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Adjoined Transcripts#

Adjoined Transcript: a transcript (RNA molecule) composed of adjoined RNA from two or more contributing transcripts.

Syntax#

Syntax five_prime_sequence_identifier ":" coord_type "." five_prime_range "::" [ linker_sequence "::" ] three_prime_sequence_identifier ":" coord_type "." three_prime_range
Examples
  • NM_002354.2:r.-358_555::NM_000251.2:r.212_*279
  • NM_152263.2:r.-115_775::aggcucccuugg::NM_002609.3:r.1580_*1924
  • NM_152263.2:r.?_775::NM_002609.3:r.1580_?
Explanation of Symbols
  • coord_type: the coordinate type, indicating the type of numbering used; r
  • five_prime_range: the range of coordinates of nucleotides included in the 5' adjoined transcript; -358_555
  • five_prime_sequence_identifier: the transcript identifier of the 5' partner of the adjoined transcript; NM_002354.2
  • linker_sequence: a nucleotide sequence that exists between two adjoined transcripts
  • three_prime_range: the range of coordinates of nucleotides included in the 3' adjoined transcript; 212_*279
  • three_prime_sequence_identifier: the transcript identifier of the 3' partner of the adjoined transcript; NM_000251.2
See also explanation of grammar used in HGVS Nomenclature.

Notes#

  • Adjoined transcripts are a product of some gene fusions.
  • The adjoined transcript syntax proposed in Community Proposal SVD WG007 and adopted here has the following limitations:
    • This syntax is for two-partner adjoined transcripts only.
    • This syntax is for RNA sequence only (no use of coding (c.) / non-coding DNA (n.) reference sequences).
    • Linker sequences are specified using General Recommendations for RNA sequence character codes, e.g. aggcucccuugg
  • This syntax REQUIRES the use of a range (not a single position) for five_prime_range / three_prime_range.
  • When the adjoined transcript junction but not the entire transcript is analyzed, the outer range bounds SHOULD be specified with ?, e.g. NM_152263.2:r.?_775::NM_002609.3:r.1580_?
  • All adjoined transcripts are described using the same format, irrespective of whether they derive from inter-chromosomal or intra-chromosomal DNA rearrangements (translocation, deletion, inversion) or other mechanisms (trans-splicing).

Examples#

  • translocation-derived adjoined transcript

    • NM_152263.2:r.-115_775::NM_002609.3:r.1580_*1924
      describes an adjoined transcript from a TPM3::PDGFRB gene fusion, where nucleotides r.-115 to r.775 (reference transcript NM_152263.2, TPM3 gene) are coupled to nucleotides r.1580 to r.*1924 (reference transcript NM_002609.3, PDGFRB gene).

  • deletion-derived adjoined transcripts

    • NM_002354.2:r.-358_555::NM_000251.2:r.212_*279
      describes an adjoined transcript from an EPCAM::MSH2 gene fusion, where nucleotides r.-358 to r.555 (reference transcript NM_002354.2, EPCAM gene) are coupled to nucleotides r.212 to r.*279 (reference transcript NM_000251.2, MSH2 gene).

    • NM_002354.2:r.?_555::guaugauuuuuuaataa::NM_000251.2:r.212_?
      describes an adjoined transcript from an EPCAM::MSH2 gene fusion, where only the fusion break point has been characterised, showing the insertion of a 17 nucleotide sequence (guaugauuuuuuaataa) between two adjoined transcripts.