Question: Consistency of clinical data from TCGA (melanoma)
3
gravatar for rachel.melamed
5.8 years ago by
United States
rachel.melamed50 wrote:

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]
tcga • 3.3k views
ADD COMMENTlink modified 5.8 years ago • written 5.8 years ago by rachel.melamed50
2
gravatar for rachel.melamed
5.8 years ago by
United States
rachel.melamed50 wrote:

I think I figured it out.  Emailing with the TCGA helpdesk helped a bit.  There's some helpful info on the corresponding enrollment form:  http://www.nationwidechildrens.org/melanoma-enrollment-form  

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.

ADD COMMENTlink written 5.8 years ago by rachel.melamed50

Nice sleuthing, Rachel. And welcome to Biostars!

ADD REPLYlink written 5.8 years ago by Cyriac Kandoth5.5k

heh thanks Cyriac!  Nice to see you on the webs. Hope we can get a drink sometime after I finish this pesky defense :)

ADD REPLYlink written 5.8 years ago by rachel.melamed50
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