Chinese Glioma Genome Atlas(CGGA):A Comprehensive Resource with Functional Genomic Data from Chinese Glioma Patients

Gliomas are the most common and malignant intracranial tumors in adults. Recent studies have revealed the significance of functional genomics for glioma pathophysiological studies and treatments. However, access to comprehensive genomic data and analytical platforms is often limited. Here, we developed the Chinese Glioma Genome Atlas(CGGA), a user-friendly data portal for the storage and interactive exploration of cross-omics data, including nearly 2000 primary and recurrent glioma samples from Chinese cohort. Currently, open access is provided to whole-exome sequencing data(286 samples), mRNA sequencing(1018 samples) and microarray data(301 samples), DNA methylation microarray data(159 samples), and microRNA microarray data(198 samples), and to detailed clinical information(age, gender, chemoradiotherapy status,WHO grade, histological type, critical molecular pathological information, and survival data). In addition, we have developed several tools for users to analyze the mutation profiles,mRNA/microRNA expression, and DNA methylation profiles, and to perform survival and gene correlation analyses of specific glioma subtypes. This database removes the barriers for researchers,providing rapid and convenient access to high-quality functional genomic data resources for biological studies and clinical applications. CGGA is available at http://www.cgga.org.cn.     

基于Pacbio第三代测序技术的厚朴基因组测序分析

厚朴为著名的传统药用植物,归于木兰科、木兰属,于我国广泛种植,其树皮、根皮、枝皮、叶片、花、果实均能入药或食用.为获取厚朴全基因组序列信息,该文以厚朴叶片DNA为材料,采用Pacbio Sequel第三代测序技术构建厚朴全基因组数据库,并利用生物信息学方法对获得的核苷酸序列进行组装、功能注释以及进化分析研究.结果表明:...     

An improved hypergeometric probability method for identification of functionally linked proteins using phylogenetic profiles

Predicting functions of proteins and alternatively spliced isoforms encoded in a genome is one of the important applications of bioinformatics in the post-genome era. Due to the practical limitation of experimental characterization of all proteins encoded in a genome using biochemical studies, bioinformatics methods provide powerful tools for function annotation and prediction. These methods also help minimize the growing sequence-to-function gap. Phylogenetic profiling is a bioinformatics approach to identify the influence of a trait across species and can be employed to infer the evolutionary history of proteins encoded in genomes. Here we propose an improved phylogenetic profile-based method which considers the co-evolution of the reference genome to derive the basic similarity measure, the background phylogeny of target genomes for profile generation and assigning weights to target genomes. The ordering of genomes and the runs of consecutive matches between the proteins were used to define phylogenetic relationships in the approach. We used Escherichia coli K12 genome as the reference genome and its 4195 proteins were used in the current analysis. We compared our approach with two existing methods and our initial results show that the predictions have outperformed two of the existing approaches. In addition, we have validated our method using a targeted protein-protein interaction network derived from protein-protein interaction database STRING. Our preliminary results indicates that improvement in function prediction can be attained by using coevolution-based similarity measures and the runs on to the same scale instead of computing them in different scales. Our method can be applied at the whole-genome level for annotating hypothetical proteins from prokaryotic genomes.     

基于简化基因组的花生InDel标记开发和功能解析

InDel在基因组中的分布密度仅次于SNP,可作为动植物群体遗传分析、分子辅助育种等研究领域的有效分子标记。花生是世界范围内重要的油料作物之一。目前,花生栽培种全基因组已经公布,为准确挖掘花生基因组信息提供了重要参考。本研究通过169份花生核心种质的GBS(Genotyping-by-sequencing)测序和比对,共获得大小分布在1～14 bp范围内的10401个InDels。染色体Arahy.16上分布的InDels最多,达741个;而在染色体Arahy.08上分布的最少,有263个。参考基因组注释信息,仅有1167个InDels分布在功能基因相关区域。经GO注释,InDel分子功能主要包括催化活性(catalytic activity)和结合(binding);生物过程主要涉及代谢过程(metabolic process)、单组织过程(single-organism process)和细胞过程(cellular process)。经KEGG通路分析发现,InDels所在的基因区域的功能主要与代谢相关。本研究开发出全基因组水平的InDel标记,并做了相应功能分类和注释,为进一步分子验证和利用提供丰富的基因资源。     

Biallelic nonsense mutations in the otogelin-like gene (OTOGL) in a child affected by mild to moderate hearing impairment

Hearing impairment is characterized by great genetic heterogeneity. We report the identification, by whole exome sequencing, of two different nonsense mutations (c.1558C>T; p.Gln520* and c.2773C>T; p.Arg925*) in the otogelin-like gene (OTOGL), in a child affected by mild to moderate isolated deafness. Parental genotypes allowed us to conclude that these mutations are present in the compound heterozygous state in the patient. In addition, our clinical data establish that the tectorial membrane and/or the outer hair cells are defective in this form of deafness.     

大豆BAC克隆基因注释

根据来源于大豆BAC克隆库中的基因组序列,与其比对的基因或蛋白质序列可以从一些数据库中搜索,如GenBank序列数据库、EMBL数据库、PDB数据库等,然后利用NCBI的Entrz程序在数据库中搜索大豆基因类似物,获取其登录号及核苷酸序列,以及这些基因编码的氨基酸序列,通过GENSCAN等软件分析,得出的是与拟南芥等物种序列比对的结果,根据GENSCAN的预测结果,可以初步得知序列长度、基因数目及具有编码某种功能蛋白的基因存在的可能性,进而对预测出的氨基酸或核苷酸序列利用数据库NCBI中的BLAST进行序列的相似性搜索及比对分析,寻找其保守区域。最后对其功能基因进行注释。     

利用eQTL构建基因-基因网络挖掘类风湿性关节炎风险基因

目的：类风湿性关节炎是一种全身的慢性炎症型疾病,可能影响许多组织和器官,主要发作于灵活的关节。全世界人群中大约有1％会患有类风湿性关节炎。目前已经证实了一些基因与类风湿性关节炎相关,但是这些基因只能解释一小部分遗传风险,因此我们需要新的策略和方法来解决这个问题。方法：表达数量性状位点（eQTL）是指能够调控基因或蛋白质表达的基因组位点,本文采用了eQTL数据构建基因一基因网络并挖掘候选类风湿性关节炎风险基因。结果：首先,利用eQTL数据,基于基因之间的共调控系数,建立基因-基因网络,我们建立了5个不同阈值（0、O．2、0．4、0．6和0．8）的基因-基因网络;然后,在OMIM和GAD数据库中搜索已经证实的与类风湿性关节炎相关的186个基因;最后我们将已证实与类风湿性关节炎相关的186个基因分别投入到这5个网络中,利用基因与基因之间的相关性来挖掘到一些可能与类风湿性关节炎相关的候选风险基因。结论：本文基于eQTL构建了基因．基因网络,结合已知类风湿性关节炎风险基因,挖掘未知风险基因,得到了较好的结果,证明了本方法的有效性,且对于类风湿性关节炎的发病机制研究具有重要价值。除了类风湿性关节炎外,本方法还可推广到其它复杂疾病中,因此本方法对人类复杂疾病的研究具有很强的学术理论价值和应用价值。     

卵巢癌侵袭转移机制的生物信息学研究进展

卵巢癌因其侵袭转移特性,致死率极高,居所有妇科恶性肿瘤之首。近年来随着高通量测序技术及生物信息学方法的快速发展,越来越多调控卵巢癌侵袭转移机制的相关生物大分子被发现。本文对卵巢癌侵袭转移机制的研究背景及现状进行了综述,归纳总结了侵袭转移机制相关调控因素,并对蛋白质组学和单细胞组学的生物信息学分析工具及数据库进行了汇总和介绍,以期为卵巢肿瘤细胞侵袭转移机制的深入研究提供理论依据和科研线索。