FHIR Chat · somatic variant reporting

Stream: genomics

Topic: somatic variant reporting

Bob Dolin (Apr 28 2021 at 00:19):

@Patrick Werner , @May Terry I've probably asked you this before, but I don't understand why some of our example reports only show c.HGVS and p.HGVS. For instance, this example [http://build.fhir.org/ig/HL7/genomics-reporting/Bundle-oncology-report-example.html] includes a variant for FBXW7 (NM_001349798.2:c.1394G>A). Presumably this is a NGS test, where a genomic variant was detected. The FBXW7 gene has multiple transcripts. Why did the lab specifically show this c.HGVS and p.HGVS?

Bob Dolin (Apr 28 2021 at 00:30):

and a corollary question - in this example [http://build.fhir.org/ig/HL7/genomics-reporting/Bundle-oncology-diagnostic.html], there is a genomic BRAF variant, and a single protein variant. Why, amongst all the BRAF transcripts, was only this protein variant included?

Patrick Werner (May 06 2021 at 10:12):

Bob Dolin said:

Patrick Werner , May Terry I've probably asked you this before, but I don't understand why some of our example reports only show c.HGVS and p.HGVS. For instance, this example [http://build.fhir.org/ig/HL7/genomics-reporting/Bundle-oncology-report-example.html] includes a variant for FBXW7 (NM_001349798.2:c.1394G>A). Presumably this is a NGS test, where a genomic variant was detected. The FBXW7 gene has multiple transcripts. Why did the lab specifically show this c.HGVS and p.HGVS?

Hi Bob, i'm not 100% if i understood the question correctly.

Patrick Werner (May 06 2021 at 10:12):

Was the question why they ended up reporting it with this specific transcript?

Bob Dolin (May 06 2021 at 13:51):

Thanks @Patrick Werner . Yes. Let's say I do NGS and detect NC_000001.11:g.1014228G>A. I could report ENST00000624697.4:c.224G>A and p.Ser75Asn, or I could report ENST00000649529.1:c.248G>A and p.Ser83Asn. I was curious how a lab decides which to report - is it, for instance, based on transcript prevalence, based on what form is typically annotated, etc?