Background: In recent years there has been a growing interest in the role of copy number variations (CNV) in genetic diseases. Though there has been rapid development of technologies and statistical methods devoted to detection in CNVs from array data, the inherent challenges in data quality associated with most hybridization techniques remains a challenging problem in CNV association studies.
Results: To help address these data quality issues in the context of family-based association studies, we introduce a statistical framework for the intensity-based array data that takes into account the family information for copy-number assignment. The method is an adaptation of traditional methods for modeling SNP genotype data that assume Gaussian mixture model, whereby CNV calling is performed for all family members simultaneously and leveraging within family-data to reduce CNV calls that are incompatible with Mendelian inheritance while still allowing de-novo CNVs. Applying this method to simulation studies and a genome-wide association study in asthma, we find that our approach significantly improves CNV calls accuracy, and reduces the Mendelian inconsistency rates and false positive genotype calls. The results were validated using qPCR experiments.
Conclusions: In conclusion, we have demonstrated that the use of family information can improve the quality of CNV calling and hopefully give more powerful association test of CNVs.
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http://dx.doi.org/10.1186/1471-2105-14-157 | DOI Listing |
Enzyme Microb Technol
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Dabie Mountain Laboratory, College of Tea and Food Science, Xinyang Normal University, Xinyang, Henan 464000, China.
2-Phenylethanol, an aromatic alcohol with a rose scent, is widely used in the cosmetics, food, and pharmaceutical industries. We designed an efficient multi-enzyme cascade pathway for production of 2-phenylethanol from styrene as the substrate. Initially, 2-phenylethanol was produced by overexpression of styrene monooxygenase A (styA), styrene monooxygenase B (styB), styrene oxide isomerase (SOI), alcohol dehydrogenase (yahK), and glucose dehydrogenase (gdh) in Escherichia coli to give 6.
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Istituto Europeo di Oncologia, IRCCS, Via Adamello 16, 20139, Milan, Italy.
Background: Predicting response to targeted cancer therapies increasingly relies on both simple and complex genetic biomarkers. Comprehensive genomic profiling using high-throughput assays must be evaluated for reproducibility and accuracy compared with existing methods.
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J Clin Med
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Departamento de Genética, Instituto Nacional de Neurología y Neurocirugía Manuel Velasco Suárez (INNNMVS), Mexico City 14269, Mexico.
: Antiseizure drugs (ASDs) are the primary therapy for epilepsy, and the choice varies according to seizure type. Epilepsy patients experience chronic mitochondrial oxidative stress and increased levels of pro-inflammatory mediators, recognizable hallmarks of biological aging; however, few studies have explored aging markers in epilepsy. Herein, we addressed for the first time the impact of ASDs on molecular aging by measuring the telomere length (TL) and mtDNA copy number (mtDNA-CN).
View Article and Find Full Text PDFJ Clin Med
December 2024
Department of Oral Medicine and Periodontology, Faculty of Medicine, University of Ljubljana, Hrvatski trg 6, 1000 Ljubljana, Slovenia.
: Periodontitis is an inflammatory disease induced by bacteria in dental plaque that can activate the host's immune-inflammatory response and invade the bloodstream. We hypothesized that a higher periodontal inflamed surface area (PISA) is associated with higher levels of inflammatory biomarkers, lower levels of antioxidants, and mitochondrial DNA copy number (mtDNAcn). : Using periodontal parameters, we calculated the PISA score, measured the levels of inflammatory biomarkers and antioxidants in the serum, and took buccal swabs for mtDNA and nuclear DNA (nDNA) extraction.
View Article and Find Full Text PDFInt J Mol Sci
January 2025
Department of Molecular Medicine, Aziz Sancar Institute of Experimental Medicine, Istanbul University, 34093 Istanbul, Türkiye.
Granulomatous mastitis (GM) is a rare, benign, but chronic and recurrent inflammatory breast disease that significantly impacts physical and psychological well-being. It often presents symptoms such as pain, swelling, and discharge, leading to diagnostic confusion with malignancy. The etiology of GM remains unclear, though autoimmune and multifactorial components are suspected.
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