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.

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

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

  • type = Gene Information

  • geneRoles

  • summary

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

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