Upload Assertions

Previous interpretations can be uploaded to My Knowledge Base at any time (e.g., during onboarding) so you can immediately start prioritizing variants and reporting based on information from your lab.

Upload Assertions

1. Navigate to the app selector (grid icon) in the top-right of the screen.

2. Select My Knowledge Base.

3. In My Knowledge Base screen, select Add Assertions in the top-right.

4. Select attached template to download the upload CSV template.

5. Edit the template by adding values to the columns. After editing, save the file.

6. Upload the template file. The maximum upload file size is 10 MB.

7. The file will begin processing. To view the processing status, select View Past Uploads icon in the top-right of the My Knowledge Base screen.

8. If a file has issues, download the file and view the issues in a new error column provided in the download. Issues can be resolved in the file and re-uploaded.

If using Excel, make sure that no auto-formatting has occurred.

Editing the CSV Template

Depending on the type of assertion you want to upload, only certain columns are required.

Required Assertion Columns

Assertion Type	Required Columns
Biological	type = Biological classificationName classificationOrder classificationBackgroundColor summary diseaseName diseaseOntology diseaseOntologyId biomarker columns
Diagnostic	type = Diagnostic classificationName classificationOrder classificationBackgroundColor summary diseaseName diseaseOntology diseaseOntologyId biomarker columns
Prognostic	type = Prognostic classificationName classificationOrder classificationBackgroundColor summary diseaseName diseaseOntology diseaseOntologyId direction biomarker columns
Therapeutic	type = Therapeutic classificationName classificationOrder classificationBackgroundColor summary diseaseName diseaseOntology diseaseOntologyId direction biomarker columns
Gene Description	type = Gene Information geneRoles summary biomarker columns (use Small Variant, Gene Level below)

Required Biomarker Columns

Depending on the type of biomarker the assertion is about, only certain columns are required.

Biomarker Type	Level	Example	Required Columns
Small Variant	Nucleotide	11:108115594 C > T	genomeBuild chromosome position ref alt geneSymbol
	Amino Acid	BRAF p.(Val600Glu)	genomeBuild transcriptId hgvsp geneSymbol
	Codon	BRAF p.(Val600)	genomeBuild transcriptId codon geneSymbol
	Exon	EGFR exon 19 deletion	genomeBuild transcriptId exon geneSymbol consequences (recommended)
	Gene	ASXL1 oncogenic variant	genomeBuild geneSymbol consequences (recommended)
Copy Number Variant	Annotation Overlap	17:37844990-37884569 gain	variantType genomeBuild chromosome position end consequences (recommended)
	Gene	TP53 copy number loss	variantType genomeBuild geneSymbol consequences (recommended)
Structural Variant	Annotation Overlap	17:37844990-37884569 deletion	variantType genomeBuild chromosome position end consequences (recommended)
	Partial fusion	ALK fusion	genomeBuild geneSymbol
	Exact fusion	EML4::ALK fusion	genomeBuild geneSymbol fusionGeneSymbol fusionPosition
RNA Splice Variant	Exon	MET exon 14 skipping	genomeBuild transcriptId exon geneSymbol consequences (recommended)
RNA Fusion Variant	Partial Fusion	ALK fusion	genomeBuild geneSymbol
	Exact Fusion	EML4::ALK fusion	genomeBuild geneSymbol fusionGeneSymbol fusionPosition
Genomic Analysis	TMB	TMB high	status
	MSI	MSI high	status
	GIS	GIS high	status

Acceptable Column Values

Column	Acceptable Values
externalid	A free text value that can be used to trace the assertion back to the originating system.
type	• Biological • Therapeutic • Prognostic • Diagnostic • Gene Information
classificationName	We recommend using the same classifications specified in the Configuration screen. Examples are as follows: For Biological: • Oncogenic • Likely Oncogenic • Uncertain Significance • Likely Benign • Benign For Therapeutic, Prognostic, Diagnostic: • Tier 1A • Tier 1B • Tier 2C • Tier 2D • Tier 3 • Tier 4
classificationOrder	We recommend using the same classifications specified in the Configuration screen. Examples are as follows: For Biological: • For Oncogenic, 1.0 • For Likely Oncogenic, 2.0 • For Uncertain Significance, 3.0 • For Likely Benign, 4.0 • For Benign, 5.0 For Therapeutic, Prognostic, Diagnostic: • For Tier 1A, 1.0 • For Tier 1B, 2.0 • For Tier 2C, 3.0 • For Tier 2D, 4.0 • For Tier 3, 5.0 • For Tier 4, 6.0 When multiple classifications map to the same AMP/ASCO/CAP tier, increment the tenths value. For example, if Level 1 and Level 2 both map to Tier 1A, the classificationOrder is as follows: • Level 1, 1.0 • Level 2, 1.1
classificationBackgroundColor	We recommend using the same classification specified in the Configuration screen. Examples are as follows: For Biological: • For Pathogenic, red • For Likely Pathogenic, pink • For Uncertain Significance, yellow • For Likely Benign, light green • For Benign, green For Therapeutic, Prognostic, Diagnostic: • For Tier 1A, red • For Tier 1B, red • For Tier 2C, violet • For Tier 2D, violet • For Tier 3, blue • For Tier 4, green
direction	For Therapeutic: • Responsive • Non-responsive • Contraindicated For Prognostic: • Favorable • Unfavorable
status	For TMB: • High • Low For MSI: • High • Stable For GIS: • High • Low
hrd	• Undetermined • Positive • Negative When interpreting biomarkers in a case, this information is visible for BRCA1/2 variants and GIS.
geneRoles	• Oncogene • Tumor Suppressor • Oncogene / Tumor Suppressor
summary	You can specify up to 30,000 characters. This information is included in PDF reports.
notes	You can specify up to 30,000 characters. This information is not included in PDF reports.
diseaseName	This can be found by searching for the disease using SNOMED International SNOMED CT Browser website.
diseaseOntology	A required field that specifies the disease ontology. We currently recommend using SNOMEDCT.
diseaseOntologyID	This can be found by searching for the disease using SNOMED International SNOMED CT Browser website.
therapy	Drug name. Multiple drug names can be specified by separating them with a pipe |.
biomarkerType	• Small variant • Copy number variant • Structural variant • RNA splice variant • RNA fusion variant • Genomic analysis (i.e., TMB, MSI, GIS)
variantType	For Copy Number Variant: • Copy number variation • Copy number loss • Copy number gain • Copy number neutral For Structural Variant: • Tandem duplication • Insertion • Deletion • Inversion • Translocation
level	For Small variants: • Nucleotide • Amino Acid • Codon • Exon • Gene For Copy number variants: • Annotation overlap • Gene For Structural variants: • Annotation overlap, if variant type is not Translocation • Partial fusion • Exact fusion For RNA splice variants: • Annotation overlap • Exon For RNA fusion variants: • Partial fusion • Exact fusion For Genomic analysis: • TMB • MSI • GIS
genomeBuild	• 37 • 38
chromosome	• 1–22 • X • Y • MT
position	The VCF position. Acceptable values are within the chromosome range.
end	The VCF position. Acceptable values are within the chromosome range.
ref	The VCF reference allele. Acceptable values are combinations of A, T, C, G.
alt	The VCF alternate allele. Acceptable values are combinations of A, T, C, G.
transcriptId	Acceptable values are RefSeq and Ensembl transcript IDs, with or without the version.
codon	Acceptable values are a three-letter hgvsp abbreviation, including prefix “p.(“ and suffix “)” and without the amino acid change, such as p.(Val600).
hgvs	Acceptable values are a three-letter hgvsp abbreviation, including prefix “p.(“ and suffix “)”, such as p.(Val600Glu).
exon	Exon #
geneSymbol	NCBI gene symbol (e.g., BRAF)
ncbiGeneId	NCBI gene ID (e.g., 673)
fusionGeneSymbol	Fusion NCBI gene symbol (e.g., ALK)
fusionNcbiGeneID	Fusion NCBI gene ID (e.g., 238)
fusionPosition	Acceptable values are 0 and 1. • Without a value, the fusion directionality is unspecified, such as EML4/ALK. • If 0 is provided, the fusion is at position 0, such as [fusion gene]-[gene]. • If 1 is provided, the fusion is at position 1, such as [gene]-[fusion gene].
consequence	When a consequence is specified, the assertion only matches to a case variant that has the consequence specified, such as EGFR exon 19 inframe deletion. For small variant, exon level: • 3_prime_UTR_variant • 5_prime_UTR_variant • coding_sequence_variant • downstream_gene_variant • frameshift_variant • inframe_deletion • inframe_insertion • intron_variant • mature_miRNA_variant • missense_variant • NMD_transcript_variant • non-coding_transcript_exon_variant • non-coding_transcript_variant • protein_altering_variant • splice_acceptor_variant • splice_donor_variant • splice_region_variant • stop_retained_variant • synonymous_variant • upstream_gene_variant For small variant, gene level: • start_lost • stop_gained • stop_lost • incomplete_terminal_codon_variant • feature_elongation • feature_truncation • splice_donor_variant • splice_acceptor_varian • splice_region_variant • frameshift_variant • inframe_deletion • inframe_insertion • missense_variant • protein_altering_variant • coding_sequence_variant • upstream_gene_variant • downstream_gene_variant • intron_variant • 5_prime_UTR_variant • 3_prime_UTR_variant • non-coding_transcript_exon_variant • non-coding_transcript_variant • synonymous_variant • start_retained_variant • stop_retained_variant • mature_miRNA_variant • NMD_transcript_variant • regulatory_region_ablation • regulatory_region_amplification • regulatory_region_variation For copy number variant, gene level: • copy_number_decrease • copy_number_increase • copy_number_change For RNA splice variant, exon level: • exon_loss_variant