# Distance-based clustering in gwas-catalog data

**URL:** <https://community.opentargets.org/t/distance-based-clustering-in-gwas-catalog-data/576>\
**Category:** Community Feedback\
**Tags:** genetics-portal\
**Created:** [4 May 2022 02:33 UTC](https://community.opentargets.org/t/distance-based-clustering-in-gwas-catalog-data/576 "2022-05-04T02:33:01Z")\
**Posts on this page:** 7\
**Page:** 1

<div class="post-metadata">

**Author:** ![Shicheng\_Guo](https://dub1.discourse-cdn.com/flex017/user_avatar/community.opentargets.org/shicheng_guo/32/217_2.png) [@Shicheng\_Guo](https://community.opentargets.org/u/Shicheng_Guo)\
**Post date:** [4 May 2022 02:33 UTC](https://community.opentargets.org/t/distance-based-clustering-in-gwas-catalog-data/576/1 "2022-05-04T02:33:01Z")

</div>

Dear Team,

I am not so clear about **distance-based clustering in gwas-catalog data** , can you give me some further explanation?

- 
  - Identify studies with an abnormally large number of reported loci compared to number of loci after distance-based clustering (±500kb). Criteria for “abnormal” are set to number of loci \> 10, and decrease in loci count after clustering of \>10%. For “abnormal” studies (N≈120), apply distance based clustering.

💬

Thanks.

Shicheng

---

<div class="post-metadata">

**Author:** ![Xiangyu](https://avatars.discourse-cdn.com/v4/letter/x/90db22/32.png) [@Xiangyu](https://community.opentargets.org/u/Xiangyu)\
**Post date:** [13 May 2022 11:41 UTC](https://community.opentargets.org/t/distance-based-clustering-in-gwas-catalog-data/576/2 "2022-05-13T11:41:20Z")

</div>

Hi Shicheng,

GWAS Catalog can contain none independent loci where summary statistics are bulk imported from supplementary tables. To correct this, the distance-based clustering step is used to remove redundant variants.

Xiangyu

---

<div class="post-metadata">

**Author:** ![Kirill\_Tsukanov](https://dub1.discourse-cdn.com/flex017/user_avatar/community.opentargets.org/kirill_tsukanov/32/31_2.png) [@Kirill\_Tsukanov](https://community.opentargets.org/u/Kirill_Tsukanov)\
**Post date:** [17 May 2022 08:18 UTC](https://community.opentargets.org/t/distance-based-clustering-in-gwas-catalog-data/576/3 "2022-05-17T08:18:39Z")

</div>

Thank you @Xiangyu. I’m going to mark this as resolved for now. @Shicheng_Guo please let us know if you have any further questions

---

<div class="post-metadata">

**Author:** ![Shicheng\_Guo](https://dub1.discourse-cdn.com/flex017/user_avatar/community.opentargets.org/shicheng_guo/32/217_2.png) [@Shicheng\_Guo](https://community.opentargets.org/u/Shicheng_Guo)\
**Post date:** [17 May 2022 20:32 UTC](https://community.opentargets.org/t/distance-based-clustering-in-gwas-catalog-data/576/4 "2022-05-17T20:32:47Z")

</div>

Thank you Xiangyu and Kirill, Can you share me the script how it was performed? or Is it shared in the github page?  
Thanks  
Shicheng

---

<div class="post-metadata">

**Author:** ![Shicheng\_Guo](https://dub1.discourse-cdn.com/flex017/user_avatar/community.opentargets.org/shicheng_guo/32/217_2.png) [@Shicheng\_Guo](https://community.opentargets.org/u/Shicheng_Guo)\
**Post date:** [17 May 2022 21:54 UTC](https://community.opentargets.org/t/distance-based-clustering-in-gwas-catalog-data/576/5 "2022-05-17T21:54:41Z")

</div>

Hi Xiangyu and Kirill,

Is there any internal discussion about my previous poster?

> [@Are you considering implementing two-sample MR?](https://community.opentargets.org/t/engage-mendelian-randomization-to-open-targets-platform/564):
>
> Dear Team, I am wondering why Mendelian Randomization (two-sample MR) is not implemented in Open Targets platform which will be very helpful for target identification and validation. Thanks. Shicheng

Thanks.

Shicheng

@Kirill_Tsukanov @Xiangyu

---

<div class="post-metadata">

**Author:** ![Kirill\_Tsukanov](https://dub1.discourse-cdn.com/flex017/user_avatar/community.opentargets.org/kirill_tsukanov/32/31_2.png) [@Kirill\_Tsukanov](https://community.opentargets.org/u/Kirill_Tsukanov)\
**Post date:** [18 May 2022 06:57 UTC](https://community.opentargets.org/t/distance-based-clustering-in-gwas-catalog-data/576/6 "2022-05-18T06:57:34Z")

</div>

I’ll let @Xiangyu get back to you about where to find the relevant code. Unmarking as resolved for now.

I’ll get back to you separately on the other post about mendelian randomisation.

---

<div class="post-metadata">

**Author:** ![Xiangyu](https://avatars.discourse-cdn.com/v4/letter/x/90db22/32.png) [@Xiangyu](https://community.opentargets.org/u/Xiangyu)\
**Post date:** [18 May 2022 08:58 UTC](https://community.opentargets.org/t/distance-based-clustering-in-gwas-catalog-data/576/7 "2022-05-18T08:58:50Z")

</div>

Hi Shicheng,

Yes, the distance based clumping is a part of the v2d processing pipeline, and the script for it is [here](https://github.com/opentargets/genetics-v2d-data/blob/master/scripts/cluster_gwas_catalog_associations.py).

Best wishes,  
Xiangyu