I'm trying to understand the clinical data for the TCGA melanoma (nationwidechildrens.org_clinical_patient_skcm.txt). From sources like https://cancerstaging.org/references-tools/quickreferences/Documents/MelanomaMedium.pdf, stage 0 (melanoma in situ, also graded Tis) is inherently not metastatic and that is why it is labeled stage 0.
But in the clinical data (partially copied below), samples that are labeled Stage 0 / Tis with no regional or distant metastases (N0 and M0), are also labeled as distant metastases. Also the patients are dead, presumably of their metastatic melanomas. This seems impossible. Maybe it was initially diagnosed as stage 0 and somehow became metastatic anyway? --but then you would not expect that to be the annotation of that tumor data in the clinical file. If I want to find all of the clinically low stage tumors, what would be the best way to do that, if not by using this field? Any ideas? Thank you!
bcr_patient_barcode tumor_status vital_status death_days_to primary_melanoma_known_dx primary_multiple_at_dx primary_at_dx_count breslow_thickness_at_diagnosis clark_level_at_diagnosis primary_melanoma_tumor_ulceration ajcc_tumor_pathologic_pt ajcc_nodes_pathologic_pn ajcc_metastasis_pathologic_pm ldh_level ajcc_pathologic_tumor_stage submitted_tumor_site submitted_tumor_site metastatic_tumor_site primary_melanoma_skin_type
TCGA-EE-A20C WITH TUMOR Dead 4601 YES NO [Not Available] [Not Available] I [Unknown] Tis N0 M0 [Not Available] Stage 0 Extremities Distant Metastasis Right back Non-glabrous skin
TCGA-ER-A2NE WITH TUMOR Dead 613 YES NO [Not Available] [Not Available] [Not Available] [Not Available] Tis N0 M0 [Not Available] Stage 0 Extremities Distant Metastasis Ileum (serosa) [Not Available]
TCGA-D3-A8GR WITH TUMOR Dead 3943 YES NO [Not Available] 0.01 I [Unknown] Tis N0 M0 [Not Available] Stage 0 Extremities Distant Metastasis Small Intestine [Not Available]
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rachelpachel •
I think I figured it out. Emailing with the TCGA helpdesk helped a bit. There's some helpful info on [the corresponding enrollment form][1]
And most of those fields pertain to the patient's primary diagnosis. Only the fields below actually pertain to the tumor specimen (plus a few other fields having to do with therapies that would lead to exclusion of the tumor)
submitted_tumor_dx_days_to submitted_tumor_site metastatic_tumor_site
days_to_submitted_specimen_dx tumor_tissue_site distant_metastasis_anatomic_site
CDE_ID:3430945 CDE_ID:3427536 CDE_ID:2961431
So, my interpretation of patient TCGA-ER-A2NE (from my original question), is: The patient originally presented in 2007 with a melanoma in situ with no metastasis, and that original melanoma was located on the extremities. 567 days later the patient had a metastasis in the ileum. This metastasis in the ileum is the sample that was submitted to TCGA. The patient died of the metastasis 613 days after diagnosis.
Therefore, what I was hoping to do (use the clinical data to find the lower grade/stage tumors) is only somewhat possible. Instead I used the TCGA barcodes to identify primary & metastasis. Hope this helps someone.
[1] http://www.nationwidechildrens.org/melanoma-enrollment-form
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rachelpachel •
Nice sleuthing, Rachel. And welcome to Biostars!
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Cyriac Kandoth
heh thanks Cyriac! Nice to see you on the webs. Hope we can get a drink sometime after I finish this pesky defense :)
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rachelpachel •
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