Mixture model-based association analysis with case-control data in genome wide association studies

ALI Fadhaa; Jian Zhang

doi:10.1515/sagmb-2016-0022

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Publication Date

Sun Jan 01 2017

Journal Name

Statistical Applications In Genetics And Molecular Biology

Volume

16

DOI

10.1515/sagmb-2016-0022

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Mixture model-based association analysis with case-control data in genome wide association studies

genome wide association studies

haplotype mixture model

odds ratios

testing for inheritance patterns

ALI Fadhaa

Jian Zhang

...Show More Authors

AbstractMultilocus haplotype analysis of candidate variants with genome wide association studies (GWAS) data may provide evidence of association with disease, even when the individual loci themselves do not. Unfortunately, when a large number of candidate variants are investigated, identifying risk haplotypes can be very difficult. To meet the challenge, a number of approaches have been put forward in recent years. However, most of them are not directly linked to the disease-penetrances of haplotypes and thus may not be efficient. To fill this gap, we propose a mixture model-based approach for detecting risk haplotypes. Under the mixture model, haplotypes are clustered directly according to their estimated disease penetrances. A theoretical justification of the above model is provided. Furthermore, we introduce a hypothesis test for haplotype inheritance patterns which underpin this model. The performance of the proposed approach is evaluated by simulations and real data analysis. The results show that the proposed approach outperforms an existing multiple testing method.

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Publication Date

Fri Jan 13 2023

Journal Name

The Plant Genome

Genome‐wide association analysis of spike and kernel traits in the U.S. hard winter wheat

Jyotirmoy

Harsimardeep S.

Jinfeng

Rami

Eric

Brent

Sunish K.

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Abstract A better understanding of the genetic control of spike and kernel traits that have higher heritability can help in the development of high‐yielding wheat varieties. Here, we identified the marker‐trait associations (MTAs) for various spike‐ and kernel‐related traits in winter wheat ( <italic>Triticum aestivum</italic> L.) through genome‐wide association studies (GWAS). An association mapping panel comprising 297 hard winter wheat accessions from the U.S. Great Plains was evaluated for eight spike‐ and kernel‐related traits in three different environments. A GWAS using 15,590 single‐nucleotide pol ... Show More

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(20)

Publication Date

Tue Jun 15 2021

Journal Name

Scientific Reports

Genome-wide association analysis permits characterization of Stagonospora nodorum blotch (SNB) resistance in hard winter wheat

Rami

Harsimardeep S.

Shaukat

Girma

Jyotirmoy

Jagdeep S.

Upinder S.

Brent

Jose L. Gonzalez

Sunish K.

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AbstractStagonospora nodorum blotch (SNB) is an economically important wheat disease caused by the necrotrophic fungus<italic>Parastagonospora nodorum</italic>. SNB resistance in wheat is controlled by several quantitative trait loci (QTLs). Thus, identifying novel resistance/susceptibility QTLs is crucial for continuous improvement of the SNB resistance. Here, the hard winter wheat association mapping panel (HWWAMP) comprising accessions from breeding programs in the Great Plains region of the US, was evaluated for SNB resistance and necrotrophic effectors (NEs) sensitivity at the seedling stage. A genome-wide association study (GWAS) was performed to identify single‐nucleotide polymorphism (SNP ... Show More

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(24)

Publication Date

Wed Feb 05 2020

Journal Name

Frontiers In Genetics

Genome-Wide Association Study Uncovers Novel Genomic Regions Associated With Coleoptile Length in Hard Winter Wheat

Jagdeep Singh

Dilkaran

Harsimardeep Singh

Navreet Kaur

Yeyan

Jyotirmoy

Rami

Brent

Sunish Kumar

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(35)

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Sun Nov 01 2026

Journal Name

Diagnostic Microbiology And Infectious Disease

Investigation in genomic signatures of helicobacter pylori through a microbial-genome wide association study exploring virulence variation

Abdulameer M.

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Publication Date

Fri Jan 01 2016

Journal Name

Machine Learning And Data Mining In Pattern Recognition

A New Strategy for Case-Based Reasoning Retrieval Using Classification Based on Association

Ahmed

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Publication Date

Thu Jan 01 2026

Journal Name

International Journal Of Dentistry

Association of Salivary HIF‐1α Level With Epithelial and Mesenchymal Markers in Smokers and Nonsmokers With Periodontitis: A Case‐Control Study

Ban Emad

Saif Sehaam

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Objectives

This case–control study aimed to investigate the relationship between the hypoxia‐related biomarker hypoxia‐inducible factor‐1α (HIF‐1α) and the epithelial‐mesenchymal transition (EMT)–associated markers E‐cadherin (E‐CAD) and N‐cadherin (N‐CAD) in saliva among smokers and nonsmokers with and without periodontitis and to assess their association with clinical periodontal parameters.

Methods

A case–control study was conducted, including 88 participants equally a

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Publication Date

Tue Jan 01 2019

Journal Name

Molecular Biology Research Communications

Association study of two single nucleotide polymorphisms rs10757278 and rs1333049 with atherosclerosis, a case-control study from Iraq

A.A.

Hanan Y. Muhsin

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Publication Date

Tue Jul 01 2025

Journal Name

Journal Of Breast Diseases

Association Between Serum Interleukin-41 Levels and Breast Cancer Status: A Case–Control Study in Iraqi Women

Zahraa

istikrar

Ali

Maryam M

Zainab

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(1)

Publication Date

Wed Nov 01 2023

Journal Name

Clinical Epidemiology And Global Health

The association of interleukin-10 single nucleotide polymorphisms (rs1800871) and serum levels in Iraqi patients with celiac disease: A case-control study

Ali

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Publication Date

Wed Sep 01 2021

Journal Name

Baghdad Science Journal

Measuring Positive and Negative Association of Apriori Algorithm with Cosine Correlation Analysis

apriori

association-rule-mining

aprioricosine-correlation-analysis

data-mining

Dewi Wisnu

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This work aims to see the positive association rules and negative association rules in the Apriori algorithm by using cosine correlation analysis. The default and the modified Association Rule Mining algorithm are implemented against the mushroom database to find out the difference of the results. The experimental results showed that the modified Association Rule Mining algorithm could generate negative association rules. The addition of cosine correlation analysis returns a smaller amount of association rules than the amounts of the default Association Rule Mining algorithm. From the top ten association rules, it can be seen that there are different rules between the default and the modified Apriori algorithm. The difference of the obta

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