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Series GSE147493 Query DataSets for GSE147493
Status Public on Mar 26, 2020
Title Transcriptome analysis in a unique cohort of untreated primary tumors collected from diagnostic prostate needle biopsies (PNBX) of localized (M0) and metastatic (M1) cases
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary PNBX were collected from 99 patients treated in the VA Greater Los Angeles (GLA-VA) Healthcare System between 2000-2016
 
Overall design 99 prostate cancer cases with archival biopsy tissue available were selected for RNA sequencing (RNAseq) from a total cohort 1927 cases identified within the GLA-VA cancer registry or procedure logs. The selected cases were divided into sub-cohorts based upon tumor burden at diagnosis or recurrence/progression documented in imaging reports, including 99mTc-methylene disphosphonate (99mTc-MDP) planar bone scintigraphy, 18F-NaF positron emission tomography (18F-NaF PET), ultrasounds, magnetic resonance imaging (MRI), computed tomography (CT) scans, and plain radiographs. Cases were designated clinical stage M1 if metastatic lesions were identified on imaging scans performed within 1 year of the diagnostic PNBX. Osteoblastic, osteolytic, and/or sclerotic bone lesions observed on bone scan were confirmed or by the presence of overlapping lesions on plain radiographs, CT or MRI imaging. Oligometastatic “oligo” disease was defined by <5 extrapelvic lymph node and/or bone metastases and no visceral metastases. Polymetastatic “poly” disease was defined as >5 metastases or any visceral involvement. M1 cases were designated M1-oligo or M0-poly based on the aforementioned tumor burden assessment. Cases that were considered M0 at diagnosis, but demonstrated eventual metastatic progression (M0-M) were designated M0-oligo or M0-poly based on tumor burden on imaging scans at the time of follow-up. Cases were designated as clinical stage M0 non-metastatic (M0-NM) if no metastatic lesions were identified at the time of last follow-up. If imaging scans were not performed, or equivocal results were obtained, the cases were categorized as MX and excluded from analysis. A significant subset of M0 cases from the original 1927 cohort did not have an indication for diagnostic imaging due to diagnosis of low- or intermediate-risk PC according to D’Amico classification
 
Contributor(s) Garraway IP, You S
Citation(s) 32380981
Submission date Mar 24, 2020
Last update date May 18, 2020
Contact name Sungyong You
E-mail(s) [email protected]
Organization name Cedars-Sinai Medical Center
Department Surgery
Lab Freeman Lab.
Street address Beverly Blvd 8400
City LA
State/province CA
ZIP/Postal code 90048
Country USA
 
Platforms (1)
GPL21290 Illumina HiSeq 3000 (Homo sapiens)
Samples (99)
GSM4432009 prostate cancer case with archival biopsy tissue 35-5a
GSM4432010 prostate cancer case with archival biopsy tissue 381-5a
GSM4432011 prostate cancer case with archival biopsy tissue 574-5a
Relations
BioProject PRJNA614979
SRA SRP253911

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE147493_Raw_count.xlsx 10.0 Mb (ftp)(http) XLSX
GSE147493_TMM_normalized_data.xlsx 22.8 Mb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
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