Open for comments - SVD-WG004


Published: November 10, 2015
Closes:  January 15, 2016


Proposal


SVD-WG004 (ISCN<>HGVS) suggest to extend the current HGVS recommendations for the description of sequence variants with the proposal below. Comments can be sent to the HGVS/HVP/HUGO Sequence Variant Description Working Group (SVD-WG), addressed to "Varnomen @ variome.org", Subject: SVD-WG004. Comments need to be sent ultimately January 15, 2016.

HGVS<>ISCN

The current HGVS recommendations (see Recommendations) do not cover translocations. One small example is given (see DNA sequence variants) but this is insufficient to properly describe the changes 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 chromosome numerical and structural 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.

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 part and a HGVS part.

Examples

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


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