The evolutionary impact of childhood cancer on the human gene pool

Ulrik Kristoffer Stoltze (), Jon Foss-Skiftesvik, Thomas van Overeem Hansen, Simon Rasmussen, Konrad J. Karczewski, Karin A. W. Wadt and Kjeld Schmiegelow ()
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Ulrik Kristoffer Stoltze: Rigshospitalet, Blegdamsvej 9
Jon Foss-Skiftesvik: Rigshospitalet, Blegdamsvej 9
Thomas van Overeem Hansen: Rigshospitalet, Blegdamsvej 9
Simon Rasmussen: University of Copenhagen, Blegdamsvej 3B
Konrad J. Karczewski: The Broad Institute of MIT and Harvard, Merkin Building, 415 Main St
Karin A. W. Wadt: Rigshospitalet, Blegdamsvej 9
Kjeld Schmiegelow: Rigshospitalet, Blegdamsvej 9

Nature Communications, 2024, vol. 15, issue 1, 1-15

Abstract: Abstract Germline pathogenic variants associated with increased childhood mortality must be subject to natural selection. Here, we analyze publicly available germline genetic metadata from 4,574 children with cancer [11 studies; 1,083 whole exome sequences (WES), 1,950 whole genome sequences (WGS), and 1,541 gene panel] and 141,456 adults [125,748 WES and 15,708 WGS]. We find that pediatric cancer predisposition syndrome (pCPS) genes [n = 85] are highly constrained, harboring only a quarter of the loss-of-function variants that would be expected. This strong indication of selective pressure on pCPS genes is found across multiple lines of germline genomics data from both pediatric and adult cohorts. For six genes [ELP1, GPR161, VHL and SDHA/B/C], a clear lack of mutational constraint calls the pediatric penetrance and/or severity of associated cancers into question. Conversely, out of 23 known pCPS genes associated with biallelic risk, two [9%, DIS3L2 and MSH2] show significant constraint, indicating that they may monoallelically increase childhood cancer risk. In summary, we show that population genetic data provide empirical evidence that heritable childhood cancer leads to natural selection powerful enough to have significantly impacted the present-day gene pool.

Date: 2024
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DOI: 10.1038/s41467-024-45975-9

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