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Microarray-based ultra-high resolution discovery of genomic deletion mutations

ABSTRACT: 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

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE55327 | GEO | 2014/02/25

SECONDARY ACCESSION(S): PRJNA239332

REPOSITORIES: GEO

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Microarray-based ultra-high resolution discovery of genomic deletion mutations

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

Discovery of previously unidentified genomic disorders from the duplication architecture of the human genome

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

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Microarray-based ultra-high resolution discovery of genomic deletion mutations.

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

Plasmodium falciparum CNV-SNP chip optimization

Project description:Optimize SNP genotyping probes and demonstrate a new P. falciparum microarray platform that includes CGH and resequencing probes on the same chip

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X chromosome-specific Array-CGH of XLMR patient

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GTF2I Mutations are Common in Thymic Epithelial Tumors

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Project description:To allow acute characterization of ABCB4 locus constitutional deletion in two patients with cholelithiasis/cholestasis, an Agilent 2X400 array CGH was used. Goal was to obtain genomic rearrangements fine characterization in order to describe ABCB4 constitutional deletions.

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Project description:Using 270K Nimblegen Comparative Genomic Hybridization (CGH) array on a set of cv. Chinese Spring deletion lines, a total of 3,671 sequence contigs and scaffolds (~7.8% of chromosome 7B physical length) were mapped into nine deletion bins. In our study we have developed 270K CGH Nimblegen array containing wheat 7B chromosome specific probes and genotyped wheat 7B deletion stocks which have terminal deletions in 7B. Our main aim was to identify absent probes (sequences) in deletion lines. Initially, spatial normalization and M-A loess normalization was performed for comparison test/reference and then clustering analysis (Mcust) was carried out. Further analysis was done on scaffolds (i.e. on larger sequences instead of probes; probes are designed from scaffolds)

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High Frequency of CNV Mutations in Combined Schizophrenia and Epilepsy

Project description:Agilent custom designed array comparative genomic hybridization (CGH) was performed on 235 samples with a dual diagnosis of schizophrenia and epilepsy and 80 samples with a dual diagnosis of bipolar and epilpsy. ArrayCGH on 191 psychiatric screened controls was also performed. A common male reference was used for all samples and controls. Samples and controls were obtained from the NIMH cell line repositories.

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