Genome Nexus Tools

Configuration File: genome_nexus_tools.json Tool Type: Local Tools Count: 4

This page contains all tools defined in the genome_nexus_tools.json configuration file.

Available Tools

GenomeNexus_annotate_mutation (Type: GenomeNexusTool)

Annotate a cancer mutation using Genome Nexus (MSK) by specifying chromosome, start, end, referen…

GenomeNexus_annotate_mutation tool specification

Tool Information:

  • Name: GenomeNexus_annotate_mutation

  • Type: GenomeNexusTool

  • Description: Annotate a cancer mutation using Genome Nexus (MSK) by specifying chromosome, start, end, reference allele, and variant allele separately. This is an alternative to the HGVS-based annotation for when you have genomic coordinates directly (GRCh37/hg19). Returns the same comprehensive annotation as GenomeNexus_annotate_variant including VEP consequences, SIFT, PolyPhen, AlphaMissense scores, cancer hotspots, and mutation assessor. Example: chr=7, start=140453136, end=140453136, ref=A, alt=T for BRAF V600E.

Parameters:

  • chromosome (string) (required) Chromosome (without ‘chr’ prefix). Examples: ‘7’, ‘17’, ‘12’, ‘X’.

  • start (integer) (required) Start position (GRCh37/hg19, 1-based).

  • end (integer) (required) End position (GRCh37/hg19, 1-based). Same as start for SNVs.

  • reference_allele (string) (required) Reference allele. Example: ‘A’.

  • variant_allele (string) (required) Variant (alternate) allele. Example: ‘T’.

Example Usage:

query = {
    "name": "GenomeNexus_annotate_mutation",
    "arguments": {
        "chromosome": "example_value",
        "start": 10,
        "end": 10,
        "reference_allele": "example_value",
        "variant_allele": "example_value"
    }
}
result = tu.run(query)

GenomeNexus_annotate_variant (Type: GenomeNexusTool)

Annotate a genomic variant using Genome Nexus (Memorial Sloan Kettering), which aggregates varian…

GenomeNexus_annotate_variant tool specification

Tool Information:

  • Name: GenomeNexus_annotate_variant

  • Type: GenomeNexusTool

  • Description: Annotate a genomic variant using Genome Nexus (Memorial Sloan Kettering), which aggregates variant annotations from multiple sources including VEP, SIFT, PolyPhen-2, AlphaMissense, cancer hotspots, and mutation assessor. Input is a GRCh37/hg19 HGVS genomic notation (e.g., ‘7:g.140453136A>T’ for BRAF V600E, ‘17:g.7577120C>T’ for TP53 R273H). Returns the most severe consequence, transcript consequences with pathogenicity scores (SIFT, PolyPhen, AlphaMissense), cancer hotspot information, and annotation summary with HGVS protein notation. This is the primary variant annotation tool for cancer genomics. Note: coordinates must be in GRCh37/hg19 assembly.

Parameters:

  • hgvsg (string) (required) Genomic variant in HGVS notation using GRCh37/hg19 coordinates. Format: ‘chr:g.posRef>Alt’. Examples: ‘7:g.140453136A>T’ (BRAF V600E), ‘17:g.7577120C>T’ (TP53 R273H), ‘12:g.25398284C>T’ (KRAS G12D).

Example Usage:

query = {
    "name": "GenomeNexus_annotate_variant",
    "arguments": {
        "hgvsg": "example_value"
    }
}
result = tu.run(query)

GenomeNexus_get_cancer_hotspots (Type: GenomeNexusTool)

Get cancer mutation hotspot annotations from Genome Nexus (MSK) for a specific genomic variant. C…

GenomeNexus_get_cancer_hotspots tool specification

Tool Information:

  • Name: GenomeNexus_get_cancer_hotspots

  • Type: GenomeNexusTool

  • Description: Get cancer mutation hotspot annotations from Genome Nexus (MSK) for a specific genomic variant. Cancer hotspots are recurrently mutated residues in cancer, curated by the Chang et al. study. Returns hotspot residue, tumor count, hotspot type (single residue or 3D cluster), and the gene symbol. Use this to check if a variant falls in a known cancer hotspot. Input is a GRCh37/hg19 HGVS genomic variant. Example: ‘7:g.140453136A>T’ (BRAF V600E) returns V600 hotspot with 897 tumors.

Parameters:

  • hgvsg (string) (required) Genomic variant in HGVS notation using GRCh37/hg19 coordinates. Format: ‘chr:g.posRef>Alt’. Examples: ‘7:g.140453136A>T’ (BRAF V600E), ‘17:g.7577120C>T’ (TP53 R273H).

Example Usage:

query = {
    "name": "GenomeNexus_get_cancer_hotspots",
    "arguments": {
        "hgvsg": "example_value"
    }
}
result = tu.run(query)

GenomeNexus_get_canonical_transcript (Type: GenomeNexusTool)

Get the canonical transcript for a gene from Genome Nexus (MSK). Returns the Ensembl transcript I…

GenomeNexus_get_canonical_transcript tool specification

Tool Information:

  • Name: GenomeNexus_get_canonical_transcript

  • Type: GenomeNexusTool

  • Description: Get the canonical transcript for a gene from Genome Nexus (MSK). Returns the Ensembl transcript ID, protein ID, protein length, RefSeq mRNA ID, CCDS ID, HUGO symbol, and Pfam protein domain annotations. Useful for determining the standard transcript to use for variant annotation, and for getting a quick overview of protein domain architecture. Input is a HUGO gene symbol (e.g., ‘TP53’, ‘BRAF’, ‘BRCA1’).

Parameters:

  • gene_symbol (string) (required) HUGO gene symbol. Examples: ‘TP53’, ‘BRAF’, ‘BRCA1’, ‘EGFR’, ‘KRAS’.

Example Usage:

query = {
    "name": "GenomeNexus_get_canonical_transcript",
    "arguments": {
        "gene_symbol": "example_value"
    }
}
result = tu.run(query)