|
| Status |
Public on Jun 01, 2022 |
| Title |
961272 |
| Sample type |
RNA |
| |
|
| Source name |
uterine serous cancer
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: metastatic USC
clinical outcome to treatment (pts=platinum sensitive ptr=platinum resistant) - ned (no evidence disease): PtS-NED
age of patient at time of surgery: 63.5
population group or ancestry (genomic analysis): Afr
ethnicity (self-reported): AA
tumor stage: IIIC
date of last chemo- therapy: 2017-01-01
date of recurrence: 2021-02-01
date of death: February-21
time to recurrence (ttr in months) \: 48.9
overall survival (os in months): 48.9
time to recurrence (months) - censored data - 1 implies censored: 1
overall survival (months) - censored data - 1 implies censored: 1
site of metastasis: LN
site of recurrence: NA
sample_name (matched primary-met): USC33M
tumor type: M-Metastatic, D-Distant, P-Primary: M
wes data (small variants/cn) (x if present): X
nanostring io 360 expression data (x if present): X
tumor purity estimate from wes analysis: 35%
favorable immune response (clis relative to tgfb1) - *marginal, **favorable, ***highlyfavorable: ***
plk3 est. cn: 2.0
plk3 cna call: Normal
tp53 cna call: Gain
log2 ratio plk3 locus: 0.012
plk3 adj. est. cn (for tumor purity): 2.0
tp53 adj. est cn (for tumor purity): 2.8
tcellextrect (est tcell proportion)-dna: 0.45
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Archived formalin-fixed paraffin-embedded tumor blocks of paired primary and metastatic tumor from 29 patients with complete clinical treatment/response information were used to obtain 5-8 unstained slides sectioned at 10-micron thickness. The unstained tissue sections were used for extraction of RNA and DNA. We used Qiagen’s Allprep DNA/RNA FFPE kit to simultaneously purify genomic DNA and total RNA from formalin-fixed, paraffin embedded (FFPE) tissue sections. DNA and RNA were released sequentially by differential solubilization of the same FFPE sample. FFPE tissue sections were first deparaffinized using xylene. The tissue was then digested with proteinase K to enable cell lysis and release of the RNA into the supernatant while the DNA and other insoluble material are precipitated. The sample was then centrifuged to separate the RNA containing supernatant from the DNA containing pellet. The RNA containing supernatant was heated to partially reverse formalin crosslinks before application to a RNeasy Mini spin column where the total RNA was bound to the membrane. An on-column DNase digestion was performed to ensure purification of DNA-free RNA. Following DNase digestion, contaminants were removed through column washing and total RNA was eluted in Nuclease-free water.
|
| Label |
NA
|
| Label protocol |
Isolated RNA was assessed by sample source using TapeStation for the percentage of fragments (fragmentation score) between 50 and 300 nt. Based on a linear function that increased input for higher fragmentation scores, the input level for samples ranged from 100 ng to 1000 ng in proportion to the fragmentation score (higher scores implied higher levels of fragmentation which led to higher input levels to the assay). After the first round of testing, all 60 samples were evaluated for provenance and consistency between paired samples. Several samples were repeated at the same or higher input levels to potentially boost detection rates for some samples that initially had low detection rates. Analysis went forward with the best of the two runs for each sample based on detection rates. A small subset of samples (patient ID #1 Met, patient ID #9 Met and Primary, patient ID #12 Met, patient ID #20 Distant Met, and patient ID#28, Primary) yielded unacceptable NanoString results from either run.
|
| |
|
| Hybridization protocol |
Samples were hybed (capture probes) based on the typical NanoString protocol
|
| Scan protocol |
Samples were scanned based on the typical NanoString protocol on the nCounter instrument
|
| Description |
USC33M
Censored data (time=outcome)
|
| Data processing |
Samples were normalized between batches using common samples that had sufficient detection. Some samples have more than 1 NanoString cartridge. The cartridge with the highest level of detection was brought forward. Genes were then separated into cancer-related and immune related genes. Immune genes were scaled to a common log2 value of 8 across samples using the entire NanoString sample profile(immune and cancer gene expression). Cancer genes were normalized separately to attempt to estimate the relative expression in non-immune cells as samples varied widely in tumor purity. Cancer genes were also normalized to a common log2 value of 8 but only using the sample profile of the cancer (non-immune) genes.
|
| |
|
| Submission date |
May 31, 2022 |
| Last update date |
Jun 01, 2022 |
| Contact name |
Wendell D Jones |
| E-mail(s) |
[email protected]
|
| Phone |
19192747824
|
| Organization name |
Q2 Solutions
|
| Street address |
2400 Ellis Rd
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27703 |
| Country |
USA |
| |
|
| Platform ID |
GPL27956 |
| Series (1) |
| GSE205209 |
PLK3 amplification and tumor immune microenvironment of metastatic tumors are linked to adjuvant treatment outcomes in uterine serous cancer |
|
