Dataset features

Specifications


Application: aCGH data analysis, FISH
Number of samples: 12
Release date: Jul 28 2006
Last update date: Mar 16 2012
Access: Public
Diseases: Aniridia, Hypopigmentation
Dataset link Array-Based Comparative Genome Hybridization in Clinical Genetics

Experimental Protocol


High-molecular weight genomic DNA was purified from patients' ’peripheral blood leukocytes. Test DNA and normal reference DNA (from an individual of the opposite sex of the test sample, except for N1 and N2) was labeled to incorporate Cy3 or Cy5 fluorophores. Equal aliquots of labeled test and reference DNA were combined and hybridized to GenoSensor Array 300 (GPL3709). This array contains 287 genomic clones, including those for each human telomere, as well as all of the known microdeletion syndromes and additional selected loci representing each chromosome arm. The GenoSensor CGH Array 300 clone list is available at http://www.vysis.com/PDF/GenoSensor300ClonesAndKey_July2004.pdf. Hybridization signal images in three colors, Cy3, Cy5 and DAPI blue were then analyzed by the GenoSensor reader system based on DAPI staining that identified target spots and their location on the grid. By analyzing the set of Cy3/Cy5 ratios (test-to-reference ratios) on all targets, the GenoSensor Array 300 Reader Software (version 1) calculates the ratio most representative of the modal DNA copy number of the sample DNA. For each target the normalized ratio, relative to the modal DNA copy number is calculated. This normalized ratio of the target indicates the degree of gain or loss of copy number, and for each clone the copy number changes are presented. For each target, a P value is calculated automatically by the GenoSensor Array 300 Reader Software (Abbott Vysis), and a P value of 0.005 or less was considered significant.

Repositories


GEO

GSE4775

BioProject

PRJNA95545

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Contact


Anat Bar-Shira