Tumor Sample Information Profile

This profile inlcudes 44 data elements to capture anatomic, sample, and testing information for each tumor sample considered. The “Specimen” sub-profile (not shown here) organize some of these elements that characterize the specimen collected for the genomic analysis.

Data Element	Data Type	Description	Terminology	Required
surg_path_id	String	The ID number from the surgical pathology report	N/A	Required
date_specimen_collected	Date	Date of profile specimen collected	N/A	Required
site_specimen	CodeableConcept	The anatomical collection site	SNOMED CT	Required
spec_type	CodeableConcept	The kind of material that forms the specimen	Code Set	Required
nci_code_sample	codeableConcept	NCI code for the specimen	NCIt	Required if known
spec_laterality	CodeableConcept	Body side of the collection site, if needed to distinguish from a similar location on the other side of the body.	SNOMED CT	Required
immunostain	CodeableConcept	IHC marker tested	Code Set	Required
er_clone	String	The antibody clone used for staining	N/A	Required if known
er_interpretation	CodeableConcept	The IHC interpretation	Code Set	Required if known
er_ihc_score	CodeableConcept	The IHC score	Code Set	Required if known
er_ihc_label	Percentage	The IHC result	N/A	Required if known
pr_clone	String	The antibody clone used for staining	N/A	Required if known
pr_interpretation	CodeableConcept	The IHC interpretation	Code Set	Required if known
pr_ihc_score	CodeableConcept	The IHC score	Code Set	Required if known
pr_ihc_label	Percentage	The IHC result	N/A	Required if known
her_clone	String	The antibody clone used for staining	N/A	Required if known
her_interpretation	CodeableConcept	The IHC interpretation	Code Set	Required if known
her_ihc_score	CodeableConcept	The IHC score	Code Set	Required if known
her_ihc_label	Percentage	The IHC result	N/A	Required if known
ar_clone	String	The antibody clone used for staining	N/A	Required if known
ar_interpretation	CodeableConcept	The IHC interpretation	Code Set	Required if known
ar_ihc_score	CodeableConcept	The IHC score	Code Set	Required if known
ar_ihc_label	Percentage	The IHC result	N/A	Required if known
pdl1_clone	String	The antibody clone used for staining	N/A	Required if known
pdl1_cps	Percentage	PDL1 CPS	N/A	Required
pdl1_ic_label	Percentage	PDL1 IC	N/A	Required
pdl1_tps	String	PDL1 TPS	N/A	Required
pdl1_ics	Percentage	PDL1 ICS	N/A	Required
her2_fish	String	HER2 FISH performed	N/A	Required
her2_fish_ratio	Decimal	HER2 FISH ratio	N/A	Required
her2_fish_interpretation	CodeableConcept	HER2 FISH interpretation	Code Set	Required
mmr_proteins	CodeableConcept	Mismatch repair proteins as assessed by immunohistochemistry	Code Set	Required
mmr_result	CodeableConcept	Mismatch repair protein assessment	Code Set	Required
mmr_protein	CodeableConcept	Impaired mismatch repair protein	Code Set	Required
fish_binary	Boolean	FISH was performed or not performed	N/A	Required
fish_assay	CodeableConcept	FISH assay	Code Set	Required
fish_result	Decimal	Gene to control ratio	N/A	Required
fish_interpretation	CodeableConcept	FISH interpretation	Code Set	Required
tumor_purity	String	The proportion of cancer cells in the tumor tissue	N/A	Required
msi_modality	CodeableConcept	How was MSI measured for this sequenced sample (choose all that apply)?	Code Set	Required
sample_reviewed_mtb	Boolean	Tumor Sample Reviewed at MTB	N/A	Required
date_mtb_disc	Date	Date of review	N/A	Required
date_cur_tumor_sample	Date	Date of curation	N/A	Required if known
cur_by_tumor_sample	String	The name of the curator who modified the instrument	N/A	Required if known

Notes

1. This profile is repeatable and more than one records can be expected per patient
2. The “Code Set” is a custom set of codes defined by the JHU Team