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
Navigate to the app selector (grid icon) in the top-right of the screen.
Select My Knowledge Base.
In My Knowledge Base screen, select Add Assertions in the top-right.
Select attached template to download the upload CSV template.
Edit the template by adding values to the columns. After editing, save the file.
Upload the template file. The maximum upload file size is 10 MB.
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.
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
Biological
type = Biological
classificationName
classificationOrder
classificationBackgroundColor
summary
diseaseName
diseaseOntology
diseaseOntologyId
Diagnostic
type = Diagnostic
classificationName
classificationOrder
classificationBackgroundColor
summary
diseaseName
diseaseOntology
diseaseOntologyId
Prognostic
type = Prognostic
classificationName
classificationOrder
classificationBackgroundColor
summary
diseaseName
diseaseOntology
diseaseOntologyId
direction
Therapeutic
type = Therapeutic
classificationName
classificationOrder
classificationBackgroundColor
summary
diseaseName
diseaseOntology
diseaseOntologyId
direction
Gene Description
Required Biomarker Columns
Depending on the type of biomarker the assertion is about, only certain columns are required.
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
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
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