Gene-based Hardy–Weinberg equilibrium test using genotype count data: application to six types of cancers

BMC Genomics, Год журнала: 2025, Номер 26(1)

Опубликована: Фев. 10, 2025

An alternative approach to investigate associations between genetic variants and disease is examine deviations from the Hardy–Weinberg equilibrium (HWE) in genotype frequencies within a case population, instead of case–control association analysis. The HWE analysis requires cases demonstrates notable ability mapping recessive variants. Allelic heterogeneity common phenomenon diseases. While gene-based successfully incorporates this heterogeneity, there are no such approaches for Therefore, we proposed test (gene-HWT) by aggregating single-nucleotide polymorphism (SNP)-level statistics gene address allelic heterogeneity. This method used only count data publicly available linkage disequilibrium information has very low computational cost. Extensive simulations demonstrated that gene-HWT effectively controls type I error at significance level outperforms SNP-level power when multiple causal gene. Using gene-HWT, analyzed genome-wide study six cancer types Japanese individuals suggest DGKE ANO3 as potential germline factors colorectal cancer. Furthermore, FSTL4 was suggested through combined across types, with particularly observed prostate cancers. These findings indicate elucidate basis complex diseases, including

Язык: Английский

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Integrative Multi-Omics Approaches for Identifying and Characterizing Biological Elements in Crop Traits: Current Progress and Future Prospects

International Journal of Molecular Sciences, Год журнала: 2025, Номер 26(4), С. 1466 - 1466

Опубликована: Фев. 10, 2025

The advancement of multi-omics tools has revolutionized the study complex biological systems, providing comprehensive insights into molecular mechanisms underlying critical traits across various organisms. By integrating data from genomics, transcriptomics, metabolomics, and other omics platforms, researchers can systematically identify characterize elements that contribute to phenotypic traits. This review delves recent progress in applying approaches elucidate genetic, epigenetic, metabolic networks associated with key plants. We emphasize potential these integrative strategies enhance crop improvement, optimize agricultural practices, promote sustainable environmental management. Furthermore, we explore future prospects field, underscoring importance cutting-edge technological advancements need for interdisciplinary collaboration address ongoing challenges. bridging this aims provide a holistic framework advancing research plant biology agriculture.

Язык: Английский

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An evolving understanding of multiple causal variants underlying genetic association signals

The American Journal of Human Genetics, Год журнала: 2025, Номер unknown

Опубликована: Фев. 1, 2025

Язык: Английский

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Using genome‐wide associations and host‐by‐pathogen predictions to identify allelic interactions that control disease resistance

The Plant Genome, Год журнала: 2025, Номер 18(1)

Опубликована: Фев. 24, 2025

Abstract Characterizing the molecular mechanisms underlying disease symptom expression has been used to improve human health and resistance in crops animal breeds. Quantitative trait loci genome‐wide association studies (GWAS) are widely identify genomic regions that involved progression. This study extends traditional GWAS significance tests of host pathogen marker main effects by utilizing dual‐genome reaction norm models evaluate importance host‐single nucleotide polymorphism (SNP) pathogen‐SNP interactions. Disease severity data from Fusarium ear rot (FER) on maize ( Zea mays L.) is demonstrate use both genomes selection for breeding identification interact across organisms impact FER development. Dual genome prediction improved heritability estimates, error variances, model accuracy while providing predictions host‐by‐pathogen interactions may be test SNP–SNP Independent populations identified significantly associated were using two different tests. Predictions dual with population structure or polygenic effects. As well, incorporating markers also included relationship matrices account structure. Subsequent evaluation protein–protein candidate genes near interacting SNPs provides a further silico method expedite genes.

Язык: Английский

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Dimensional and transdiagnostic phenotypes in psychiatric genome-wide association studies

Molecular Psychiatry, Год журнала: 2023, Номер 28(12), С. 4943 - 4953

Опубликована: Июль 4, 2023

Язык: Английский

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