemiological approach, while emphasising the need for well characterised population groups and valid biomarkers.

Antioxidants↗
PubMed2004

Does haplotype diversity predict power for association mapping of disease susceptibility?

Many recent studies have established that haplotype diversity in a small region may not be greatly diminished when the number of markers is reduced to a smaller set of "haplotype-tagging" single-nucleotide polymorphisms (SNPs) that identify the most common haplotypes. These studies are motivated by the assumption that retention of haplotype diversity assures retention of power for mapping disease susceptibility by allelic association. Using two bodies of real data, three proposed measures of diversity, and regression-based methods for association mapping, we found no scenario for which this assumption was tenable. We compared the chi-square for composite likelihood and the maximum chi-square for single SNPs in diplotypes, excluding the marker designated as causal. All haplotype-tagging methods conserve haplotype diversity by selecting common SNPs. When the causal marker has a range of allele frequencies as in real data, chi-square decreases faster than under random selection as the haplotype-tagging set diminishes. Selecting SNPs by maximizing haplotype diversity is inefficient when their frequency is much different from the unknown frequency of the causal variant. Loss of power is minimized when the difference between minor allele frequencies of the causal SNP and a closely associated marker SNP is small, which is unlikely in ignorance of the frequency of the causal SNP unless dense markers are used. Therefore retention of haplotype diversity in simulations that do not mirror genomic allele frequencies has no relevance to power for association mapping. TagSNPs that are assigned to bins instead of haplotype blocks also lose power compared with random SNPs. This evidence favours a multi-stage design in which both models and density change adaptively.

Gene Frequency↗
PubMed2004

Positional cloning by linkage disequilibrium.

Recently, metric linkage disequilibrium (LD) maps that assign an LD unit (LDU) location for each marker have been developed (Maniatis et al. 2002). Here we present a multiple pairwise method for positional cloning by LD within a composite likelihood framework and investigate the operating characteristics of maps in physical units (kb) and LDU for two bodies of data (Daly et al. 2001; Jeffreys et al. 2001) on which current ideas of blocks are based. False-negative indications of a disease locus (type II error) were examined by selecting one single-nucleotide polymorphism (SNP) at a time as causal and taking its allelic count (0, 1, or 2, for the three genotypes) as a pseudophenotype, Y. By use of regression and correlation, association between every pseudophenotype and the allelic count of each SNP locus (X) was based on an adaptation of the Malecot model, which includes a parameter for location of the putative gene. By expressing locations in kb or LDU, greater power for localization was observed when the LDU map was fitted. The efficiency of the kb map, relative to the LDU map, to describe LD varied from a maximum of 0.87 to a minimum of 0.36, with a mean of 0.62. False-positive indications of a disease locus (type I error) were examined by simulating an unlinked causal SNP and the allele count was used as a pseudophenotype. The type I error was in good agreement with Wald's likelihood theorem for both metrics and all models that were tested. Unlike tests that select only the most significant marker, haplotype, or haploset, these methods are robust to large numbers of markers in a candidate region. Contrary to predictions from tagging SNPs that retain haplotype diversity, the sample with smaller size but greater SNP density gave less error. The locations of causal SNPs were estimated with the same precision in blocks and steps, suggesting that block definition may be less useful than anticipated for mapping a causal SNP. These results provide a guide to efficient positional cloning by SNPs and a benchmark against which the power of positional cloning by haplotype-based alternatives may be measured.

Alleles↗
PubMed2004

The impact of SNP density on fine-scale patterns of linkage disequilibrium.

Linkage disequilibrium (LD) is a measure of the degree of association between alleles in a population. The detection of disease-causing variants by association with neighbouring single nucleotide polymorphisms (SNPs) depends on the existence of strong LD between them. Previous studies have indicated that the extent of LD is highly variable in different chromosome regions and different populations, demonstrating the importance of genome-wide accurate measurement of LD at high resolution throughout the human genome. A uniform feature of these studies has been the inability to detect LD in regions of low marker density. To investigate the dependence of LD patterns on marker selection we performed a high-resolution study in African-American, Asian and UK Caucasian populations. We selected over 5000 SNPs with an average spacing of approximately 1 SNP per 2 kb after validating ca 12 000 SNPs derived from a dense SNP collection (1 SNP per 0.3 kb on average). Applications of different statistical methods of LD assessment highlight similar areas of high and low LD. However, at high resolution, features such as overall sequence coverage in LD blocks and block boundaries vary substantially with respect to marker density. Model-based linkage disequilibrium unit (LDU) maps appear robust to marker density and consistently influenced by marker allele frequency. The results suggest that very dense marker sets will be required to yield stable views of fine-scale LD in the human genome.

Black or African American↗
PubMed2004

Mapping genes for common diseases: the case for genetic (LD) maps.

We examine the current effort to develop a haplotype map of the human genome and suggest an alternative approach which represents linkage disequilibrium patterns in the form of a metric LD map. LD maps have some of the useful properties of genetic linkage maps but have a much higher resolution which is optimal for SNP-based association mapping of common diseases. The studies that have been undertaken to date suggest that LD and recombination maps show some close similarities because of abundant, narrow, recombination hot spots. These hot spots are co-localised in all populations but, unlike linkage maps, LD maps differ in scale for different populations because of differences in population history. The prospects for developing optimized panels of SNPs and the use of linkage disequilibrium maps in disease gene localisation are assessed in the light of recent evidence.

Chromosome Mapping↗
PubMed2004

MaGIC: a program to generate targeted marker sets for genome-wide association studies.

High-throughput genotyping technologies such as DNA pooling and DNA microarrays mean that whole-genome screens are now practical for complex disease gene discovery using association studies. Because it is currently impractical to use all available markers, a subset is typically selected on the basis of required saturation density. Restricting markers to those within annotated genomic features of interest (e.g., genes or exons) or within feature-rich regions, reduces workload and cost while retaining much information. We have designed a program (MaGIC) that exploits genome assembly data to create lists of markers correlated with other genomic features. Marker lists are generated at a user-defined spacing and can target features with a user-defined density. Maps are in base pairs or linkage disequilibrium units (LDUs) as derived from the International HapMap data, which is useful for association studies and fine-mapping. Markers may be selected on the basis of heterozygosity and source database, and single nucleotide polymorphism (SNP) markers may additionally be selected on the basis of validation status. The import function means the method can be used for any genomic features such as housekeeping genes, long interspersed elements (LINES), or Alu repeats in humans, and is also functional for other species with equivalent data. The program and source code is freely available at http://cogent.iop.kcl.ac.uk/MaGIC.cogx.

Algorithms↗
PubMed2003

Haplotypic analysis of the MMP-9 gene in relation to coronary artery disease.

Matrix metalloproteinase-9 (MMP-9) plays an important role in the pathogenesis of atherosclerosis, the pathology underlying the majority of coronary artery disease. We previously identified several polymorphisms in the gene encoding MMP-9. In this study we tested the hypothesis that variation in the matrix metalloproteinase-9 gene influences the development of atherosclerosis. Three common polymorphisms, i.e. -1562C>T, R+279Q and +6C>T, were analysed in 1510 white subjects undergoing coronary angiography. Analyses of individual polymorphisms showed that the frequencies of the C/T and T/T genotypes of the -1562C>T polymorphism were significantly higher in patients with coronary stenosis than in those with a normal angiogram. Logistic regression analyses indicated that individuals carrying the -1562T allele had an approx. 1.5-fold higher risk of developing coronary stenosis (OR 1.49, 95% CI 1.039-2.144), which was equivalent to an over 30% reduction in risk of coronary stenosis in individuals not carrying this allele (OR 0.670, 95% CI 0.467-0.963). The three polymorphisms studied were found to be in strong linkage disequilibrium. Haplotype analyses showed that the C-G-C haplotype (-1562C, +279Q and +6C) was associated with a protective effect against atherosclerosis. Individuals carrying this haplotype were at reduced risk of developing coronary stenosis (OR 0.695, 95% CI 0.530.92). Furthermore, the C-G-C haplotype was associated with less severe coronary atherosclerosis, i.e. carriers of this haplotype were at a lower risk of having coronary stenosis in more than one coronary artery (OR 0.796, 95% CI 0.640.99). These data, together with the previous finding that the -1562T allele has a higher transcriptional activity than the -1562C allele, support the notion that genetic variation with an effect on MMP-9 expression influences the development and progression of atherosclerosis.

Case-Control Studies↗
PubMed2003

Linkage disequilibrium in human populations.

Whereas the human linkage map appears on limited evidence to be constant over populations, maps of linkage disequilibrium (LD) vary among populations that differ in gene history. The greatest difference is between populations of sub-Saharan origin and populations remotely derived from Africa after a major bottleneck that reduced their heterozygosity and altered their Malecot parameters, increasing the intercept M that reflects association in founders and decreasing the exponential decline epsilon. Variation among populations within this ethnic dichotomy is much smaller. These observations validate use of a cosmopolitan LD map based on a sizeable sample representing a large population reliably typed for markers at high density. Then an LD map for a region or isolate within an ethnic group may be created by fitting the sample LD to the cosmopolitan map, estimating Malecot parameters simultaneously. The cosmopolitan map scaled by epsilon recovers 95% of the information that a local map at the same density gives and therefore more than the information in a low-resolution local map. Relative to a Eurasian cosmopolitan map the scaling factors are estimated to be 0.82 for isolates of European descent, 1.53 for Yorubans, and 1.74 for African Americans. These observations are consistent with a common bottleneck (perhaps but not necessarily speciation) approximately 173,500 years ago, if the bottleneck associated with migration out of Africa was 100,000 years ago. Eurasian populations (especially isolates with numerous cases) are efficient for genome scans, and populations of recent African origin (such as African Americans) are efficient for identification of causal polymorphisms within a candidate sequence.

Chromosome Mapping↗
PubMed2002

Properties of linkage disequilibrium (LD) maps.

A linkage disequilibrium map is expressed in linkage disequilibrium (LD) units (LDU) discriminating blocks of conserved LD that have additive distances and locations monotonic with physical (kb) and genetic (cM) maps. There is remarkable agreement between LDU steps and sites of meiotic recombination in the one body of data informative for crossing over, and good agreement with another method that defines blocks without assigning an LD location to each marker. The map may be constructed from haplotypes or diplotypes, and efficiency estimated from the empirical variance of LD is substantially greater for the rho metric based on evolutionary theory than for the absolute correlation r, and for the LD map compared with its physical counterpart. The empirical variance is nearly three times as great for the worst alternative (r and kb map) as for the most efficient approach (rho and LD map). According to the empirical variances, blocks are best defined by zero distance between included markers. Because block size is algorithm-dependent and highly variable, the number of markers required for positional cloning is minimized by uniform spacing on the LD map, which is estimated to have approximately equal 1 LDU per locus, but with much variation among regions. No alternative representation of linkage disequilibrium (some of which are loosely called maps) has these properties, suggesting that LD maps are optimal for positional cloning of genes determining disease susceptibility.

Chromosome Mapping↗
PubMed2002

A novel approach for identifying candidate imprinted genes through sequence analysis of imprinted and control genes.

Through the sequence analysis of 27 imprinted human genes and a set of 100 control genes we have developed a novel approach for identifying candidate imprinted genes based on the differences in sequence composition observed. The imprinted genes were found to be associated with significantly reduced numbers of short interspersed transposable element (SINE) Alus and mammalian-wide interspersed repeat (MIR) repeat elements, as previously reported. In addition, a significant association between imprinted genes and increased numbers of low-complexity repeats was also evident. Numbers of the Alu classes AluJ and AluS were found to be significantly depleted in some parts of the flanking regions of imprinted genes. A recent study has proposed that there is active selection against SINE elements in imprinted regions. Alternatively, there may be differences in the rates of insertion of Alu elements. Our study indicates that this difference extends both upstream and downstream of the coding region. This and other consistent differences between the sequence characteristics of imprinted and control genes has enabled us to develop discriminant analysis, which can be used to screen the genome for candidate imprinted genes. We have applied this function to a number of genes whose imprinting status is disputed or uncertain.

Female↗
PubMed2002

IL-16 regulation of human mast cells/basophils and their susceptibility to HIV-1.

AIDS patients often contain HIV-1-infected mast cells (MCs)/basophils in their peripheral blood, and in vivo-differentiated MCs/basophils have been isolated from the blood of asthma patients that are HIV-1 susceptible ex vivo due to their surface expression of CD4 and varied chemokine receptors. Because IL-16 is a ligand for CD4 and/or an undefined CD4-associated protein, the ability of this multifunctional cytokine to regulate the development of human MCs/basophils from nongranulated progenitors residing in cord or peripheral blood was evaluated. After 3 wk of culture in the presence of c-kit ligand, IL-16 induced the progenitors residing in the blood of normal individuals to increase their expression of chymase and tryptase about 20-fold. As assessed immunohistochemically, >80% of these tryptase(+) and/or chymase(+) cells expressed CD4. The resulting cells responded to IL-16 in an in vitro chemotaxis assay, and this biologic response could be blocked by anti-IL-16 and anti-CD4 Abs as well as by a competitive peptide inhibitor corresponding to a sequence in the C-terminal domain of IL-16. The additional finding that IL-16 induces calcium mobilization in the HMC-1 cell line indicates that IL-16 acts directly on MCs and their committed progenitors. IL-16-treated MCs/basophils also are less susceptible to infection by an M/R5-tropic strain of HIV-1. Thus, IL-16 regulates MCs/basophils at a number of levels, including their vulnerability to retroviral infection.

Antiviral Agents↗
PubMed2002

The power and statistical behaviour of allele-sharing statistics when applied to models with two disease loci.

We have evaluated the power for detecting a common trait determined by two loci, using seven statistics, of which five are implemented in the computer program SimWalk2, and two are implemented in GENEHUNTER. Unlike most previous reports which involve evaluations of the power of allele-sharing statistics for a single disease locus, we have used a simulated data set of general pedigrees in which a two-locus disease is segregating and evaluated several nonparametric linkage statistics implemented in the two programs. We found that the power for detecting linkage using the S(all) statistic in GENEHUNTER (GH, version 2.1), implemented as statistic E in SimWalk2 (version 2.82), is different in the two. The P values associated with statistic E output by SimWalk2 are consistently more conservative than those from GENEHUNTER except when the underlying model includes heterogeneity at a level of 50% where the P values output are very comparable. On the other hand, when the thresholds are determined empirically under the null hypothesis, S(all) in GENEHUNTER and statistic E have similar power.

Alleles↗