Community Consultation

Proposal SVD-WG004 (ISCN<>HGVS)

The proposal suggests to extend the HGVS recommendations to allow description of complex variants incl. those covered so far by the ISCN (e.g. transpositions, translocations, chromothripsis, marker chromosomes, etc.). In addition it includes suggestions to harmonise the HGVS and ISCN recommendations, removing discrepancies as much as possible.


HGVS <> ISCN

The current HGVS recommendations [(see Recommendations)]/recommendations/general/) do not cover translocations. One small example is given (see DNA sequence variants) but this is insufficient to properly describe such changes when detected. The SVD-WG has received the request to extend the HGVS recommendations to include the description of translocations.

Historically the description of translocations is the responsibility of the ISCN committee. The ISCN recommendations cover the description of numerical and structural chromosomal changes detected using microscopic/cytogenetic techniques, while the HGVS recommendations cover the description of changes at the nucleotide level detected using sequencing. Given the increased use of sequencing technologies to characterize chromosomal abnormalities the ISCN committee and the HGVS/HVP/HUGO Sequence Variant Description Working Group (SVD-WG) have thoroughly checked and discussed the recommendations of both committees. The committees decided to design one format that, wherever possible, leaves existing standards intact but that also draws a clear border between ISCN and HGVS. Discussions concentrated around earlier proposals for the description of translocations, e.g. as presented at the HGVS/ASHG meeting in Boston (see presentation), and a paper from Ordulu et al. (2014) reporting sequencing results of structural chromosome rearrangements.


Proposal

The committees propose that as soon as nucleotide positions are used in the description of rearrangements, HGVS nomenclature is followed and descriptions are split in a ISCN and a HGVS part.

the basics
HGVS additions

Examples

Note the format: the variant is first described using ISCN nomenclature, next using HGVS.