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Polygenic score

The two graphics illustrate sampling distributions of polygenic scores and the predictive ability of stratified sampling on polygenic risk score with increasing age. + The left panel shows how risk—(the standardized PRS on the x-axis)—can separate 'cases' (i.e., individuals with a certain disease, (red)) from the 'controls' (individuals without the disease, (blue)). The y-axis (vertical axis) indicates how many in each group are assigned a certain score. + At the right panel, the same population is divided into three groups according to their predicted risk, i.e., their assigned score, as high (red), middle (gray), or low (blue). The y-axis shows the observed risk amounts, where the x-axis shows the groups separating in risk as they age—corresponding with the predicted risk scores.

In genetics, a polygenic score (PGS) is a number that summarizes the estimated effect of many genetic variants on an individual's phenotype. The PGS is also called the polygenic index (PGI) or genome-wide score; in the context of disease risk, it is called a polygenic risk score (PRS or PR score[1]) or genetic risk score. The score reflects an individual's estimated genetic predisposition for a given trait and can be used as a predictor for that trait.[2][3][4][5][6] It gives an estimate of how likely an individual is to have a given trait based only on genetics, without taking environmental factors into account; and it is typically calculated as a weighted sum of trait-associated alleles.[7][8][9]

Recent progress in genetics has developed polygenic predictors of complex human traits, including risk for many important complex diseases[10][11] that are typically affected by many genetic variants, each of which confers a small effect on overall risk.[12][13] In a polygenic risk predictor the lifetime (or age-range) risk for the disease is a numerical function captured by the score which depends on the states of thousands of individual genetic variants (i.e., single-nucleotide polymorphisms, or SNPs).

Polygenic scores are widely used in animal breeding and plant breeding due to their efficacy in improving livestock breeding and crops.[14] In humans, polygenic scores are typically generated from data of genome-wide association study (GWAS). They are an active area of research spanning topics such as learning algorithms for genomic prediction; new predictor training; validation testing of predictors; and clinical application of PRS.[15][16][17][4][11] In 2018, the American Heart Association named polygenic risk scores as one of the major breakthroughs in research in heart disease and stroke.[18]

  1. ^ Gregory, Gillian; Das Gupta, Kuheli; Meiser, Bettina; Barlow-Stewart, Kristine; Geelan-Small, Peter; Kaur, Rajneesh; Scheepers-Joynt, Maatje; McInerny, Simone; Taylor, Shelby; Antill, Yoland; Salmon, Lucinda; Smyth, Courtney; Young, Mary-Anne; James, Paul A; Yanes, Tatiane (February 2022). "Polygenic risk in familial breast cancer: Changing the dynamics of communicating genetic risk". Journal of Genetic Counseling. 31 (1): 120–129. doi:10.1002/jgc4.1458. hdl:1959.4/unsworks_78566. PMID 34223688. S2CID 235732957.
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  5. ^ Yanes T, Meiser B, Kaur R, Scheepers-Joynt M, McInerny S, Taylor S, et al. (March 2020). "Uptake of polygenic risk information among women at increased risk of breast cancer". Clinical Genetics. 97 (3): 492–501. doi:10.1111/cge.13687. hdl:11343/286783. PMID 31833054. S2CID 209342044.
  6. ^ Vilhjálmsson BJ, Yang J, Finucane HK, Gusev A, Lindström S, Ripke S, et al. (October 2015). "Modeling Linkage Disequilibrium Increases Accuracy of Polygenic Risk Scores". American Journal of Human Genetics. 97 (4): 576–592. doi:10.1016/j.ajhg.2015.09.001. PMC 4596916. PMID 26430803.
  7. ^ Dudbridge F (March 2013). "Power and predictive accuracy of polygenic risk scores". PLOS Genetics. 9 (3): e1003348. doi:10.1371/journal.pgen.1003348. PMC 3605113. PMID 23555274.
  8. ^ Torkamani A, Wineinger NE, Topol EJ (September 2018). "The personal and clinical utility of polygenic risk scores". Nature Reviews. Genetics. 19 (9): 581–590. doi:10.1038/s41576-018-0018-x. PMID 29789686. S2CID 46893131.
  9. ^ Lambert SA, Abraham G, Inouye M (November 2019). "Towards clinical utility of polygenic risk scores". Human Molecular Genetics. 28 (R2): R133 – R142. doi:10.1093/hmg/ddz187. PMID 31363735.
  10. ^ Regalado A (8 March 2019). "23andMe thinks polygenic risk scores are ready for the masses, but experts aren't so sure". MIT Technology Review. Retrieved 2020-08-14.
  11. ^ a b Lello L, Raben TG, Yong SY, Tellier LC, Hsu SD (October 2019). "Genomic Prediction of 16 Complex Disease Risks Including Heart Attack, Diabetes, Breast and Prostate Cancer". Scientific Reports. 9 (1): 15286. Bibcode:2019NatSR...915286L. doi:10.1038/s41598-019-51258-x. PMC 6814833. PMID 31653892.
  12. ^ Visscher PM, Wray NR, Zhang Q, Sklar P, McCarthy MI, Brown MA, Yang J (July 2017). "10 Years of GWAS Discovery: Biology, Function, and Translation". American Journal of Human Genetics. 101 (1): 5–22. doi:10.1016/j.ajhg.2017.06.005. PMC 5501872. PMID 28686856.
  13. ^ Spiliopoulou A, Nagy R, Bermingham ML, Huffman JE, Hayward C, Vitart V, et al. (July 2015). "Genomic prediction of complex human traits: relatedness, trait architecture and predictive meta-models". Human Molecular Genetics. 24 (14): 4167–4182. doi:10.1093/hmg/ddv145. PMC 4476450. PMID 25918167.
  14. ^ Spindel JE, McCouch SR (December 2016). "When more is better: how data sharing would accelerate genomic selection of crop plants". The New Phytologist. 212 (4): 814–826. doi:10.1111/nph.14174. PMID 27716975.
  15. ^ "Modern genetics will improve health and usher in "designer" children". The Economist. 2019-11-09. Retrieved 2021-04-12.
  16. ^ "Test could predict risk of future heart disease for just £40". The Guardian. 2018-10-08. Retrieved 2021-04-12.
  17. ^ Raben TG, Lello L, Widen E, Hsu SD (2021-01-14). "From Genotype to Phenotype: polygenic prediction of complex human traits". arXiv:2101.05870 [q-bio].
  18. ^ "Big picture genetic scoring approach reliably predicts heart disease". Science Daily. 2019-06-11. Retrieved 2021-04-12.

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