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Tutorial: a guide to performing polygenic risk score analyses

bioRxiv, 2018
A polygenic score (PGS) or polygenic risk score (PRS) is an estimate of an individual’s genetic liability to a trait or disease, calculated according to their genotype profile and relevant genome-wide association study (GWAS) data.
S. Choi, Timothy Shin Heng Mak, P. O’Reilly   +2 more
semanticscholar   +2 more sources

Deep neural network improves the estimation of polygenic risk scores for breast cancer [PDF]

A. Badr\'e, L. Zhang, W. Muchero, J.C. Reynolds, C. Pan (2021). Deep neural network improves the estimation of polygenic risk scores for breast cancer. Journal of Human Genetics, 66(4), 359-369, 2023
Polygenic risk scores (PRS) estimate the genetic risk of an individual for a complex disease based on many genetic variants across the whole genome. In this study, we compared a series of computational models for estimation of breast cancer PRS. A deep neural network (DNN) was found to outperform alternative machine learning techniques and established ...
arxiv   +1 more source

Development and validation of a trans-ancestry polygenic risk score for type 2 diabetes in diverse populations

Genome Medicine, 2022
Type 2 diabetes (T2D) is a worldwide scourge caused by both genetic and environmental risk factors that disproportionately afflicts communities of color.
T. Ge, M. Irvin, A. Patki, V. Srinivasasainagendra, Yen-Feng Lin, H. Tiwari, N. Armstrong, Barbara Benoit, Chia-Yen Chen, Karmel W. Choi, J. Cimino, Brittney H. Davis, O. Dikilitas, Bethany Etheridge, Y. Feng, V. Gainer, Hailiang Huang, G. Jarvik, C. Kachulis, E. Kenny, Atlas Khan, K. Kiryluk, L. Kottyan, I. Kullo, C. Lange, N. Lennon, A. Leong, E. Malolepsza, Ayme D. Miles, S. Murphy, B. Namjou, Renuka Narayan, Mark J O'Connor, J. Pacheco, E. Perez, L. Rasmussen-Torvik, E. Rosenthal, D. Schaid, M. Stamou, M. Udler, Wei-Qi Wei, Scott T. Weiss, M. Ng, J. Smoller, Matthew S. Lebo, J. Meigs, N. Limdi, E. Karlson   +47 more
semanticscholar   +1 more source

The roles of MMP8/MMP10 polymorphisms in ischemic stroke susceptibility

Brain and Behavior, Volume 12, Issue 12, December 2022., 2022
Abstract Background Ischemic stroke (IS), a multifactorial and polygenic disease, is the most common cause of death. This study aimed to determine the roles of MMP8/MMP10 polymorphisms in IS susceptibility in the Chinese Han population. Methods MMP8 rs1940475 and rs3765620, and MMP10 rs17860949 from 700 IS patients and 700 controls were genotyped by ...
Yong Zhao, Qi Zhang, Xiaobo Zhang, Yu Zhang, Ying Lu, Xiaojuan Ma, Weiping Li, Xiaochen Niu, Gejuan Zhang, Mingze Chang, Wenzhen Shi, Ye Tian   +11 more
wiley   +1 more source

Identifying individuals with high risk of Alzheimer’s disease using polygenic risk scores

Nature Communications, 2021
While polygenic risk scores have been shown to be correlated with disease risk, there is little agreement on how the score should be calculated. Here the authors investigate risk scores for Alzheimer’s disease, finding that the most effective approach ...
Ganna Leonenko, Emily Baker, Joshua Stevenson-Hoare, Annerieke Sierksma, Mark Fiers, Julie Williams, Bart de Strooper, Valentina Escott-Price   +7 more
doaj   +1 more source

Polygenic risk scores: a biased prediction? [PDF]

Genome Medicine, 2018
A new study highlights the biases and inaccuracies of polygenic risk scores (PRS) when predicting disease risk in individuals from populations other than those used in their derivation. The design bias of workhorse tools used for research, particularly genotyping arrays, contributes to these distortions.
Francisco M. De La Vega, Carlos D. Bustamante   +1 more
openaire   +3 more sources

HIVEP3 cooperates with ferroptosis gene signatures to confer adverse prognosis in acute myeloid leukemia

Cancer Medicine, Volume 11, Issue 24, Page 5050-5065, December 2022., 2022
The aberrant expression pattern and prognostic implications of HIVEP3 in AML were explored and validated based on versatile bioinformatics tools. A LASSO model which combined HIVEP3 with ferroptosis regulators was created to predict the prognosis for AML patients.
Xiaoning Zhang, Xiaoyu Zhang, Kuo Liu, Wenwen Li, Jiazheng Wang, Peng Liu, Wanshan Ma   +6 more
wiley   +1 more source

Implementation and implications for polygenic risk scores in healthcare [PDF]

Human Genomics, 2021
AbstractIncreasing amounts of genetic data have led to the development of polygenic risk scores (PRSs) for a variety of diseases. These scores, built from the summary statistics of genome-wide association studies (GWASs), are able to stratify individuals based on their genetic risk of developing various common diseases and could potentially be used to ...
John L. Slunecka, Matthijs D. van der Zee, Jeffrey J. Beck, Brandon N. Johnson, Casey T. Finnicum, René Pool, Jouke-Jan Hottenga, Eco J. C. de Geus, Erik A. Ehli   +8 more
openaire   +4 more sources

Polygenic Risk Scores Expand to Obesity [PDF]

Cell, 2019
Obesity is one of the most serious health challenges of our time. In this issue of Cell, Khera and co-authors demonstrate the striking ability of genetics, in the form of a polygenic risk score, to identify those individuals at high risk for obesity.
Ali Torkamani, Eric J. Topol
openaire   +3 more sources

Design and user experience testing of a polygenic score report: a qualitative study of prospective users

BMC Medical Genomics, 2021
Background Polygenic scores—which quantify inherited risk by integrating information from many common sites of DNA variation—may enable a tailored approach to clinical medicine. However, alongside considerable enthusiasm, we and others have highlighted a
Deanna G. Brockman, Lia Petronio, Jacqueline S. Dron, Bum Chul Kwon, Trish Vosburg, Lisa Nip, Andrew Tang, Mary O’Reilly, Niall Lennon, Bang Wong, Kenney Ng, Katherine H. Huang, Akl C. Fahed, Amit V. Khera   +13 more
doaj   +1 more source