Target types

  • Updated

Tapestri Designer currently allows five target identifiers to describe targets – gene, region, dbSNP, COSMIC, and HGVS. Designer supports all five target identifiers for the catalog human genome hg19 (GRCh37) and only region targets for the catalog mouse genome mm10 (GRCm38) and custom genomes.

For each type, we provide the following information:

Identifier: Valid identifier for the target from the source database

Entry: The beginning portion of the target ID

Source: The databases used to identify the targets

Examples: Sample valid inputs. For CSV files, they should contain three columns: target type, target ID, and target name (optional). The file can have a header row or not. When pasting or typing in the target, the format is comma (,) separated "target type, target ID, target name" or tab-separated. Name is an optional field, which is a text identifier for the amplicon to make it understandable to the user. Each name should be a unique identifier within a panel.

Gene

  • Identifier: Official HGNC gene symbol, not NCBI 
  • Entry: Gene symbol
  • Source: HGNC
  • Genomes supported: The gene type supports numerous genomes, but Tapestri Designer only supports hg19 (GRCh37). Designer converts the genes to hg19-based regions.
  • CDS regions: Targets only the gene’s CDS region. To design amplicons for the entire gene, add the regions for the introns within that gene. 
  • Examples
    • Gene,BRCA1,breast cancer gene
    • Gene,TP53

Region

  • Identifier: N/A
  • Entry: "chr" prefix is optional, when specifying chromosomes X and Y, X and Y must be capitalized
  • Source: mm10, hg19 or custom genome assembly 
  • Genomes supported: The region type supports numerous genomes, but Tapestri Designer only supports catalog genomes hg19 (GRCh37), mm10 (GRCm38), and custom genomes. Convert hg38 (GRCh38) coordinates to hg19 using the USCS Liftover Tool. Or upload your own custom hg38 genome by following the steps listed here.
  • CDS regions: Both CDS and non-CDS regions are supported.
  • Coordinate system: Input should be in one-based format
  • Examples: 
    • Region,chr7:100-200,Region 1
    • Region,7:100-200,Region 2
    • Region,chr7:100..200
    • Region,7:100..200 (COSMIC style)
    • Region,X:155270560-155270560
    • Region,chr1:220138518-220138518

dbSNP

  • Identifier: SNP ID
  • Entry: "rs" is a required part of the id
  • Source: dbSNP (build 151); remove extra parentheses
  • Genomes supported: dbSNP supports human and non-human genomes, but they are phasing out non-human support. Designer converts the dbSNP IDs to hg19-based regions.
  • CDS regions: Both CDS and non-CDS regions are supported.
  • Examples
    • dbSNP,rs1042522,TP53:R72P
    • dbSNP,rs4680
    • dbSNP,rs121913237,My var
    • dbSNP,rs66816424
    • COSMIC
  • Identifier: COSMIC ID
  • Entry: COSM is a required part of the id
  • Source: COSMIC DB (v84)
  • Genomes supported: COSMIC supports only the human genome. Designer converts the COSMIC IDs to hg19-based regions.
  • CDS regions: Both CDS and non-CDS regions are supported.
  • Examples
    • COSMIC,COSM564,NRAS
    • COSMIC,COSM10648,Most common TP53 mutation
    • COSMIC,COSM6932

Note: Currently, Designer only supports COSMIC IDs with the COSM prefix.

HGVS

  • Identifier: HGVS ID
  • Entry: We support anything VarSome supports, which is most of varnomen.hgvs.org
  • Source: VarSome
  • Genomes supported: HGVS supports multiple human genomes, but Tapestri Designer only supports hg19 (GRCh37). Designer converts the HGVS IDs to hg19-based regions.
  • CDS regions: Both CDS and non-CDS regions are supported.
  • Examples
    • Protein format based
      • HGVS,NRAS:G12D,My mutation (protein format)
      • HGVS,NM_000546.5(TP53):R248Q (Specify the transcript ID when a gene has multiple isoforms. This forces VarSome to fetch the coordinates for the specified transcript and not all the transcripts and limits ambiguity in targets.)
    • cDNA format based (indels must be in cDNA format)
      • HGVS,KRAS:c.38G>A,G13D
      • HGVS,KIT:c.1672_1716del,KIT deletion 
      • HGVS,APC:c.3905dup
      • HGVS,RET:c.1894_1906delinsAGCT
      • HGVS,NM_005228.5(EGFR):c.2308_2309insGTT
      • HGVS,NM_001304360.2:c.-19-2656C>T
    • Chromosome—position—ref seq—variant seq
      • HGVS,chr6-161127501-A-G,substitution
      • HGVS,chr6-161127501-A-,deletion
      • HGVS,6-161127501--G,insertion
    • Chromosome—position—ref_seq_length—variant_seq
      • HGVS,15-73027478-1-C,substitution 1
      • HGVS,22:39777823:0:CAA,insertion 1
      • HGVS,chr22:38482353:42:,deletion 1
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