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Sample GSM1621485 Query DataSets for GSM1621485
Status Public on Oct 06, 2015
Title sample_05-MP-006 [copy number]
Sample type genomic
 
Source name Breast cancer, CHER-LOB Arm B, pre-treated
Organism Homo sapiens
Characteristics disease state: HER2-positive breast cancer
tissue: breast cancer
cher-lob arm: B
arm description: chemotherapy+lapatinib
pcr (1=yes): 0
Treatment protocol CHER-LOB is a phase II, randomized, multicenter, trial in which 121 patients with primary HER2-positive breast cancer were randomized to receive preoperative chemotherapy with weekly paclitaxel times 12 followed by 4 courses of 3-weekly FEC (fluorouracil, epirubicin and cyclophosphamide) plus either trastuzumab (Arm A), lapatinib (Arm B) or the combination of trastuzumab and lapatinib (Arm C). The trial design, eligibility criteria, statistical analysis, and clinical results including response, surgery outcomes and treatment safety are described in details elsewhere.
Growth protocol NA
Extracted molecule genomic DNA
Extraction protocol Qiagen DNeasy Blood & Tissue Kit (manufacturer's protocol).
Label Biotin
Label protocol Affymetrix (manufacturer's protocol).
 
Hybridization protocol Affymetrix® Genome-Wide Human SNP Nsp/Sty 6.0 (manufacturer's protocol).
Scan protocol Affymetrix GeneChip Scanner 3000 7G (manufacturer's protocol).
Data processing Affymetrix® Genotyping Console.
 
Submission date Feb 27, 2015
Last update date Oct 06, 2015
Contact name Enrico Tagliafico
E-mail(s) enrico.tagliafico@unimore.it
Organization name University of Modena and Reggio Emilia
Department Center for Genome Research
Street address Via Campi 287
City Modena
State/province MO
ZIP/Postal code 41126
Country Italy
 
Platform ID GPL6801
Series (2)
GSE66398 Prospective biomarker analysis of the randomized CHER-LOB study evaluating the dual anti-HER2 treatment with chemotherapy plus trastuzumab and lapatinib as neoadjuvant therapy for HER2-positive breast cancer [copy number]
GSE66399 Prospective biomarker analysis of the randomized CHER-LOB study evaluating the dual anti-HER2 treatment with chemotherapy plus trastuzumab and lapatinib as neoadjuvant therapy for HER2-positive breast cancer

Data table header descriptions
ID_REF
VALUE CN STATE
CHROMOSOME
POSITION
LOG2 RATIO
SMOOTH SIGNAL
LOH
ALLELE DIFFERENCE

Data table
ID_REF VALUE CHROMOSOME POSITION LOG2 RATIO SMOOTH SIGNAL LOH ALLELE DIFFERENCE
CN_473963 3.000000 1 61723 0.584150 2.877078 nan nan
CN_473964 3.000000 1 61796 0.245988 2.876980 nan nan
CN_473965 3.000000 1 61811 0.381036 2.876960 nan nan
CN_473981 3.000000 1 62908 0.332581 2.875490 nan nan
CN_473982 3.000000 1 62925 0.465104 2.875467 nan nan
CN_497981 3.000000 1 72764 -0.084978 2.862351 nan nan
CN_502615 3.000000 1 85924 1.451985 2.845057 nan nan
CN_502613 3.000000 1 85986 -0.034769 2.844976 nan nan
CN_502614 3.000000 1 86312 -0.028319 2.844552 nan nan
CN_502616 3.000000 1 86329 -0.341953 2.844530 nan nan
CN_502843 3.000000 1 98590 0.185746 2.828772 nan nan
CN_466171 3.000000 1 228694 0.853725 2.980044 nan nan
CN_468414 3.000000 1 229063 -0.012195 2.980169 nan nan
CN_468412 3.000000 1 229146 -0.003644 2.980198 nan nan
CN_468413 3.000000 1 229161 0.788231 2.980203 nan nan
CN_470565 3.000000 1 229607 -0.349679 2.980354 nan nan
CN_468424 3.000000 1 235658 0.462254 2.982426 nan nan
CN_468425 3.000000 1 235716 0.502841 2.982446 nan nan
CN_460512 2.000000 1 356431 -0.830376 1.543687 nan nan
CN_460513 2.000000 1 356530 0.415047 1.543689 nan nan

Total number of rows: 1813281

Table truncated, full table size 114166 Kbytes.




Supplementary file Size Download File type/resource
GSM1621485_05-MP-006.CEL.gz 27.4 Mb (ftp)(http) CEL
GSM1621485_05-MP-006.CN5.CNCHP.gz 34.9 Mb (ftp)(http) CNCHP
Processed data included within Sample table
Processed data provided as supplementary file
Processed data are available on Series record

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