Updated manuscript: How are pathology_free_text_diagnosis and pathology_diagnosis` being used?

[cansavvy]

What section of the manuscript should be updated?

The clinical-data-harmonization section: https://github.com/AlexsLemonade/OpenPBTA-manuscript/blob/master/content/03.methods.md#clinical-data-harmonization

and the molecular subtyping section: https://github.com/AlexsLemonade/OpenPBTA-manuscript/blob/master/content/03.methods.md#molecular-subtyping

Proposed changes

Two things would be helpful:

• I'm suspecting that the Notes column might be the same pathology_free_text_diagnosis is this true? If yes, can that be added or explained? If it isn't, can we add an explanation about pathology_free_text_diagnosis to that table?

• In the molecular-subtyping, can we add one sentence that specifies what variable is being used for molecular subtyping? I think based on the series of issues filed in OpenPBTA-analysis, this would be pathology_diagnosis now, but those issues also mention something about searching for samples using pathology_free_text_diagnosis?

I'm a bit confused on how pathology_free_text_diagnosis should be used in analyses - or is it only for record keeping? But this may be a question for over on OpenPBTA-analysis

[jharenza]

• I'm suspecting that the Notes column might be the same pathology_free_text_diagnosis is this true? If yes, can that be added or explained? If it isn't, can we add an explanation about pathology_free_text_diagnosis to that table?

These are not the same. Notes was meant for tracking when/how we got from pathology_diagnosis to integrated_diagnosis, if there was a change. I tracked an issue here to update this to be a bit more informative, but still on the list of to-dos. Also, thanks for adding this ticket )(also on my to-dos) - YES, we do have to add pathology_free_text_diagnosis to the harmonization table, and as well, have to update logic for CNS_region, per #106. Someone at D3b will take care of those.

*In the molecular-subtyping, can we add one sentence that specifies what variable is being used for molecular subtyping? I think based on the series of issues filed in OpenPBTA-analysis, this would be pathology_diagnosis now, but those issues also mention something about searching for samples using pathology_free_text_diagnosis?
*

Sure - as background, I created this ticket to explain the new way the pbta-histologies.tsv file is being created. With V17, we could not implement all SQL rules because the subtyping is currently done as follows:

molecular subtyping module	variable being used
LGAT	short_histology
HGG	short_histology
embryonal	broad_histology
EPN	integrated_diagnosis
EWS	short_histology
MB	integrated_diagnosis

However, I hesitate adding this to the methods, since we will replace all of these with use of pathology_diagnosis and pathology_free_text_diagnosis, which I expect to happen with V18. But, I agree this should be documented somewhere -- perhaps in the data-formats.md file, which looks like it is a bit out of date re: subtyping anyway? Thoughts, @jaclyn-taroni?

Re:pathology_free_text_diagnosis and searching - we added this because during the clinical data refresh, some samples which previously had a pathology_diagnosis of a specific cancer were updated to Other, and some of those were previously subtyped (see table below). If pathology_diagnosis == Other, then we should search pathology_free_text_diagnosis to determine whether a sample fits that cohort for subtyping (most relevant to embryonal tumors).

Kids_First_Biospecimen_ID	pathology_diagnosis	pathology_free_text_diagnosis
BS_QB7YGKN1	Other	glioneuronal tumor
BS_2Z9JQDPV	Other	non- langerhans histiocytosis (jxg- cns)
BS_F5BZSF3Q	Other	inclusion cyst
BS_02W5H7K5	Other	rosai-dorfman disease
BS_FEPRNEXX	Other	ependymoblastoma
BS_MGY2V5N4	Other	neuroepithelial neoplasm
BS_F6V1Y4QS	Other	neuroepithelial neoplasm
BS_BM95DGCQ	Other	prolactinoma
BS_8WPNFT03	Other	non- langerhans histiocytosis (jxg- cns)
BS_VQEPFE1P	Other	meningioangiomatosis
BS_06XH7EVF	Other	osteoblastoma
BS_R1RMKH1B	Other	ganglioneuroma
BS_B61168DE	Other	malignant melanocytic neoplasm
BS_8D52JK1Q	Other	malignant melanocytic neoplasm
BS_JSPR854S	Other	perineuroma
BS_CXN0498B	Other	osteoblastoma
BS_5KK9P7XD	Other	meningioangiomatosis
BS_MS87PMR7	Other	rathke cleft cyst
BS_W6AC5J3C	Other	meningioangiomatosis
BS_9R82A3VT	Other	dermoid cyst
BS_Z72QAZC7	Other	dermoid cyst
BS_8Q8CAY84	Other	hamartoma
BS_QBR4WCQ2	Other	myxoid spindle cell tumor
BS_AHT9PKVE	Other	embryonal tumor, nos, congenital type
BS_3ZASRA3A	Other	epidermoid cyst
BS_1135HC0V	Other	cortical tubers
BS_BVD7PWP5	Other	choroid plexus cyst
BS_9G69F50J	Other	ossifying fibroma
BS_NDFDQBCZ	Other	myofibroblastic tumor
BS_BS5X4H0Y	Other	dermoid inclusion cyst
BS_4Z6F1HJZ	Other	myxoid spindle cell tumor
BS_HCP5C912	Other	meningioangiomatosis
BS_H83DTMT2	Other	dermoid cyst
BS_Z4S81HG1	Other	myofibroblastic tumor
BS_886M7JMG	Other	arteriovenous malformation
BS_69VS8PS1	Other	embryonal tumor with multilayer rosettes, ros (who grade iv)
BS_MCM78YPC	Other	reactive connective tissue
BS_Q807ENGY	Other	perineuroma
BS_W50WEJE7	Other	ossifying fibroma
BS_9XWJ88Q1	Other	osteoblastoma
BS_37GTVG4N	Other	embryonal tumor with multilayer rosettes, ros (who grade iv)
BS_XKXDH0YJ	Other	atypical lymphoid infiltrate
BS_Z7G68ZS2	Other	atypical lymphoid infiltrate
BS_AA164D3A	Other	dermoid cyst
BS_1T19NFJ8	Other	epilepsy, chronic rasmussen encephalitis
BS_KK0JWATQ	Other	reactive connective tissue
BS_N5VYY66W	Other	meningioangiomatosis
BS_TPX7YY57	Other	epilepsy, chronic rasmussen encephalitis
BS_N9BF56FP	Other	fibromyxoid lesion
BS_B8T7M0WV	Other	arteriovenous malformation
BS_4XPPZTGG	Other	xanthogranuloma
BS_0HW7W7SD	Other	medullooepithelioma
BS_N9SMBR24	Other	fibroma
BS_49F4RAA4	Other	rosai-dorfman disease
BS_B24PKKQB	Other	hamartoma
BS_6R7SFVV2	Other	ganglioneuroma
BS_T1QMEH1N	Other	xanthogranuloma
BS_V2MDX7HG	Other	inclusion cyst
BS_AQMKA8NC	Other	ependymoblastoma
BS_ZH1FBX50	Other	cortical tubers
BS_F9WKPDFG	Other	choroid plexus cyst
BS_DVCQ8XDZ	Other	meningioangiomatosis
BS_947CK40E	Other	dermoid cyst
BS_92MT680S	Other	fibromyxoid lesion
BS_32VQRFDS	Other	osteoblastoma
BS_QZFEB94Q	Other	fibroma
BS_7BW0YRPY	Other	embryonal tumor, nos, congenital type

[jharenza]

I am working on this today

[jharenza]

closed with #126