|
| Status |
Public on Feb 17, 2011 |
| Title |
9609_Child_Father (Agilent 244K) |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
peripheral blood
|
| Organism |
Homo sapiens |
| Characteristics |
developmental state: Developmental Delay
tissue: peripheral blood
family: 9609
family member: Child
phenotype: idiopathic MR
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from blood samples using the Puregene DNA kit
|
| Label |
Cy3
|
| Label protocol |
3 μg of high-quality genomic DNA were digested with RsaI and AluI and labeled with Cyanine-3 or Cyanine-5 using a random priming method. Two arrays were used for each trio, one in which the child’s DNA was hybridized against the father’s DNA, and another in which the child’s DNA was hybridized against the mother’s DNA. Equal amounts of the child’s and one parent’s DNA were labeled with opposite fluorochromes and hybridized to the array
|
| |
|
| Channel 2 |
| Source name |
peripheral blood
|
| Organism |
Homo sapiens |
| Characteristics |
family: 9609
family member: Father
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from blood samples using the Puregene DNA kit
|
| Label |
Cy5
|
| Label protocol |
3 μg of high-quality genomic DNA were digested with RsaI and AluI and labeled with Cyanine-3 or Cyanine-5 using a random priming method. Two arrays were used for each trio, one in which the child’s DNA was hybridized against the father’s DNA, and another in which the child’s DNA was hybridized against the mother’s DNA. Equal amounts of the child’s and one parent’s DNA were labeled with opposite fluorochromes and hybridized to the array
|
| |
|
| |
| Hybridization protocol |
3 day hyb at 65C in Agilent Hyb Oven
|
| Scan protocol |
5um scan with Agilent Scanner and Agilent Scanner Control Software v7.0
|
| Data processing |
Captured images were analysed with Feature Extraction v 9.1 and CGH Analytics 3.5.14 using the ADM-1 algorithm to identify regions with consistently high or low log2 ratio. This algorithm does not rely on a window size but rather samples immediately adjacent probes and uses the average normalized log2 ratios of all probes in a genomic interval to determine the deviation of the log2 ratio from its expected value of zero. A user-defined stringency threshold of 6, the recommended default value, was set. Two other methods were also used to assist in the aberration calls. A centralization process was performed that assumes the log2 ratio values are centered at zero and re-centers the data by finding a constant value to add to or subtract from all log2 values. The program uses a default of a 10 probe window to average the log2 ratios. Also, a “fuzzy zero” method, which applies a global error mode to all aberrant intervals identified by the ADM-1 algorithm, was used to avoid erroneous aberration calls when the errors were correlated.
|
| |
|
| Submission date |
Feb 10, 2011 |
| Last update date |
Feb 17, 2011 |
| Contact name |
Tracy Tucker |
| E-mail(s) |
tbtucker@interchange.ubc.ca
|
| Organization name |
University of British Columbia
|
| Street address |
Box 153 4480 Oak Street
|
| City |
Vancouver |
| ZIP/Postal code |
V6H3V4 |
| Country |
Canada |
| |
|
| Platform ID |
GPL4091 |
| Series (2) |
| GSE27229 |
Prospective comparison of genome-wide aCGH platforms for the detection of CNVs in MR (Agilent 244K) |
| GSE27367 |
Prospective comparison of genome-wide aCGH platforms for the detection of CNVs in MR |
|
