|
| Status |
Public on Dec 10, 2021 |
| Title |
Bone marrow cells - SNP array (AL3182A7400M6) |
| Sample type |
genomic |
| |
|
| Source name |
Bone marrow cells
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: Ph-positive ALL
treatment: HCVAD_plus_ponatinib
tissue: bone marrow
cell type: leukemic cell
Sex: Male
age_diagnosis: 57
outcome: Complete Response
|
| Treatment protocol |
Samples were either bone marrow aspirate or peripheral blood obtained from previously untreated patients.
|
| Growth protocol |
Not applicable
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from bone marrow or peripheral blood samples using a QIAamp DNA Mini kit (QIAGEN, Hilden, Germany).
|
| Label |
C-Bio and A-DNP
|
| Label protocol |
standard Illumina protocol
|
| |
|
| Hybridization protocol |
According to the hybridazation protocol in manufacture's Reference Guide
|
| Scan protocol |
According to the scan protocol in manufacture's Reference Guide
|
| Data processing |
Genomic DNA extracted from patient-derived leukemic cells was genotyped using Infinium HumanCytoSNP-850K-12 v2.1 BeadChips (Illumina).
The raw log R ratio was used for ASCAT (allele-specific copy number analysis of tumors) algorithm to identify allele-specific copy-number alterations.
The log R ratio (LRR)
|
| |
|
| Submission date |
Dec 07, 2021 |
| Last update date |
Dec 10, 2021 |
| Contact name |
Yuya Sasaki |
| E-mail(s) |
imagingbio0311@gmail.com
|
| Organization name |
M.D. Anderson Cancer Center
|
| Street address |
1515 Holcombe Blvd
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77054 |
| Country |
USA |
| |
|
| Platform ID |
GPL31039 |
| Series (2) |
| GSE190390 |
Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios [CytoSNP] |
| GSE190397 |
Philadelphia chromosome (Ph)-positive acute lymphoblastic leukemia (ALL) |
|
