New Perspective on GWAS: East Asian Populations from the Viewpoint of Selection Pressure and Linear Algebra with AI

Kanazawa, Masayuki

doi:10.1101/2022.05.27.493710

Cited by 2 publications

(2 citation statements)

References 15 publications

(19 reference statements)

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“…A total of 731 immunophenotypes were included, including absolute cell counts (AC) (n = 118), median fluorescence intensity (MFI) reflecting surface antigen levels (n = 389), morphology parameter (MP) (n = 32), and relative cell count (RC) (n = 192). Specifically, the MFI, AC, and RC features contained B cells, conventional dendritic cells (cDCs), mature T cells, monocytes, myeloid cells, TBNK (T cells, B cells, natural killer cells) and regulatory T (Treg) cells, while the MP feature contained cDCs and TBNK cells only ( Kanazawa, 2022 ). The original immune signature GWAS used data from 3,757 Europeans with no overlap.…”

Section: Methodsmentioning

confidence: 99%

Exploring the immunological landscape of osteomyelitis through mendelian randomization analysis

Long,

Gong,

et al. 2024

Front. Genet.

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Background:Osteomyelitis is a severe bone marrow infection, whose pathogenesis is not yet fully understood. This study aims to explore the causal relationship between immune cell characteristics and osteomyelitis, hoping to provide new insights for the prevention and treatment of osteomyelitis.Methods:Based on two independent samples, this study employed a two-sample Mendelian randomization (MR) analysis to assess the causal relationship between 731 immune cell characteristics (divided into seven groups) and osteomyelitis. Genetic variants were used as proxies for risk factors to ensure that the selected instrumental variables meet the three key assumptions of MR analysis. Genome-Wide Association Studies (GWAS) data for immune characteristics were obtained from the public GWAS catalog, while data for osteomyelitis was sourced from the FinnGen.Results:At a significance level of 0.05, 21 immune phenotypes were identified as having a causal relationship with osteomyelitis development. In the B cell group, phenotypes such as Memory B cell % B cell (percentage of memory B cells within the total B cell population, % finger cell ratio), CD20− %B cell (percentage of B cells that do not express the CD20 marker on their surface), and Memory B cell % lymphocyte showed a positive causal relationship with osteomyelitis, while Naive-mature B cell %B cell and IgD-CD38-absolute cell counts (AC) phenotypes showed a negative causal relationship. In addition, specific immune phenotypes in the conventional dendritic cells (cDCs) group, Myeloid cell group, TBNK (T cells, B cells, natural killer cells) cell group, T cell maturation stage, and Treg cell group also showed significant associations with osteomyelitis. Through reverse MR analysis, it was found that osteomyelitis had no significant causal impact on these immune phenotypes, suggesting that the occurrence of osteomyelitis may not affect these immune cell phenotypes.Conclusion:To our knowledge, this is the first study to shed light on the causal relationship between specific immune cell characteristics and the development of osteomyelitis, thereby providing a new perspective to understand the immune mechanism of osteomyelitis. These findings are significant for formulating targeted prevention and treatment strategies, and hold promise to improve the treatment outcomes for patients with osteomyelitis.

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Section: Methodsmentioning

confidence: 99%

Exploring the immunological landscape of osteomyelitis through mendelian randomization analysis

Long,

Gong,

et al. 2024

Front. Genet.

View full text Add to dashboard Cite

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“…Speci cally, the MFI, AC and RC features contained B cells, CDCs, mature T cells, monocytes, myeloid cells, TBNK (T cells, B cells, natural killer cells) and Treg cells, while the MP feature contained CDCs and TBNK cells (15). The original immune signature GWAS used data from 3757 Europeans with no overlap.…”

Section: Immunity-wide Gwas Data Sourcesmentioning

confidence: 99%

Osteomyelitis and immune cell phenotypes: a study based on a Mendelian randomisation approach

Long,

Dong,

et al. 2023

Preprint

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Background: Osteomyelitis is a severe bone marrow infection, whose pathogenesis is not fully understood. This study aims to explore the causal relationship between immune cell characteristics and osteomyelitis, in hopes of providing new insights for the prevention and treatment of osteomyelitis. Methods: Based on two independent samples, this study employed a two-sample Mendelian randomization (MR) analysis to assess the causal relationship between 731 immune cell characteristics (divided into 7 groups) and osteomyelitis. Genetic variants were used as proxies for risk factors to ensure the selected instrumental variables meet the three key assumptions of MR analysis. GWAS data for immune characteristics came from the public GWAS catalog, while data for osteomyelitis was sourced from the Finnish database. Results: At a significance level of 0.05, 21 immune phenotypes were identified as having a causal relationship with the development of osteomyelitis. In the B cell group, phenotypes such as Memory B cell %B cell, CD20- %B cell, and Memory B cell %lymphocyte showed a positive causal relationship with osteomyelitis, while Naive-mature B cell %B cell and IgD- CD38- AC phenotypes showed a negative causal relationship. In addition, specific immune phenotypes in the cDC cell group, Myeloid cell group, TBNK cell group, T cell maturation stage, and Treg cell group also showed significant associations with osteomyelitis. Through reverse MR analysis, it was found that osteomyelitis had no significant causal impact on these immune phenotypes, suggesting that the occurrence of osteomyelitis might not in turn affect these immune cell phenotypes. Conclusion: This study reveals for the first time the causal relationship between specific immune cell characteristics and the development of osteomyelitis, providing a new perspective for understanding the immune mechanism of osteomyelitis. These findings are significant for formulating targeted prevention and treatment strategies, and hold promise for improving the clinical treatment outcomes of patients’ osteomyelitis.

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New Perspective on GWAS: East Asian Populations from the Viewpoint of Selection Pressure and Linear Algebra with AI

Cited by 2 publications

References 15 publications

Exploring the immunological landscape of osteomyelitis through mendelian randomization analysis

Exploring the immunological landscape of osteomyelitis through mendelian randomization analysis

Osteomyelitis and immune cell phenotypes: a study based on a Mendelian randomisation approach

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