detection of copy number variation using snp genotyping

... regression model for raw copy number estimation of both SNP and CN markers Figure 7a gives an example of raw copy numbers for a 394-marker region Algorithm for copy number variant detection Key to our ... analytical tool for the analysis of copy number variation using whole genome SNP genotyping data It was originally developed for Illumina arrays, but version 1.1 of this software supports Affymetrix ... for high-resolution copy number variation detection in whole-genome SNP genotyping data Genome Res 2007, 17:1665-1674 Pinto D, Marshall C, Feuk L, Scherer SW: Copy- number variation in control...

Ngày tải lên: 09/08/2014, 20:20

... methods 73 4.1 Study I (Genomic copy number variations in three Southeast Asian 73 populations) 4.2 Study II (A population-based study of copy number variants and regions of 76 homozygosity in healthy ... changes, (b) tandem repeats, (c) indels, (d) structural variations (copy number variations and copy neutral variations) and (e) regions of homozygosity Figure 2a – Single nucleotide changes (adapted ... community in Metropolitan Denver, Colorado, USA Chr - chromosome CNP – copy number polymorphism CN – copy number CNV – copy number variation CTDSPL - CTD (carboxy-terminal domain, RNA polymerase II,...

Ngày tải lên: 10/09/2015, 15:47

... genome-wide copy number variation detection of single EBV-transformed cells using the GADA algorithm Single-cell CNV detection of all seven EBV-transformed cells Each row represents the profile of one ... 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 sample ... step Detection of copy number variation After the exploration of the amplification bias, we checked the impact of genome composition artifacts and recurrent genome artifacts on the performance of...

Ngày tải lên: 09/08/2014, 23:20

... example of CNV due to the deletion of a homoeologous copy of a gene Deletion of a gene in the A genome of Td resulted in the disappearance of three bases, T, A and A, in the alignment a GSS or SNP ... features of SNP sites will be the presence of an IVS in one of the two wheat lines (A and G in Figure 2a) and a monomorphism for one of the variants in another line (G in Figure 2a) Patterns of variation ... P = 0.77 for synonymous SNPs) Out of 20 loss -of- function (LOF) SNPs, a lower fraction was found in the genome of cultivated wheat In addition, we identified seven cases of reverse mutations resulting...

Ngày tải lên: 09/08/2014, 23:20

... CY: Gene copy- number variation and associated polymorphisms of complement component C4 in human systemic lupus erythematosus (SLE): low copy number is a risk factor for and high copy number is ... vitiligo, the 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, ... SD, standard deviation; N, number Page of Liu et al Journal of Biomedical Science 2011, 18:71 http://www.jbiomedsci.com/content/18/1/71 Page of Table Distribution of C4 polymorphisms in individuals...

Ngày tải lên: 10/08/2014, 10:20

... 1) Figure (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 ... as most of the dimer variants are likely to cause frameshifts deposited research Repeat copy- number and extent of variation reports Figure variation Weighted scatter-plot of the pattern of detected ... given copy- number (indicated on the x-axis, rounded to the nearest whole number) (a) Non-variants, N = 88,850; (b) variants, N = 249; copynumber for variants represents the average copy- number...

Ngày tải lên: 14/08/2014, 14:21

... al., 2007; Shendure, 2008) 1.2.4 SNP Genotyping Arrays SNP genotyping arrays are widely used in high-throughput identification of SNPs On a SNP genotyping array, each SNP allele is represented by ... Subset of CNV Regions Detected Between KB1 and ABT Genomes Appendix F 175 177 CNV-seq, a new method to detect copy number variation using high-throughput sequencing 193 Summary Copy Number Variation ... given up many times Table of Contents Introduction 1.1 Copy Number Variation 1.1.1 What is Copy Number Variation? 1.1.2 Brief History of CNV Discovery ...

Ngày tải lên: 11/09/2015, 10:01

... and characterized In anticipation of the identification of new markers in the future and the possibility of using cocktails, we are focusing on the development of a universal probe, based on iron ... Figure Detection of cell-nanoparticle association by fluorescent immunodetection and confocal microscopy Her2 antigen was detected on the surface of MCF7/Her2-18 cells by indirect immunofluorescence ... Mexico School of Medicine, MSC07 4025, University of New Mexico, Albuquerque, NM 87131, USA 3Department of Pathology, University of New Mexico School of Medicine, MSC08 46401 University of New Mexico,...

Ngày tải lên: 22/03/2014, 17:20

... look resections of high risk patients and if the improvement in the rate of detection of flat lesions in the follow-up may improve the use of additional treatment and the prognosis of these patients ... maintenance schedule However, the detection rate of these otherwise undiagnosed lesions is higher with photodynamic screening The limitations of this study are the small number of patients included However, ... cystoscopy should be recommended in the early follow-up of high risk patients Author details Department of Urology, San Gerardo Hospital, University of Milano-Bicocca, Monza, Italy 2Department of...

Ngày tải lên: 18/06/2014, 16:20

... “Global variation in copy number in the human genome,” Nature, vol 444, no 7118, pp 444–454, 2006 [2] D Pinkel, R Seagraves, D Sudar et al., “High resolution analysis of DNA copy number variation usingcomparative ... major direct role of DNA copy number alteration in the transcriptional program of human breast tumors,” Proceedings of the National Academy of Sciences of the United States of America, vol 99, ... versatile statistical analysis algorithm to detect genome copy number variation, ” Proceedings of the National Academy of Sciences of the United States of America, vol 101, no 46, pp 16292–16297, 2004...

Ngày tải lên: 21/06/2014, 11:20

... analysis of results was performed using STATA 9.0 (Texas, USA) Phage assay The details of the assay and production of phage D29 have been described previously [8] Indicator plates for detection of ... However, when concentration of rifampicin was increased to or 10 μg/ml the number of strains found resistant by the phage Page of (page number not for citation purposes) Annals of Clinical Microbiology ... in all regions of the world Incidences of MDR exceeding 10% of TB caseloads have been reported in parts of Central Asia, China, Eastern Europe, Russia and Africa [1] The prognosis of patients with...

Ngày tải lên: 08/08/2014, 19:20

... to recent genotyping arrays, such as the Affymetrix SNP 6.0 or the Illumina BeadChips, which generate allele-specific signals (with the exception of subsets of non -genotyping copy number probes) ... be harboring a fair proportion of common and more older CNVs, similar to the occurrence of common SNPs [1] A number of previous CNV studies also used some or all of the Yoruba individuals, making ... thorough catalog of shorter CNVs in the genome, including an assessment of the age of these variations Even at a resolution of approximately 200 bp, our genome scan detected only a fraction of the CNVs...

Ngày tải lên: 09/08/2014, 20:20

... 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 ... identification of SNPs associated with disease, these studies also allow quantitative assessment of the genome A total of five GWASs of PD have been published so far However, analyses of struc­ tural ... existence of several rare CNVs causing the same disorders in a proportion of patients The number of individuals carrying a given CNV at a known gene locus is frequently small Nevertheless, discovery of...

Ngày tải lên: 11/08/2014, 12:20

... The number of expressed genes in each tissue was estimated by counting the number of microarray features measuring absolute expression of at least one copy per cell, and converting this set of ... one copy per cell or more Copy- number estimates from expressed transcripts were summed to estimate the number of mRNA molecules per cell for each tissue, as well as the mean and median copy numbers ... upstream of 60-mer oligonucleotide probes when possible, or less than 650 bp downstream, and copy number was estimated using serial dilutions of RNA, in vitro transcribed from mouse cDNAs, at known copy...

Ngày tải lên: 14/08/2014, 14:21

... coverage of the targeted regions, to reduce the number of genes identified for which termination would be ethically questionable (for example, BRCA, AZF), and to reduce the number of regions of uncertain ... 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 and gene ... prenatal diagnosis, one of us (CLC) presented a study by targeted BAC array of a series of 49 fetuses with multiple anatomical malformations and normal karyotype Most of the known recurrent microdeletion...

Ngày tải lên: 14/08/2014, 21:20

... lymphocytic leukemia; CNA, copy number aberration; CNV, copy number variation; CV, coefficient of variation; FISH, fluorescent in situ hybridization; HMM, hidden Markov model; LOH, loss of heterozygosity; ... heterozygous SNPs in size (Figure 5b) Hence, SOMATICs obtains sensitivities similar to the segmentation strategy at the expense of identifying a larger number of false positive regions The detection of copy ... Estimation of tumor cell content from simulated data using segmentation Tumor cells (%) Tumor cells using hemizygous loss (%)* Tumor cells using single copy gain (%)† Tumor cells using copy neutral...

Ngày tải lên: 14/08/2014, 20:22

... function of the number of sources, Ns , is the vector of parameters needed for the model that generated the data Y The criteria are composed of the negative of the ˆ ˆ log-likelihood function of the ... both of these methods, the estimate of the number of sources is that value of Ns which minimizes the criterion In [9] there is a more thorough discussion concerning determining the number of degrees ... than sensors, then the rank of SCS is equal to the number of signals incident on the array or, equivalently, the number of sources If there are Ns sources, then SCS is of rank Ns and its Ns eigenvalues...

Ngày tải lên: 16/12/2013, 04:15

... strains of Japanese encephalitis virus, 28 strains of St Louis encephalitis virus, 172 strains of West Nile virus and 24 strains of yellow fever virus using BLASTn [22] The genome sequences of the ... Effect of geographical variation in dengue virus on the performance of the primer cocktail Each of the four serotypes of dengue virus can be classified into several genotypes, defined as a group of ... for probes or primers for the detection of that pathogen against that host background It was found that 99.99% of all possible 11-mers, 70% of all 15-mers and 5% of all 18-mers are present in...

Ngày tải lên: 14/02/2014, 19:20

... were an artefact of the genotyping assay or a result of unequal allele distribution CYP17 copy number determination Relative copy number determinations were performed for each of the three putative ... samples, a melting peak area ratio of : is indicative of gene duplication [26] An example of gene quantification using hybridization probes is the detection of the autosomal dominant demyelinating ... and 631) Genotyping CYP17 Subsequent to the identification of two unique CYP17 isoforms (ACS) and ACS+) in the South African Angora goat population, a number of goats were genotyped using a restriction...

Ngày tải lên: 07/03/2014, 06:20

... made using a pH-3c digital A solution of 40.0 mL of dimethylformamide in 40.0 mL of methylene chloride was chilled in an ice bath A solution of 37.0 mL of phosphorus oxychloride in 35.0 mL of methylene ... conditions for the analysis of O2–Æ, the effect of buffer solution and the concentration of the fluorescent probe were investigated Effect of pH and buffer concentration The pH of the medium has a large ... compilation ª 2007 FEBS J J Gao et al Selective detection of superoxide anion radicals Scheme A mechanism for the reaction of DBZTC with O2–Æ of reaction of O2–Æ with DBZTC is as follows (Scheme 2)...

Ngày tải lên: 16/03/2014, 11:20