Data Dictionary

1. Discrete Copy Number Data

Field	Required?	Description
Hugo_Symbol	Required*	HUGO gene symbol (*one of Hugo_Symbol or Entrez_Gene_Id required)
Entrez_Gene_Id	Required*	Entrez Gene numeric identifier (*one of Hugo_Symbol or Entrez_Gene_Id required)
[SAMPLE_ID columns]	Required	A sample ID. This field can only contain numbers, letters, points, underscores and hyphens.
cbp_driver	Optional	Custom driver annotation: Putative_Driver, Putative_Passenger, Unknown, NA
cbp_driver_annotation	Optional	Free-text description of driver annotation (max 80 chars). *This field must be present if the cbp_driver is also present in the MAF file
cbp_driver_tiers	Optional	Driver tier label, e.g. 'Highly actionable' (max 20 chars). *This field must be present if the cbp_driver_tiers_annotation is also present in the MAF file
cbp_driver_tiers_annotation	Optional	Description of driver tier (max 80 chars). *This field must be present if the cbp_driver_tiers is also present in the MAF file

2. Continuous Copy Number Data

Field	Required?	Description
Hugo_Symbol	Required*	HUGO gene symbol (*one of Hugo_Symbol or Entrez_Gene_Id required)
Entrez_Gene_Id	Required*	Entrez Gene numeric identifier (*one of Hugo_Symbol or Entrez_Gene_Id required)
[SAMPLE_ID columns]	Required	One column per sample; continuous copy number or log2 value per gene-sample pair

3. Segmented Data (SEG)

Should follow this format. Link does not work from cBioPortal.

Field	Required?	Description
ID	Required	Sample identifier
chrom	Required	Index of the chromosome column
loc.start	Required	Index of the start position column
loc.end	Required	Index of the end position column
num.mark	Required	Index of a probe or description column
seg.mean	Required	No description provided (might be under the data tab on IGV.org )

4. Expression Data (mRNA / microRNA)

Field	Required?	Description
Hugo_Symbol	Recommended*	HUGO gene symbol (*one of Hugo_Symbol or Entrez_Gene_Id required)
Entrez_Gene_Id	Recommended*	Entrez Gene numeric identifier (preferred; reduces ambiguity)
[SAMPLE_ID columns]	Required	One column per sample; real-number expression value or NA per gene-sample pair

5. Mutation Data (MAF)

Field	Required?	Description
Hugo_Symbol	Required	A HUGO gene symbol.
Entrez_Gene_Id	Recommended	A Entrez Gene numeric identifier.
Center	Optional	The sequencing center.
NCBI_Build	Required	Genome Reference Consortium Build used by variant calling software. Must be GRCh37 or GRCh38 for human, GRCm38 for mouse.
Chromosome	Required	A chromosome number, e.g. '7'.
Start_Position	Recommended	Start position of the event. Required for Cancer Hotspots annotations.
End_Position	Recommended	End position of the event. Required for Cancer Hotspots annotations.
Strand	Optional	Strand of the mutation. Assumed to be reported for the + strand.
Variant_Classification	Required	Translational effect of variant allele, e.g. Missense_Mutation, Nonsense_Mutation, Silent, Splice_Site, Frame_Shift_Del, etc. (TCGA MAF values).
Variant_Type	Optional	Variant type, e.g. SNP, DNP, INS, DEL, etc.
Reference_Allele	Required	The plus strand reference allele at this position.
Tumor_Seq_Allele1	Optional	Primary data genotype (allele 1).
Tumor_Seq_Allele2	Required	Primary data genotype (variant allele).
dbSNP_RS	Optional	Latest dbSNP rs ID for this position.
dbSNP_Val_Status	Optional	dbSNP validation status.
Tumor_Sample_Barcode	Required	Sample ID — either a TCGA barcode (patient ID extracted automatically) or a literal SAMPLE_ID from the clinical data file.
Matched_Norm_Sample_Barcode	Optional	Sample ID for the matched normal sample.
Match_Norm_Seq_Allele1	Optional	Primary data genotype for matched normal (allele 1).
Match_Norm_Seq_Allele2	Optional	Primary data genotype for matched normal (allele 2).
Tumor_Validation_Allele1	Optional	Secondary data from orthogonal technology (tumor allele 1).
Tumor_Validation_Allele2	Optional	Secondary data from orthogonal technology (tumor allele 2).
Match_Norm_Validation_Allele1	Optional	Secondary data from orthogonal technology (normal allele 1).
Match_Norm_Validation_Allele2	Optional	Secondary data from orthogonal technology (normal allele 2).
Verification_Status	Optional	Second pass results from independent attempt using same methods. Values: Verified, Unknown, or NA.
Validation_Status	Optional	Second pass results from orthogonal technology. Values: Valid, Invalid, Untested, Inconclusive, Redacted, Unknown, or NA.
Mutation_Status	Optional	Somatic or Germline are displayed in the Mutations tab. None, LOH, and Wildtype will not be loaded. Other values displayed as text.
Sequencing_Phase	Optional	Indicates current sequencing phase.
Sequence_Source	Optional	Molecular assay type used to produce the analytes used for sequencing.
Validation_Method	Optional	The assay platforms used for the validation call.
Score	Optional	Not used by cBioPortal.
BAM_File	Optional	Not used by cBioPortal.
Sequencer	Optional	Instrument used to produce primary data.
HGVSp_Short	Required	Amino acid change in HGVS notation, e.g. p.V600E.
t_alt_count	Optional	Variant allele count (tumor).
t_ref_count	Optional	Reference allele count (tumor).
n_alt_count	Optional	Variant allele count (normal).
n_ref_count	Optional	Reference allele count (normal).
cbp_driver	Optional	Custom driver annotation: Putative_Driver, Putative_Passenger, Unknown, NA, or empty.
cbp_driver_annotation	Optional	Free-text description of the driver annotation (max 80 chars).
cbp_driver_tiers	Optional	Driver tier label, e.g. 'Highly actionable' (max 20 chars).
cbp_driver_tiers_annotation	Optional	Description of the driver tier value (max 80 chars).
ASCN.ASCN_METHOD	Optional (ASCN)	Method used to obtain allele-specific copy number data, e.g. FACETS.
ASCN.CCF_EXPECTED_COPIES	Optional (ASCN)	Cancer-cell fraction if mutation exists on major allele.
ASCN.CCF_EXPECTED_COPIES_UPPER	Optional (ASCN)	Upper error bound for cancer-cell fraction estimate.
ASCN.EXPECTED_ALT_COPIES	Optional (ASCN)	Estimated number of copies harboring the mutant allele.
ASCN.CLONAL	Optional (ASCN)	Clonal status: Clonal, Subclonal, or Indeterminate.
ASCN.TOTAL_COPY_NUMBER	Optional (ASCN)	Total copy number of the gene.
ASCN.MINOR_COPY_NUMBER	Optional (ASCN)	Copy number of the minor allele.
ASCN.ASCN_INTEGER_COPY_NUMBER	Optional (ASCN)	Absolute integer copy-number estimate.
Site2_Region	Recommended	Region type: 5_Prime_UTR, 3_Prime_UTR, Promoter, Exon, or Intron
Site2_Chromosome	Recommended	Chromosome of gene 2
Site2_Position	Recommended	Genomic position of breakpoint at gene 2
NCBI_Build	Optional	Genome reference build: GRCh37 or GRCh38
Class	Optional	Deletion, Duplication, Insertion, Inversion, or Translocation
Event_Info	Optional	Free-text description of the event, e.g. 'TMPRSS2-ERG fusion'
Annotation	Optional	Free-text description of the gene/transcript rearrangement
Site1_Ensembl_Transcript_Id	Optional	Ensembl transcript ID of gene 1 (required for SV tab visualization)
Site2_Ensembl_Transcript_Id	Optional	Ensembl transcript ID of gene 2 (required for SV tab visualization)
DNA_Support	Optional	Yes or No — fusion detected from DNA data
RNA_Support	Optional	Yes or No — fusion detected from RNA data
SV_Length	Optional	Length of the structural variant in bases
Tumor_Split_Read_Count	Optional	Number of split reads supporting the call in tumor
Tumor_Paired_End_Read_Count	Optional	Number of paired-end reads supporting the call in tumor
Comments	Optional	Any free-text comments

6. Methylation Data

Field	Required?	Description
Hugo_Symbol	Required*	HUGO gene symbol (*one of Hugo_Symbol or Entrez_Gene_Id required)
Entrez_Gene_Id	Required*	Entrez Gene numeric identifier (*one of Hugo_Symbol or Entrez_Gene_Id required)
[SAMPLE_ID columns]	Required	One column per sample; methylation beta-value per gene-sample pair

7. Protein Level Data (RPPA / Mass Spectrometry)

Two-dimensional matrix: one row per antibody, one column per sample. Values are log2 protein expression levels or Z-scores.

Field	Required?	Description
Composite.Element.REF	Required	Antibody identifier encoding gene symbol(s)/Entrez ID(s) and antibody ID, e.g. 'BRAF|B-Raf-M-NA' or 'MAPK1 MAPK3|MAPK_PT202_Y204'
[SAMPLE_ID columns]	Required	One column per sample; real-number protein level per antibody-sample pair

8. Structural Variant Data (SV)

Field	Required?	Description
Sample_Id	Required	Sample identifier as defined in the clinical sample file
SV_Status	Required	SOMATIC or GERMLINE
Site1_Hugo_Symbol	Recommended	HUGO gene symbol of gene 1 (left/3' site)
Site1_Ensembl_Transcript_Id	Optional	Ensembl transcript ID of gene 1 (required for SV tab visualization)
Site1_Entrez_Gene_Id	Recommended	Entrez Gene identifier of gene 1
Site1_Region_Number	Recommended	Region number of Site 1, e.g. exon 2
Site1_Region	Recommended	Region type: 5_Prime_UTR, 3_Prime_UTR, Promoter, Exon, or Intron
Site1_Chromosome	Recommended	Chromosome of gene 1
Site1_Contig	Optional	The contig of Site 1
Site1_Position	Recommended	Genomic position of breakpoint at gene 1
Site1_Description	Optional	Description of this event at site 2. This could be the location of the 2nd breakpoint in case of a fusion event.
Site2_Hugo_Symbol	Recommended	HUGO gene symbol of gene 2 (right/5' site)
Site2_Ensembl_Transcript_Id	Optional	Ensembl transcript ID of gene 2 (required for SV tab visualization)
Site2_Entrez_Gene_Id	Recommended	Entrez Gene identifier of gene 2
Site2_Region_Number	Recommended	Region number of Site 2
Site2_Region	Recommended	Region type: 5_Prime_UTR, 3_Prime_UTR, Promoter, Exon, or Intron
Site2_Chromosome	Recommended	Chromosome of gene 2
Site2_Contig	Optional	The contig of Site 2
Site2_Position	Recommended	Genomic position of breakpoint at gene 2
Site2_Description	Optional	Description of this event at site 1. This could be the location of the 1st breakpoint in case of a fusion event.
Site2_Effect_On_Frame	Optional	The effect of frame reading in gene 2. Frame_shift or InFrame (free text)
NCBI_Build	Optional	Genome reference build: GRCh37 or GRCh38
Class	Optional	Deletion, Duplication, Insertion, Inversion, or Translocation
Tumor_Split_Read_Count	Optional	Number of split reads supporting the call in tumor
Tumor_Paired_End_Read_Count	Optional	Number of paired-end reads supporting the call in tumor
Event_Info	Optional	Free-text description of the event, e.g. 'TMPRSS2-ERG fusion'
Connection_Type	Optional	Which direction the connection is made
Breakpoint_Type	Optional	PRECISE or IMPRECISE which explain the resolution. Fill in PRECISE if the breakpoint resolution is known down to the base pair
Annotation	Optional	Free-text description of the gene/transcript rearrangement
DNA_Support	Optional	Yes or No — fusion detected from DNA data
RNA_Support	Optional	Yes or No — fusion detected from RNA data
SV_Length	Optional	Length of the structural variant in bases
Normal_Read_Count	Optional	The total number of reads of the normal tissue.
Tumor_Read_Count	Optional	The total number of reads of the tumor tissue.
Normal_Variant_Count	Optional	The number of reads of the normal tissue that have the variant/allele.
Tumor_Variant_Count	Optional	The number of reads of the tumor tissue that have the variant/allele.
Normal_Paired_End_Read_Count	Optional	The number of paired-end reads of the normal tissue that support the call.
Normal_Split_Read_Count	Optional	The number of split reads of the normal tissue that support the call.
Comments	Optional	Any free-text comments

9. Fusion Data (DEPRECATED — use Structural Variant Data instead)

This format is deprecated. New studies should use the Structural Variant (SV) format above.

Field	Required?	Description
Hugo_Symbol	Required	HUGO gene symbol
Entrez_Gene_Id	Required	Entrez Gene numeric identifier
Center	Required	Sequencing center
Tumor_Sample_Barcode	Required	Sample ID
Fusion	Required	Description of the fusion, e.g. 'TMPRSS2-ERG fusion'
DNA_support	Required	Fusion detected from DNA: yes or no
RNA_support	Required	Fusion detected from RNA: yes or no
Method	Required	Algorithm/tool used for fusion detection
Frame	Required	in-frame or frameshift
Fusion_Status	Optional	Assesment of mutation type: SOMATIC, GERMLINE, UNKNOWN, or empty.

10. Timeline Data

Field	Required?	Description
PATIENT_ID	Required	Patient identifier from the dataset
START_DATE	Required	Days from date of diagnosis (day 0) to event start
STOP_DATE	Required	Days from date of diagnosis to event end (blank if point-in-time event)
EVENT_TYPE	Required	Category of event: TREATMENT, LAB_TEST, IMAGING, STATUS, SPECIMEN, or any custom type
TREATMENT_TYPE	Optional	For TREATMENT events: Medical Therapy or Radiation Therapy
SUBTYPE	Optional	For TREATMENT events: Chemotherapy, Hormone Therapy, Targeted Therapy, etc.
AGENT	Optional	For TREATMENT events: agent name with number of cycles if applicable
TEST	Optional	For LAB_TEST events: type of test performed
RESULT	Optional	For LAB_TEST events: corresponding test result value
DIAGNOSTIC_TYPE	Optional	For IMAGING events: diagnostic tool used (MRI, CT scan, etc.)
STATUS	Optional	For STATUS events: best response or disease progression stage
SPECIMEN_SITE	Optional	For SPECIMEN events: site from which specimen was collected
SPECIMEN_TYPE	Optional	For SPECIMEN events: tissue or blood
STYLE_SHAPE	Optional	Render shape for this event: circle, square, triangle, diamond, star, or camera
STYLE_COLOR	Optional	Hexadecimal color value for rendering this event, e.g. #ffffff
Agent_Class	Optional	Suggested for TREATMENT events to classify agents into groups
Diagnostic_Type_Detailed	Optional	Suggested for IMAGING events as a detailed description
Source	Optional	Appears as a suggested column for IMAGING, STATUS, and SPECIMEN events

11. GISTIC 2.0 Data

Field	Required?	Description
chromosome	Required	Chromosome number (without 'chr' prefix)
peak_start	Required	Start coordinate of the region of maximal amplification or deletion
peak_end	Required	End coordinate of the region of maximal amplification or deletion
genes_in_region	Required	Comma-separated list of HUGO gene symbols in the wide peak
amp	Required	1 for amplification, 0 for deletion
cytoband	Required	Cytogenetic band specification including chromosome (Giemsa stain)
q_value	Required	Q-value (FDR-corrected p-value) of the peak region

12. MutSig Data

Field	Required?	Description
rank	Required	Gene rank by significance
gene	Required	HUGO gene symbol
N (or Nnon)	Required	Number of bases covered
n (or nnon)	Required	Number of mutations observed
p	Required	P-value: probability mutations are due to background processes
q	Required	Q-value: p-value corrected for multiple testing

13. Gene Panel Data (Gene Panel Matrix)

Field	Required?	Description
SAMPLE_ID	Required	Sample identifier
[stable_id columns]	Required	One column per genetic profile (e.g. 'mutations', 'gistic'); value is gene panel stable_id or NA if not profiled

14. Gene Set Data (GSVA Scores and P-values)

Field	Required?	Description
geneset_id	Required	Gene set name (uppercase); must match across score and p-value files
[SAMPLE_ID columns]	Required	Score file: GSVA score between -1.0 and 1.0, or NA. P-value file: p-value for the score

15. Generic Assay Data (incl. Arm-Level CNA, Mutational Signatures)

Field	Required?	Description
entity_stable_id	Required	Stable identifier for the assay entity (e.g. '1p', '1q', 'SBS1' for mutational signatures)
Name	Required	A column from generic_entity_meta_properties (using the property name as the column header)
Description	Required	Another generic_entity_meta_properties column
URL	Required	Another generic_entity_meta_properties column
[SAMPLE_ID columns]	Required	One column per sample; numeric value per entity-sample pair