Trimming, weighting, and grouping SNPs in human case-control association studies

The search for genes underlying complex traits has been difficult and often disappointing. The main reason for these difficulties is that several genes, each with rather small effect, might be interacting to produce the trait. Therefore, we must search the whole genome for a good chance to find these genes. Doing this with tens of thousands of SNP markers, however, greatly increases the overall probability of false-positive results, and current methods limiting such error probabilities to acceptable levels tend to reduce the power of detecting weak genes. Investigating large numbers of SNPs inevitably introduces errors (e.g., in genotyping), which will distort analysis results. Here we propose a simple strategy that circumvents many of these problems. We develop a set-association method to blend relevant sources of information such as allelic association and Hardy-Weinberg disequilibrium. Information is combined over multiple markers and genes in the genome, quality control is improved by trimming, and an appropriate testing strategy limits the overall false-positive rate. In contrast to other available methods, our method to detect association to sets of SNP markers in different genes in a real data application has shown remarkable success.

The p53MH algorithm and its application in detecting p53-responsive genes

A computer algorithm, p53MH, was developed, which identifies putative p53 transcription factor DNA-binding sites on a genomewide scale with high power and versatility. With the sequences from the human and mouse genomes, putative p53 DNA-binding elements were identified in a scan of 2,583 human genes and 1,713 mouse orthologs based on the experimental data of el-Deiry et al. [el-Deiry, W. S., Kern, S. E., Pietenpol, J. A., Kinzler, K. W. & Vogelstein, B. (1992) Nat. Genet. 1, 45-49] and Funk et al. [Funk, W. D., Pak, D. T., Karas, R. H., Wright, W. E. & Shay, J. W. (1992) Mol. Cell. Biol. 12, 2866-2871] (http://linkage.rockefeller.edu/p53). The p53 DNA-binding motif consists of a 10-bp palindrome and most commonly a second related palindrome linked by a spacer region. By scanning from the 5' to 3' end of each gene with an additional 10-kb nucleotide sequence appended at each end (most regulatory DNA elements characterized in the literature are in these regions), p53MH computes the binding likelihood for each site under a discrete discriminant model and then outputs ordered scores, corresponding site positions, sequences, and related information. About 300 genes receiving scores greater than a theoretical cut-off value were identified as potential p53 targets. Semiquantitative reverse transcription-PCR experiments were performed in 2 cell lines on 16 genes that were previously unknown regarding their functional relationship to p53 and were found to have high scores in either proximal promoter or possible distal enhancer regions. Ten (approximately 63%) of these genes responded to the presence of p53.

Laryngeal muscle fibre types

The internal laryngeal muscles have evolved to subserve the highly specialized functions of airways protection, respiration, and phonation. Their contractile properties, histochemistry, biochemical properties, myosin heavy chain (MyHC) expression and their regulation by nerves and hormones are reviewed and compared with limb muscle fibres. Cricothyroid, the vocal cord tensor, is limb-like in MyHC composition and fibre type properties, while the vocal fold abductor and adductors are allotypically different, with capacity for expressing an isoform of MyHC that is kinetically faster than the fastest limb MyHC. In rats and rabbits the faster isoform is the extraocular (EO) MyHC, while in carnivores, it is the IIB MyHC. These adaptations enable the abductor and adductor muscles to remain always faster than the cricothyroid as the latter changes in speed during evolution to match changing metabolic and respiratory rates in relation to scaling with body mass. Such phylogenetic plasticity is vital to the airways protection and respiratory functions of these muscles. The posterior cricoarythenoid, the abductor muscle, is tonically driven during expiration, and consequently has a slower fibre type profile than the principal adductor, the thyroarythenoid. The human thyroarythenoid appears not to express EO or IIB MyHC significantly, but is unique in expressing the slow-tonic MyHC. The concepts of allotype and phylogenetic plasticity help to explain differences in fibre type between limb and laryngeal muscles and between homologous laryngeal muscles in different species. Laryngeal muscle fibres exhibit physiological plasticity as do limb muscles, being subject to neural and hormonal modulation.

p53 tumor suppressor protein regulates the levels of huntingtin gene expression

The p53 protein is a transcription factor that integrates various cellular stress signals. The accumulation of the mutant huntingtin protein with an expanded polyglutamine tract plays a central role in the pathology of human Huntington's disease. We found that the huntingtin gene contains multiple putative p53-responsive elements and p53 binds to these elements both in vivo and in vitro. p53 activation in cultured human cells, either by a temperature-sensitive mutant p53 protein or by gamma-irradiation (gamma-irradiation), increases huntingtin mRNA and protein expression. Similarly, murine huntingtin also contains multiple putative p53-responsive elements and its expression is induced by p53 activation in cultured cells. Moreover, gamma-irradiation, which activates p53, increases huntingtin gene expression in the striatum and cortex of mouse brain, the major pathological sites for Huntington's disease, in p53+/+ but not the isogenic p53-/- mice. These results demonstrate that p53 protein can regulate huntingtin expression at transcriptional level, and suggest that a p53 stress response could be a modulator of the process of Huntington's disease.

Selecting SNPs in two-stage analysis of disease association data: a model-free approach

For large numbers of marker loci in a genomic scan for disease loci, we propose a novel 2-stage approach for linkage or association analysis. The two stages are (1) selection of a subset of markers that are 'important' for the trait studied, and (2) modelling interactions among markers and between markers and trait. Here we focus on stage 1 and develop a selection method based on a 2-level nested bootstrap procedure. The method is applied to single nucleotide polymorphisms (SNPs) data in a cohort study of heart disease patients. Out of the 89 original SNPs the method selects 11 markers as being 'important'. Conventional backward stepwise logistic regression on the 89 SNPs selects 7 markers, which are a subset of the 11 markers chosen by our method.

Scan statistics to scan markers for susceptibility genes

Scan statistics are applied to combine information on multiple contiguous genetic markers used in a genome screen for susceptibility loci. This information may be, for example, allele sharing proportions for sib pairs or logarithm of odds (lod) scores in general small families. We focus on a dichotomous outcome variable, for example, case and control individuals or affected-affected versus affected-unaffected siblings, and suitable single-marker statistics. A significant scan statistic based on the single-marker statistics represents evidence of the presence of a susceptibility gene. For a given length of the scan statistic, we assess its significance by Monte Carlo permutation tests. Comparing P values for varying lengths of scan statistics, we treat the smallest observed P value as our statistic of interest and determine its overall significance level. We applied this method to a genome screen with autism families. The result was informative and surprising: A susceptibility region was found (genome-wide significance level, P = 0.038), which is missed with conventional approaches.

Effects of food and sucralfate on a single oral dose of 500 milligrams of levofloxacin in healthy subjects

The effects of food and sucralfate on the pharmacokinetics of levofloxacin following the administration of a single 500-mg oral dose were investigated in a randomized, three-way crossover study with young healthy subjects (12 males and 12 females). Levofloxacin was administered under three conditions: fasting, fed (immediately after a standardized high-fat breakfast), and fasting with sucralfate given 2 h following the administration of levofloxacin. The concentrations of levofloxacin in plasma and urine were determined by high-pressure liquid chromatography. By noncompartmental methods, the maximum concentration of drug in serum (Cmax), the time to Cmax (Tmax), the area under the concentration-time curve (AUC), half-life (t1/2), clearance (CL/F), renal clearance (CLR), and cumulative amount of levofloxacin in urine (Ae) were estimated. The individual profiles of the drug concentration in plasma showed little difference among the three treatments. The only consistent effect of the coadministration of levofloxacin with a high-fat meal for most subjects was that levofloxacin absorption was delayed and Cmax was slightly reduced (Tmax, 1.0 and 2.0 h for fasting and fed conditions, respectively [P = 0.002]; Cmax, 5.9 +/- 1.3 and 5.1 +/- 0.9 microg/ml [90% confidence interval = 0.79 to 0.94] for fasting and fed conditions, respectively). Sucralfate, which was administered 2 h after the administration of levofloxacin, appeared to have no effect on levofloxacin's disposition compared with that under the fasting condition. Mean values of Cmax and AUC from time zero to infinity were 6.7 +/- 3.2 microg/ml and 47.9 +/- 8.4 microg x h/ml, respectively, following the administration of sucralfate compared to values of 5.9 +/- 1.3 microg/ml and 50.5 +/- 8.1 microg x h/ml, respectively, under fasting conditions. The mean t1/2, CL/F, CLR, and Ae values were similar among all three treatment groups. In conclusion, the absorption of levofloxacin was slightly delayed by food, although the overall bioavailability of levofloxacin following a high-fat meal was not altered. Finally, sucralfate did not alter the disposition of levofloxacin when sucralfate was given 2 h after the administration of the antibacterial agent, thus preventing a potential drug-drug interaction.

Multi-locus interactions predict risk for post-PTCA restenosis: an approach to the genetic analysis of common complex disease

The complexity of recognizing the potential contribution of a number of possible predictors of complex disorders is increasingly challenging with the application of large-scale single nucleotide polymorphism (SNP) typing. In the search for putative genetic factors predisposing to coronary artery restenosis following balloon angioplasty, we determined genotypes for 94 SNPs representing 62 candidate genes, in a prospectively assembled cohort of 342 cases and 437 controls. Using a customized coupled-logistic regression procedure accounting for both additive and interactive effects, we identified seven SNPs in seven genes that, together, showed a statistically significant association with restenosis incidence (P <0.0001), accounting for 11.6% of overall variance observed. Among them are candidate genes for cardiovascular pathophysiology (apolipoprotein-species and NOS), inflammatory response (TNF receptor and CD14), and cell-cycle control (p53 and p53-associated protein). Our results emphasize the need to account for complex multi-gene influences and interactions when assessing the molecular pathology of multifactorial medical entities.

Differential expression of myosin heavy chain isoforms between abductor and adductor muscles in the human larynx

OBJECTIVE

This study examines the differential expression of myosin heavy chain (MyHC) components in human laryngeal muscle groups.

STUDY DESIGN

A battery of monospecific monoclonal antibodies in Western blots was used to determine expression of IIX, extraocular-specific (EOM), and IIB MyHCs for the thyroarytenoid (TA), vocalis (VOC), lateral cricoarytenoid (LCA), cricothyroid (CT), and posterior cricoarytenoid (PCA) muscles obtained from fresh cadaver specimens.

RESULTS

Fast IIX MyHC was only expressed in the TA, VOC, and LCA muscles. Fast IIA and slow MyHCs were expressed in all laryngeal muscles including the CT and PCA. The CT with mixed phonatory and respiratory function and the PCA with respiratory function did not express IIX MyHC. The 2 MyHC isoforms associated with the highest speeds of contraction in rat laryngeal muscle, namely, the EOM MyHC and IIB MyHC, were not detected in human laryngeal muscles. Novel MyHC bands were not detected in SDS-PAGE gels or Western blots using a broad specificity MyHC antibody.

CONCLUSION

The profile of MyHC expression in human laryngeal muscles differs from that observed in human extraocular and masticator muscles, and other mammalian species. Our data demonstrate that IIX MyHC expression is associated primarily with muscles affecting glottic closure and is absent in CT and PCA.

SIGNIFICANCE

A higher percentage of IIX MyHC is expected to impart a high speed of shortening to the TA and LCA muscles. The absence of IIX MyHC in muscles with respiratory (PCA) and mixed respiratory/phonatory function (CT) further supports the inference that the physiologic difference between laryngeal muscles is reflected in the molecular composition of contractile protein.

Cytoskeletal neurofilament gene expression in brain tissue from Alzheimer's disease patients. I. Decrease in NF-L and NF-M message

The cytoskeletal changes seen in brains of patients with Alzheimer's disease include neurofibrillary tangles, neuritic plaques, Hirano bodies, and granulovacuolar degeneration. Northern and slot blot analyses were used to investigate the expression of the genes coding for actin, tubulin, neurofilaments, and histone in brain tissue from Alzheimer's disease patients and normal aged controls. We found a marked decrease of 94% in the expression of the neurofilament gene coding for the medium size subunit (150 kDa) and a 73% decrease in the expression of the gene coding for the small subunit (68 kDa) in Alzheimer's disease patients as compared to controls. Expression of the other genes, such as actin and histone, did not show any significant difference. Expression of the gene coding for medium size, neurofilament gene was not decreased in other neurodegenerative diseases, such as amyotrophic lateral sclerosis and Parkinson's disease. This abnormality in neurofilament gene expression may explain some of the pathologic features found in Alzheimer's disease patients.

Distribution of developmental myosin heavy chains in adult rabbit extraocular muscle: identification of a novel embryonic isoform absent in fetal limb

PURPOSE

To identify embryonic and neonatal/fetal myosin heavy chains (MyHCs) in rabbit extraocular muscle (EOM) by electrophoretic and immunochemical analyses and to describe the distribution of these two MyHC isoforms in the endplate zone (EPZ) and the distal and proximal segments of EOM fibers.

METHODS

SDS-PAGE and Western blot analysis using monoclonal antibodies (mAbs) against embryonic and neonatal/fetal MyHCs were performed on MyHC isoforms from rabbit adult and neonatal EOM and fetal limb muscles. Immunohistochemical analysis was performed along the entire length of the rabbit superior rectus muscles, using these and other mAbs.

RESULTS

Western blot analysis showed that adult rabbit EOM had two embryonic MyHC bands: a weakly stained band that comigrated with the embryonic MyHC from fetal limb muscles, and a strongly stained band of lower electrophoretic mobility for which there was no limb counterpart. Three anti-embryonic MyHC mAbs stained muscle fibers, predominantly in the orbital layer, and staining was localized distal and proximal to the EPZ but not in the EPZ itself. There, most fibers expressed the EOM-specific fast MyHC, although some fibers expressed alpha-cardiac MyHC. Anti-neonatal/fetal MyHC mAb failed to stain in Western blot analysis but stained scattered fibers predominantly in the global layer, and there was no specific absence of staining at the EPZ.

CONCLUSIONS

There are two electrophoretically distinct isoforms of embryonic MyHCs in adult rabbit EOM. These isoforms are expressed in orbital fibers but are excluded from the EPZ, where EOM-specific fast MyHC is strongly expressed. Neonatal and fetal MyHC is weakly expressed in the EOM, but is not excluded from the EPZ.

UVA-induced oxidative damage in retinal pigment epithelial cells after H2O2 or sparfloxacin exposure

Retinal impairment is one of the leading causes of visual loss in an aging human population. To explore a possible cause for retinal damage in the human population, we have monitored DNA oxidation in human retinal pigment epithelial (RPE) cells after exposure to hydrogen peroxide (H2O2) or the quinolone antibacterial sparfloxacin. When H2O2- or sparfloxacin-exposed cells were further exposed to ultraviolet A (UVA) irradiation, oxidative damage to the DNA of these cells was greatly increased over baseline values. This RPE+pharmaceutical-UVA cell system was developed to mimic in vivo retinal degeneration, seen in mouse studies using quinolone and UVA exposure. DNA damage produced by sparfloxacin and UVA in RPE cells could be remedied by the use of antioxidants, indicating a possible in vivo method for prevention or minimization of retinal damage in humans

Statistical multilocus methods for disequilibrium analysis in complex traits

Hundreds of thousands of SNP markers are being generated with the purpose of carrying out case-control association studies for complex traits, which are thought to be due to multiple underlying susceptibility genes. The number of markers is typically much larger than the number of observations so that joint analysis of marker genotypes and their interactions is not feasible. We discuss a two-stage approach to first select a small subset of markers and then model the effects of the selected markers on disease. Examples of two procedures for marker selection are given with subsequent modeling of main and interaction effects. The approaches are applied to a data set with 89 SNPs in lieu of a genome screen with many more markers.

A train of thoughts on gene mapping

Complex traits, by definition, are the pheonotypic outcome from multiple interacting genes. The traditional analysis of association studies on complex traits is to test one locus at a time, but a better approach is to analyze all markers simultaneously. We previously proposed a two-stage approach, first selecting the influential markers and then modeling main and interaction effects of these markers. Here we introduce alternative approaches to marker selection and discuss issues regarding analytical tools for disease gene mapping, marker selection, and statistical modeling.

A measure of phase ambiguity in pairs of SNPs in the presence of linkage disequilibrium

The extent of haplotype ambiguity in a string of single-nucleotide polymorphisms (SNPs) was quantified by Hodge et al. [Nat Genet 1999;21:360]. In their measure, the level of ambiguity increases with increasing numbers of loci and as loci become more polymorphic. That work assumed linkage equilibrium (LE). However, linkage disequilibrium (LD) provides additional information about the haplotypes at a site, thereby diluting the level of ambiguity. The ambiguity vanishes altogether when LD reaches its maximum value. Here, we introduce the ambiguity measure, Phi, to allow for LD (between pairs of SNPs). We derive the formula Phi = 4x(2)x(3) for ambiguity in individuals, where x(1), x(2), x(3) and x(4) are the probabilities of the A(1)A(2), A(1)B(2), B(1)A(2) and B(1)B(2) haplotypes, respectively, and w.l.o.g. x(1)x(4) > or = x(2)x(3). Alternatively, Phi can be expressed in terms of the allele frequencies and the LD parameter delta. We also extend the formula to triads of two parents plus one child. We estimate our measure Phi for relevant SNPs in the published lipoprotein lipase (LPL) gene dataset [Clark et al., Am J Hum Genet 1998;63:595; Nickerson et al., Nat Genet 1998;19:233], obtaining values ranging from a low of 0 to a high of 0.11 among adjacent pairs of sites. In genome-wide LD studies to map common disease genes, a dense map of SNPs may be utilized to detect association between a marker and disease. Therefore, the measurement of ambiguity can potentially help investigators to determine a more efficient map, designed to minimize ambiguity and subsequent information loss.

Ascertainment and anticipation in family studies

Many human diseases show anticipation; that is, disease occurs earlier (or with greater severity) in successive generations. In a computer simulation, we assessed the degree of anticipation that one would expect to see in two-generation breast cancer families. Under reasonable assumed distributions for age at cancer onset, number of children, and mortality, we find a consistent earlier mean age at diagnosis in daughters than in mothers, but the same mean age at diagnosis in affected aunts and nieces. We compare these results with published pedigree data for familial breast cancer that show substantial anticipation in affected daughters compared to their mothers. We find that at least some anticipation is expected in human disease families even when the disease is stable and families are ascertained without obvious sampling bias. We further demonstrate that such anticipation is reduced when comparing affected children to the parents' affected siblings.

Two approaches for consolidating results from genome scans of complex traits: selection methods and scan statistics

This work has two purposes: (i) empirically selecting levels of significance that maximize the fraction of markers close to a gene (hit rate) when performing linkage analyses of simulated data and (ii) evaluating the utility of a previously reported scan statistic on the same data. Genotype data were simulated from a trait model of seven susceptibility genes. For purpose (i), five statistics were evaluated on all marker loci in fifty replicates; two-point lod and heterogeneity lod scores maximized over dominance (mlod, mhlod), a multi-allelic TDT test, an affected sib-pair test (ASP), and a model-free test on all sib-pairs (ALL_SIBS). Within each replicate the fraction of markers (hit rate) significant at specified levels of significance and also (a) within fifty markers of, or (b) on the same chromosome as a major gene was calculated. For purpose (ii), scan statistics of length 15 were calculated for each chromosome and their empirical significance levels estimated on the basis of 500 replicates generated under no linkage. The scan statistic was applied to the mhlod scores from one replicate (Replicate 5). Empirical p-values for the scan statistic were determined by computing mhlod scores on 500 replicates of simulated null data. For purpose (i), significance levels between 0.001 and 0.01 had the greatest hit rate for all five methods and both criteria. For criterion (a) at the 0.001 level of significance, both mlod and mhlod displayed the highest hit rates, approximately 0.4 for each. For criterion (b), all methods but ALL_SIBS and ASP had hit rates ranging between 0.4 and 0.5. For purpose (ii), the scan statistic proved equally or more powerful than the single-locus statistic for two of the seven susceptibility genes while the remaining five genes were not detected.

Chronic swim stress enhances the motoric inhibiting effects of a muscarinic agonist

The authors previously demonstrated that chronic inescapable swim stress and footshock increase the capacity of a fixed dose of a muscarinic agonist to produce hypothermia in the rat. This project was designed to determine whether chronic inescapable swim stress in cold water would render a low dose of a muscarinic agonist, devoid of an effect on motor behavior in the naive rat (i.e., prior to subjection to the course of swim stress), an inhibitor of mobility. The study involved two groups of rats, an experimental group which received arecoline and a control group which received saline five minutes prior to being placed in an open field. Number of crossings, the dependent variable, was measured in both groups before and after a 14-day course of twice daily inescapable swim stress of 10 minutes duration at 12 degrees C. The arecoline-treated group, as hypothesized, exhibited a significantly greater reduction in number of crossings than the saline-treated groups following the course of swim stress.

Sequence diversity of gap junction proteins

This paper summarizes our understanding of the molecular organization of gap junction proteins. There appear to be overall similarities in the organization of heart and liver junctions in terms of general domains, even though the molecular sizes of the two proteins are quite different. Sequence data on the amino-terminal regions of these two proteins show 43% of the residues to be identical and 25% more to be homologous. The major intrinsic protein of lens (MIP), believed by many to be the lens-fibre junction protein, does not show such sequence homology with the known portions of junction proteins from either heart or liver. Yet the sequence of MIP, which is completely known, suggests a conformation for this molecule quite compatible with a junctional role. It thus appears that molecules potentially involved in junction formation will prove to form a rather diverse family, with special characteristics of organ-specific molecules that may well be related to their function.

Developmental, physiologic and phylogenetic perspectives on the expression and regulation of myosin heavy chains in mammalian skeletal muscles

The kinetics of myosin controls the speed and power of muscle contraction. Mammalian skeletal muscles express twelve kinetically different myosin heavy chain (MyHC) genes which provides a wide range of muscle speeds to meet different functional demands. Myogenic progenitors from diverse craniofacial and somitic mesoderm specify muscle allotypes with different repertoires for MyHC expression. This review provides a brief synopsis on the historical and current views on how cell lineage, neural impulse patterns, and thyroid hormone influence MyHC gene expression in muscles of the limb allotype during development and in adult life and the molecular mechanisms thereof. During somitic myogenesis, embryonic and foetal myoblast lineages form slow and fast primary and secondary myotube ontotypes which respond differently to postnatal neural and thyroidal influences to generate fully differentiated fibre phenotypes. Fibres of a given phenotype may arise from myotubes of different ontotypes which retain their capacity to respond differently to neural and thyroidal influences during postnatal life. This gives muscles physiological plasticity to adapt to fluctuations in thyroid hormone levels and patterns of use. The kinetics of MyHC isoforms vary inversely with animal body mass. Fast 2b fibres are specifically absent in muscles involved in elastic energy saving in hopping marsupials and generally absent in large eutherian mammals. Changes in MyHC expression are viewed in the context of the physiology of the whole animal. The roles of myoblast lineage and thyroid hormone in regulating MyHC gene expression are phylogenetically the most ancient while that of neural impulse patterns the most recent.

Arecoline-associated changes in open-field behavior following swim stress in the rat. A possible relationship to water temperature

The rat exhibits a reduction in movement in an open field following a 14-day course of forced swim stress at 12 degrees C. The decrease in movement is greater in rats receiving arecoline relative to those receiving saline prior to placement in the open field. The authors report that when water temperature is increased to 20 degrees, there is a categorical difference in the results. The saline control group exhibits a rise and the arecoline group no change in crossings.

Mechanism of post-tetanic depression of slow muscle fibres

A brief tetanic stimulation has a very different effect on the subsequent isometric twitch force of fast and slow skeletal muscles. Fast muscle responds with an enhanced twitch force which doubles that of the pre-tetanic value, whereas slow muscle depresses the post-tetanic twitch by about 20%. Twitch potentiation of fast muscle has long been known to be due to myosin light chain 2 phosphorylation. It is proposed that post-tetanic twitch depression in slow muscle is due to the dephosphorylation of the slow isoform of the thick filament protein, myosin-binding protein-C, by Ca2+/calmodulin-activated phosphatase calcineurin, whilst its phosphorylation underlies the force enhancement due to β-adrenergic stimulation in slow and fast muscle.