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Series GSE4240 Query DataSets for GSE4240
Status Public on Feb 16, 2006
Title High Resolution Mapping of DNA Copy Alterations in Human Chromosome 22 Using High Density Tiling Oligonucleotide Arrays
Organism Homo sapiens
Experiment type Genome variation profiling by genome tiling array
Summary 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)
 
Overall design The overall goal of the study was the detection of the precise boundaries of chromosomal aberrations involved in disease. Maskless array synthesis was used to construct custom isothermal arrays containing up to 385,000 oligonucleotides, either tiling the non-repetitive regions of chromosome 22, or focussing on the beta-globin locus on chromosome 11. Genomic DNA isolated from patients (Cy3) was co-hybridized with a reference DNA pool (Promega; Cy5).
 
Contributor(s) Urban AE, Korbel JO, Selzer R, Richmond T, Cubells JF, Popescu GV, Hacker A, Green R, Emanuel BS, Gerstein MB, Weissman SM, Snyder M
Citation(s) 16537408
Submission date Feb 14, 2006
Last update date Mar 16, 2012
Contact name Jan Oliver Korbel
Phone +1 203 432 5405
Fax +1 203 432 5175
URL http://bioinfo.mbb.yale.edu/array/
Organization name Yale University
Street address 266 Whitney Avenue
City New Haven
State/province CT
ZIP/Postal code 06520
Country USA
 
Platforms (3)
GPL3448 YALE/NIMBLEGEN_HUMAN-CHR22_372K_v1.0
GPL3449 YALE/NIMBLEGEN HUMAN-CHR11-beta-globin-locus 6K v1.0
GPL3450 YALE/NIMBLEGEN HUMAN-CHR11-beta-globin-locus 3K v1.0
Samples (16)
GSM96607 Patient-04-018_HR-CGH_rep1 (Experiment-ID: 36320)
GSM96608 Patient-04-018_HR-CGH_rep2 (Experiment-ID: 38516)
GSM96609 Patient-04-018_HR-CGH_rep3 (Experiment-ID: 42719)
Relations
BioProject PRJNA94897

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