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Sample GSM1621445 Query DataSets for GSM1621445
Status Public on Oct 06, 2015
Title sample_01-EG-009 [copy number]
Sample type genomic
 
Source name Breast cancer, CHER-LOB Arm A, pre-treated
Organism Homo sapiens
Characteristics disease state: HER2-positive breast cancer
tissue: breast cancer
cher-lob arm: A
arm description: chemotherapy+trastuzumab
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 2.000000 1 61723 0.032927 1.231654 nan nan
CN_473964 2.000000 1 61796 -0.059169 1.231481 nan nan
CN_473965 2.000000 1 61811 0.032911 1.231445 nan nan
CN_473981 2.000000 1 62908 -0.122083 1.228846 nan nan
CN_473982 2.000000 1 62925 -0.319946 1.228806 nan nan
CN_497981 2.000000 1 72764 0.020281 1.205812 nan nan
CN_502615 1.000000 1 85924 -0.570692 1.176088 nan nan
CN_502613 1.000000 1 85986 -0.395338 1.175951 nan nan
CN_502614 1.000000 1 86312 -0.851002 1.175232 nan nan
CN_502616 1.000000 1 86329 -2.099290 1.175195 nan nan
CN_502843 1.000000 1 98590 -0.145498 1.148837 nan nan
CN_466171 3.000000 1 228694 0.721823 2.492097 nan nan
CN_468414 3.000000 1 229063 -0.140636 2.492167 nan nan
CN_468412 3.000000 1 229146 0.004738 2.492182 nan nan
CN_468413 3.000000 1 229161 0.198869 2.492185 nan nan
CN_470565 3.000000 1 229607 -0.120479 2.492270 nan nan
CN_468424 3.000000 1 235658 0.401160 2.493421 nan nan
CN_468425 3.000000 1 235716 0.171348 2.493433 nan nan
CN_460512 3.000000 1 356431 1.376003 12.057818 nan nan
CN_460513 3.000000 1 356530 1.505254 12.057821 nan nan

Total number of rows: 1813281

Table truncated, full table size 114212 Kbytes.




Supplementary file Size Download File type/resource
GSM1621445_01-EG-009.CEL.gz 26.9 Mb (ftp)(http) CEL
GSM1621445_01-EG-009.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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