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Mixture model-based association analysis with case-control data in genome wide association studies
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Abstract<p>Multilocus 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.</p>
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Publication Date
Sat Jan 01 2022
Journal Name
Proceeding Of The 1st International Conference On Advanced Research In Pure And Applied Science (icarpas2021): Third Annual Conference Of Al-muthanna University/college Of Science
Interleukin 2−330 single nucleotide polymorphism association with type 1 diabetes in Iraqi patients
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Type 1 diabetes (T1D) is an autoimmune disease with chronic nature resulting from a combination of both factors genetic and environmental. The genetic contributors of T1D among Iraqis are unexplored enough. The study aimed to shed a light on the contribution between genetic variation of interleukin2 (IL2) gene to T1D as a risk influencer in a sample of Iraqi patients. The association between IL2−330 polymorphism (rs2069762) was investigated in 322 Iraqis (78 T1D patients and 244 volunteers as controls). Genotyping for the haplotypes using polymerase chain reaction test – specific sequence primer (PCR-SSP) for (GG, GT, and TT) genotypes corresponding to (G and T) alleles were performed. A significant association revealed a decreased freq

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Publication Date
Thu Feb 01 2024
Journal Name
Baghdad Science Journal
Association of pvc genes expression with Biofilm formation in Clinical Isolates of Pseudomonas aeruginosa
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PvcABCD are cluster of genes found in Pseudomonas aeruginosa. The research was designed to examine the relationship between the pvc genes expression and cupB gene, which plays a crucial role in the development of biofilm, and rhlR, which regulates the expression of biofilm-related genes, and to investigate whether the pvc genes form one or two operons. The aims were achieved by employing qRT-PCR technique to measure the gene expression of genes of interest. It was found that out of 25 clinical isolates, 21 isolates were qualified as P.aeruginosa. Amongst, 18(85.7%) were evaluated as biofilm producers, 10 (47.6%), 5 (23.8%), and 3 (14.2%) were evaluated as strong, moderate and weak producers respectively, while, 3 (14.2%) were considered

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Publication Date
Mon Feb 01 2021
Journal Name
Meta Gene
Association analysis of FTO gene polymorphisms rs9939609 and obesity risk among the adults: A systematic review and meta-analysis
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Publication Date
Sun Jan 01 2023
Journal Name
The Egyptian Journal Of Hospital Medicine
Association of Microrna-153-3p Expression in Response to Treatment with Imatinib in Patients with Chronic Myeloid Leukemia
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The study aimed to establish the association of miR-153-3p expression with treatment response to IM in CML patients. Sixty CML patients were included and divided into two groups consistent with their response to treatment whether sensitive or resistant to IM. Ten healthy normal participants were enrolled as control group. RNA was extracted from serum to work out miR-153-3p expression utilizing real-time quantitative reverse transcription polymerase chain reaction. The primers were supplied by Macrogen Inc. Twenty seven patients were sensitive to imatinib and 33 were resistant to imatinib. The ratio of male to female was 1.14:1. The bulk (58%) of patients were within the age range of 41-60 years. Weight and gender did not significantly diffe

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Publication Date
Wed Apr 08 2020
Journal Name
Biochemical & Cellular Archives .
PURIFICATION OF RHODANESE (RHD) AND ITS ASSOCIATION WITH MDA AND PEROXYNITRITE IN PATIENTS WITH TYPE II DIABETES.
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Publication Date
Tue Jun 25 2024
Journal Name
World Academy Of Sciences Journal
Expression of programmed death ligand 1 in patients with triple‑negative breast cancer: Association with clinicopathological parameters
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The utilization of targeted therapy for programmed death ligand 1 (PD‑L1) has emerged as a prominent focus in contemporary clinical trials, particularly in the context of immune checkpoint inhibitors. The prognostic significance of the expression of PD‑L1 in invasive mammary cancer remains a subject of discussion in clinical oncology, requiring further exploration, despite its recognition as a biomarker for responsiveness to anti‑PDL1 immunotherapy. The present study was conducted to investigate the immunohistological expression of PD‑L1 in women with triple‑negative breast cancer (TNBC), with a particular focus for searching for the associated clinical and pathological characteristics. The present retrospective study examined the

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Publication Date
Sun Mar 30 2025
Journal Name
Journal Of Systems Science And Mathematical Sciences
SCREENING TESTS FOR DISEASE RISK HAPLOTYPE SEGMENTS IN GENOME BY USE OF PERMUTATION
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The haplotype association analysis has been proposed to capture the collective behavior of sets of variants by testing the association of each set instead of individual variants with the disease.Such an analysis typically involves a list of unphased multiple-locus genotypes with potentially sparse frequencies in cases and controls.It starts with inferring haplotypes from genotypes followed by a haplotype co-classification and marginal screening for disease-associated haplotypes.Unfortunately,phasing uncertainty may have a strong effects on the haplotype co-classification and therefore on the accuracy of predicting risk haplotypes.Here,to address the issue,we propose an alternative approach:In Stage 1,we select potential risk genotypes inste

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Publication Date
Sun Mar 06 2016
Journal Name
Baghdad Science Journal
Association of Glutathione–S-Transferase (GSTP1) Genetic Polymorphism in Iraqi Patients with Diabetes Mellitus Type2
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Glutathione S-transferases (GSTs) are enzymes that included, in a more range of detoxifying reactions by conjugation of glutathione, to electrophilic material. Polymorphisms n the genes that responsible of GSTs affect, the function of the GSTs. GSTs play an active role in protection of cell against oxidative stress mechanism. Polymorphisms of GSTP1 at codon 105 amino acids forms GSTP1 important site for bind of hydrophobic electrophiles and the substitution of Ile/Val affect substrate specially catalytic activity of the enzyme and may correlate with reach to different diseases in human like diabetes mellitus type2 disease. Correlation between these polymorphisms and changes in the parameters file of diabetic patients has also bee

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Publication Date
Mon Nov 23 2015
Journal Name
Sultan Qaboos University Medical Journal
Association of Higher Defensin β-4 Genomic Copy Numbers with Behçet’s Disease in Iraqi Patients
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Publication Date
Tue Jun 01 2021
Journal Name
International Medical Journal Vol. 28, Supplement No. 1, Pp. 46 - 48 , June 2021
Association of enamel defects with nutritional status among primary schools students in Al-Najaf city
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