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Cryptic variation & melanoma risk

Gene Expression
By Razib Khan
Apr 22, 2009 5:18 PMNov 5, 2019 9:36 AM

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One of the funnier aspects of the discovery of genes correlated with physical traits is that finding the genetic variant which explains 75% of the variation in blue eyes is interesting, but it isn't as if you now have a better way to find blue eyed people (though it is important for forensic work). But now there is apparently working on looking at pigmentation genes and how they effect melanoma risk in a manner which isn't visible to the eye: Dark Hair? Don't Burn? Your Genes May Still Put You At Risk For Melanoma:

Overall, the presence of certain MC1R variants was associated with a more than two-fold risk of melanoma, but this risk was largely confined to those patients who would not usually be considered to be at elevated risk. Although those with dark hair are not thought to be at increased risk for melanoma, if they had dark hair and also inherited certain MC1R genetic variants, their risk for melanoma increased 2.4-fold. However, no elevated risk was associated with these same MC1R variants in those with blond or red hair. MC1R was also associated with increased risk among those with dark eye color (3.2-fold increase), who did not freckle (8-fold increase), who tanned after repeated sun exposure (2.4 fold increase) or who tanned immediately without burning (9.5-fold increase). People with these characteristics are usually thought to be at reduced risk for melanoma.

MC1R is melanocortin 1 receptor, and it's involved in pigmentation pathways. In fact its importance was known well before most of the newer loci yielded by genomic techniques. There are particular variants which are associated with red hair, for example. Additionally in Europeans it is very polymorphic, with a host of different loss of function mutations floating around. It seems likely that these data point to cryptic phenotypic variation which clinical assessment through visual inspection isn't picking up. In other words, coarse binning into categories like "dark hair" and "normal complexion" don't reflect the variation even within those categories. I may be that people on the fairer side of normal are at particular risk because doctors don't think to warm them to take precautions, as they would someone with red hair.

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