Alex H. Wagner, PhD

Representation of copy number variation in cancer is difficult due to the confluence of tumor purity, clonality, and technical error in whole-tumor NGS assays. To account for this, CNVs are...

Molecular type attribute

3

Sequences are currently untyped, but may benefit from DNA/RNA/AA designation. This was an early design decision I think we should revisit. Starting this thread as a place to collect use...

Categorical variation

10

Some variants are described in terms of exculsionary criteria. These will need to be considered in our model. See https://civicdb.org/events/genes/5/summary/variants/2408/summary#variant for an example.

Document new design decision: explicit attributes

2

Design decision: - be explicit about everything - NULL doesn’t work in some implementations - no mixing of basic types with VRS types

Explicit IUPAC tables

1

Currently, we link to the [Wikipedia IUPAC tables](https://en.wikipedia.org/wiki/International_Union_of_Pure_and_Applied_Chemistry#Amino_acid_and_nucleotide_base_codes), and previously the [genome.jp IUPAC tables](https://www.genome.jp/kegg/catalog/codes1.html) which have some slight differences (termination and gap codes). We should be explicit about what we...

Reverse complement attribute was not included in the information model documentation for DerivedSequenceExpression. Also include in figure revision for #324.

Allele Normalization

2

We need to refine Allele Normalization in VRS v1.2 to account for various sequence expression types. The following was discussed in the 5/24/21 VRS call: - Normalize LiteralSequenceExpression as SequenceState...

Consider IUPAC Ambiguity Codes and amino acid ambiguity

3

Currently we allow all IUPAC ambiguity codes for VRS, but no parallel mechanism for amino acids. Section 1.4.1 of v4.2 of the VCF specification under Ref and Alt, only A,...

ENSEMBL transcripts not versioned

7

When trying to refer to ensembl transcripts we cannot find by version in the 20210129 data release.

**What is the SO term name and accession?** This involves the SO relationship, [`is_consecutive_sequence_of`](http://www.sequenceontology.org/browser/current_release/term/is_consecutive_sequence_of). **Describe what you would like to change.** The definition has a few typos and omissions from...