Add information about diagnosis changes to histologies file

[jharenza]

What data file(s) does this issue pertain to?

pbta-histologies.tsv

What release are you using?

V15

Put your question or report your issue here.

@adamresnick requests us add information about how the integrated_diagnosis was obtained. This is generally in the Notes column when it was a change, however, some other aspects are not captured.

Requested info:

1. Whether this was changed due to molecular lesion findings
2. Whether this was changed due to a QC issue (entails going back to pathology reports to see if there was an input database error)
3. Whether it was changed to conform to WHO 2016 Classification nomenclature.

The first two scenarios only apply to changes in diagnosis, while 3 may be applicable to everything, and all of those changes will be at least a 1, but sometimes could be a 2. See table below I sent to the pathology dept at CHOP for changes we have thus far.

Kids_First_Participant_ID	Kids_First_Biospecimen_ID	sample_id	pathology_diagnosis	integrated_diagnosis	molecular_subtype	Notes from Path inspection	Action	Therapy
PT_00G007DM	BS_K07KNTFY	7316-272	Medulloblastoma	Embryonal tumor with multilayer rosettes	ETMR, C19MC-altered	Path report had "medulloblastoma" handwritten, but final dx ETMR with multilayer rosettes
PT_00G007DM	BS_QWNBZ9RJ	7316-272	Medulloblastoma	Embryonal tumor with multilayer rosettes	ETMR, C19MC-altered	Path report had "medulloblastoma" handwritten, but final dx ETMR with multilayer rosettes
PT_01MZ62KG	BS_P39SQPTS	7316-447	Pineoblastoma	Embryonal tumor with multilayer rosettes	ETMR, C19MC-altered	Path report PNET/pineoblastoma; "there are scattered true rosettes (Flexner-Wintersteiner)"
PT_01MZ62KG	BS_TE8QFF7T	7316-447	Pineoblastoma	Embryonal tumor with multilayer rosettes	ETMR, C19MC-altered	Path report PNET/pineoblastoma; "there are scattered true rosettes (Flexner-Wintersteiner)"
PT_5BWZA0NT	BS_BFDEZK1C	7316-1102	Supratentorial or Spinal Cord PNET	Diffuse midline glioma	DMG, H3 K28	No path report available
PT_5BWZA0NT	BS_MB7WN0ZB	7316-1102	Supratentorial or Spinal Cord PNET	Diffuse midline glioma	DMG, H3 K28	No path report available
PT_6Q0NPVP3	BS_5JM573JC	7316-2255	Ganglioglioma	Diffuse midline glioma	DMG, H3 K28	Path report ganglioglioma with extensive chondroid metaplasia
PT_6Q0NPVP3	BS_E5H6CFYT	7316-2255	Ganglioglioma	Diffuse midline glioma	DMG, H3 K28	Path report ganglioglioma with extensive chondroid metaplasia
PT_7E3V3JFX	BS_G16NM5WJ	7316-506	Ependymoma	Diffuse midline glioma	DMG, H3 K28	Path report posterior fossa ependymoma
PT_7E3V3JFX	BS_J8VX4D17	7316-506	Ependymoma	Diffuse midline glioma	DMG, H3 K28	Path report posterior fossa ependymoma
PT_80NVYCBS	BS_KSKZ9J7J	7316-765	Ependymoma	CNS Embryonal Tumor	CNS HGNET-MN1	Path report anaplastic ependymoma
PT_9BZETM0M	BS_5P1TN10Z	7316-158	Supratentorial or Spinal Cord PNET	High-grade glioma	HGG, H3 G35	Path report PNET
PT_9BZETM0M	BS_STNH7YSX	7316-158	Supratentorial or Spinal Cord PNET	High-grade glioma	HGG, H3 G35	Path report PNET
PT_9BZETM0M	BS_TV5B86ZD	7316-158	Supratentorial or Spinal Cord PNET	High-grade glioma	HGG, H3 G35	Path report PNET
PT_T8V9ES93	BS_H1XPVS9A	7316-1106	High-grade glioma/astrocytoma (WHO grade III/IV)	High-grade glioma - should be LGG?	BRAF V600E	No path report available
PT_T8V9ES93	BS_J4E9SW51	7316-1106	High-grade glioma/astrocytoma (WHO grade III/IV)	High-grade glioma - should be LGG?	BRAF V600E	No path report available
PT_X648RVMK	BS_N6N147BY	7316-238	High-grade glioma/astrocytoma (WHO grade III/IV)	Embryonal tumor with multilayer rosettes	ETMR, C19MC-altered	Path report handwritten "high grade glioma"; final dx infiltrating glioneuronal neoplasm
PT_X71D7G5S	BS_C6ZZ3FY5	7316-1105	Supratentorial or Spinal Cord PNET	High-grade glioma	HGG, H3 G35	No path report available

cc @baileyckelly @chris-s-friedman @yuankunzhu @allisonheath

[jharenza]

closing this, as we do update via subtyping modules