Candidate Gene Identification for Systemic Lupus Erythematosus Using Network Centrality Measures and Gene Ontology

Systemic lupus erythematosus (SLE) commonly accredited as “the great imitator” is a highly complex disease involving multiple gene susceptibility with non-specific symptoms. Many experimental and computational approaches have been used to investigate the disease related candidate genes. But the limited knowledge of gene function and disease correlation and also lack of complete functional details about the majority of genes in susceptible locus, encumbrances the identification of SLE related candidate genes. In this paper, we have studied the human immunome network (undirected) using various graph theoretical centrality measures integrated with the gene ontology terms to predict the new candidate genes. As a result, we have identified 8 candidate genes, which may act as potential targets for SLE disease. We have also carried out the same analysis by replacing the human immunome network with human immunome signaling network (directed) and as an outcome we have obtained 5 candidate genes as potential targets for SLE disease. From the comparison study, we have found these two approaches are complementary in nature.     

Genome-Wide Analysis of Copy Number Variation Identifies Candidate Gene Loci Associated with the Progression of Non-Alcoholic Fatty Liver Disease

Between 10 and 25% of individuals with non-alcoholic fatty liver disease (NAFLD) develop hepatic fibrosis leading to cirrhosis and hepatocellular carcinoma (HCC). To investigate the molecular basis of disease progression, we performed a genome-wide analysis of copy number variation (CNV) in a total of 49 patients with NAFLD [10 simple steatosis and 39 non-alcoholic steatohepatitis (NASH)] and 49 matched controls using high-density comparative genomic hybridization (CGH) microarrays. A total of 11 CNVs were found to be unique to individuals with simple steatosis, whilst 22 were common between simple steatosis and NASH, and 224 were unique to NASH. We postulated that these CNVs could be involved in the pathogenesis of NAFLD progression. After stringent filtering, we identified four rare and/or novel CNVs that may influence the pathogenesis of NASH. Two of these CNVs, located at 13q12.11 and 12q13.2 respectively, harbour the exportin 4 (XPO4) and phosphodiesterase 1B (PDE1B) genes which are already known to be involved in the etiology of liver cirrhosis and HCC. Cross-comparison of the genes located at these four CNV loci with genes already known to be associated with NAFLD yielded a set of genes associated with shared biological processes including cell death, the key process involved in ‘second hit’ hepatic injury. To our knowledge, this pilot study is the first to provide CNV information of potential relevance to the NAFLD spectrum. These data could prove invaluable in predicting patients at risk of developing NAFLD and more importantly, those who will subsequently progress to NASH.     

两个位点主基因控制的质量—数量性状的遗传分析

应用极大似然法和EM算法提出了关于两个位点主基因控制的质量．数量性状的遗传分析方法,参照质量性状两位点互作在F_2代的分离比率建立了7种遗传假设及其似然比测验的程序,讨论了应用这一方法时应注意的几个问题．     

Genome-Wide Association in Tomato Reveals 44 Candidate Loci for Fruit Metabolic Traits

Genome-wide association studies have been successful in identifying genes involved in polygenic traits and are valuable for crop improvement. Tomato (Solanum lycopersicum) is a major crop and is highly appreciated worldwide for its health value. We used a core collection of 163 tomato accessions composed of S. lycopersicum, S. lycopersicum var cerasiforme, and Solanum pimpinellifolium to map loci controlling variation in fruit metabolites. Fruits were phenotyped for a broad range of metabolites, including amino acids, sugars, and ascorbate. In parallel, the accessions were genotyped with 5,995 single-nucleotide polymorphism markers spread over the whole genome. Genome-wide association analysis was conducted on a large set of metabolic traits that were stable over 2 years using a multilocus mixed model as a general method for mapping complex traits in structured populations and applied to tomato. We detected a total of 44 loci that were significantly associated with a total of 19 traits, including sucrose, ascorbate, malate, and citrate levels. These results not only provide a list of candidate loci to be functionally validated but also a powerful analytical approach for finding genetic variants that can be directly used for crop improvement and deciphering the genetic architecture of complex traits.In crops, linkage mapping has proved invaluable for detecting quantitative trait loci (QTLs) for traits of interest and to unravel their underlying genetic architecture. This approach is based on the analysis of the segregation of polymorphism between the parental lines and their progeny. However, one of the limitations of this approach is the reduced number of recombination events that occur per generation (for review, see Korte and Farlow, 2013). This leads to extended linkage blocks that reduce the accuracy of the linkage mapping. An alternative to linkage-based mapping studies is to perform linkage disequilibrium (LD) mapping in a population of theoretically unrelated individuals. The ancestral polymorphism segregating through this population (or panel) is far more informative compared with the polymorphism of the parental lines of the linkage mapping population (Mauricio, 2001). LD mapping, also known as genome-wide association (GWA), relies on the natural patterns of LD in the population investigated. The aim of GWA is to reveal trait-associated loci by taking advantage of the level of LD. Depending on the decay of LD, the mapping resolution can be narrowed from a large genomic portion where the level of LD is relatively high to a single marker when the LD level is very low.Following domestication, crops are prone to (1) increased levels of LD, (2) population structure (remote common ancestry of large groups of individuals), and (3) cryptic relatedness (the presence of close relatives in a sample of unrelated individuals; Riedelsheimer et al., 2012). Population structure and cryptic relatedness may lead to false-positive association in GWA studies (Astle and Balding, 2009), but their effect is now relatively well accounted for in mixed linear models (for review, see Sillanpää, 2011; Listgarten et al., 2012). The problem of high LD in GWA scans also must be taken into account: Segura et al. (2012) investigated this difficulty by proposing a multilocus mixed model (MLMM) that handles the confounding effect of background loci that may be present throughout the genome due to LD. This approach revealed multiple loci in LD and associated with sodium concentration in leaves in Arabidopsis (Arabidopsis thaliana), while previous methods failed to identify this complex pattern (Segura et al., 2012).In parallel, the development of cost-effective high-throughput sequencing technologies has identified increasingly dense variant loci necessary to conduct GWA scans, especially in model species such as rice (Oryza sativa) for agronomic traits (Huang et al., 2010) or maize (Zea mays) for drought tolerance (Lu et al., 2010; for review, see Soto-Cerda and Cloutier, 2012). However, GWA is not restricted to model species and is becoming increasingly widespread in nonmodel ones such as sunflower (Helianthus annuus; Mandel et al., 2013) and tomato (Solanum lycopersicum; Xu et al., 2013), where numerous associations have been successfully identified for traits related to plant architecture (branching in the case of sunflower) and fruit quality (e.g. fresh weight in tomato).Tomato is a crop of particular interest, as the fruit are an important source of fiber and nutrients in the human diet and a model for the study of fruit development (Giovannoni, 2001). Over the last two decades, numerous QTLs have been identified for traits such as fresh weight using linkage approaches (Frary et al., 2000; Zhang et al., 2012; Chakrabarti et al., 2013) but also for other fruit-related traits such as fruit ascorbic acid levels (Stevens et al., 2007), sensory and instrumental quality traits (Causse et al., 2002), sugar and organic acids (Fulton et al., 2002), and metabolic components (Schauer et al., 2008). Large tomato germplasm collections have been characterized at the molecular level using simple sequence repeat (Ranc et al., 2008) and single-nucleotide polymorphism (SNP) markers (Blanca et al., 2012; Shirasawa et al., 2013), giving insights into population structure, tomato evolutionary history, and the genetic architecture of traits of agronomic interest. These screens of nucleotide diversity were made possible (for review, see Bauchet and Causse, 2012) in the last couple of years due to the release of the tomato genome sequence (Tomato Genome Consortium, 2012) and derived genomic tools such as a high-density SNP genotyping array (Sim et al., 2012). The combination of large germplasm collections, high-throughput genomic tools, and traits of economic interest provide a framework to apply genome-wide association study (GWAS) in this species. In tomato, previous association studies have been limited to a targeted region (e.g. chromosome 2; Ranc et al., 2012), used low-density genome-wide-distributed SNP markers (Xu et al., 2013), or investigated a limited number of agronomic traits with low precision on the association panel (Shirasawa et al., 2013).Using tomato as a model, we aimed to investigate the genetic architecture of traits related to fruit metabolic composition at high resolution. To reach this objective, we carried out an investigation into LD patterns at the genome-wide scale and a GWA scan using the MLMM approach. We present results on the genetic architecture of fruit metabolic composition for metabolites such as organic acids, amino acids, sugars, and ascorbate in tomato.     

水稻早衰突变体LS-es1的基因定位及候选基因分析

衰老是植物发育末期自主发生且不可逆的适应性反应, 叶片早衰相关分子机制研究对水稻(Oryza sativa)遗传改良以及抗衰老品种培育有重要意义。LS-es1是通过EMS诱变粳稻品种TP309获得的稳定遗传的早衰突变体。对LS-es1及其野生型的表型观察和生理生化分析表明, LS-es1叶片中积累了大量活性氧且细胞死亡更多, 同时LS-es1与产量相关的农艺性状均显著下降, 这也验证了LS-es1早衰的特征。对LS-es1及其野生型幼苗进行外源激素处理, 结果表明LS-es1对水杨酸(SA)、脱落酸(ABA)和茉莉酸甲酯(MeJA)更敏感。用图位克隆方法将LS-es1基因定位在水稻第7号染色体长臂46.2 kb区间内, 该区间共包括8个开放阅读框(ORF)。对该区间内的基因进行生物信息学分析, 结果发现Os07g0275300和Os07g0276000两个候选功能基因与早衰途径相关, 并且这2个基因的表达量在野生型和突变体中差异较大。研究结果为进一步克隆LS-es1基因并深入研究其生物学功能奠定了基础。     

两个基因座位的遗传平衡原理

由于许多教科书中关于连锁平衡的介绍,多是引用结论或是推导不太严谨,使学生在学习群体遗传学时对理解连锁平衡的原理感到困难。本文从遗传平衡的基本条件出发,通过较严谨的数学推导,介绍了两个基因座的连锁平衡条件、平衡过程等原理,供教师和学生在群体遗传学教学中参考。Abstract: Because linkage equilibrium is introduced by directly quoting the conclusions or imprecise mathematical reasoning in most of textbooks, many students are puzzled with the problem of linkage equilibrium when they learn population genetics. Based on the radical conditions of genetic equilibrium, the principle of linkage equilibrium condition and process, for two gene loci is introduced by precise mathematical reasoning. The article may provide reference to teachers and students in the teaching and learning of population genetics.     

玉米叶形相关性状的Meta-QTL及候选基因分析

叶长、叶宽、叶面积及叶夹角不仅影响玉米(Zea mays)光合效率, 也是株型的重要构成因素。通过对620个叶形QTL进行整合, 构建不同遗传背景下的叶形QTL整合图谱, 利用元分析发掘出22个叶长、22个叶宽、12个叶面积以及17个叶夹角mQTL; 进一步运用生物信息学手段, 确定44个与叶片发育密切相关的候选基因。分析发现, 仅有NAL7-like、YABBY6- like和GRF2等13个基因位于mQTL区间内, 而玉米中已克隆的KNOTTED1、AN3/GIF1、rgd1/lbl1、mwp1及SRL2-like、HYL1-like和CYCB2;4-like等水稻(Oryza sativa)和拟南芥(Arabidopsis thaliana)叶形同源基因位于未被整合的QTL内; 对44个候选基因在叶片长、宽、厚发育过程中基部-末端、中央-边缘、远轴-近轴的调控机理进行归纳分析, 发现玉米中仅有少数几个候选基因被报道, 揭示了叶形发育的部分分子机理。因此, 对玉米叶形相关mQTL/QTL及基因进行全面深入的分析, 不仅有助于增加对其遗传结构的了解, 发掘更多候选基因, 阐明叶形发育和形成的分子机制, 还可为耐密理想株型的分子标记辅助选择提供依据。     

水稻早衰突变体LS-es1的基因定位及候选基因分析

衰老是植物发育末期自主发生且不可逆的适应性反应, 叶片早衰相关分子机制研究对水稻(Oryza sativa)遗传改良以及抗衰老品种培育有重要意义。LS-es1是通过EMS诱变粳稻品种TP309获得的稳定遗传的早衰突变体。对LS-es1及其野生型的表型观察和生理生化分析表明, LS-es1叶片中积累了大量活性氧且细胞死亡更多, 同时LS-es1与产量相关的农艺性状均显著下降, 这也验证了LS-es1早衰的特征。对LS-es1及其野生型幼苗进行外源激素处理, 结果表明LS-es1对水杨酸(SA)、脱落酸(ABA)和茉莉酸甲酯(MeJA)更敏感。用图位克隆方法将LS-es1基因定位在水稻第7号染色体长臂46.2 kb区间内, 该区间共包括8个开放阅读框(ORF)。对该区间内的基因进行生物信息学分析, 结果发现Os07g0275300和Os07g0276000两个候选功能基因与早衰途径相关, 并且这2个基因的表达量在野生型和突变体中差异较大。研究结果为进一步克隆LS-es1基因并深入研究其生物学功能奠定了基础。     

Fine Mapping and Candidate Gene Search of Quantitative Trait Loci for Growth and Obesity Using Mouse Intersubspecific Subcongenic Intercrosses and Exome Sequencing

Although growth and body composition traits are quantitative traits of medical and agricultural importance, the genetic and molecular basis of those traits remains elusive. Our previous genome-wide quantitative trait locus (QTL) analyses in an intersubspecific backcross population between C57BL/6JJcl (B6) and wild Mus musculus castaneus mice revealed a major growth QTL (named Pbwg1) on a proximal region of mouse chromosome 2. Using the B6.Cg-Pbwg1 intersubspecific congenic strain created, we revealed 12 closely linked QTLs for body weight and body composition traits on an approximately 44.1-Mb wild-derived congenic region. In this study, we narrowed down genomic regions harboring three (Pbwg1.12, Pbwg1.3 and Pbwg1.5) of the 12 linked QTLs and searched for possible candidate genes for the QTLs. By phenotypic analyses of F₂ intercross populations between B6 and each of four B6.Cg-Pbwg1 subcongenic strains with overlapping and non-overlapping introgressed regions, we physically defined Pbwg1.12 affecting body weight to a 3.8-Mb interval (61.5–65.3 Mb) on chromosome 2. We fine-mapped Pbwg1.3 for body length to an 8.0-Mb interval (57.3–65.3) and Pbwg1.5 for abdominal white fat weight to a 2.1-Mb interval (59.4–61.5). The wild-derived allele at Pbwg1.12 and Pbwg1.3 uniquely increased body weight and length despite the fact that the wild mouse has a smaller body size than that of B6, whereas it decreased fat weight at Pbwg1.5. Exome sequencing and candidate gene prioritization suggested that Gcg and Grb14 are putative candidate genes for Pbwg1.12 and that Ly75 and Itgb6 are putative candidate genes for Pbwg1.5. These genes had nonsynonymous SNPs, but the SNPs were predicted to be not harmful to protein functions. These results provide information helpful to identify wild-derived quantitative trait genes causing enhanced growth and resistance to obesity.     

Evidence for Close Linkage of Human Amylase Loci

HUMAN α-amylase (α-1,4-glucan 4-glucanohydrolase, E.C. 3.2.1.1) is primarily in the pancreas and salivary glands and can be detected in serum and urine (UAmy) as well as in saliva (SaAmy) and duodenal secretions. The SaAmy locus (Amy₁) has at least three mutant alleles with the combined frequency of electrophoretic variant phenotypes totalling approximately 0.01 in Caucasian Americans¹. Subsequently, UAmy was shown to be a convenient source of pancreatic amylase. The pancreatic amylase locus (Amy₂) has at least two mutant alleles in Caucasian and Afro-Americans². The variant UAmy Ss is common in Caucasians whereas UAmy Sp has been found only in Afro-Americans; the frequency of variant phenotypes is 0·086 in each population².     

Fine Mapping and Candidate Gene Analysis of the Leaf-Color Gene ygl-1 in Maize

A novel yellow-green leaf mutant yellow-green leaf-1 (ygl-1) was isolated in self-pollinated progenies from the cross of maize inbred lines Ye478 and Yuanwu02. The mutant spontaneously showed yellow-green character throughout the lifespan. Meanwhile, the mutant reduced contents of chlorophyll and Car, arrested chloroplast development and lowered the capacity of photosynthesis compared with the wild-type Lx7226. Genetic analysis revealed that the mutant phenotype was controlled by a recessive nuclear gene. The ygl-1 locus was initially mapped to an interval of about 0.86 Mb in bin 1.01 on the short arm of chromosome 1 using 231 yellow-green leaf individuals of an F₂ segregating population from ygl-1/Lx7226. Utilizing four new polymorphic SSR markers, the ygl-1 locus was narrowed down to a region of about 48 kb using 2930 and 2247 individuals of F₂ and F₃ mapping populations, respectively. Among the three predicted genes annotated within this 48 kb region, GRMZM2G007441, which was predicted to encode a cpSRP43 protein, had a 1-bp nucleotide deletion in the coding region of ygl-1 resulting in a frame shift mutation. Semi-quantitative RT-PCR analysis revealed that YGL-1 was constitutively expressed in all tested tissues and its expression level was not significantly affected in the ygl-1 mutant from early to mature stages, while light intensity regulated its expression both in the ygl-1 mutant and wild type seedlings. Furthermore, the mRNA levels of some genes involved in chloroplast development were affected in the six-week old ygl-1 plants. These findings suggested that YGL-1 plays an important role in chloroplast development of maize.     

Linkage Relationships of Seventeen Human Gene Loci as determined by Man-Mouse Somatic Cell Hybrids

Electrophoretic studies of the enzymes produced by sixty-four independently derived hybrid clones have made possible the detection of autosomal linkages on human chromosomes.     

GroupRank: Rank Candidate Genes in PPI Network by Differentially Expressed Gene Groups

Many cell activities are organized as a network, and genes are clustered into co-expressed groups if they have the same or closely related biological function or they are co-regulated. In this study, based on an assumption that a strong candidate disease gene is more likely close to gene groups in which all members coordinately differentially express than individual genes with differential expression, we developed a novel disease gene prioritization method GroupRank by integrating gene co-expression and differential expression information generated from microarray data as well as PPI network. A candidate gene is ranked high using GroupRank if it is differentially expressed in disease and control or is close to differentially co-expressed groups in PPI network. We tested our method on data sets of lung, kidney, leukemia and breast cancer. The results revealed GroupRank could efficiently prioritize disease genes with significantly improved AUC value in comparison to the previous method with no consideration of co-exprssed gene groups in PPI network. Moreover, the functional analyses of the major contributing gene group in gene prioritization of kidney cancer verified that our algorithm GroupRank not only ranks disease genes efficiently but also could help us identify and understand possible mechanisms in important physiological and pathological processes of disease.     

Global Analysis of the Human Pathophenotypic Similarity Gene Network Merges Disease Module Components

The molecular complexity of genetic diseases requires novel approaches to break it down into coherent biological modules. For this purpose, many disease network models have been created and analyzed. We highlight two of them, “the human diseases networks” (HDN) and “the orphan disease networks” (ODN). However, in these models, each single node represents one disease or an ambiguous group of diseases. In these cases, the notion of diseases as unique entities reduces the usefulness of network-based methods. We hypothesize that using the clinical features (pathophenotypes) to define pathophenotypic connections between disease-causing genes improve our understanding of the molecular events originated by genetic disturbances. For this, we have built a pathophenotypic similarity gene network (PSGN) and compared it with the unipartite projections (based on gene-to-gene edges) similar to those used in previous network models (HDN and ODN). Unlike these disease network models, the PSGN uses semantic similarities. This pathophenotypic similarity has been calculated by comparing pathophenotypic annotations of genes (human abnormalities of HPO terms) in the “Human Phenotype Ontology”. The resulting network contains 1075 genes (nodes) and 26197 significant pathophenotypic similarities (edges). A global analysis of this network reveals: unnoticed pairs of genes showing significant pathophenotypic similarity, a biological meaningful re-arrangement of the pathological relationships between genes, correlations of biochemical interactions with higher similarity scores and functional biases in metabolic and essential genes toward the pathophenotypic specificity and the pleiotropy, respectively. Additionally, pathophenotypic similarities and metabolic interactions of genes associated with maple syrup urine disease (MSUD) have been used to merge into a coherent pathological module.Our results indicate that pathophenotypes contribute to identify underlying co-dependencies among disease-causing genes that are useful to describe disease modularity.     

ncRNA候选基因sptl的克隆与初步分析

在用suc2信号肽捕获系统对小鼠胚胎cDNA文库筛选的过程中,反复获得一个相同的强阳性克隆,命名为sptl.对该克隆的序列分析表明插入序列由697 bp组成,6个开放阅读框中共有37个启始密码子(ATG)和80个终止密码子(TGA、TAG、TAA);没有较大的有意义开放读框存在.经BLAST分析,结果显示该序列定位于小鼠第17号染色体长臂,没有发现同源基因.Northern blot和RT-PCR分析表明,该序列仅表达于小鼠卵巢组织,全长约4.5～5.0kb.酵母转化和序列截短实验提示,该序列能够介导蔗糖转换酶向细胞外的分泌.因此,推测sptl很有可能是一个新的非编码RNA的一部分,参与蛋白质的分泌过程.