Genomics Profile

This profile inlcudes 37 data elements to capture all information for the gene and variant as retrieved from the genomic report and processed and annotated by the bioinformatics pipelines. The “Cytogenetic Location” sub-profile (not shown here) groups the elements for the cytogenetic location of the variant detected.

Data Element	Data Type	Description	Terminology	Required
surg_path_id_genomic	String	The ID number from the surgical pathology report	N/A	Required
tumor_prof_case_id_genomic	String	The tumor profiling case ID	N/A	Required
gene_name_hgnc	CodeableConcept	The gene name	HGNC	Required
gene_id_hgnc_id	CodeableConcept	The gene id	HGNC	Required if known
mutation_type	CodeableConcept	Is the mutation reported as a sequence or structural alteration (amplification, deletion or fusion/rearrangement)?	Code Set	Required
structural_type	CodeableConcept	Type of structural mutation	Code Set	Required
five_prime_partner	String	5’ fusion partner	N/A	Required
three_prime_partner	String	3’ fusion partner	N/A	Required
fusion_breakpoint	String	Exact breakpoint or any information from NGS report	N/A	Required
genome_assembly	CodeableConcept	The genome assembly	HGNC	Required if known
cytogen_loc	String	The full cytogenetic location	N/A	Required if known
cytogen_loc_chromosome	CodeableConcept	The cytogenetic location (chromosome)	Code Set	Required
cytogen_loc_start_pos	Integer	The cytogenetic location (start position)	N/A	Required
cytogen_loc_end_pos	Integer	The cytogenetic (end position)	N/A	Required
reference_allele	CodeableConcept	Reference Allele (A, T, C, G)	Code Set	Required
altered_allele	CodeableConcept	Altered Allele (A, T, C, G)	Code Set	Required
refseq_id	CodeableConcept	Reference sequence ID by NCBI	NCBI RefSeq	Required if known
ensembl_id	CodeableConcept	The Ensembl ID	Ensembl	Required
mutation_class	CodeableConcept	The mutation classification based on the provided codes	Code Set	Required
nucleotide_change_hgvs	CodeableConcept	The symbolic representation of a genetic structural variant reported using HGVS nomenclature (gHGVS)	HGVS	Required
cosmic	CodeableConcept	The variation ID assigned by Cosmic	COSMIC	Required
cdna_change_hgvs	String	The change in the coding DNA	N/A	Required
amino_acid_change_hgvs	CodeableConcept	The symbolic representation of an amino acid variant reported using HGVS nomenclature (pHGVS)	HGVS	Required
dbsnp	CodeableConcept	The variation ID assigned by DBSNP	NCBI dbSNP	Required
clinvar	CodeableConcept	The variation ID assigned by ClinVar	NCBI ClinVar	Required
allelic_state	CodeableConcept	The classification of allelic state using one of the five provided codes	LOINC	Required
mutation_vaf	Percentage	The allele frequency represents the incidence of a gene variant in a population	N/A	Required
cn_fold	Integer	The genomic trait involving the number of copies of a particular gene present in the genome of an individual	N/A	Required
variant_origin	CodeableConcept	The genomic class of the specimen being analyzed, for example, germline	Code Set	Required
genomics_germline_disc	Boolean	Record whether the MTB discussed the potential germline finding	N/A	Required if known
genomics_clonal_heme_disc	Boolean	Record whether the MTB discussed the potential germline finding	N/A	Required if known
variant_clin_significance	CodeableConcept	The variant clinical significance depending on pathogenicity	Code Set	Required
genomics_mtb_recs	CodeableConcept	MTB’s recommendation based on the genomic findings	Code Set	Required
genomics_report_recs	CodeableConcept	The recommendation listed on NGS report	Code Set	Required
vus	Boolean	The mutation is listed as a VUS in the NGS report	N/A	Required
date_cur_genomics	Date	Date of curation	N/A	Required
cur_by_genomics	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