Genome-wide association study of pain sensitivity assessed by questionnaire and the cold pressor test
Authors: Fontanillas Pierre , Kless Achim ,   23andMe Research Team, Bothmer John , Tung Joyce Y. 
Published: November 2019

Altered pain sensitivity is believed to play an important role in the development of chronic pain, a common debilitating condition affecting an estimated 1 in 5 adults. Pain sensitivity varies broadly between individuals, and it is notoriously difficult to measure at scale in large populations. Although pain sensitivity is known to be moderately heritable, only a small number of genetic studies have been published and they have had limited success in identifying the genetic architecture of pain sensitivity. In this study, we deployed an online pain sensitivity questionnaire (PSQ) and an at-home version of the cold pressor test (CPT) in a large genotyped cohort. We performed genome-wide association studies (GWAS) on the PSQ score (n = 25,321) and CPT duration (n = 6,853). Despite a reasonably large sample size, we identified only one genome-wide significant locus associated with the PSQ score, which was located in the TSSC1 gene (rs58194899, OR = 0.950 [0.933-0.967], P-value = 1.9*10−8). This gene is responsible for intracellular cell trafficking and it could modulate pain sensitivity via changes in neuroplasticity. PSQ score is genetically correlated with chronic and acute pain, including chronic neck and shoulder pain (rg = 0.71), fracture (0.71), rheumatoid arthritis (0.68), osteoarthritis (0.38), and pneumothorax (0.82). PSQ score was also genetically correlated with known risk factors, such as the length of working week (0.65), noisy workplace (0.41), smoking (0.36), or extreme BMI (0.23). Gene-based analysis followed by pathway analysis showed that GWAS results were enriched for genes expressed in the brain, predominantly in the frontal cortex and basal ganglia, and enriched for genes involved in neuronal development and glutamatergic synapse signaling pathways. Finally, we confirmed that females with red hair were more sensitive to pain and found that genetic variation in the MC1R gene was associated with an increase in pain sensitivity as assessed by the PSQ. Overall, we detailed the genetic background of pain sensitivity using scalable at-home procedures that may serve as a blueprint for larger genetic studies.

Author Summary

Despite decades of research and many advances in our understanding of the physical, emotional, and psychological aspects, the genetic contribution to pain sensitivity is still largely unknown. We administered a pain sensitivity questionnaire in parallel with an experimental cold pressor test in a large, genotyped cohort of 31,000 research participants, and found a novel genome-wide genetic association in TSSC1. This gene is responsible for intracellular cell trafficking and it could modulate pain sensitivity via changes in neuroplasticity. Overall, the pain sensitivity measurements revealed strong positive genetic correlations with chronic and acute pain conditions, as well as with unhealthy traits and behaviors, such as obesity, smoking, or difficult working conditions. The genetic association results also suggested, perhaps unsurprisingly, that only the brain tissues could be relevant for pain sensitivity, and identified enrichments for glutamatergic synapse pathways. Despite the complexity of pain sensitivity, our study demonstrated that it is now possible to deploy sophisticated pain questionnaires online and perform experimental medicine tests in at-home settings to further study the genetic architecture of pain sensitivity.