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Copy number variation related disease genes

Frontiers of Electrical and Electronic Engineering in China 2018年第2期6卷 99-112页

作者： Chaima Aouiche Xuequn Shang Bolin Chen School of Computer Science Northwestern Polytechnical University Xi'an 710072 China

Background： One of the most important and challenging issues in biomedicine and genomics is how to identify disease related genes. Datasets from high-throughput biotechnologies have been widely used to overcome this issue from various perspectives, e.g., epigenomics, genomics, transcriptomics, proteomics, metabolomics. At the genomic level, copy number variations （CNVs） have been recognized as critical genetic variations, which contribute significantly to genomic diversity. They have been associated with both common and complex diseases, and thus have a large influence on a variety of Mendelian and somatic genetic disorders. Results： In this review, based on a variety of complex diseases, we give an overview about the critical role of using CNVs for identifying disease related genes, and discuss on details the different high-throughput and sequencing methods applied for CNV detection. Some limitations and challenges concerning CNV are also highlighted. Conclusions： Reliable detection of CNVs will not only allow discriminating driver mutations for various diseases, but also helps to develop personalized medicine when integrating it with other genomic features.

关键词： CNV disease gene complex disease targeted approach genome-wide approach whole exome sequencing

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Understanding tissue-specificity with human tissue-specific regulatory networks

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Science China(Information Sciences) 2016年第7期59卷 51-60页

作者： Weili GUO Lin ZHU Suping DENG Xingming ZHAO Deshuang HUANG College of Electromics and Information Engineering Tongji University

Tissue-specificity is important for the function of human body. However, it is still not clear how the functional diversity of different tissues is achieved. Here we construct gene regulatory networks in 13 human tissues by integrating large-scale transcription factor(TF)-gene regulations with gene and protein expression data. By comparing these regulatory networks, we find many tissue-specific regulations that are important for tissue identity. In particular, the tissue-specific TFs are found to regulate more genes than those expressed in multiple tissues, and the processes regulated by these tissue-specific TFs are closely related to tissue ***, the regulations that are present in certain tissue are found to be enriched in the tissue associated disease genes, and these networks provide the molecular context of disease genes. Therefore, recognizing tissuespecific regulatory networks can help better understand the molecular mechanisms underlying diseases and identify new disease genes.

关键词： tissue-specificity gene regulatory network transcription factor tissue-specific regulation disease gene

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Exome sequencing greatly expedites the progressive research of Mendelian diseases

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Frontiers of Medicine 2014年第1期8卷 42-57页

作者： Xuejun Zhang Institute of Dermatology and Department of Dermatology First Affiliated Hospital Anhui Medical University Hefei 230032 China' StateKey Laboratory Incubation Base of Dermatology Ministry of Science and Technology of China Hefei 230032 China

The advent of whole-exome sequencing （WES） has facilitated the discovery of rare structure and functional genetic variants. Combining exome sequencing with linkage studies is one of the most efficient strategies in searching disease genes for Mendelian diseases. WES has achieved great success in the past three years for Mendelian disease genetics and has identified over 150 new Mendelian disease genes. We illustrate the workflow of exome capture and sequencing to highlight the advantages of WES. We also indicate the progress and limitations of WES that can potentially result in failure to identify disease-causing mutations in part of patients. With an affordable cost, WES is expected to become the most commonly used tool for Mendelian disease gene identification. The variants detected cumulatively from previous WES studies will be widely used in future clinical services.

关键词： genetics whole-exome sequencing Mendelian disease disease gene

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