Genome-wide copy number analysis of cerebrospinal fluid tumor cells and their corresponding archival primary tumors.
A debilitating complication of breast cancer is the metastatic spread of tumor cells to the leptomeninges or cerebrospinal fluid (CSF). Patients diagnosed with this aggressive clinical syndrome, known as leptomeningeal carcinomatosis, have very poor prognosis. Despite improvements in detecting cerebrospinal fluid tumor cells (CSFTCs), information regarding their molecular biology is extremely limited. In our recent work, we utilized a protocol previously used for circulating tumor cell isolation to purify tumor cells from the CSF. We then performed genomic characterization of CSFTCs as well as archival tumors from the same patient. Here, we describe the microarray data and quality controls associated with our study published in the Cancer Research journal in 2013 [1]. We also provide an R script containing code for quality control of microarray data and assessment of copy number calls. The microarray data has been deposited into Gene Expression Omnibus under accession # GSE46068.
Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA ; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA.
Mark Jesus M
MJ
Magbanua
Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA ; Helen Diller Family Comprehensive Cancer Center Computational Biology Core, University of California San Francisco, San Francisco, California, USA.
Ritu
R
Roy
Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA ; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA.
Eduardo V
EV
Sosa
Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA ; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA.
Louai
L
Hauranieh
Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA ; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA.
Andrea
A
Kablanian
Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA ; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA.
Lauren E
LE
Eisenbud
Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA ; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA.
Artem
A
Ryazantsev
Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA ; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA.
Alfred
A
Au
Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA ; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA.
Janet H
JH
Scott
Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA ; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA.
Michelle
M
Melisko
Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA ; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA.
John W
JW
Park