the bedrocks of the genome wide association approach

... involved in drafting the manuscript and have reviewed and approved the final version Acknowledgements We thank Jennifer Dackor for her curation of the genome- wide association studies of smoking behavior ... practice in the hope of reducing the burden of smoking in our society Until the goal of personalized cessation treatment is realized, all smokers should be encouraged to quit, regardless of genotype ... health improvements [18] and reduce the likelihood of harm; such harm could include a lowering of the motivation to quit or of the self-efficacy for quitting, both of which could undermine quitting...

Ngày tải lên: 11/08/2014, 12:20

... (LD) The top ranked SNPs (that is, the SNP with the most extreme Pvalue) are forced into the model first We then calculate the residual effect of each of the other SNPs after accounting for the ... estimate of the predicted probability of an individual being a MS case (P-Hat) The median of the cumulative genetic risk in the case group is 0.90, and in the control group 0.01 Quantiles of the estimated ... (Hosmer-Lemeshow goodness -of- fit test [30] was implemented to assess ‘lack of fit’ of the selected model; P > 0.05 indicates that there is no evidence of a lack of fit of the selected model) aHLA-DRB1,...

Ngày tải lên: 11/08/2014, 12:21

... could thereby have resulted in reduced power for detecting associations Although none of the observed association signals achieved stringent levels of genome wide significance, likely due to the ... colleagues in Indonesia and the Netherlands for their help in the collection and analysis of clinical data from the clinics We also thank colleagues at the Genome Institute of Singapore, Meah Wee ... with one another [22] The result of the lambda inflation factor calculated according to the method of Devlin and Roeder [19], had a value close to 1, which further confirmed that there was minimal...

Ngày tải lên: 06/03/2014, 04:20

... discover the genetic contribution to the disease etiology, with the exception of the strong association in the HLA region, other genetic associations are largely unconfirmed We hypothesize that ... determine the concentration The number of samples in each pool dictated the amount each sample contributes to the pool The final volume of each pool was 46.5 μL This represents a pool for each of the ... disease will be identified using an unbiased genome- wide association approach Herein, we used a DNA pooling technology to perform the first genome- wide association study in Behçet's disease We identify...

Ngày tải lên: 09/08/2014, 14:20

... (TYRP-1), on the cell membrane of the melanosomes, resulting in a shift of pigment synthesis from pheomelanin to eumelanin The variants of the genes encoding these proteins are listed The corresponding ... SNP at each locus with genomewide significance (P 

Ngày tải lên: 11/08/2014, 12:20

... GWAS, genome- wide association studies; RA, rheumatoid arthritis Competing interests This study was financially supported partly by the grant from the Ministry of Health, Labor and Welfare of Japan ... Gorlov IP, Gallick GE, Gorlova OY, Amos C, Logothetis CJ: GWAS meets microarray: are the results of genome wide association studies and geneexpression profiling consistent? Prostate cancer as an example ... al Arthritis Research & Therapy 2010, 12:401 http://arthritis-research.com/content/12/2/401 Page of Table Candidate genes identified from rheumatoid arthritis genome- wide association studies Gene...

Ngày tải lên: 12/08/2014, 11:23

... Figure Flow chart of genome wide scan of SNPs associated with CAD 77 Figure Summary of genome wide association of 2,379 samples on 796,922 SNPs The left panel was the Manhattan plot of 2,379 samples ... search of genetic variants on a genome wide scale Therefore, association analysis provides a much more effective way to unveil the genetic basis of CAD 2.3 Genome wide association studies of coronary ... to study the etiology of CAD to facilitate the prediction and prevention of CAD 1.2 Overview of the epidemiology of coronary artery disease Cardiovascular disease is the leading cause of morbidity...

Ngày tải lên: 09/09/2015, 08:17

... either claiming replication or the lack of it The replication of the variants in the paper by Suarez-Gestal and colleagues therefore represents the tip of the iceberg because it has confirmed the ... less) and there was some sample duplication between them The other factor that may contribute to the diversity of strongly associated SNPs between different studies is the heterogeneity of the disease ... greater density of markers This scale of experiment, which is proving successful for other complex diseases, would offset the loss of power associated with the heterogeneity of lupus In complex...

Ngày tải lên: 09/08/2014, 14:22

... two alleles The allele that appears in the majority of a population is termed the major allele, the other is called the minor allele In our illustration, the genotypes of the SNPs for the 1st, 2nd ... test the same null hypothesis but the latter assumes the HWE The null hypothesis to be tested is: H0 : the frequency for allele “a” in the case group is the same as in the control group The general ... which only considers the interaction term Therefore, when there is a single association in the genetic model (main effect), the power of the test which considers the association of single SNPs is...

Ngày tải lên: 09/09/2015, 10:06

... hundreds of thousands of SNPs, there are only a few that contribute to the disease Thus, the task of genome- wide studies is to detect the genetic variants of common diseases from a huge number of SNPs ... collection of genotypes of densely spaced SNPs throughout the whole genome is becoming the norm, which moves genome- wide associate studies from the futuristic to the realistic In fact, in these tens ... 4.3 The procedure of the final selection step 68 4.4 Summary 70 CONTENTS v The Application of the Generalized Tournament Approach in Genomewide Association...

Ngày tải lên: 11/09/2015, 16:05

... specify the mode of inheritance of the trait being studied, that means we have known the number of loci involved, the number of alleles at each locus and their frequencies, and the penetrance of each ... an odd number of crossovers occur between two loci, there is a recombination between the two loci The closer the loci are together, the smaller the probability of a recombination The recombination ... QTL MAPPING AND GENOME- WIDE ASSOCIATION STUDY HAO YING (Master of Science, National University of Singapore ) A THESIS SUBMITTED FOR THE DEGREE OF DOCTOR OF PHILOSOPHY DEPARTMENT OF STATISTICS...

Ngày tải lên: 11/09/2015, 16:06

... Manhattan plot of Genome- Wide Association Study for NBA in LW_2 196 SI 2: Manhattan plot of Genome- Wide Association Study for NBA in LW_2a 196 SI 3: Manhattan plot of Genome- Wide Association ... Manhattan plot of Genome- Wide Association Study for NBA in LW_3 197 SI 5: Manhattan plot of Genome- Wide Association Study for NBA in LR_1 197 SI 6: Manhattan plot of Genome- Wide Association ... Manhattan plot of Genome- Wide Association Study for NBA in LR_3 198 SI 8: Manhattan plot of Genome- Wide Association Study for NBA in LR_3a 198 SI 9: Manhattan plot of Genome- Wide Association...

Ngày tải lên: 26/11/2015, 10:18

... Clearly, a subset of the test markers remain in the tail of this more conservative distribution A further indication of the neutrality of the gene-associated marker scores from the empirical distribution ... 'Gene' indicates the gene in which the SNP is located or the nearest gene in the case of the last SNP 'Microsatellite name' is the name given to the microsatellites flanking the SNP; the same name ... frequency of the selected allele, a reduction of variability and an excess of rare variants [10] Therefore, a lower number of heterozygotes than expected are observed On the other hand, the positive...

Ngày tải lên: 14/08/2014, 17:22

... analysis revealed that the counterpart genomic regions on the human genome of many of these eight QTL are linked to RA For five of the eight small-effect QTL the DBA/1 alleles are the arthritis-enhancing ... upregulated after induction of CIA The expression of these genes reached a peak at the onset phase of the disease and functional clustering results revealed that they are related to the immune response ... differentially expressed – most of them were upregulated (78 out of 102) – while at the onset phase of the disease, only 26 genes were differentially expressed At the chronic phase of the disease, 184 differentially...

Ngày tải lên: 09/08/2014, 10:20

... dePamphilis CW: Widespread genome duplications throughout the history of flowering plants Genome Res 2006, 16:738-749 The Arabidopsis Genome Initiative: Analysis of the genome sequence of the flowering ... indicates the genome split at around MYA (Figure 5g) Detection of a peak reflecting 3R in the Bo and Bna genomes but absence of this peak in the Br genome and between the other Brassica genomes ... inferences of the number and timing of polyploidy events, and we now discuss the impact of these events on the structure and evolution of the Brassica 'A' genome (Figure 6) Ks estimates suggest that the...

Ngày tải lên: 09/08/2014, 20:20

... 4C) of the cells during the 24-h time series (b) Expression profiles of early cell cycle genes (c) Expression profiles of late cell cycle genes Error bars represent standard errors of the mean of ... the ability of the cells to recover from starvation (b) Expression profiles of early cell cycle genes at the time of sampling during the light experiment (c) Expression profiles of early cell ... yoelii; Thean, Theileria annulata; Thepa, Theileria parva; Parte, Paramecium tetraurelia, Tetth, Tetrahymena thermophila aNumber of cyclins versus total number of genes calculated with the number of...

Ngày tải lên: 09/08/2014, 20:21

... (p)ppGpp-deficient However, due to the sensitivity of the assay, the presence of trace amounts of (p)ppGpp in the rsh mutant, possibly resulting from the presence of an as yet unidentified synthetase gene, cannot ... CH00371 and the ECF sigma factor ecfG2/PF00052 The log2 ratios of the array data were compared to the log ratios of the qPCR results 16S rRNA was not used as a reference gene as the level of mRNA/rRNA ... altered morphology of the R etli rsh mutant Furthermore, expression of the global iron-responsive regulator RirA that controls the synthesis of heme, FeS-clusters and bacterioferritin in rhizobia,...

Ngày tải lên: 09/08/2014, 22:23

... stretches of the genome which are inherited from either of the ancestral populations Moreover, the structure of an admixed genome contains information on the timing of the admixture event itself The ... the genomes of the descendants of an Page of 18 admixture event are composed of different combinations of these ancestral blocks (Figure 1) Hence, by screening the genome of an individual of mixed ... the average of g Note that the level l of a wavelet is defined as the logarithm base 1/2 of the halfperiod p of the wave, where period is measured as a fraction of the length of the entire signal:...

Ngày tải lên: 09/08/2014, 22:23

... not express relying solely on the absence of their EST clones Nonetheless, the availability of EST clones for the rest of the OsCam and OsCML genes indicate that they are expressed and indeed ... those of the plant CaM consensus sequence Other residues in the Ca2+-binding loop are also conserved with only the exception of aspartate (D) at residue 11 of the fourth EF hand in OsCaM3 Among the ... other potential myristoylated glycines either terminal or internal were found among the rest of the OsCML proteins In addition, to determine the possible localization of the OsCML proteins, their...

Ngày tải lên: 12/08/2014, 05:20

... data), and not by the others, then the distributional deviations must fall within the detection spectra of that method but outside the detection spectra of the other methods In the EGF receptor ... parameters control the types of categories modeled: the number of genes in the category (N); the proportion of modulated genes (π); and the mean and standard deviation of the modulated gene scores ... an approach would yield results tables similar to Table 1, and offers the benefit of allowing the user to make indirect conclusions about the characteristics of the distributional deviations of...

Ngày tải lên: 14/08/2014, 07:21