microarray based genome wide association studies using pooled dna

... doi:10.1186/ar2937 Cite this article as: Sugino H, et al.: DNA microarray analysis of rheumatoid arthritis susceptibility genes identified by genome- wide association studies Arthritis Research & Therapy 2010, ... 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 ... Table Candidate genes identified from rheumatoid arthritis genome- wide association studies Gene GeneID PMID Gene expression (up or down) Microarray P valuesa CD244 605554 18794858 Up 1.0 x 10–16...

Ngày tải lên: 12/08/2014, 11:23

... stratification in genome- wide association studies Nat Genet 2006, 38: 904-909 10 Li M, Li C, Guan W: Evaluation of coverage variation of SNP chips for genome- wide association studies Eur J Hum ... Non-replication and inconsistency in the genome- wide association setting Hum Hered 2007, 64:203213 Neale BM, Purcell S: The positives, protocols and perils of genome- wide association Am J Med Genet 2008, ... Merrill JT, Gilkeson GS, Seldin MF, Yin H, Baechler EC, Li QZ, Wakeland EK, Bruner GR, et al.: Genome- wide association scan in women with systemic lupus erythematosus identifies susceptibility variants...

Ngày tải lên: 09/08/2014, 14:22

... CDKN2A/B [12] No association BCC, no association to CM KRT5, G138E substitution [12] No association BCC, no association to CM 7q32 adjacent to KLF14 [12] No association BCC, no association to CM ... effort from ten GenoMEL groups with 1,650 cases and 1,065 controls The team identified five loci on chromosomes 2, 5, 9, 11 and 16, with at least one SNP at each locus with genomewide significance ... Arg142His and p.Ile155Thr) based on strong familial association with RHC phenotype; and (c) three ‘r’ alleles (p.Val60Leu, p.Val92Met, and p.Arg163Gln) with weaker association with the RHC phenotype...

Ngày tải lên: 11/08/2014, 12:20

... CAD Genome wide association analysis, which is a powerful tool to identify genetic variants, is commonly employed to identify novel genetic variants currently Most genome wide association studies ... experimental studies As with all findings of association studies, there are genetic variants with genome- wide significance that could not be replicated successfully in other studies For example, the association ... 2.3.1 GWAS of CAD Genome wide association studies have identified multiple genetic variants associated with CAD Most of the associations have been replicated in independent studies, indicating...

Ngày tải lên: 09/09/2015, 08:17

... in Genomewide Association Studies 72 5.1 Introduction to the multiple testing for genome- wide association studies 73 5.2 The generalized tournament screening cum EBIC approach for genomewide association ... Subsection 1.3.2 1.3.1 Feature selection methods in genome- wide association studies In genome- wide association studies, a large number of statistical studies have been developed to detect genetic variants ... the dimension P is large Such a problem has become especially prevalent in genome- wide association studies A genome- wide association study (GWAS) is a promising way to detect genetic variants responsible...

Ngày tải lên: 11/09/2015, 16:05

... possible candidate genes based on the unbiased genome- wide pooling association study Individual case-control genotyping using TaqMan SNP Genotyping Assays confirmed the genetic association between ... 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 ... provided written informed consent DNA pooling studies For the initial discovery phase of novel genetic associations, we used a DNA pooling genotyping methodology DNA pools were generated from cases...

Ngày tải lên: 09/08/2014, 14:20

... MS: A genome- wide scalable SNP genotyping assay using microarray technology Nat Genet 2005, 37(5):549-554 Purcell S, Cherny SS, Sham PC: Genetic Power Calculator: design of linkage and association ... analysis Analysis of association statistics After sample and SNP quality control, statistics of association were calculated using the PLINK software package [26] For detecting associations in the ... 10-7 (0.05/95,207) is required to declare genome wide significance in this study Stage 3: testing TB association in Russian cohort Among the top SNP associations detected in the first two stages...

Ngày tải lên: 06/03/2014, 04:20

... GR: Genomewide association for nicotine dependence and smoking cessation success in NIH research volunteers Mol Med 2009, 15:21-27 Guessous I, Gwinn M, Khoury MJ: Genome- wide association studies ... the final version Acknowledgements We thank Jennifer Dackor for her curation of the genome- wide association studies of smoking behavior and editorial assistance This work was funded by the University ... Am J Prev Med 2007, 33:S398-S405 Crowley JJ, Sullivan PF, McLeod HL: Pharmacogenomic genome- wide association studies: lessons learned thus far Pharmacogenomics 2009, 10:161-163 Uhl GR, Liu QR,...

Ngày tải lên: 11/08/2014, 12:20

... multiple sclerosis identified by a genomewide study N Engl J Med 2007, 357:851-862 12 Australian and New Zealand Multiple Sclerosis Genetics Consortium: Genome- wide association study identifies new ... Matthews PM, Hauser SL, Gibson RA, Oksenberg JR, Barnes MR: Pathway and network -based analysis of genome- wide association studies in multiple sclerosis Hum Mol Genet 2009, 18:2078-2090 Purcell SM, ... 131:3118-3131 Nannya Y, Taura K, Kurokawa M, Chiba S, Ogawa S: Evaluation of genomewide power of genetic association studies based on empirical data from the HapMap project Hum Mol Genet 2007, 16:2494-2505...

Ngày tải lên: 11/08/2014, 12:21

... tests) AND linkage AND genome- scan OR scan OR genome OR genomewide OR genome- wide OR LOD OR microsatellite) Limits were set on the search including; published in English, human studies, published ... combining studies in the meta-analyses using these different provocation stimuli Significantly, using asthma as a phenotype we did not identify any chromosomal region as showing genomewide significance ... In the analyses of the BHR phenotype significant linkage was not driven by studies using a specific agonist i.e studies using both methacholine and histamine provocation contributed to the signal...

Ngày tải lên: 12/08/2014, 15:21

... Introduction 1.1 1.1.1 Motivation Genome- wide association studies (GWAS) A genome- wide association study (GWAS) searches for inherent expression (genetic patterns) from a genome that is potentially ... been successfully applied to the identification of genome- wide associations in casecontrol studies RF can also be applied to population association studies with multivariate quantitative traits, ... 1.1.1 Genome- wide association studies (GWAS) 1.1.2 Computational challenges in GWAS 1.1.3 Big data, Hadoop and associated technologies 1.1.4 Hadoop in genome analysis ...

Ngày tải lên: 09/09/2015, 10:06

... 50 CONTENTS v TDT in Genome- wide Association Study 57 4.1 FDR-controlling procedure 58 4.2 Genome- wide TDT procedure using logistic model and feature selection ... 64 4.2.3 Genome- wide mapping procedure 67 4.2.4 4.3 Introduction to logistic model for TDT 62 Genome- wide TDT for QTL mapping 71 Numerical studies ... Genetic markers are the regions of DNA that vary between individuals Linkage studies are based on the recombination In linkage studies, some markers and the disease-causing genes are assumed to be...

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 Study ... 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 Study ... 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

... flies and mammalian genomes, discovering large sets of known and novel motifs Genome Biology 2005, 6:R18 http://genomebiology.com/2005/6/2/R18 Genome Biology 2005, information Genome Biology 2005, ... above, using the new conserved sets The full information for the 398 k-mers is available at [9] Known regulatory elements Using known transcription factor binding site motifs, genome- wide in ... downloaded 765 microarray conditions for S cerevisiae, 555 conditions for C elegans, 156 conditions for D melanogaster, and 1,384 Genome Biology 2005, 6:R18 http://genomebiology.com/2005/6/2/R18 Genome...

Ngày tải lên: 14/08/2014, 14:21

... Chia KS The pursuit of genome- wide association studies: where are we now? Journal of Human Genetics 55: 195-206 (2010) 15 Ku CS*, Chia KS The success of the genome- wide association approach: a ... population -based CNV studies in different populations using SNP genotyping microarrays) The limitations of ROMA and the BAC-CGH arrays have been overcome in later studies by using higher resolution microarrays ... 500 GWAS (A Catalog of Published Genome- Wide Association Studies: http://www .genome. gov/26525384) Almost all the GWAS have used the commercially available whole -genome SNP genotyping arrays from...

Ngày tải lên: 10/09/2015, 15:47

... report concerning intergenic expression in M tuberculosis genome and show that microarray- based transcriptional evidence would facilitate genome- wide gene finding MATERIALS AND METHODS 2.1 Bacterial ... RNA samples were sent to the UCI DNA core and further checked through a quality and quantity test based on electrophoresis before microarray hybridization 2.3 Microarray hybridization In this ... conducted a genome- wide expression analysis on intergenic regions using the Affymetrix GeneChip Each intergenic sequence is subject to gene prediction and coding potential analysis based on bioinformatics...

Ngày tải lên: 22/06/2014, 19:20

... introns in the human genome as expected with the smaller genome size The species is highly polymorphic relative to other species with sequenced genomes Using thermal DNA reassociation experiments, ... from the same individual are then pooled and hybridized under conditions that favor binding of uncut DNA over cut DNA to the array tiles DNA that matches the known genome sequence is cut by the restriction ... urchins Pespeni et al Genome Biology 2010, 11:R44 http://genomebiology.com/2010/11/4/R44 differ from each other in about 4% of the nucleotide pairs in single-copy DNA [49] Genome assembly revealed...

Ngày tải lên: 09/08/2014, 20:21

... presumably neutrally evolving subgenomes, the NCNR subgenome and the AR subgenome, were constructed based on the March 2006 build of the human genome (hg18) The NCNR subgenome was constructed by excluding ... are male biased too: a whole -genome analysis in rodents Genome Res 2004, 14:567-573 Lunter G, Ponting CP, Hein J: Genome- wide identification of human functional DNA using a neutral indel model ... binding sites were obtained from the UCSC Genome Browser per 1Mb window of the human genome, based on hg18 annotations of the human genome in the UCSC Genome Browser GC content was obtained from...

Ngày tải lên: 09/08/2014, 22:24

... genes Cumulative distribution (a) Genome Biology 2007, 0.2 −5 Gene score information Genome Biology 2007, 8:R74 interactions We proceeded to apply all methods to real microarray data, starting with ... between the threshold-free methods (commented under Results) Genome Biology 2007, 8:R74 http://genomebiology.com/2007/8/5/R74 (a) Genome Biology 2007, Method relationships (Spearman metric) (b) ... First MDS component 0.2 0.3 −0.2 −0.1 0.1 First MDS component 0.2 The ontological analysis of genome- wide studies relies fundamentally on the validity and continued growth of ontologies providing...

Ngày tải lên: 14/08/2014, 07:21

... level was used as the suggestive level, which was inferred from the 5% genome- wide level using: À Á19 P chromosome % À À P genome ð2Þ to correct the multiple tests [7] RESULTS The pubertal stage ... Figure A 1% genome- wide significant QTL was found at position 114 cM on SSC1 (Fig 1A) and the Erhualian allele at this locus is favourable for decreased age at puberty A 0.1% genome- wide significant ... oestrus sign was observed 2.3 Genotyping Genomic DNA was extracted from pig ear tissues or blood using the standard phenol/chloroform method All DNA samples were quantified with a DU640 spectrophotometer...

Ngày tải lên: 14/08/2014, 13:21