scholarly journals MCKAT, a multi-dimensional copy number variant kernel association test

2021 ◽  
Author(s):  
Nastaran Maus Esfahani ◽  
Daniel Catchpoole ◽  
Javed Khan ◽  
Paul J. Kennedy
Keyword(s):  
Copy Number ◽  
Kernel Method ◽  
Random Effect ◽  
Random Effect Model ◽  
Score Test ◽  
Copy Number Variant ◽  
Association Test ◽  
P Value ◽  
Single Pair ◽  
Related Trait

AbstractBackgroundCopy number variants (CNVs) are the gain or loss of DNA segments in the genome. Studies have shown that CNVs are linked to various disorders, including autism, intellectual disability, and schizophrenia.Consequently, the interest in studying a possible association of CNVs to specific disease traits is growing. However, due to the specific multi-dimensional characteristics of the CNVs, methods for testing the association between CNVs and the disease-related traits are still underdeveloped. We propose a novel multi-dimensional CNV kernel association test (MCKAT) in this paper. We aim to find significant associations between CNVs and disease-related traits using kernel-based methods.ResultsWe address the multi-dimensionality in CNV characteristics. We first design a single pair CNV kernel, which contains three sub-kernels to summarize the similarity between two CNVs considering all CNV characteristics. Then, aggregate single pair CNV kernel to the whole chromosome CNV kernel, which summarizes the similarity between CNVs in two or more chromosomes. Finally, the association between the CNVs and disease-related traits is evaluated by comparing the similarity in the trait with kernel-based similarity using a score test in a random effect model. We apply MCKAT on genome-wide CNV datasets to examine the association between CNVs and disease-related traits, which demonstrates the potential usefulness the proposed method has for the CNV association tests. We compare the performance of MCKAT with CKAT, a uni-dimensional kernel method. Based on the results, MCKAT indicates stronger evidence, smaller p-value, in detecting significant associations between CNVs and disease-related traits in both rare and common CNV datasets.ConclusionA multi-dimensional copy number variant kernel association test can detect significantly associated CNVs with any disease-related trait. MCKAT can help biologists detect significantly associated CNVs with any disease-related trait across a patient group instead of examining the CNVs case by case in each subject.

scholarly journals MCKAT: a multi-dimensional copy number variant kernel association test

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Nastaran Maus Esfahani ◽  
Daniel Catchpoole ◽  
Javed Khan ◽  
Paul J. Kennedy
Keyword(s):  
Copy Number ◽  
Kernel Method ◽  
Random Effect ◽  
Random Effect Model ◽  
Score Test ◽  
Copy Number Variants ◽  
Copy Number Variant ◽  
Association Test ◽  
Single Pair ◽  
Related Trait

Abstract Background Copy number variants (CNVs) are the gain or loss of DNA segments in the genome. Studies have shown that CNVs are linked to various disorders, including autism, intellectual disability, and schizophrenia. Consequently, the interest in studying a possible association of CNVs to specific disease traits is growing. However, due to the specific multi-dimensional characteristics of the CNVs, methods for testing the association between CNVs and the disease-related traits are still underdeveloped. We propose a novel multi-dimensional CNV kernel association test (MCKAT) in this paper. We aim to find significant associations between CNVs and disease-related traits using kernel-based methods. Results We address the multi-dimensionality in CNV characteristics. We first design a single pair CNV kernel, which contains three sub-kernels to summarize the similarity between two CNVs considering all CNV characteristics. Then, aggregate single pair CNV kernel to the whole chromosome CNV kernel, which summarizes the similarity between CNVs in two or more chromosomes. Finally, the association between the CNVs and disease-related traits is evaluated by comparing the similarity in the trait with kernel-based similarity using a score test in a random effect model. We apply MCKAT on genome-wide CNV datasets to examine the association between CNVs and disease-related traits, which demonstrates the potential usefulness the proposed method has for the CNV association tests. We compare the performance of MCKAT with CKAT, a uni-dimensional kernel method. Based on the results, MCKAT indicates stronger evidence, smaller p-value, in detecting significant associations between CNVs and disease-related traits in both rare and common CNV datasets. Conclusion A multi-dimensional copy number variant kernel association test can detect statistically significant associated CNV regions with any disease-related trait. MCKAT can provide biologists with CNV hot spots at the cytogenetic band level that CNVs on them may have a significant association with disease-related traits. Using MCKAT, biologists can narrow their investigation from the whole genome, including many genes and CNVs, to more specific cytogenetic bands that MCKAT identifies. Furthermore, MCKAT can help biologists detect significantly associated CNVs with disease-related traits across a patient group instead of examining each subject’s CNVs case by case.

scholarly journals Comparative efficacy between ketamine, memantine, riluzole and d-cycloserine in patients diagnosed with drug resistant depression: a meta-analysis

2019 ◽  
Vol 8 (6) ◽  
pp. 1132
Author(s):  
Nishita H. Darji ◽  
Devang A. Rana ◽  
Supriya D. Malhotra
Keyword(s):  
Rating Scale ◽  
Meta Analysis ◽  
Random Effect ◽  
Random Effect Model ◽  
Fixed Effect ◽  
P Value ◽  
Drug Resistant ◽  
Effect Model ◽  
Resistant Depression ◽  
Glutamate Modulators

Background: Glutamate modulators are having immense potential and are newer entities for treating drug resistant depression. The objectives were to generate statistical evidence on basis of existing data of ketamine, memantine, riluzole and d-cycloserine in resistant depression.Methods: A total of 14 RCTs following PRISMA guidelines and matching inclusion and exclusion criteria were collected of ketamine (5), memantine (3), riluzole (2) and d-cycloserine (4) vs placebo in drug resistant depression. Only RCTs with primary diagnosis of drug resistant depression (Previously on two standard antidepressant therapy) were included. Studies with treatment response rate, 50% reduction in total score of the depression rating scale-Montgomery-Åsberg Depression Rating Scale or the Hamilton Depression Rating Scale or Beck Depression Inventory was chosen as clinical outcome measure. RevMan 5.3 software was used for the analysis.Results: In ketamine group using random effect model SMD was 2.122 (95% CI 0.659-3.584). P-value was statistically significant (random effect p <0.005 and in fixed effect <0.001). In memantine group, using random effect model -0.963 was SMD and (95% CI -1.958-0.0324). P-value was <0.001, significant in fixed effect. In riluzole group, SMD was -0.564 with (95% CI -3.927-2.799) in random effect. P-value was 0.741. In d-cycloserine group SMD was 0.316 with (95% CI -1.252-1.885) in random effect. P-value was 0.690.Conclusions: Ketamine showed best efficacy followed by memantine. Riluzole and DCS as such have no efficacy although its acts by same glutamate pathway. More molecular based research is required in use of glutamate modulators in resistant depression.

scholarly journals Weight Change and Its Predictors among Newly Initiated ART Clients in Dessie City, Northeast Ethiopia, July 2020. Longitudinal Data Analysis

2020 ◽  
Author(s):  
Zinabu Fentaw ◽  
Reta Dewau ◽  
Muluken Chanie ◽  
Mequannent Melaku ◽  
Melaku Yalew ◽  
...  
Keyword(s):  
Antiretroviral Therapy ◽  
Opportunistic Infection ◽  
Weight Change ◽  
Random Effect ◽  
Random Effect Model ◽  
Least Square ◽  
Clinical Staging ◽  
P Value ◽  
Positive Weight ◽  
Therapy Clients

Abstract Background The weight of HIV/AIDS patients is one of the classifications WHO clinical staging of the diseases. A positive weight change in antiretroviral therapy patients is one of the expected clinical outcomes within a few months after the initiation of antiretroviral therapy in previously naïve patients. But the weight change varies across clients, and the reason for this variation and the effect of time-varying clinical profiles on the weight of the clients is not well investigated. Method: A retrospective cohort study was conducted in Dessie City Health Facility in July 2020. The data were collected using a simple random sampling method in adult antiretroviral therapy clients who were enrolled to care between January to June 2019. Totally, 58 charts were reviewed within three months interval for 6 consecutive observations per chart. The data were entered into Epi-data, and analyzed using Stata 14. The effect of Panel and random effect model was assessed using Breusch and Pagan and Hausman's test, respectively. Finally, the Random Effect Generalize Least Square model was fitted, and variables with a p-value less than 0.05 were considered as the predictors of weight change. Result A total of 58 clients chart with 322 observations were assessed and the mean age (standard deviation) of participants were 37 (10) and 30 (51.7%) of them were female clients. The absence of opportunistic infection (β:1.85; 95% CI:0.66–3.03) the interaction of opportunistic infection and months on Antiretroviral Therapy (β:0.09; 95% CI:0.05–0.13) and advanced WHO clinical stage (β: -3.52; 95% CI: -6.71-(-0.34)) were significantly associated with the weight of adult Antiretroviral Therapy user overtime. Conclusion There is a significant positive weight change after imitation of Antiretroviral Therapy. The absence of opportunistic infection and its interaction with time have a positive change on the weight of adult Antiretroviral Therapy clients whereas, experiencing advanced WHO stage disease over time has a negative effect on the weight change.

Clinical outcome for continuous versus intermittent chemotherapy for unresectable metastatic colorectal cancer: Comparative analysis after first-line therapy.

2018 ◽  
Vol 36 (4_suppl) ◽  
pp. 825-825
Author(s):  
Nadine Abdallah ◽  
AMR Mohamed ◽  
Hibah Ismail ◽  
Wei Chen ◽  
Alaa Akhras ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Statistical Tests ◽  
Random Effect ◽  
Random Effect Model ◽  
Primary Objective ◽  
Induction Treatment ◽  
P Value ◽  
First Line ◽  
Free Interval ◽  
Significant Difference

825 Background: Colorectal cancer (CRC) is the third most common and second most lethal cancer in the U.S, with almost 50% of patients developing metastatic disease. Although survival of metastatic CRC (mCRC) has improved significantly, current treatment strategies are associated with many adverse effects. With no prospect of cure, goals of treatment should consider both quantity and quality of life. Interruption of chemotherapy after induction can represent a means to achieve this balance. Methods: The primary objective of this meta-analysis is to assess the effect of continuation vs interruption of systemic therapy in terms of survival in patients with unresectable mCRC after first line treatment. Among 15 prospective studies published from 2009-2017, 9 qualified for inclusion. Random-effect model was used for pooled effects within two main categories: continuous chemotherapy vs chemotherapy-free interval after first line induction. Studies with maintenance fluoropyrimidine and/or bevacizumab were excluded. Primary endpoint was median progression free survival (PFS) and secondary endpoint was median overall survival (OS). z statistics were used for comparing subgroups. All statistical tests were two-sided. P values < 0.05 were considered significant. Results: 1366 patients (55% males) were included in the final analysis. Induction treatment was 5-FU or capecitabine-based chemotherapy with either oxaliplatin or irinotecan with or without bevacizumab. After stratifying for induction status, there was no statistically significant difference in median PFS between continuous vs chemotherapy free interval [Median PFS 4.74-month (95% CI 3.87-5.61) vs 3.52 month (95% CI 2.97-4.07), z-test adjusted p value 0.1383]. No significant difference in median OS between both groups [Median OS 16.95-month (95% CI 15.40-18.50) vs 18.35 month (95% CI 15.17-21.54)]. Conclusions: In mCRC patients, the superiority of continuous chemotherapy was not demonstrated. Further studies should shed light on patient and tumor characteristics most likely to benefit from continuous chemotherapy to limit delivery of cytotoxic therapy to this subset of patients.

scholarly journals Validity of the Family‐Based Association Test for Copy Number Variant Data in the Case of Non‐Linear Intensity‐Genotype Relationship

2012 ◽  
Vol 36 (8) ◽  
pp. 895-898 ◽  
Author(s):  
Manuela Zanda ◽  
Suna Onengut ◽  
Neil Walker ◽  
John A. Todd ◽  
David G. Clayton ◽  
...  
Keyword(s):  
Copy Number ◽  
Copy Number Variant ◽  
Association Test ◽  
The Family ◽  
Non Linear ◽  
Family Based ◽  
Linear Intensity

scholarly journals Toxoplasmosis infection among pregnant women in Africa: A systematic review and meta-analysis

PLoS ONE ◽  
2021 ◽  
Vol 16 (7) ◽  
pp. e0254209
Author(s):  
Tamirat Tesfaye Dasa ◽  
Teshome Gensa Geta ◽  
Ayalnesh Zemene Yalew ◽  
Rahel Mezemir Abebe ◽  
Henna Umer Kele
Keyword(s):  
Systematic Review ◽  
Pregnant Women ◽  
Democratic Republic Of Congo ◽  
Meta Analysis ◽  
Random Effect ◽  
Random Effect Model ◽  
Congenital Toxoplasmosis ◽  
Protozoan Parasite ◽  
P Value ◽  
Toxoplasma Infection

The epidemiology of toxoplasmosis in pregnancy is a major issue in public health. Toxoplasmosis is caused by the protozoan parasite. Toxoplasma parasite is at high risk for life-threatening diseases during pregnancy. Congenital toxoplasmosis results from a maternal infection acquired during gestation. Therefore, this systematic review and meta-analysis was aimed to determine the seropositive prevalence of toxoplasmosis infection among pregnant women who attended antenatal care in a health facility in Africa. A systematic review and meta-analysis of published and unpublished studies were included. Databases such as MEDLINE, PubMed, EMBASE, CINAHL, Web of Science, African Journals Online were used with relevant search terms. The quality of the articles was critically evaluated using the tool of the Joanna Briggs Institute. Data were extracted on Microsoft word 2016. Meta-analysis was conducted using STATA 14 software. The heterogeneity and publication bias were assessed using the I2 statistics and Egger’s test, respectively. Forest plots were used to present the pooled prevalence and odds ratio with a 95% confidence interval of meta-analysis using the random effect model. In total, 23 studies comprising 7,579 pregnant women across ten countries in Africa were included in this meta-analysis. The overall prevalence of seropositive toxoplasmosis among pregnant women in Africa was 51.01% (95% CI; 37.66, 64.34). The heterogeneity test showed that heterogeneity was high, I2 = 99.6%, P-value < 0.001. The variables responsible for the source of heterogeneity were included from Cameroon, the Democratic Republic of Congo, and Ethiopia. Overall prevalence of toxoplasmosis in Africa showed that more than one-half of pregnant women were infected. The risk of acquiring toxoplasmosis infection during pregnancy is high; hence, preventive measures to avoid exposure of pregnant women to Toxoplasma infection should be strictly applied.

scholarly journals COMPARISON OF VILLAGE DEVELOPMENT BEFORE AND AFTER VILLAGE FUND IMPLEMENTATION IN NAGAN RAYA DISTRICT

2021 ◽  
pp. 18-35
Author(s):  
Arroyyan Ramly
Keyword(s):  
Time Series Data ◽  
Random Effect ◽  
Random Effect Model ◽  
Secondary Data ◽  
Primary Data ◽  
Series Data ◽  
P Value ◽  
Analysis Method ◽  
Effect Model ◽  
The Village

This study aims to analyze and see the effectiveness of the distribution of the use of village funds in Kuala Subdistrict, Nagan Raya Regency and its relationship with poverty levels. The data used is in the form of time series data from 2015 to 2018 which is collected through primary and secondary data. Primary data were obtained by directly visiting villages in the Kuala sub-district. Meanwhile, secondary data were obtained from the website of the Central Statistics Agency (BPS), document review, articles related to the object of research. This study conducted observations of 10 villages as a sample of 17 villages in Kuala District. The analysis method uses panel data regression with the random effect model (REM) analysis method. From the regression results of the random effect model, it was found that the village fund variable had a positive and significant effect on poverty with a probability of 0.0000 = p-value α = 5%. Then the village fund allocation variable has a significant negative effect on poverty with a probability of 0.0000 = p-value α = 5%. This means that adding 1% of village funds or increasing village funds will reduce poverty in Kuala Subdistrict, Nagan Raya Regency.

scholarly journals Association test using Copy Number Profile Curves (CONCUR) enhances power in rare copy number variant analysis

2020 ◽  
Vol 16 (5) ◽  
pp. e1007797
Author(s):  
Amanda Brucker ◽  
Wenbin Lu ◽  
Rachel Marceau West ◽  
Qi-You Yu ◽  
Chuhsing Kate Hsiao ◽  
...  
Keyword(s):  
Copy Number ◽  
Copy Number Variant ◽  
Association Test ◽  
Copy Number Profile ◽  
Variant Analysis

A systematic and meta-analysis study on the prevalence of tuberculosis and relative risk factors for prisoners in Iran

2021 ◽  
Vol 21 ◽  
Author(s):  
Sedigheh Taherpour ◽  
Mojtaba Mousavi Bazzaz ◽  
Hamidreza Naderi ◽  
Saeed Samarghandian ◽  
Alireza Amirabadizadeh ◽  
...  
Keyword(s):  
Risk Factors ◽  
Meta Analysis ◽  
Random Effect ◽  
Random Effect Model ◽  
Random Model ◽  
Health Interventions ◽  
P Value ◽  
Analysis Study ◽  
Effect Model ◽  
Related Risk

Introduction: This study aimed to evaluate the incidence of Tuberculosis (TB) among prisoners in Iran, by performing a systematic and meta-analysis study on the related articles. Methodology: Scopus, Iran doc, Cochrane, Pubmed, Medline, Embase and Iran Medex, Magiran, SID, Google Scholar, and EBSCO were searched. After quality assessment of the articles, a fixed or random model, as appropriate, was used to pool the results in a meta-analysis. Heterogeneity between the studies was assessed using I-square and Q-test. Results: The overall sample size of included studies was 19562 that 64 of them were with TB. The highest prevalence of tuberculosis was related to the study of Rasht, 517 in 100,000 but the lowest rate was related to the study of Sought Khorasan, 25 in 100,000. The ES of the random effect model is 0.003 (95% CI, 0.001-0.005) and p-value <0.0001. The Higgins’ I2 of all studies is 86.55%, and the p-value of the Cochrane Q statistics is <0.001, indicating that there is heterogeneity. Based on the Egger regression plot (t=2.18, p = 0.08, CI 95%: -0.001, 0.005) no publication bias existed. Conclusion: The frequency of TB among the prisoners in Iran was low. Due to important limitations in this study, it is not possible to indicate the exact prevalence of TB among prisoners in Iran and compare this with the general population. More studies are needed to assess the related risk factor for designing health interventions plan to decrease the incidence rate of TB among prisoners.

scholarly journals Efektivitas Pemanfaatan Dana Desa dalam Mengentaskan Kemiskinan di Kecamatan Kuala, Kab Nagan Raya

2020 ◽  
Vol 4 (1) ◽  
Author(s):  
Ar Royyan Ramly ◽  
Wahyuddin Wahyuddin ◽  
Muslim A. Djalil ◽  
Mirna Indriani
Keyword(s):  
Time Series ◽  
Random Effect ◽  
Random Effect Model ◽  
P Value ◽  
Effect Model

Penelitian ini bertujuan menganalisa dan melihat efektifitas distribusi pemanfaatan dana desa di Kecamatan Kuala Kabupaten Nagan Raya dan hubungannya dengan tingkat kemiskinan. Data yang digunakan berupa data time series dari tahun 2015 hingga tahun 2018 yang dikumpulkan melalui data primer dan sekunder. Data primer diperoleh dengan mendatangi langsung ke desa-desa di kecamatan kuala. Sementara data sekunder diperoleh dari website Badan Pusat Statistik (BPS), telaah dokumen, artikel yang berhubungan dengan objek penelitian. Penelitian ini melakukan observasi terhadap 10 desa sebagai sample dari 17 desa di Kecamatan Kuala. Metode analisa mengunakan regresi data panel dengan metode analisa random effect model (REM). Dari hasil regresi model random effect ditemukan bahwa variabel dana desa berpengaruh positif dan signifikan terhadap kemisikinan dengan Probabilitas sebesar  0,0000 = p-value α = 5%. Kemudian variabel alokasi dana desa berpengaruh negatif signifikan terhadap kemiskinan dengan Probabilitas sebesar  0,0000 = p-value α = 5%. Artinya dengan menambahkan 1% dana desa atau meningkatkan dana desa akan mengurangi kemiskinan di Kecamatan Kuala Kabupaten Nagan Raya

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