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  • 1
    Publication Date: 2018-07-03
    Description: Genes, Vol. 9, Pages 331: SEGF: A Novel Method for Gene Fusion Detection from Single-End Next-Generation Sequencing Data Genes doi: 10.3390/genes9070331 Authors: Hai Xu Xiaojin Wu Dawei Sun Shijun Li Siwen Zhang Miao Teng Jianlong Bu Xizhe Zhang Bo Meng Weitao Wang Geng Tian Huixin Lin Dawei Yuan Jidong Lang Shidong Xu With the development and application of next-generation sequencing (NGS) and target capture technology, the demand for an effective analysis method to accurately detect gene fusion from high-throughput data is growing. Hence, we developed a novel fusion gene analyzing method called single-end gene fusion (SEGF) by starting with single-end DNA-seq data. This approach takes raw sequencing data as input, and integrates the commonly used alignment approach basic local alignment search tool (BLAST) and short oligonucleotide analysis package (SOAP) with stringent passing filters to achieve successful fusion gene detection. To evaluate SEGF, we compared it with four other fusion gene discovery analysis methods by analyzing sequencing results of 23 standard DNA samples and DNA extracted from 286 lung cancer formalin fixed paraffin embedded (FFPE) samples. The results generated by SEGF indicated that it not only detected the fusion genes from standard samples and clinical samples, but also had the highest accuracy and sensitivity among the five compared methods. In addition, SEGF was capable of detecting complex gene fusion types from single-end NGS sequencing data compared with other methods. By using SEGF to acquire gene fusion information at DNA level, more useful information can be retrieved from the DNA panel or other DNA sequencing methods without generating RNA sequencing information to benefit clinical diagnosis or medication instruction. It was a timely and cost-effective measure with regard to research or diagnosis. Considering all the above, SEGF is a straightforward method without manipulating complicated arguments, providing a useful approach for the precise detection of gene fusion variation.
    Electronic ISSN: 2073-4425
    Topics: Biology
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  • 2
    Publication Date: 2018-05-11
    Description: Genes, Vol. 9, Pages 247: Journey into Bone Models: A Review Genes doi: 10.3390/genes9050247 Authors: Julia Scheinpflug Moritz Pfeiffenberger Alexandra Damerau Franziska Schwarz Martin Textor Annemarie Lang Frank Schulze Bone is a complex tissue with a variety of functions, such as providing mechanical stability for locomotion, protection of the inner organs, mineral homeostasis and haematopoiesis. To fulfil these diverse roles in the human body, bone consists of a multitude of different cells and an extracellular matrix that is mechanically stable, yet flexible at the same time. Unlike most tissues, bone is under constant renewal facilitated by a coordinated interaction of bone-forming and bone-resorbing cells. It is thus challenging to recreate bone in its complexity in vitro and most current models rather focus on certain aspects of bone biology that are of relevance for the research question addressed. In addition, animal models are still regarded as the gold-standard in the context of bone biology and pathology, especially for the development of novel treatment strategies. However, species-specific differences impede the translation of findings from animal models to humans. The current review summarizes and discusses the latest developments in bone tissue engineering and organoid culture including suitable cell sources, extracellular matrices and microfluidic bioreactor systems. With available technology in mind, a best possible bone model will be hypothesized. Furthermore, the future need and application of such a complex model will be discussed.
    Electronic ISSN: 2073-4425
    Topics: Biology
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