Improving genetic risk prediction across diverse population by disentangling ancestry representations

Article Multidisciplinary Sciences

Quantifying portable genetic effects and improving cross-ancestry genetic prediction with GWAS summary statistics

Jiacheng Miao et al.

Summary: X-Wing is a statistical framework that improves the predictive performance of polygenic risk scores in ancestrally diverse populations.

NATURE COMMUNICATIONS (2023)

Add to Collection

Article Genetics & Heredity

SDPRX: A statistical method for cross- population prediction of complex traits

Geyu Zhou et al.

Summary: Polygenic risk score (PRS) has been proven highly useful in biomedical research for identifying high-risk individuals based on their genotypes. However, the limited transferability of PRS developed in Europeans to non-European populations has hindered its broader application. To address this, a statistical method called SDPRX is developed, which effectively integrates genome-wide association study data from different populations. SDPRX adjusts for linkage disequilibrium differences and characterizes the joint distribution of variant effect sizes in different populations. Simulation and real trait applications demonstrate that SDPRX improves prediction accuracy in non-European populations compared to existing methods.

AMERICAN JOURNAL OF HUMAN GENETICS (2023)

Add to Collection

Article Biochemical Research Methods

Deep learning-based identification of genetic variants: application to Alzheimer's disease classification

Taeho Jo et al.

Summary: This paper proposes a deep learning-based approach for identification of phenotype-associated SNPs and developing a classification model for AD. The final classification model achieves good accuracy in terms of area under the curve.

BRIEFINGS IN BIOINFORMATICS (2022)

Add to Collection

Article Genetics & Heredity

Improving polygenic prediction in ancestrally diverse populations

Yunfeng Ruan et al.

Summary: PRS-CSx is a method that improves cross-population polygenic prediction by integrating GWAS summary statistics from multiple populations. It can enhance the predictive performance of polygenic risk scores in non-European populations and reduce healthcare disparities.

NATURE GENETICS (2022)

Add to Collection

Article Genetics & Heredity

Leveraging fine-mapping and multipopulation training data to improve cross-population polygenic risk scores

Omer Weissbrod et al.

Summary: PolyPred and PolyPred(+) methods greatly improve cross-population polygenic prediction accuracy, particularly when applied to diseases and complex traits in UK Biobank populations. This is crucial for reducing health disparities in non-European populations.

NATURE GENETICS (2022)

Add to Collection

Article Genetics & Heredity

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

Adrien Badre et al.

Summary: Polygenic risk scores (PRS) estimate genetic risk for complex diseases based on genetic variants across the genome. A deep neural network (DNN) outperformed other models in estimating breast cancer PRS, successfully separating the population into high-risk and normal-risk subpopulations, with better recall and precision rates.

JOURNAL OF HUMAN GENETICS (2021)

Add to Collection

Article Genetics & Heredity

Tractor uses local ancestry to enable the inclusion of admixed individuals in GWAS and to boost power

Elizabeth G. Atkinson et al.

Summary: Tractor is a statistical framework and software package that leverages local ancestry to include admixed individuals in association studies, boosting GWAS power and improving the resolution of association signals.

NATURE GENETICS (2021)

Add to Collection

Article Genetics & Heredity

Genome-wide meta-analysis, fine-mapping and integrative prioritization implicate new Alzheimer's disease risk genes

Jeremy Schwartzentruber et al.

Summary: A genome-wide AD meta-analysis identified 37 risk loci, including new associations near CCDC6, TSPAN14, NCK2, and SPRED2. By fine-mapping SNPs and using functional annotation, 21 SNPs with >50% probability of being causally involved in AD risk were identified. Protein interaction networks and tissue-specific expression helped prioritize genes, leading to the discovery of likely causal genes.

NATURE GENETICS (2021)

Add to Collection

Article Genetics & Heredity

A unified framework for cross-population trait prediction by leveraging the genetic correlation of polygenic traits

Mingxuan Cai et al.

Summary: This study introduces a cross-population analysis framework for polygenic risk score (PRS) construction, which leverages trans-ancestry genetic correlation to improve risk prediction accuracy in non-European populations and incorporates population-specific effects to enhance PRS construction. The methods show significant savings in computational time and memory usage, and through simulation studies demonstrate accurate and efficient PRS construction across various genetic architectures.

AMERICAN JOURNAL OF HUMAN GENETICS (2021)

Add to Collection

Editorial Material Obstetrics & Gynecology

Race and Genetic Ancestry in Medicine-A Time for Reckoning With Racism

[Anonymous]

Summary: The article underscores the importance of considering race and ethnicity in biomedical research and clinical practice. While race/ethnicity data have been used to assess differences in clinical measures and outcomes, there are challenges and controversies that need to be carefully analyzed. It is crucial to continue using racial/ethnic categories to address health inequities until more precise predictors are available.

OBSTETRICAL & GYNECOLOGICAL SURVEY (2021)

Add to Collection

Article Multidisciplinary Sciences

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

Ganna Leonenko et al.

Summary: Polygenic Risk Scores for Alzheimer's disease offer unique possibilities for reliably identifying individuals at high and low risk. The study shows that the best prediction accuracy is achieved with a model including APOE and a polygenic score excluding APOE. Standardizing PRS against the population mean makes individuals' scores comparable between studies.

NATURE COMMUNICATIONS (2021)

Add to Collection

Review Clinical Neurology