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Add a variant page link to primAD #2547

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anneodonnell opened this issue Mar 14, 2022 · 2 comments
Open

Add a variant page link to primAD #2547

anneodonnell opened this issue Mar 14, 2022 · 2 comments

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@anneodonnell
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Is your feature request related to a problem? Please describe.
primAD has sequence data from ~1000 primates from many different species and is helpful to look at variation in this database, similar to looking at gnomAD. We would want to know the primate AF for a variant, as this is some evidence that the variant is tolerated. In these 1000 primates, there is as much variation seen as there is in the 60,000 people in ExAC.

Describe the solution you'd like
Add AC/AFs from primAD as a reference population dataset, with link to the primAD variant page - BUT only for the primate data. primAD also has a copy of the gnomAD data which we already have in seqr, so we would want the data just for primates.

Describe alternatives you've considered
It would be ok to just have the link if the variant is in primates in primAD, though having AC/AF would be helpful but not essential. It would not be helpful to have a link on every variant.

We would not plan to filter on primAD AF at this stage as we are getting used to the data, though there is some chance it could change in the future.

We might need to add the primAD data as some type of annotation in the loading pipeline too - that might require a special request of the primAD team.

Additional context
gnomAD is going to need something similar to might be similar - at least in terms of knowing which variants are present in primates and worth linking to (doesn't need the AC/AF probably) so could coordinate on effort. Yanshen Yang is the contact on the Illumina side for primAD if there are questions.

@hanars
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hanars commented Mar 14, 2022

Adding to seqr requires pipeline update. first - created broadinstitute/seqr-loading-pipelines#320 to track that work

@lynnpais
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Talked to Anne about this a few weeks ago where we decided to defer on adding PrimAD AC/AF info to seqr. Moving to Icebox.

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