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Polygenic risk scores for prediction of breast cancer risk in Asian populations.


ABSTRACT:

Purpose

Non-European populations are under-represented in genetics studies, hindering clinical implementation of breast cancer polygenic risk scores (PRSs). We aimed to develop PRSs using the largest available studies of Asian ancestry and to assess the transferability of PRS across ethnic subgroups.

Methods

The development data set comprised 138,309 women from 17 case-control studies. PRSs were generated using a clumping and thresholding method, lasso penalized regression, an Empirical Bayes approach, a Bayesian polygenic prediction approach, or linear combinations of multiple PRSs. These PRSs were evaluated in 89,898 women from 3 prospective studies (1592 incident cases).

Results

The best performing PRS (genome-wide set of single-nucleotide variations [formerly single-nucleotide polymorphism]) had a hazard ratio per unit SD of 1.62 (95% CI = 1.46-1.80) and an area under the receiver operating curve of 0.635 (95% CI = 0.622-0.649). Combined Asian and European PRSs (333 single-nucleotide variations) had a hazard ratio per SD of 1.53 (95% CI = 1.37-1.71) and an area under the receiver operating curve of 0.621 (95% CI = 0.608-0.635). The distribution of the latter PRS was different across ethnic subgroups, confirming the importance of population-specific calibration for valid estimation of breast cancer risk.

Conclusion

PRSs developed in this study, from association data from multiple ancestries, can enhance risk stratification for women of Asian ancestry.

SUBMITTER: Ho WK 

PROVIDER: S-EPMC7612481 | biostudies-literature | 2022 Mar

REPOSITORIES: biostudies-literature

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Publications

Polygenic risk scores for prediction of breast cancer risk in Asian populations.

Ho Weang-Kee WK   Tai Mei-Chee MC   Dennis Joe J   Shu Xiang X   Li Jingmei J   Ho Peh Joo PJ   Millwood Iona Y IY   Lin Kuang K   Jee Yon-Ho YH   Lee Su-Hyun SH   Mavaddat Nasim N   Bolla Manjeet K MK   Wang Qin Q   Michailidou Kyriaki K   Long Jirong J   Wijaya Eldarina Azfar EA   Hassan Tiara T   Rahmat Kartini K   Tan Veronique Kiak Mien VKM   Tan Benita Kiat Tee BKT   Tan Su Ming SM   Tan Ern Yu EY   Lim Swee Ho SH   Gao Yu-Tang YT   Zheng Ying Y   Kang Daehee D   Choi Ji-Yeob JY   Han Wonshik W   Lee Han-Byoel HB   Kubo Michiki M   Okada Yukinori Y   Namba Shinichi S   Park Sue K SK   Kim Sung-Won SW   Shen Chen-Yang CY   Wu Pei-Ei PE   Park Boyoung B   Muir Kenneth R KR   Lophatananon Artitaya A   Wu Anna H AH   Tseng Chiu-Chen CC   Matsuo Keitaro K   Ito Hidemi H   Kwong Ava A   Chan Tsun L TL   John Esther M EM   Kurian Allison W AW   Iwasaki Motoki M   Yamaji Taiki T   Kweon Sun-Seog SS   Aronson Kristan J KJ   Murphy Rachel A RA   Koh Woon-Puay WP   Khor Chiea-Chuen CC   Yuan Jian-Min JM   Dorajoo Rajkumar R   Walters Robin G RG   Chen Zhengming Z   Li Liming L   Lv Jun J   Jung Keum-Ji KJ   Kraft Peter P   Pharoah Paul D B PDB   Dunning Alison M AM   Simard Jacques J   Shu Xiao-Ou XO   Yip Cheng-Har CH   Taib Nur Aishah Mohd NAM   Antoniou Antonis C AC   Zheng Wei W   Hartman Mikael M   Easton Douglas F DF   Teo Soo-Hwang SH  

Genetics in medicine : official journal of the American College of Medical Genetics 20211215 3


<h4>Purpose</h4>Non-European populations are under-represented in genetics studies, hindering clinical implementation of breast cancer polygenic risk scores (PRSs). We aimed to develop PRSs using the largest available studies of Asian ancestry and to assess the transferability of PRS across ethnic subgroups.<h4>Methods</h4>The development data set comprised 138,309 women from 17 case-control studies. PRSs were generated using a clumping and thresholding method, lasso penalized regression, an Emp  ...[more]

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