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Flag trans QTLs in credible set dataset. #3718

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DSuveges opened this issue Jan 14, 2025 · 3 comments · May be fixed by opentargets/gentropy#973
Open
4 tasks

Flag trans QTLs in credible set dataset. #3718

DSuveges opened this issue Jan 14, 2025 · 3 comments · May be fixed by opentargets/gentropy#973
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@DSuveges
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Data Relates to Open Targets data team Platform Issues related to Open Targets Platform

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@DSuveges
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The UKB PPP not only provides cis, but also trans QTL loci as well. By looking at the credible set data it is not apparent which one are cis vs trans. This ticket captures the following actions:

  • Assess impact on study-locus schema.
  • Adding logic to assess if the QTL locus is trans vs cis.
  • If new field is required prepare backed to ingest and expose via API.
  • Assess required action on the frontend.
@DSuveges DSuveges self-assigned this Jan 14, 2025
@d0choa
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d0choa commented Jan 14, 2025

After a quick bibliography search, I concluded the consensus of defining cis as anything within 5Mb of the TSS is well-established

@buniello buniello added Data Relates to Open Targets data team Platform Issues related to Open Targets Platform labels Jan 14, 2025
@DSuveges
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DSuveges commented Jan 14, 2025 •
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Some stats

  • All QTL credible sets: 2,043,037
  • Number of credible sets where at least one of the tag is on a different chromosome than the gene: 15,793 (0.7%) from 2,103 studies, all from UKB_PPP
  • The number of credible stets where at least one of the tags are further away than 5MB from the TSS of the gene is 955 (0.04%) from 465 studies, all from UKB_PPP

@DSuveges
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Some of the 16k transQTLs:

+--------------------------------+-------+
|studyLocusId                    |isTrans|
+--------------------------------+-------+
|00bd8ad3db97f5aa19ad74923f52406f|true   |
|00d4a716964d6b14b0f70c873aa6c06f|true   |
|019615c92ef665ac157a7384976d1ad7|true   |
|019ea8c9a704192d95c5888c3df78143|true   |
|01af8f338b522bea2e20d9c30da82b0c|true   |
|01c15338dde3d34919e0eceb7ac83c38|true   |
|01f258ef824c793b32e95b2bb0d348c1|true   |
|02360063c93d52174f300ed3842b472a|true   |
|0250f5faac990a4acf4649e100138422|true   |
|03a0b75f6faee796b7b2c76056cbd3d8|true   |
|03d7fd1b5c5cc8382dc019838f5750a1|true   |
|04a78fad2a98c58b2ed1177702611f47|true   |
|05708f6d4434a21b033dbb09d941a7ea|true   |
|070decd2eb433a0185deecf8244cd071|true   |
|073d140302240a4aeb1691f036c75e55|true   |
|08a0428fe3d953bc0d8396a54718b83c|true   |
|0ad39d865ac94ccf991f613b83c31b8c|true   |
|0b185fa4ba2e1a2481c064738caea1a3|true   |
|0bb88e6faad545c5d35e36d52b97344b|true   |
|0bf657334812ab640e6ae0fc33532efa|true   |
+--------------------------------+-------+
only showing top 20 rows

@DSuveges DSuveges linked a pull request Jan 15, 2025 that will close this issue
feat(qtls): flagging trans QTL credible sets opentargets/gentropy#973
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feat(qtls): flagging trans QTL credible sets opentargets/gentropy
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@d0choa @DSuveges @buniello