Microarray-based ultra-high resolution discovery of genomic deletion mutations
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE55327 | GEO | 2014/02/25
SECONDARY ACCESSION(S): PRJNA239332
REPOSITORIES: GEO
Similar Datasets
Project description:The use of a graduated series of Arabidopsis thaliana genomic deletion mutations (of sizes ranging from 4 bp to ~5 kb) to optimize CGH-based genomic deletion detection Microarray-based ultra-high resolution discovery of genomic deletion mutations
2014-02-25 | E-GEOD-55327 | biostudies-arrayexpress
Project description:BackgroundOligonucleotide microarray-based comparative genomic hybridization (CGH) offers an attractive possible route for the rapid and cost-effective genome-wide discovery of deletion mutations. CGH typically involves comparison of the hybridization intensities of genomic DNA samples with microarray chip representations of entire genomes, and has widespread potential application in experimental research and medical diagnostics. However, the power to detect small deletions is low.ResultsHere we use a graduated series of Arabidopsis thaliana genomic deletion mutations (of sizes ranging from 4 bp to ~5 kb) to optimize CGH-based genomic deletion detection. We show that the power to detect smaller deletions (4, 28 and 104 bp) depends upon oligonucleotide density (essentially the number of genome-representative oligonucleotides on the microarray chip), and determine the oligonucleotide spacings necessary to guarantee detection of deletions of specified size.ConclusionsOur findings will enhance a wide range of research and clinical applications, and in particular will aid in the discovery of genomic deletions in the absence of a priori knowledge of their existence.
| S-EPMC3998191 | biostudies-literature
Project description:This entry is part of a study comparing various array CGH platforms. In addition to the submitted data the following BT474 profiles were analyzed in this study: GSM69198 , GSM73557 and data from http://research.dfci.harvard.edu/meyersonlab/snp/snp.htm Keywords: Comparitive Genomic Hybridization (CGH) Platform Comparison
2007-02-15 | GSE6415 | GEO
Project description:We present a novel method of using commercial oligonucleotide expression microarrays for aCGH, enabling DNA copy number measurements and expression profiles to be combined using the same platform. This method yields aCGH data from genomic DNA without complexity reduction at a median resolution of approximately 17,500 base pairs. Due to the well-defined nature of oligonucleotide probes, DNA amplification and deletion can be defined at the level of individual genes and can easily be combined with gene expression data. Keywords: genomic DNA, CGH, Copy Number Variation
2007-03-29 | GSE7364 | GEO
Project description:Genomic disorders are characterized by the presence of flanking segmental duplications that predispose these regions to recurrent rearrangement. Based on the duplication architecture of the genome we investigated 130 regions which we hypothesized as candidates for novel genomic disorders 1. We tested 290 patients with mental retardation by BAC array CGH, identifying sixteen pathogenic rearrangements, including four patients with de novo microdeletions of 17q21.31. Using oligonucleotide arrays we refined the breakpoints of this microdeletion, defining a 478 kb critical region containing six genes that were deleted in all four cases. The breakpoints of this deletion, and of four other pathogenic rearrangements in 1q21.1, 15q13, 15q24 and 17q12 were mapped to flanking segmental duplications, suggesting that these are also sites of recurrent rearrangement. In common with the 17q21.31 deletion, these breakpoint regions are also sites of copy number polymorphism in controls, indicating that these may be inherently unstable genomic regions. Keywords: BAC comparative genomic hybridization of individuals with mental retardation and congenital anomalies
2006-08-10 | GSE5373 | GEO
Project description:The Males Experiment: This experiment was done to test the sensitivity of our array in detecting single copy losses of probes to the X chromosome. Males (XO) have just one X chromosome, while hermaphrodites (XX) have two. CB4856 and JU258: This experiment was done to determine the natural copy number variation that exists in a wild C. elegans isolate. Extensive natural copy number variation exists in this strain. gkDf2 (VC100): This control experiment was done to confirm that we could reliably detect a large 50-kb homozygous deletion on chromosome X using this array. gk329 (VC766): This control experiment was done to confirm that we could reliably detect a homozygous 1-kb single-gene deletion on the X chromosome. This deletion targets the gene ceh-39. For gk291 (VC615): This control experiment was done to confirm that we could reliably detect a heterozygous (single copy) single-gene 1-kb deletion on chromsome II. This deletion targets the gene dab-1. All other experiments: This experiment was done in an effort to detect novel balanced single copy losses on chromosome II in mutagenized strains. Mutants were previously screened for homozygous lethal mutations on chromosome II, and these mutations were then balanced with the mIn1 balancer chromosome to generate the mutant strain screened in this experiment. Keywords: comparative genomic hybridization
2006-11-18 | GSE6294 | GEO
Project description:Deletions and amplifications of the human genomic sequence (Copy Number Polymorphisms, or 'CNPs') are the cause for numerous diseases and a potential cause of phenotypic variation in the normal population. Comparative Genomic Hybridization (CGH) has been developed as a useful tool for detecting alterations in DNA copy number that involve blocks of DNA several kilobases or greater in size. We have developed High-Resolution CGH (HR-CGH) to detect accurately and with relatively little bias the presence and extent of chromosomal aberrations in human DNA. Maskless array synthesis was used to construct arrays containing 393,000 oligonucleotides with isothermal probes of 45-85 bp in length; arrays tiling the β-globin locus and chromosome 22q were prepared. Arrays with 9 bp tiling path were used to map a 622 bp heterozygous deletion in the β-globin locus. Arrays with an 85 bp tiling path were used to analyze DNA from patients with copy number changes in the pericentromeric region of chromosome 22. Heterozygous deletions and duplications as well as partial triploidies and partial tetraploidies of portions of chromosome 22q were mapped with high resolution in each patient, and the precise breakpoint of two deletions was confirmed by DNA sequencing. Additional peaks potentially corresponding to known and novel additional CNPs were also observed. Our results demonstrate that HR-CGH allows the detection of copy-number changes in any given region of the human genome comprehensively and at an unprecedented level of resolution. Keywords: high resolution comparative genome hybridization (HR-CGH)
2006-02-16 | GSE4240 | GEO
Project description:BackgroundHigh-resolution HLA genotyping is a critical diagnostic and research assay. Current methods rarely achieve unambiguous high-resolution typing without making population-specific frequency inferences due to a lack of locus coverage and difficulty in exon-phase matching. Achieving high-resolution typing is also becoming more challenging with traditional methods as the database of known HLA alleles increases.ResultsWe designed a cDNA amplicon-based pyrosequencing method to capture 94% of the HLA class I open-reading-frame with only two amplicons per sample, and an analogous method for class II HLA genes, with a primary focus on sequencing the DRB loci. We present a novel Galaxy server-based analysis workflow for determining genotype. During assay validation, we performed two GS Junior sequencing runs to determine the accuracy of the HLA class I amplicons and DRB amplicon at different levels of multiplexing. When 116 amplicons were multiplexed, we unambiguously resolved 99%of class I alleles to four- or six-digit resolution, as well as 100% unambiguous DRB calls. The second experiment, with 271 multiplexed amplicons, missed some alleles, but generated high-resolution, concordant typing for 93% of class I alleles, and 96% for DRB1 alleles. In a third, preliminary experiment we attempted to sequence novel amplicons for other class II loci with mixed success.ConclusionsThe presented assay is higher-throughput and higher-resolution than existing HLA genotyping methods, and suitable for allele discovery or large cohort sampling. The validated class I and DRB primers successfully generated unambiguously high-resolution genotypes, while further work is needed to validate additional class II genotyping amplicons.
| S-EPMC3575390 | biostudies-literature
Project description:Optimize SNP genotyping probes and demonstrate a new P. falciparum microarray platform that includes CGH and resequencing probes on the same chip
2011-04-01 | GSE28287 | GEO
Project description:Ultra high resolution breakpoint mapping using custom oligonucleotide arrays and array painting The two derivative chromosomes from 4 patients with balanced translocations were flow sorted, differentially labelled and hybridised to custom oligonucleotide arrays designed to cover the potential breakpoint region at high resolution. Single hybridisations with no replicates.
2010-07-01 | E-GEOD-4297 | biostudies-arrayexpress