|
| Status |
Public on Dec 11, 2010 |
| Title |
MA7 |
| Sample type |
genomic |
| |
|
| Source name |
MA7
|
| Organism |
Homo sapiens |
| Characteristics |
Sex: female
parent twin pair: 3
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
To extract DNA we used a standard phenol-chloroform method. The detailed method is attached in a pdf document.
|
| Label |
C-Bio and A-DNP
|
| Label protocol |
Standard Illumina protocol
|
| |
|
| Hybridization protocol |
Standard Illumina protocol
|
| Scan protocol |
Standard Illumina protocol
|
| Data processing |
To normalize the data I used Illumina Genome Studio's Genotyping Module version 1.5.16. The data was normalized using a cluster file of 782 individuals of Mexican American descent who were genotyped as part of the San Antonio Family Heart and San Antonio Family Diabetes/Gallbladder studies.
To identify regions that differed in copy number between pair samples I used circular binary segmentation (CBS) applied to the absolute value of the difference between b-allele ratios. Applying CBS to b-allele ratio differences is a novel approach. To implement CBS I used DNAcopy 1.16.0. The statistical approach I used is described here: (VENKATRAMAN, E. S., and A. B. OLSHEN, 2007 A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics 23: 657-663). I used PennCNV (Sat, 01 May 2010 version) to identify germline copy number variants in all of the samples. I used the available trio information and a posteriori trio calling to identify de novo CNVs.
|
| |
|
| Submission date |
Dec 02, 2010 |
| Last update date |
Dec 11, 2010 |
| Contact name |
August Nolan Blackburn |
| E-mail(s) |
[email protected]
|
| Phone |
2105670544
|
| Organization name |
University of Texas Health Science Center at San Antonio
|
| Department |
Medicine - Clinical Epidemiology
|
| Lab |
Lehman Lab
|
| Street address |
7702 Floyd Curl
|
| City |
San Antonio |
| State/province |
Texas |
| ZIP/Postal code |
78229 |
| Country |
USA |
| |
|
| Platform ID |
GPL6984 |
| Series (1) |
| GSE25826 |
Investigation of somatic copy number variation in MZ twins |
|
