A Likelihood-Based Framework for Variant Calling and De Novo Mutation Detection in Families

Family samples, which can be enriched for rare causal variants by focusing on families with multiple extreme individuals and which facilitate detection of de novo mutation events, provide an attractive resource for next-generation sequencing studies. Here, we describe, implement, and evaluate a likelihood-based framework for analysis of next generation sequence data in family samples. Our framework is able to identify variant sites accurately and to assign individual genotypes, and can handle de novo mutation events, increasing the sensitivity and specificity of variant calling and de novo mutation detection. Through simulations we show explicit modeling of family relationships is especially useful for analyses of low-frequency variants and that genotype accuracy increases with the number of individuals sequenced per family. Compared with the standard approach of ignoring relatedness, our methods identify and accurately genotype more variants, and have high specificity for detecting de novo mutation events. The improvement in accuracy using our methods over the standard approach is particularly pronounced for low-frequency variants. Furthermore the family-aware calling framework dramatically reduces Mendelian inconsistencies and is beneficial for family-based analysis. We hope our framework and software will facilitate continuing efforts to identify genetic factors underlying human diseases.     

A Strategy to Identify de Novo Mutations in Common Disorders such as Autism and Schizophrenia

There are several lines of evidence supporting the role of de novo mutations as a mechanism for common disorders, such as autism and schizophrenia. First, the de novo mutation rate in humans is relatively high, so new mutations are generated at a high frequency in the population. However, de novo mutations have not been reported in most common diseases. Mutations in genes leading to severe diseases where there is a strong negative selection against the phenotype, such as lethality in embryonic stages or reduced reproductive fitness, will not be transmitted to multiple family members, and therefore will not be detected by linkage gene mapping or association studies. The observation of very high concordance in monozygotic twins and very low concordance in dizygotic twins also strongly supports the hypothesis that a significant fraction of cases may result from new mutations. Such is the case for diseases such as autism and schizophrenia. Second, despite reduced reproductive fitness¹ and extremely variable environmental factors, the incidence of some diseases is maintained worldwide at a relatively high and constant rate. This is the case for autism and schizophrenia, with an incidence of approximately 1% worldwide. Mutational load can be thought of as a balance between selection for or against a deleterious mutation and its production by de novo mutation. Lower rates of reproduction constitute a negative selection factor that should reduce the number of mutant alleles in the population, ultimately leading to decreased disease prevalence. These selective pressures tend to be of different intensity in different environments. Nonetheless, these severe mental disorders have been maintained at a constant relatively high prevalence in the worldwide population across a wide range of cultures and countries despite a strong negative selection against them². This is not what one would predict in diseases with reduced reproductive fitness, unless there was a high new mutation rate. Finally, the effects of paternal age: there is a significantly increased risk of the disease with increasing paternal age, which could result from the age related increase in paternal de novo mutations. This is the case for autism and schizophrenia³. The male-to-female ratio of mutation rate is estimated at about 4–6:1, presumably due to a higher number of germ-cell divisions with age in males. Therefore, one would predict that de novo mutations would more frequently come from males, particularly older males⁴. A high rate of new mutations may in part explain why genetic studies have so far failed to identify many genes predisposing to complexes diseases genes, such as autism and schizophrenia, and why diseases have been identified for a mere 3% of genes in the human genome. Identification for de novo mutations as a cause of a disease requires a targeted molecular approach, which includes studying parents and affected subjects. The process for determining if the genetic basis of a disease may result in part from de novo mutations and the molecular approach to establish this link will be illustrated, using autism and schizophrenia as examples.     

家养动物复杂性状基因定位的统计分析和实验设计

复杂性状基因定位的研究是人类、动植物研究中的1个热点领域。在畜禽的研究中,其目的是定位与生产性状、繁殖性状和疾病相关的基因。在人类中,复杂性状基因定位的研究具有极大的挑战性。尽管基因定位的结果积累得很快,但能得以确认的结果却很少。关于畜禽基因定位的研究结果同样也增长很快,目前在鸡、猪、奶牛等物种中几个大尺度的基因定位工作也正在开展中。虽然在不远的将来能够得到新的、可确信的结果,但是如何精确地理解这些复杂性状的基因仍然需要一定的时间。近来,复杂性状基因定位的方法已被用于通过基因表达的数据研究转录调节因子的定位工作中,这是基因定位研究中1个新的领域。基因定位的统计分析和实验设计是基因定位研究中的关键性步骤,研究的目的在于讨论畜禽复杂性状基因定位的统计分析和实验设计的研究进展及今后的发展。     

Emergence,Retention and Selection: A Trilogy of Origination for Functional De Novo Proteins from Ancestral LncRNAs in Primates

While some human-specific protein-coding genes have been proposed to originate from ancestral lncRNAs, the transition process remains poorly understood. Here we identified 64 hominoid-specific de novo genes and report a mechanism for the origination of functional de novo proteins from ancestral lncRNAs with precise splicing structures and specific tissue expression profiles. Whole-genome sequencing of dozens of rhesus macaque animals revealed that these lncRNAs are generally not more selectively constrained than other lncRNA loci. The existence of these newly-originated de novo proteins is also not beyond anticipation under neutral expectation, as they generally have longer theoretical lifespan than their current age, due to their GC-rich sequence property enabling stable ORFs with lower chance of non-sense mutations. Interestingly, although the emergence and retention of these de novo genes are likely driven by neutral forces, population genetics study in 67 human individuals and 82 macaque animals revealed signatures of purifying selection on these genes specifically in human population, indicating a proportion of these newly-originated proteins are already functional in human. We thus propose a mechanism for creation of functional de novo proteins from ancestral lncRNAs during the primate evolution, which may contribute to human-specific genetic novelties by taking advantage of existed genomic contexts.     

单位点孢子体-配子体互作模型中不育基因的位置和效应的估计方法

水稻籼粳亚种间杂交F1通常表现为高度不育,这种不育性的一种遗传学解释称为单位点孢子体-配子体互作模型.为了研究这种不育性,提出了一种统计方法,可以估计单位点孢子体-配子体互作模型中不育基因位点的位置和效应.该方法利用回交群体中呈现异常分离的标记位点,用最大似然法对不育基因与标记位点之间的重组率和雌配子存活率进行估计.由于所依据的是非连续变异的遗传标记的分离,而不是连续分布的配子育性指标,因此可以避免由育性直接估计所带来的重组率结果的不稳定.     

Integrated Source Apportionment,Screening Risk Assessment,and Risk Mapping of Heavy Metals in Surface Sediments: A Case Study of the Dongting Lake,Middle China

Surface sediment samples were collected from 10 typical locations throughout the Dongting Lake, China, in January 2009. Samples were assayed by atom absorption spectrophotometer and cold atomic fluorescent spectrophotometer for Pb, Cd, As, Hg. In order to investigate the spatial distribution characteristics, sources, and potential ecological risks of heavy metals, the geostatistics method, potential ecological risk index, and multivariate statistical analysis were applied. The results showed that except for the content of Hg, the contents of Pb, Cd, and As had similar spatial distribution characteristics. The average contents of Cd and As exceeded the second class contents of the National Standard for Soil Environment Quality (GB15618-1995), especially that for Cd. The potential ecological risk posed by these heavy metals decreased in the order of the outlet of the Dongting Lake > the East Dongting Lake > the South Dongting Lake > the West Dongting Lake spatially. From the results of multivariate statistical analysis, Pb and Cd, as the first group, were considered to be rooted in mining smelting processes for developed mining and heavy industry. And Hg, as the second group, was mainly derived from parent material weathering, while As was probably considered to originate from both sources above.     

Maternal Genes and Facial Clefts in Offspring: A Comprehensive Search for Genetic Associations in Two Population-Based Cleft Studies from Scandinavia

Background

Fetal conditions can in principle be affected by the mother''s genotype working through the prenatal environment.

Methodology/Principal Findings

Genotypes for 1536 SNPs in 357 cleft candidate genes were available from a previous analysis in which we focused on fetal gene effects [1]. After data-cleaning, genotypes for 1315 SNPs in 334 autosomal genes were available for the current analysis of maternal gene effects. Two complementary statistical methods, TRIMM and HAPLIN, were used to detect multi-marker effects in population-based samples from Norway (562 case-parent and 592 control-parent triads) and Denmark (235 case-parent triads). We analyzed isolated cleft lip with or without cleft palate (iCL/P) and isolated cleft palate only (iCP) separately and assessed replication by looking for genes detected in both populations by both methods. In iCL/P, neither TRIMM nor HAPLIN detected more genes than expected by chance alone; furthermore, the selected genes were not replicated across the two methods. In iCP, however, FLNB was identified by both methods in both populations. Although HIC1 and ZNF189 did not fully satisfy our stringency criterion for replication, they were strongly associated with iCP in TRIMM analyses of the Norwegian triads.

Conclusion/Significance

Except for FLNB, HIC1 and ZNF189, maternal genes did not appear to influence the risk of clefting in our data. This is consistent with recent epidemiological findings showing no apparent difference between mother-to-offspring and father-to-offspring recurrence of clefts in these two populations. It is likely that fetal genes make the major genetic contribution to clefting risk in these populations, but we cannot rule out the possibility that maternal genes can affect risk through interactions with specific teratogens or fetal genes.     

Sustainable Consumption of Food: A Framework for Analyzing Scenarios about Changes in Diets

This article describes the integration of life-cycle assessment methods with a new input-output model of the world economy to analyze the environmental and economic implications of alternative future diets. The article reviews findings by industrial ecologists about the energy and land required for the production and consumption of alternative foods and diets in several European countries. It also reviews attributes of foods and diets identified by nutritionists as reducing the risks of obesity and major chronic diseases related to the diets of the affluent. The predominantly plant-based Mediterranean-type diet emerges as a dietary scenario that could satisfy both sets of concerns. The likely implications for agriculture and for farm policies of a shift toward this diet from the current average diet in the United States are discussed and shown to be substantial. The one-country studies reviewed in the article provide substantial insights into the potential ramifications of dietary change. Many of the limitations of these studies could be overcome by conducting the analysis in a global framework that represented the relationships among consumption, production, and trade and the physical constraints within which they operate. Analysis of the environmental and economic implications of alternative scenarios describing healthy diets can help stimulate more intensive dialogue, debate, and action among the interested parties; such analysis can both benefit from and contribute to initiatives such as the World Health Organization's global strategy on diet and health, which intends to enlist the support of governments, corporations, and civil society.     

Exercise-Induced Neuroprotection in SMA Model Mice: A Means for Determining New Therapeutic Strategies

Due to the prevalence of neuromuscular disorders such as amyotrophic lateral sclerosis and spinal muscular atrophy in modern societies, defining new and efficient strategies for the treatment of these two neurodegenerative diseases has become a vital and still unfulfilled urge. Several lines of experimental evidence have emphasized the benefits of regular exercise training in mouse models for these affections in terms of life span increase and improvement of both motor capacities and motoneuron survival. Identifying molecules that could mimic the neuroprotective effects of exercise represents a promising way to find novel therapies. Some of the effects of exercise are caused by the overproduction of circulating neurotrophic factors, such as IGF-I, whereas others may be due to modifications of the intrinsic properties of the motoneurons within the spinal cord. The causal relationship that links these potential effects of exercise training and the improvement of motor capacity and life span expectancy is consequently discussed.     

Confidence Intervals for the Relative Risk Ratio Parameter from Survival Data Under a Random Censorship Model in Biomedical and Epidemiologic Studies (By Simulation)

The present paper reports the results of a Monte Carlo simulation study to examine the performance of several approximate confidence intervals for the Relative Risk Ratio (RRR) parameter in an epidemiologic study, involving two groups of individuals. The first group consists of n₁ individuals, called the experimental group, who are exposed to some carcinogen, say radiation, whose effect on the incidence of some form of cancer, say skin cancer, is being investigated. The second group consists of n₂ individuals (called the control group) who are not exposed to the carcinogen. Two cases are considered in which the life times (or time to cancer) in the two groups follow (i) the exponential and (ii) the Weibull distributions. The case when the life times follow a Rayleigh distribution follows as a particular case. A general random censorship model is considered in which the life times of the individuals are censored on the right by random censoring times following (i) the exponential and (ii) the Weibull distributions. The Relative Risk Ratio parameter in the study is defined as the ratio of the hazard rates in the two distributions of the times to cancer. Approximate confidence intervals are constructed for the RRR parameter using its maximum likelihood estimator (m.l.e) and several other methods, including a method due to FIELLER. SPROTT'S (1973) and Cox's (1953) suggestions, as well as the Box-Cox (1964) transformation, are also utilized to construct approximate confidence intervals. The performance of these confidence intervals in small samples is investigated by means of some Monte Carlo simulations based on 500 random samples. Our simulation study indicates that many of these confidence intervals perform quite well in samples of size 10 and 15, in terms of the coverage probability and expected length of the interval.     

A rapid method for differentiating Saccharomyces sensu stricto strains from other yeast species in an enological environment

During programs for the selection of enological yeasts, several hundred natural isolates are usually screened. The scope of these operations is to isolate strains possessing good fermentative properties without necessarily arriving at a precise species designation: in other words, to detect strains belonging to the Saccharomyces sensu stricto complex. In the present study, a pair of primers, designed within the variable D1/D2 region of the 26S subunit of ribosomal yeast RNA, have been constructed. These generate an amplification fragment of 471 bp that is specific for the seven Saccharomyces sensu stricto species, while no signal was obtained for Saccharomyces sensu lato strains (17 species) or for another 18 selected species commonly found in enological environments. A second pair of primers was also constructed, within the 18S rRNA gene, composed of perfectly conserved sequences common for all 42 yeast species examined, which generate a 900 bp (c.) band for all strains. This was used as a positive experimental control in multiplex PCR analysis using all four primers.     

A Bayesian MCMC Approach to Assess the Complete Distribution of Fitness Effects of New Mutations: Uncovering the Potential for Adaptive Walks in Challenging Environments

The role of adaptation in the evolutionary process has been contentious for decades. At the heart of the century-old debate between neutralists and selectionists lies the distribution of fitness effects (DFE)—that is, the selective effect of all mutations. Attempts to describe the DFE have been varied, occupying theoreticians and experimentalists alike. New high-throughput techniques stand to make important contributions to empirical efforts to characterize the DFE, but the usefulness of such approaches depends on the availability of robust statistical methods for their interpretation. We here present and discuss a Bayesian MCMC approach to estimate fitness from deep sequencing data and use it to assess the DFE for the same 560 point mutations in a coding region of Hsp90 in Saccharomyces cerevisiae across six different environmental conditions. Using these estimates, we compare the differences in the DFEs resulting from mutations covering one-, two-, and three-nucleotide steps from the wild type—showing that multiple-step mutations harbor more potential for adaptation in challenging environments, but also tend to be more deleterious in the standard environment. All observations are discussed in the light of expectations arising from Fisher’s geometric model.     

A Bootstrap-Based Covariate Selection Method for Modeling the Risk of Lightning-Induced Fires at a Local Scale: A Case Study in Northwest Spain

In lightning-induced fire risk prediction models, the number of potential predictors is usually high, with some redundancy among them. It is therefore important to select the best subset of predictors that obtain models with the greatest discrimination capacity. With this aim in mind, the logistic generalized linear model was used to estimate lightning-induced fire occurrence using a case study of the province of León (northwest Spain). A bootstrap-based test was used to obtain the optimal number of predictors and to model this optimal number of predictors displaying the largest area under the receiver operating characteristics curve. The results show that of the 16 variables initially considered, only three were necessary to obtain the model with the best discriminatory capacity for estimating lightning-induced fire occurrence. Moreover, this model can be considered equivalent to another nine alternative models with three covariates. Both the optimal and the equivalent models are useful in the spatially explicit assessment of fire risk, the planning and coordination of regional efforts to identify areas at greatest risk, and the design of long-term wildfire management strategies. The methodology used for this case study can be applied to other wildfire risk assessment situations where multiple and interconnected covariates are available.     

Tryptic Peptide Mapping Studies on the Regulatory Subunits of Type II Protein Kinases from Cerebral Cortex and Heart. Evidence for Overall Structural Divergence and Differences in the Autophosphorylation and cAMP-binding Domains

Abstract: Regulatory subunits of type II cAMP-dependent protein kinases (RII) (EC 2.7.1.37) from bovine brain and heart exhibit similar physicochemical and functional properties in vitro . However, the two forms of RII are markedly different in their (a) antigenic determinants, (b) cell and tissue distribution, and (c) subcellular localization. This suggests that each of these cAMP-binding proteins may possess some unique structural features. To assess the degree of overall divergence between the primary structures of brain RII and heart RII, tryptic peptides derived from the two proteins were mapped by reverse phase HPLC on a C₁₈ column. When the column effluent was monitored at 280 nm, 15 peptides were found only in the heart RII digest, while 5 other peptides were obtained only from brain RII. More complex HPLC profiles were observed by following peptide absorbance at 210 nm, but a similar level of diversity was apparent: 13 brain-RII-specific and 15 heart-RII-specific tryptic peptides were identified and resolved with a gradient (0–50%) of acetonitrile in 0.1% trifluoroacetic acid. In complementary experiments, classical two-dimensional mapping analyses revealed that several ³²P-labeled tryptic fragments derived from autophosphorylated and photoaffinity-labeled brain RII were separate and distinct from the ³²P-peptides isolated from similarly treated heart RII. The HPLC mapping data document a structural basis for the immunological disparity between brain RII and heart RII and suggest that the two cAMP-binding proteins are different proteins rather than interconvertible forms of a single protein. The two-dimensional maps further indicate that significant structural dissimilarities between brain RII and heart RII also occur within the functionally conserved autophosphorylation and cAMP-binding domains.