Variant Calling Challenge

Open innovation challenge for experts in variant calling and an interest in auto-immune diseases.

The challenge

GWAS and eQTL datasets have been used in auto-immune disease target identification for many years for and the available datasets and resources have been frequently mined. There are however many RNA Sequencing (RNASeq) datasets which have not been fully explored for potential nucleotide changes which may influence disease. As clonal expansion of immune cells due to somatic driver mutations (usually called Clonal Hematopoesis of Indeterminant Potential, CHIP) is well described [1], [2] and has been linked to cardiovascular risk [ 3], we hypothesize that that searching for somatic mutations in auto-immune diseases might yield interesting results. 

The aim of this variant calling challenges is to create new sustainable partnerships with external academic experts to mine RNASeq datasets for nucleotide variants (DNA or RNA) which may associate with or drive auto-immune or inflammatory disease. By looking at somatic mutations or aberrant RNA editing events, we hope to we find hits and thus targets which are not already captured by public GWAS data.  Even if the hits are not common drivers, downstream pathway or network analysis of infrequent mutations might reveal previously under-appreciated pathogenic pathways.  Diseases of particular interest include lupus, multiple sclerosis, or rheumatoid arthritis; however, other auto-immune diseases are also in-scope if suitable datasets exist.

We are looking for submissions which include both some pilot results (using public data to demonstrate the feasibility of the variant calling and the downstream interpretation) and a proposal for an expansion to more public data or to our own clinical RNASeq datasets. 

We will evaluate your submission by the criteria innovativeness, potential (analytical, scientific and/or medical), team strength and strategic fit. The best team wins 10 000 EUR and the chance to present their work to our scientists.


[1] What is Clonal Hematopoiesis of Indeterminate Potential (CHIP)? Dana Farber Insight Blog March 19, 2019

[2] Cook et. al, 2020 Clonal hematopoiesis and inflammation: Partners in leukemogenesis and comorbidity Experimental Hematology Vol. 83: 85-94 

[3] Libby and Ebert, 2018. CHIP (Clonal Hematopoiesis of Indeterminate Potential) Circulation 138:666–668

Who can participate?

Experts in variant calling and with an interest in auto-immune diseases. This challenge is not open to HCPs.

The application process has closed, come back in the future to learn about new opportunities to engage.

How does it work?

  • Submission is by completing the Application Form (with Terms and Conditions of the challenge) and submitting by e-mail to before 23:59 (CET) by 30. April 2021. 
  • You need to submit a description of your expertise in the field and proof of your track record.
  • Proof of your track record may be provided by providing a non-confidential description of a completed variant calling use case including a description of how you performed variant calling and the associated the variants (individually, by gene, by pathway) with disease. 
  • For the variant calling use case, you may include relevant public RNA sequencing data, to look for somatic mutations or aberrant RNA editing events that may be driving the expansion of pathogenic immune cells or otherwise altering immune function.
  • Your expertise in the field may be demonstrated by providing a short scientific CV with publication record. Experience in immune biology is also helpful.  
  • We will evaluate all submissions received by the submission deadline by the criteria innovativeness, potential (analytical, scientific and/or medical), team strength and strategic fit. 
  • The best team wins 10 000 EUR and the chance to present their work to our scientists. 
  • You retain any rights that you hold with the use case, any tools you use and publishing rights you may have.
  • Merck KGaA, Darmstadt, Germany retains the exclusive right to make any press release or any kind of public communication about the competition and the winning proposal. Confidential details on project content will not be revealed.


Merck KGaA, Darmstadt, Germany awards a EUR 10,000 prize to the winning proposal based on the criteria innovativeness, potential (analytical, scientific and/or medical), team strength and strategic fit. Furthermore, selected participants have the chance to gain access to potential collaborations within us.


Terms & Conditions and Application Form click here