|
| Status |
Public on Sep 25, 2008 |
| Title |
MMCONTROL53_NSP |
| Sample type |
genomic |
| |
|
| Source name |
PERIPHERAL BLOOD
|
| Organism |
Homo sapiens |
| Characteristics |
PB MM CONTROL - NSP CHIP
Number: 53
Control
Treatment: 1- Pamidronate
Gender: male
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
AUTOMATED DNA EXTRACTION MAGNA PURE
|
| Label |
BIOTIN
|
| Label protocol |
Following restriction enzyme digestion, biotin labeled DNA was prepared according to the Affymetrix protocol from 500ng of starting DNA (GeneChip Mapping 500K Assay Manual, Affymetrix, 2005).
|
| |
|
| Hybridization protocol |
Mapping 500K arrays were hybridized according to the Affymetrix protocol (GeneChip Mapping 500K Assay Manual, Affymetrix, 2005) using an Affymetrix hybridization oven.
|
| Scan protocol |
Mapping 500K arrays were scanned according to the Affymetrix protocol (GeneChip Mapping 500K Assay Manual, Affymetrix, 2005) using a GS3000 scanner.
|
| Description |
NA
|
| Data processing |
Genotypes were determined using the BRLMM algorithm (Bayesian Robust Linear Model with Mahalanobis distance classifier) with cases and controls undergoing a joint cluster analysis. Before the analysis, quality filtering tests (of both samples and SNP’s) were carried out to ensure a robust association test. The criteria for exclusion were: 1) call rate<90%, 2) minor allele frequency, MAF<5% and 3) deviations from Hardy-Weinberg equilibrium with a low enough significance (p<0.00001). Sexual chromosomes were not considered in the SNP analysis.
|
| |
|
| Submission date |
Jul 01, 2008 |
| Last update date |
Sep 24, 2008 |
| Contact name |
Maria Eugenia Sarasquete |
| E-mail(s) |
sarasquete@hotmail.com
|
| Phone |
0034-923-291629
|
| Fax |
0034-923-269066
|
| Organization name |
Hospital Universitario de Salamanca
|
| Department |
Hematology
|
| Lab |
Molecular Biology
|
| Street address |
Paseo San Vicente 58-182
|
| City |
salamanca |
| State/province |
salamanca |
| ZIP/Postal code |
37007 |
| Country |
Spain |
| |
|
| Platform ID |
GPL3718 |
| Series (1) |
| GSE11948 |
Bisphosphonate related osteonecrosis of the jaw is associated with polymorphisms of the cytochrome P450 CYP2C8 in MM |
|
