During the VA call today, @javild reviewed the Molecular Consequence VA type found here.
Steve Hart and others mentioned the importance of being able to use the variant representation (subject) to be able to represent or at least discover all equivalent transcript representations of the variant, so that alternate forms do not get lost or discovered when digesting/using variant annotations of this nature.
Examples verbalized,
"using refseq transcript version 3 verses 4 should be mapped"
"using refseq vs. ensembl transcripts should be mapped"
It was not clear to me if some subset of multiple "isoforms" for a given gene should be considered equivalent in this case. (I think not). But there was a related discussion about whether VA types like MolConseq should be able to be aggregated, when the statement was the same or similar for multiple isoforms of the same underlying genomic variant.
@mbrush indicated that we (VA) is starting with the notion that we would define atomic annotation records for now and then consider aggregate VA statements.
We (VR) need to also consider the consideration that the VA MolConsq annotations can be alleles, haplotypes, CNVs or SVs (see @javild for more examples of CNVs and SVs for this type of annotation).
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4 years ago
During the VA call today, @javild reviewed the Molecular Consequence VA type found here.
Steve Hart and others mentioned the importance of being able to use the variant representation (subject) to be able to represent or at least discover all equivalent transcript representations of the variant, so that alternate forms do not get lost or discovered when digesting/using variant annotations of this nature.
Examples verbalized, "using refseq transcript version 3 verses 4 should be mapped" "using refseq vs. ensembl transcripts should be mapped"
It was not clear to me if some subset of multiple "isoforms" for a given gene should be considered equivalent in this case. (I think not). But there was a related discussion about whether VA types like MolConseq should be able to be aggregated, when the statement was the same or similar for multiple isoforms of the same underlying genomic variant. @mbrush indicated that we (VA) is starting with the notion that we would define atomic annotation records for now and then consider aggregate VA statements.
We (VR) need to also consider the consideration that the VA MolConsq annotations can be alleles, haplotypes, CNVs or SVs (see @javild for more examples of CNVs and SVs for this type of annotation).