Mohammed, M. A. | Search bioRxiv

bioRxiv2019

In silico analysis of CDC73 gene revealing 11 novel SNPs associated with Jaw Tumor Syndrome

Back groundhyperparathyroidism-jaw tumor (HPT-JT) is an autosomal dominant disorder with variable expression, with an estimated prevalence of 6.7 per 1,000 population. Genetic testing for predisposing CDC73 (HRPT2) mutations has been an important clinical advance, aimed at early detection and/or treatment to prevent advanced disease. The aim of this study is to assess the effect of SNPs on CDC73 structure and function using different bioinformatics tools.\n\nMethodComputational analysis using eight different in-silico tools including SIFT, PROVEAN, PolyPhen-2, SNAP2, PhD-SNP, SNPs&GO, PMut and Imutant were used to identify the impact on the structure and/or function of CDC73 gene that might be causing jaw tumour.\n\nResultsFrom (733) SNPs identified in the CDC73 gene we found that only Eleven were deleterious to the function and structure of protein and expected to cause syndrome.\n\nConclusionEleven substantial genetic/molecular aberrations in CDC73 gene were identified that could serve as actionable targets for chemotherapeutic intervention in patients whose disease is no longer surgically curable.

bioinformatics↗

bioRxiv2019

In silico analysis of IDH3A gene revealed Novel mutations associated with Retinitis Pigmentosa

BackgroundRetinitis Pigmentosa (RP) refers to a group of inherited disorders characterized by the death of photoreceptor cells leading to blindness. The aim of this study is to identify the pathogenic SNPs in the IDH3A gene and their effect on the structure and function of the protein. Methodwe used different bioinformatics tools to predict the effect of each SNP on the structure and function of the protein. Result20 deleterious SNPs out of 178 were found to have a damaging effect on the protein structure and function. Conclusionthis is the first in silico analysis of IDH3A gene and 20 novel mutations were found using different bioinformatics tools, and they could be used as diagnostic markers for Retinitis Pigmentosa.

bioinformatics↗

bioRxiv2018

Overview of biomedical and public health reviews in Ethiopia from 1970 to 2018: trends, methodological qualities, gaps and future directions

IntroductionGlobally, there has been a dramatic increment of narrative reviews, systematic reviews and overview publication rates. In Ethiopia, only small number of reviews are published and no overviews conducted in biomedical and public health disciplines. Therefore, we aimed to (1) assess the trend of narrative and systematic reviews in Ethiopia, (2) examine their methodological quality and (3) suggest future directions for improvement.\n\nMethodsPubMed, EMBASE, Web of Science, SCOPUS, CINHAL, WHO Global Index Medicus, Cochrane Library and PsycINFO electronic databases were searched and supplemented by hand searching as well. All narrative reviews and systematic reviews with or without a meta-analysis from 1970 to April 2018 were included. The International Narrative Systematic assessment (INSA) for narrative reviews and A MeaSurement Tool to Assess Systematic Reviews (AMSTAR-2) for systematic reviews with or without a meta-analysis were used for quality appraisal. Fishers exact test at the p-value threshold of 0.05 was used to compare the differences in methodological quality.\n\nResultsOf the 2,201 initially identified articles, 106 articles published from 1970 to 2018 were eligible for full-text review. Among included reviews, 50.9% were narrative reviews, 16% were systematic reviews and 33.1% were systematic reviews with meta-analyses. Twenty-nine percent were published in Ethiopia and 43.4% were published after 2015. 85.1% of narrative reviews poorly described the characteristics of included studies and 63.8% did not report a conflict of interest. In systematic reviews, 89.6%, 91.7%, and 100% did not register/publish the protocol, justifying the selection of the study designs for inclusion and report sources of funding for the primary studies respectively. Overall, 55.3% of narrative reviews and 75% of systematic reviews with or without meta-analysis had poor methodological quality.\n\nConclusionsAlthough publication rate of narrative and systematic reviews have risen in Ethiopia, half of the narrative reviews and three-quarters of the systematic reviews had poor methodological quality. We recommend authors to strictly follow standardized quality assessment tools during conducting reviews. Moreover, immediate interventions such as providing methodological training and employers, editors and peer-reviewers should carefully evaluate all reviews before submission or publication.\n\nWhat is new?O_ST_ABSKey findingsC_ST_ABSO_LIThe publication rate of narrative and systematic reviews have risen in Ethiopia.\nC_LIO_LIAlmost half of narrative reviews and three-fourths of systematic reviews with or without meta-analysis had poor scientific methodological quality.\nC_LI\n\nWhat this adds to what is knownO_LITo our knowledge, this is the first overview of its kind providing insight into the publication trend of narrative and systematic reviews, and their methodological rigor in Ethiopia.\nC_LI\n\nWhat is the implication, what should change nowO_LIOur review shows that the methodological quality of reviews in biomedical and public health discipline in Ethiopia is substantially low and urges immediate intervention.\nC_LIO_LIWe recommended authors to strictly follow standardized quality assessment tools during designing, conducting and reporting (systematic)reviews.\nC_LI

scientific communication and education↗