|
| Status |
Public on Dec 01, 2022 |
| Title |
CleftProband_106 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
genomic DNA from whole blood
|
| Organism |
Homo sapiens |
| Characteristics |
Sex: male
syndromic versus non-syndromic: syndromic
cleft type: cleft lip and cleft palate
cleft laterality: right
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from whole blood samples using the Quickgene610L.
|
| Label |
Cy3
|
| Label protocol |
1 ug of case DNA was labeled with Cy3-coupled nonamers and 1 ug of control DNA (from an unaffected male from the Philippines) was labeled with Cy5-coupled nonamers.
|
| |
|
| Channel 2 |
| Source name |
DNA from an unaffected male from the Philippines
|
| Organism |
Homo sapiens |
| Characteristics |
Sex: male
cleft type: unaffected
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from whole blood samples using the Quickgene610L.
|
| Label |
Cy5
|
| Label protocol |
1 ug of case DNA was labeled with Cy3-coupled nonamers and 1 ug of control DNA (from an unaffected male from the Philippines) was labeled with Cy5-coupled nonamers.
|
| |
|
| |
| Hybridization protocol |
34 ug of each labeled DNA was co-hybridized to a Roche NimbleGen human whole genome tiling microarray (Human CGH 2.1M Whole-Genome Tiling v2.0D Array)
|
| Scan protocol |
Arrays were scanned on a Roche NimbleGen microarray scanner.
|
| Data processing |
532.tif and 635.tif files were analyzed using DEVA software to generate a data_summary.txt file and segMNT.txt file. Data_summary.txt files were analyzed using Nexus 7 Software to generate NexusData.bed files and then compared to the segMNT.txt file using BEDTOOLS 50% reciprocal overlap function. Only calls which shared a reciprocal overlap of 50% or greater were retained for further analysis.
BioDiscovery’s FASST2 Segmentation Algorithm, a Hidden Markov Model (HMM) based approach, was the algorithm used to make copy number calls using Nexus 7 Software. The significance threshold for segmentation was set at 1.0E-6 also requiring a minimum of 3 probes per segment and a maximum probe spacing of 1000 between adjacent probes before breaking a segment. The log ratio thresholds for single copy gain and single copy loss were set at 0.3 and -0.3, respectively. A 3:1 sex chromosome gain threshold was set to 1.2 and a 4:1 sex chromosome gain threshold was set to 1.7. NimbleGen's DEVA segMNT algorithm, which minimizes squared error relative to the segment means, was used as a second algorithm for all copy number calls after data extraction, LOESS spatial correction and background correction. Default parameters were used with the exception of setting the minimum segment difference to 0.3 and requiring a minimum of 3 probes per segment.
|
| |
|
| Submission date |
Aug 27, 2022 |
| Last update date |
Dec 02, 2022 |
| Contact name |
J. Robert Manak |
| Organization name |
The University of Iowa
|
| Department |
Biology and Pediatrics
|
| Lab |
Manak Lab
|
| Street address |
455 Biology Building, 129 East Jefferson Street
|
| City |
Iowa City |
| State/province |
Iowa |
| ZIP/Postal code |
52242 |
| Country |
USA |
| |
|
| Platform ID |
GPL23665 |
| Series (2) |
| GSE212166 |
CNV analysis of 869 individuals from the Philippines with cleft lip and/or cleft palate |
| GSE212296 |
Genome-wide analysis of copy number variation in humans with cleft lip and/or cleft palate identifies COBLL1, RIC1, and ARHGEF38 as clefting genes |
|
