Assertions Upload

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

1. Navigate to the app selector (grid icon) at the top-right of the screen and select My Knowledge Base.

2. In My Knowledge Base, under Add New Knowledge, select Add Assertions.

3. Select attached template to download the upload template.

4. Edit the template by adding values to the columns. For more information on the applicable columns and values, refer to CSV Template and Uploading Gene Descriptions . To view existing assertions as examples, refer to Existing Assertion Entries.

5. After editing, save the file in the CSV format. The maximum permitted file size is 10 MB.

6. Upload the template file. For more information, refer to Uploading the Template.

CSV Template

The template is in CSV format and contains the following columns:

Column	Description
externalid	An optional external reference ID that can be used to trace the assertion back to your system.
type	A required field that specifies the assertion type. Acceptable values are as follows. • Biological • Therapeutic • Prognostic • Diagnostic • Predictive • Gene Information
classificationName	A required field that specifies the assertion classification. Examples are as follows. For Biological: • Pathogenic • Likely Pathogenic • Uncertain Significance • Likely Benign • Benign For Therapeutic, Prognostic, Diagnostic: • Tier 1A • Tier 1B • Tier 2C • Tier 3 • Tier 4 When interpreting biomarkers in a case, the default values are the same as the examples. In the Configuration screen, you can customize and set the prioritization of these values. We recommend using the same classification here and in the Configurations screen. For moreinformation, refer to Custom Actionability Classification
classificationOrder	A required field that specifies the assertion classification. Examples are as follows. For Biological: • For Pathogenic, 1.0 • For Likely Pathogenic, 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 interpreting biomarkers in a case, the default values are the same as the examples. In the Configuration screen, you can customize and set the prioritization of these values. We recommend using the same classification here and in the Configurations screen. For moreinformation, refer to Custom Actionability Classification When multiple classifications map to the same AMP/ASCO/CAP tier, increment the tenthsvalue 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	A required field that specifies the assertion classification. 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 •or Tier 2D, violet • For Tier 3, blue • For Tier 4, green When interpreting biomarkers in a case, the default values are the same as the examples. In the Configuration screen, you can customize and set the prioritization of these values. We recommend using the same classification here and in the Configurations screen. For moreinformation, refer to Custom Actionability Classification
direction	A required field for Therapeutic and Prognostic that specifies the direction of the assertion. Acceptable values are as follows. For Therapeutic: • Responsive • Non-responsive • Contraindicated For Prognostic: • Favorable • Unfavorable
status	A required field for TMB, MSI, and GIS assertions Acceptable values are as follows. • High • Low
hrd	A required field. Acceptable values are as follows. • Undetermined • Positive • Negative When interpreting biomarkers in a case, this information is visible for BRCA1/2 variants andGIS.
geneRoles	An optional field used for the gene description assertion. Acceptable values are as follows. • Oncogene • Tumor Suppressor • Oncogene / Tumor Suppressor
summary	An optional field where an interpretation summary can be added. You can specify up to30,000. characters. This information is included in PDF reports.
notes	An optional field where interpretation notes can be added. You can specify up to 30,000characters. This information is not included in PDF reports.
diseaseName	An optional field that specifies the disease name. The system can determine the name based on the diseaseOntology and diseaseOntologyId provided.
diseaseOntology	A required field that specifies the disease ontology. We currently recommend using SNOMEDCT. The SNOMEDCT ID can be found by navigating to an existing case and searching for the disease in the Case Details or assertion form. The ID can also be found by using the International Edition browser at the SNOMED International SNOMED CT Browser website.
diseaseOntologyID	A required field that specifies the disease ontology ID.
therapy	A required field for Therapeutic that specifies the therapy. Multiple drug names can bespecified by separating them with a pipe.
biomarkerType	A required field that specifies the type of biomarker the assertion is for. • Acceptable values are as follows. • Small variant • Copy number variant • Structural variant • RNA splice variant • RNA fusion variant • Genomic analysis (ie, TMB, MSI, GIS)
variantType	A required field for Copy number variant and Structural variant. Acceptable values are as follows. 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	A required field that specifies the curation level. Acceptable values are as follows. 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	A required field that specifies the genome build. Acceptable values are as follows. • 37 • 38
chromosome	A required field for levels nucleotide and annotation overlap that specifies the chromosome. Acceptable values are as follows. • 1–22 • X • Y • MT
position	A required field for levels nucleotide and annotation overlap that specifies the VCF position. Acceptable values are within the chromosome range.
end	A required field for level annotation overlap that specifies the VCF end position. Acceptable values are within the chromosome range.
ref	A required field for level nucleotide that specifies the VCF reference allele. Acceptable values are combinations of A, T, C, G.
alt	A required field for level nucleotide that specifies the VCF alternate allele. Acceptable values are combinations of A, T, C, G.
transcriptId	A required field for the following curation levels that specifies the transcript ID. • Nucleotide • Amino acid • Codon • Exon Acceptable values are RefSeq and Ensembl transcript IDs, with or without the version.
codon	A required field for level codon that specifies the codon. Acceptable values are a three-letter hgvsp abbreviation, including prefix “p.(“ and suffix “)” and without the amino acid change, such as p.(Val600). Only missense variants aresupported.
hgvsp	A required field for level amino acid that specifies the hgvsp. Acceptable values are a three-letter hgvsp abbreviation, including prefix “p.(“ and suffix “)”, such as p.(Val600Glu).
exon	A required field for level exon that specifies the exon. The acceptable value is [exon #].
geneSymbol	A required field. If the NCBI gene ID is not provided, then the following levels specify thegene symbol: • Gene • Partial fusion • Exact fusion
ncbiGeneId	A required field. If the gene symbol is not provided, then the following levels specify the NCBIgene ID: • Gene • Partial fusion • Exact fusion
fusionGeneSymbol	A required field for level exact fusion. If the fusion NCBI gene ID is not provided, this fieldspecifies the fusion gene symbol.
fusionNcbiGeneID	A required field for level exact fusion. If the fusion gene symbol is not provided, this fieldspecifies the fusion NCBI gene ID. An optional field for level partial fusion.
fusionPosition	An optional field for levels partial fusion and exact fusion that specifies the fusiondirectionality. 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	An optional field for levels exon and gene that specifies the consequence. When a consequence is specified, the assertion only matches to a case variant that has heconsequence specified, such as EGFR exon 19 inframe deletion. Acceptable values are the following sequence ontology values: 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

Uploading the Template

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

After the content has been added to the template, it can be uploaded for processing.

1. In the Add Assertions dialog, drag and drop or select the file to upload. The maximum permitted file size is 10 MB. Any initial validation errors are displayed (for example, missing required headers, incorrect file type).

2. After the file has been uploaded, view the processing status for each file by selecting View Uploads.

3. When completed, view the number of rows processed, including rows that have issues. 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.

Uploading Gene Descriptions

Upload gene descriptions through the CSV template used to upload assertions. To upload gene descriptions, the following fields are required:

• type (for the gene description, the value must be Gene Information)

• geneRoles

• summary

• biomarkerType

• level (for the gene description, the value must be Gene)

• genomeBuild

• geneSymbol

• nbciGeneId

Existing Assertion Entries

Assertions in the knowledge base, created either by upload or within a case, can be downloaded at any time.

1. In the My Knowledge Base screen, select Download to View.