Methods for DNA copy number variation analysis using high throughput sequencing

... detect copy number variation using high- throughput sequencing 193 Summary Copy Number Variation (CNV) is an important class of genetic variation, which has been traditionally studied using microarray-based ... Manuscripts Xie, C and M T Tammi (2009) CNV-seq, a new method to detect copy number variation using high- throughput sequencing BMC Bioinformatics 10, 80 (Appendix F, cited 23 times as of 27 Dec 2010) ... Introduction 1.1 Copy Number Variation 1.1.1 What is Copy Number Variation? Every individual genome is different, including the genomes of identical twins (Notini et al., 2008) Genomic variations have...

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Báo cáo y học: "miRTRAP, a computational method for the systematic identification of miRNAs from high throughput sequencing data" pptx

... of all miR loci in the Ciona genome Altogether, miRTRAP generated an apparent false negative rate of approximately 5% and a false discovery rate of approximately 19% To systematically compare ... endogenous human Argonautes and their miRNA partners in RNA silencing Proc Natl Acad Sci USA 2008, 105:7964-7969 33 Katayama S, Tomaru Y, Kasukawa T, Waki K, Nakanishi M, Nakamura M, Nishida H, Yap CC, ... to other genomes will reveal additional novel miRs Materials and methods Library preparation, sequencing and Northern analysis Ciona stage-specific small RNA library preparation and Illumina sequencing...

báo cáo hóa học:" Research Article A Bayesian Analysis for Identifying DNA Copy Number Variations Using a Compound Poisson Process" docx

... algorithm for copy number analysis in SNP data An algorithm called reversible jump aCGH (RJaCGH) for identifying copy number alterations was introduced in Rueda and D´az-Uriarte [16] This RJaCGH ... Fibroblast Cell-Lines Datasets There are many approaches (computational or statistical) now available for analyzing aCGH data in the relative literature But many of those approaches, especially ... Picard, S Robin, M Lavielle, C Vaisse, and J.-J Daudin, A statistical approach for array CGH data analysis, ” BMC Bioinformatics, vol 6, article 27, 2005 [11] W R Lai, M D Johnson, R Kucherlapati,...

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Báo cáo y học: "An optimization framework for unsupervised identification of rare copy number variation from SNP array data." doc

... other SNP arrays, including earlier versions of the Affymetrix platform, Illumina arrays, or array comparative genomic (a) 2.5 Raw copy number Raw copy number 3.0 hybridization Any platform that ... Birdsuite platform [17] QuantiSNP [26] is an analytical tool for the analysis of copy number variation using whole genome SNP genotyping data It was originally developed for Illumina arrays, but version ... segments of consistent copy number The Affymetrix SNP array was originally designed so that each SNP is interrogated by 24 to 40 unique probes Of these, half are perfectly complementary to the...

Báo cáo y học: "Targeted analysis of nucleotide and copy number variation by exon capture in allotetraploid wheat genome" pdf

... consistency of a pool of baits in the capture assay The sensitivity of capture baits was estimated by calculating their minimum folding energy (PMFE), hybridization folding energy (PHFE), hairpin score ... this article as: Saintenac et al.: Targeted analysis of nucleotide and copy number variation by exon capture in allotetraploid wheat genome Genome Biology 2011 12:R88 Submit your next manuscript ... efficiency of selection and recombination [37,44] The effect of selection on local variation was inferred by studying the distribution of SNPs in coding and noncoding regions of the wheat genome...

Báo cáo y học: " FISH Oracle: a web server for flexible visualization of DNA copy number data in a genomic contex" ppsx

... Shinomiya T, Date K, Hagiwara A, Yamaguchi T, Takahashi T, Nakamura Y, Abe T, Inazawa J: Gains, losses, and amplifications of genomic materials in primary gastric cancers analyzed by comparative genomic ... source data In particular, two different kinds of data are stored in two separate databases: genome annotation data (as available in the Ensembl database [37]) and segmented array CGH data The ... for the user The web- based applications for processing array CGH data (see introduction) are mainly offered as publicly available web servers Additionally CAPweb and arrayCGHbase can be obtained...

Báo cáo khoa học: " Effective methods for the production of immunoglobulin Y using immunogens of Bordetella bronchiseptica , Pasteurella multocida and Actinobacillus pleuropneumoniae" docx

... 199 6, 6 0, 886-888 Yokoyama, H ., Paralta, R C ., Diaz, R ., Sendo, S ., Effective methods for the production of immunoglobulin Y using immunogens of Bordetella bronchiseptica, Pasteurella multocida and ... Li, X ., Nakano, T ., Sunwoo, H H ., Peak, B H ., Chae, H S ., and Sim, J S Effects of egg and yolk weights on yolk antibodies (IgY) production in laying chickens Poultry Sci 199 8, 7 7, 266-270 Marandi, ... Immun 1992 6 0, 998-1007 30 Yokoyama, H ., Paralta, R C ., Diaz, R ., Sendo, S ., Ikemori, Y and Kodama, Y Detection of passage and absorption of chicken egg yolk immunoglobulins in the gastrointestinal...

Báo cáo y học: " Single-cell copy number variation detection" pptx

... have been validated by the corresponding genomic DNA using a 250 K Affymetrix SNP array with the help of SNP copy number, loss-of-heterozygosity, and heterozygous SNPs The karyotype of each EBV-transformed ... that only few probes display an aneuploidy copy number and most probes display diploid copy numbers does not hold generally (for example, consider heavily rearranged blastomeres, tumor cells, and ... well as analyzed on a 250 K Affymetrix SNP array to confirm real aberrant regions A deleted region on a SNP array presents only a single allele and is indicated by loss-of-heterozygosity Diploid...

Báo cáo y học: "Association between copy number variation of complement component C4 and Graves’ disease" ppsx

... distribution of copy number for total C4, C4 isotypes as well as C4 polymorphisms did not associate with the occurrence of myxedema (Table 3) The distribution of copy number for total C4, C4 isotypes ... individuals with 4, and copies of C4, C4A and C4B genes, especially those with A2B2 polymorphism may have higher risk, whereas those with...

Báo cáo khoa hoc:" Comparison of nanoparticle-mediated transfection methods for DNA expression plasmids: efficiency and cytotoxicity" potx

... Cite this article as: Durán et al.: Comparison of nanoparticle-mediated transfection methods for DNA expression plasmids: efficiency and cytotoxicity Journal of Nanobiotechnology 2011 9:47 ... 37°C and 5% CO2 For each protocol the incubation of cells with the transfection reagents and without DNA was considered as the negative control The plasmid DNA uptake of pIRES-hrGFPII-eIL-12 and ... immunology and cancer research would benefit from improved transfection efficiencies, high reproducibility and low toxicity of the required transfection approach High transfection efficiency for plasmid...

báo cáo khoa học: " Copy number variation in Parkinson’s disease" docx

... promoter and at intron fragments (red) Pathogenic copy number variation in autosomal dominant Parkinson’s disease A seminal discovery in the study of PD was the report of missense mutations in the SNCA ... Toft and Ross Genome Medicine 2010, 2:62 http://genomemedicine.com/content/2/9/62 (a) Page of Individual inferred relative copy number: Chr4 Inferred copy number 87 88 89 90 91 92 93 Mb ... mutations in the SNCA gene, encoding the αsynuclein protein, in dominantly inherited disease [6] This was the first evidence that genomic variation could result in an inherited form of PD The subsequent...

Báo cáo sinh học: " Precision of methods for calculating identity-by-descent matrices using multiple mar" pot

... 15 cM 2.5 Index for information from the markers An information index was presented in order to provide some understanding of the precision of the methods for calculating IBD matrices It considers ... results of a comparison of a deterministic method and an MCMC based method for calculating IBD matrices for a number of scenarios of population structure, density of marker map, and heterozygosity of ... objective of this study was to evaluate methods for calculating matrices conditional on multiple markers regarding the precision of the matrices and their performance in common animal breeding applications...

Báo cáo y học: "Tandem repeat copy-number variation in protein-coding regions of human genes" docx

... approximately in 5,000 transcripts in dinucleotide tandem repeats [48]: in our survey of 5,304 sequences containing 8,449 dinucleotide repeats, we found an incidence of 36 frameshifting dinucleotide ... (see copy-numbers Distribution offollowing page) of tandem repeats Distribution of copy-numbers of tandem repeats The x-axis indicates the number of tandem repeat loci of a given unit length (indicated ... level of polymorphism One is that these proteins are typically under low selective constraint, as repetitive regions in protein- and DNA-binding proteins are often substantially structurally disordered...

Báo cáo y học: " Copy number variation goes clinical" pps

... several years on defining the impact of nucleotide and copy number variation on geneexpression phenotypes He gave an update on a new association survey currently in progress, comparing nucleotide variations ... to accurately identify functional sequences that are variable in copy number, and provide new insights into mechanisms generating chromosomal rearrangements New whole-genome CNV genotyping platforms ... ancestry They have discovered 11,700 CNVs of more than 500 bp in size Genome Biology 2009, 10:301 http://genomebiology.com/2009/10/1/301 Genome Biology 2009, and have defined precisely CNV boundaries...

Level set methods for MRE image processing and analysis

... formulation for robust MRE elastogram segmentation Finally, we propose a hybrid level set model for piecewise constant modeling of MRE elasticity 30 CHAPTER NEW LEVEL SET METHODS FOR MRE Level set methods ... for MRE image processing and analysis First, a numerical platform – level set diffusion (LSD) – is derived for noise suppression and image enhancement Second, we design a unified level set formulation ... the methods of image processing and analysis for dynamic MRE, although some should be applicable to static MRE as well Level set methods (LSMs) define a numerical framework for representing and...

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