Discrepancies Between GEO Page and its article - Seeking Clarification

Question

[JACKY]

How should I interpret the information from the article GSE145281? On the GEO page, it mentions bladder cancer. However, the article itself specifies that the samples are from both metastatic urothelial cancer and metastatic RCC. Which is the correct classification?

Additionally, there's a discrepancy in the number of samples. The GEO page lists only 18 samples, while the article mentions 1,445 patients. Could you clarify the actual number of samples used?

Lastly, the paper indicates that the sample sites are both Peripheral blood mononuclear cells and tumors. In contrast, the GEO page only mentions peripheral blood mononuclear cells. Which source provides the accurate information?

It's not clear why the data and the numbers are not precisely summarized in the GEO page. Here is a summary of the questions I need :

1. What cancer exactly are we dealing with here?
2. What is the number of samples?
3. What is the sampling site?

Thank you!

[GenoMax]

This appears to be "renal cancer" . Summary data from 18 samples was submitted in GEO: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE145281

Raw data analyzed in this study has been submitted to the European Genome-Phenome Archive (EGA) with accession numbers EGAS00001004008, EGAS00001004229 and EGAS00001004230. Raw and processed count matrix of single cell RNAseq data has been submitted to Gene Expression Omnibus (GEO) with accession number GSE145281.

Using EntrezDirect you can get information about the samples (truncated due to space):

$ esearch -db bioproject -query "PRJNA606594" | elink -target biosample | efetch
1: Blood1
Identifiers: BioSample: SAMN14122094; GEO: GSM4317763
Organism: Homo sapiens
Attributes:
    /source name="Blood"
    /patient="donor1"
    /sex="male"
    /tissue="Blood"
Accession: SAMN14122094 ID: 14122094

2: Blood2
Identifiers: BioSample: SAMN14122093; GEO: GSM4317764
Organism: Homo sapiens
Attributes:
    /source name="Blood"
    /patient="donor2"
    /sex="female"
    /tissue="Blood"
Accession: SAMN14122093 ID: 14122093

[JACKY]

I don't fully understand your answer sir. How come you infered that this is renal cancer, although in the GEO it clearly says "bladder cancer from a Phase II trial IMvigor210" ?

And what about sampling site and number of samples ?

[GenoMax]

Bladder is part of the renal system plus one of the EGA submissions denotes these as renal cancer samples: https://ega-archive.org/search/egas00001004230

And what about sampling site and number of samples ?

That info is in the EntrezDirect search I showed you above.