A Bayes factor approach with informative prior for rare genetic variant analysis from next generation sequencing data

The discovery of rare genetic variants through next generation sequencing is a very challenging issue in the field of human genetics. We propose a novel region‐based statistical approach based on a Bayes Factor (BF) to assess evidence of association between a set of rare variants (RVs) located on the same genomic region and a disease outcome in the context of case‐control design. Marginal likelihoods are computed under the null and alternative hypotheses assuming a binomial distribution for the RV count in the region and a beta or mixture of Dirac and beta prior distribution for the probability of RV. We derive the theoretical null distribution of the BF under our prior setting and show that a Bayesian control of the false Discovery Rate can be obtained for genome‐wide inference. Informative priors are introduced using prior evidence of association from a Kolmogorov‐Smirnov test statistic. We use our simulation program, sim1000G, to generate RV data similar to the 1000 genomes sequencing project. Our simulation studies showed that the new BF statistic outperforms standard methods (SKAT, SKAT‐O, Burden test) in case‐control studies with moderate sample sizes and is equivalent to them under large sample size scenarios. Our real data application to a lung cancer case‐control study found enrichment for RVs in known and novel cancer genes. It also suggests that using the BF with informative prior improves the overall gene discovery compared to the BF with noninformative prior.     

The rates of introgression and barriers to genetic exchange between hybridizing species: sex chromosomes vs autosomes

Interspecific crossing experiments have shown that sex chromosomes play a major role in reproductive isolation between many pairs of species. However, their ability to act as reproductive barriers, which hamper interspecific genetic exchange, has rarely been evaluated quantitatively compared to Autosomes. This genome-wide limitation of gene flow is essential for understanding the complete separation of species, and thus speciation. Here, we develop a mainland-island model of secondary contact between hybridizing species of an XY (or ZW) sexual system. We obtain theoretical predictions for the frequency of introgressed alleles, and the strength of the barrier to neutral gene flow for the two types of chromosomes carrying multiple interspecific barrier loci. Theoretical predictions are obtained for scenarios where introgressed alleles are rare. We show that the same analytical expressions apply for sex chromosomes and autosomes, but with different sex-averaged effective parameters. The specific features of sex chromosomes (hemizygosity and absence of recombination in the heterogametic sex) lead to reduced levels of introgression on the X (or Z) compared to autosomes. This effect can be enhanced by certain types of sex-biased forces, but it remains overall small (except when alleles causing incompatibilities are recessive). We discuss these predictions in the light of empirical data comprising model-based tests of introgression and cline surveys in various biological systems.     

Evading resistance to gene drives

Gene drives offer the possibility of altering and even suppressing wild populations of countless plant and animal species, and CRISPR technology now provides the technical feasibility of engineering them. However, population-suppression gene drives are prone to select resistance, should it arise. Here, we develop mathematical and computational models to identify conditions under which suppression drives will evade resistance, even if resistance is present initially. Previous models assumed resistance is allelic to the drive. We relax this assumption and show that linkage between the resistance and drive loci is critical to the evolution of resistance and that evolution of resistance requires (negative) linkage disequilibrium between the two loci. When the two loci are unlinked or only partially so, a suppression drive that causes limited inviability can evolve to fixation while causing only a minor increase in resistance frequency. Once fixed, the drive allele no longer selects resistance. Our analyses suggest that among gene drives that cause moderate suppression, toxin-antidote systems are less apt to select for resistance than homing drives. Single drives of moderate effect might cause only moderate population suppression, but multiple drives (perhaps delivered sequentially) would allow arbitrary levels of suppression. The most favorable case for evolution of resistance appears to be with suppression homing drives in which resistance is dominant and fully suppresses transmission distortion; partial suppression by resistance heterozygotes or recessive resistance are less prone to resistance evolution. Given that it is now possible to engineer CRISPR-based gene drives capable of circumventing allelic resistance, this design may allow for the engineering of suppression gene drives that are effectively resistance-proof.     

Repeated horizontal gene transfer of GALactose metabolism genes violates Dollo’s law of irreversible loss

Dollo’s law posits that evolutionary losses are irreversible, thereby narrowing the potential paths of evolutionary change. While phenotypic reversals to ancestral states have been observed, little is known about their underlying genetic causes. The genomes of budding yeasts have been shaped by extensive reductive evolution, such as reduced genome sizes and the losses of metabolic capabilities. However, the extent and mechanisms of trait reacquisition after gene loss in yeasts have not been thoroughly studied. Here, through phylogenomic analyses, we reconstructed the evolutionary history of the yeast galactose utilization pathway and observed widespread and repeated losses of the ability to utilize galactose, which occurred concurrently with the losses of GALactose (GAL) utilization genes. Unexpectedly, we detected multiple galactose-utilizing lineages that were deeply embedded within clades that underwent ancient losses of galactose utilization. We show that at least two, and possibly three, lineages reacquired the GAL pathway via yeast-to-yeast horizontal gene transfer. Our results show how trait reacquisition can occur tens of millions of years after an initial loss via horizontal gene transfer from distant relatives. These findings demonstrate that the losses of complex traits and even whole pathways are not always evolutionary dead-ends, highlighting how reversals to ancestral states can occur.     

牛磺酸上调基因1(TUG1)对肝纤维化的作用及其机制*

目的:探讨牛磺酸上调基因1(TUG1)在肝纤维化中的作用机制。方法:按照文献建立TGF-β1(5 ng/ml)刺激的活化肝星状细胞模型和经典的1%DMN(1 ml/kg/d)致大鼠肝纤维化模型,将肝纤维化大鼠和活化肝星状细胞(HSC)均分为模型对照组、阴性对照组(沉默TUG1阴性对照)、siRNA干扰组(TUG1基因沉默组)。实验结束后利用苏木精-伊红(HE)染色检测大鼠肝脏组织病理变化;采用逆转录-聚合酶链反应(RT-PCR)法、蛋白免疫印记(Western blot)分别测定大鼠肝组织及活化肝星状细胞中α-平滑肌肌动蛋白(α-SMA)、TUG1、I型胶原蛋白(collagenI)、基质金属蛋白酶-2(MMP-2)、金属蛋白酶组织抑制因子(TIMP-1)、Smad2、Smad3表达水平。结果:肝组织病理学检查显示,沉默TUG1能够明显缓解肝脏纤维化病理改变,Western blot结果显示,沉默TUG1能够显著降低大鼠肝组织和活化肝星状细胞中TUG1、α-SMA、collagenI、MMP-2、TIMP-1、Smad2、Smad3基因与蛋白表达水平(P＜0.05)。与模型对照组相比,阴性对照组的TUG1、α-SMA的蛋白与基因水平明显升高(P＜0.05)。与模型对照组和阴性对照组相比,siRNA干扰组中TUG1, α-SMA, collagenI, MMP-2, TIMP-1, Smad2 and Smad3的蛋白和基因水平显著降低(P＜0.05),而在模型对照组和阴性对照组中TUG1, α-SMA, collagenI, MMP-2, TIMP-1, Smad2 and Smad3的蛋白和基因表达水平之间差异无显著性。结论:TUG1在肝纤维化组织和活化的肝星状细胞中显著上调,沉默TUG1可能通过抑制转化生长因子-β1(TGF-β1)/Smad信号通路改善1%DMN致大鼠肝纤维化病理损伤,降低活化肝星状细胞中纤维化相关蛋白水平,发挥抗肝纤维化的作用。