ielis commented 6 months ago

Not all phenopackets include variants with exact CNV coordinates and sometimes all we have is a gene and a Sequence Ontology term (e.g. )

For instance PMID_36446582_Novara2017_P2 includes the following genomic interpretation:

"genomicInterpretations": [
          {
            "subjectOrBiosampleId": "Novara, 2017_P2",
            "interpretationStatus": "CAUSATIVE",
            "variantInterpretation": {
              "variationDescriptor": {
                "id": "var_WqTwGolKqoDWrueIvbQUFXsZr",
                "label": "16q24.2-q24.3 (87340135_89335428)x1 (hg19)",
                "geneContext": {
                  "valueId": "HGNC:21316",
                  "symbol": "ANKRD11"
                },
                "moleculeContext": "genomic",
                "structuralType": {
                  "id": "SO:1000029",
                  "label": "chromosomal_deletion"
                },
                "allelicState": {
                  "id": "GENO:0000135",
                  "label": "heterozygous"
                }
              }
            }
          }
        ]

We only know about a chromosomal_deletion of ANKRD11.

We need to devise a strategy for including such CNVs into the analysis.

lnrekerle commented 2 weeks ago

156

@ielis @pnrobinson Is this issue needed when we have another that should cover this? Or is the legacy CNV some how different than other structural variants?

ielis commented 2 weeks ago

No, this is indeed a duplicate of #156. Let's close it and deal with the issue elsewhere.

monarch-initiative / genophenocorr

Handling phenopackets with legacy CNV #119

156