|
| Status |
Public on Feb 06, 2016 |
| Title |
CML-58 |
| Sample type |
genomic |
| |
|
| Source name |
Blood
|
| Organism |
Homo sapiens |
| Characteristics |
sample id: CML-58
chronic phase: Chronic Phase-Under Treatment-58-Hydroxyurea , Zyloric and Imatinib treated nine months
age: 32 years
gender: Female
|
| Treatment protocol |
All patients were commenced to Imatinib treatment alone or in combination with Hydrea/Hydroxyurea. Importantly, in some cases when patients failed to achieve time dependent molecular targets we switched to nilotinib or high dose Imatinib. Clinical outcomes included molecular response on the basis of BCR-ABL1
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from fresh tumor tissue using a QIAamp DNA mini kit (Qiagen, Germany) according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotin labelled fragmented DNA were prepared according to the standard OncoScan™ Array protocol (Affymetrix).
|
| |
|
| Hybridization protocol |
Briefly, the 75 ng DNA/sample were hybridized to MIP probe for 17 hours followed by gap filling with AT/GC. After removing the un-ligated (non gap-filled, linear) probes through exonuclease treatment, the cleavage enzyme was added to linearize the gap-filled circular MIP Probes. This was followed by amplification and enrichment of the gap-filled, linearized MIP probe through 1st and 2nd PCR. The enriched product was digested by HaeIII enzyme and hybridized to the OncoScan™ Array for 17 hours at 49 degree C at 60rpm.
|
| Scan protocol |
GeneChips were scanned using the Gene Chip Scanner, Affymetrix
|
| Description |
Chronic Phase-Under Treatment-58-Hydroxyurea , Zyloric and Imatinib treated nine months; 32 years Female
|
| Data processing |
The .cel file generated after scanning, was converted to OSCHP files through Oncoscan Console Software (Biodiscovery, Inc., CA USA). Further the OSCHP file was analyzed through tumor Scan (TuScan) and BioDiscovery’s SNP-FASST2 algorithm using the Nexus Express for Oncoscan software version 3.0 and 7.5 (Biodiscovery, Inc., CA USA). The TuScan algorithm creates segmentation to differentiate between adjacent clusters of probes and determines the copy number changes. The BioDiscovery’s SNP-FASST2 algorithm, a proprietary variation of a hidden Markov model (HMM) is used to identify the allelic event calls.
|
| |
|
| Submission date |
Feb 04, 2016 |
| Last update date |
Feb 06, 2016 |
| Contact name |
Neetu Singh |
| E-mail(s) |
neetuaashi@yahoo.com
|
| Phone |
9984801444
|
| Organization name |
King George's Medical University
|
| Department |
Center for Advance Research
|
| Street address |
Chowk
|
| City |
Lucknow |
| ZIP/Postal code |
226003 |
| Country |
India |
| |
|
| Platform ID |
GPL18602 |
| Series (2) |
| GSE77571 |
Combination of multiomics approach and BCR-ABL based molecular testing: A better way to monitor treatment regimen and disease progression in Chronic Myeloid Leukemia [OncoScan] |
| GSE77573 |
Combination of multiomics approach and BCR-ABL based molecular testing: A better way to monitor treatment regimen and disease progression in Chronic Myeloid Leukemia |
|
