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Status |
Public on Dec 10, 2021 |
Title |
Bone marrow cells - SNP array (1009724-4) |
Sample type |
genomic |
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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: 38 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 |
Cy3 and Cy5
|
Label protocol |
standard Illumina protocol
|
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|
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 |
The raw data retrieved from an Illumina Omni2.5-8 SNP array was processed using GenomeStudio 2.0. 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)
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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 |
GPL18952 |
Series (2) |
GSE190392 |
Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios [Omni2.5] |
GSE190397 |
Philadelphia chromosome (Ph)-positive acute lymphoblastic leukemia (ALL) |
|