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...

Ngày tải lên: 11/09/2015, 10:01

... of all miR loci in the Ciona genome Altogether, miRTRAP generated an apparent false negative rate of approxi- mately 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, Nis...

Ngày tải lên: 09/08/2014, 20:21

... 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 approac...

Ngày tải lên: 21/06/2014, 11:20

... 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...

Ngày tải lên: 09/08/2014, 20:20

... 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 Bi...

Ngày tải lên: 09/08/2014, 23:20

... 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...

Ngày tải lên: 10/08/2014, 09:22

... 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 a...

Ngày tải lên: 07/08/2014, 15:20

... 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 blastomere...

Ngày tải lên: 09/08/2014, 23:20

... 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

Ngày tải lên: 10/08/2014, 10:20

... 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 upta...

Ngày tải lên: 11/08/2014, 08:20

... 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...

Ngày tải lên: 11/08/2014, 12:20

... 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...

Ngày tải lên: 14/08/2014, 13:21

... 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...

Ngày tải lên: 14/08/2014, 14:21

... 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 C...

Ngày tải lên: 14/08/2014, 21:20

... 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 imag...

Ngày tải lên: 09/09/2015, 18:50