An intuitive risk factors search algorithm: usage of the Bayesian network technique in personalized medicine

The article focuses on the application of the Bayesian networks (BN) technique to problems of personalized medicine. The simple (intuitive) algorithm of BN optimization with respect to the number of nodes using naive network topology is developed. This algorithm allows to increase the BN prediction quality and to identify the most important variables of the network. The parallel program implementing the algorithm has demonstrated good scalability with an increase in the computational cores number, and it can be applied to the large patients database containing thousands of variables. This program is applied for the prediction for the unfavorable outcome of coronary artery disease (CAD) for patients who survived the acute coronary syndrome (ACS). As a result, the quality of the predictions of the investigated networks was significantly improved and the most important risk factors were detected. The significance of the tumor necrosis factor-alpha gene polymorphism for the prediction of the unfavorable outcome of CAD for patients survived after ACS was revealed for the first time.     

试论新农村建设与城市化的协同发展

中国目前仍有8亿多的农村人口,建设新农村是一项重大的抉择。但中国的新农村建设是在中国现代化发展很不充分的情况下提出的。新农村建设与工业化、城市化或总体来讲的现代化是密切相关的,有其系统规定性。在研究“中国的社会主义新农村建设是什么”、“工业化、城市化和现代化的过程”、“中国大陆城市化的滞后及原因”的基础上,提出“协同新农村建设与城市化的构想”。     

Polymorphic fundatrices in thimbleberry aphid — ecology and maintenance

The thimbleberry aphid,Masonaphis maxima (Mason) lives on patches of plants that support 3,4 or 5 generations depending on site and weather. The life cycle requires sexual females and males to produce overwintering eggs. The eggs hatch in the spring to produce the first ’fundatrix’ generation; subsequent generations are produced parthenogenically. Males and other morphs are produced by wingless virginoparae, but sexual females are produced by ’gynoparae’, a winged morph that is specialized to produce only sexual females. The fundatrices have no indication of the number of generations that the plants will support in the current year. There are two fundatrix types that coexist in different ratios depending on the number of generations supported by the patch the previous year. One type produces sexual females in generations 3 and 5, and males in generations 4 and 5; the other type produces sexual females in generations 4 and 5, and males in generations 3, 4 and 5. The dimorphism adapts the aphid to its heterogeneous and somewhat unpredictable environment. The role of sex in the maintenance of the dimorphism is discussed. This is the first report of fundatrix polymorphism and consequent differential sex expression in aphids.     

EEFSEC基因、染色体17q24和染色体11q13.2基因变异与前列腺癌的关联研究

目的探索EEFSEC基因(rs10934853,A)、染色体17q24区(rs1859962,T)和染色体11q13.2(rs7931342,T)的基因变异类型与前列腺癌患病发病风险的关联,分析这些基因型与前列腺癌患者临床特征的关系。方法采用病例对照研究设计,比较病例组中124例患者和对照组中138例正常对照者的EEFSEC基因(rs10934853,A)、染色体17q24区(rs1859962,T)和染色体11q13.2(rs7931342,T)等位基因和基因型频率的差异,并探讨各基因变异与患者的确诊年龄,BMI,Gleason评分,PSA浓度,肿瘤分期等临床特征之间的关联。结果 EEFSEC基因(rs10934853,A)、染色体17q24区(rs1859962,T)和染色体11q13.2(rs7931342,T)的基因型和等位基因在病例组和对照组中的频率分布差异均无统计学意义(P0.05),然而,EEFSEC基因(rs10934853,A)和染色体17q24区(rs1859962,T)存在更强的基因-基因协同的交互作用(P=0.0396,OR=1.722,95%CI=1.0244~2.8944);病例组基因型-表型观察指标关联分析表明,3个SNPs与PCa患者的年龄、Gleason评分、PSA浓度及烟酒均无关联(P0.05),然而,染色体17q24区(rs1859962,T)位点与食用蛋类有关(P=0.005)。结论 EEFSEC基因(rs10934853,A),17q24(rs1859962,T)和11q13.2(rs7931342,T)位点可能与我国北方人群前列腺癌的发病风险无关联,但是存在有基因之间增加PCa发病风险的协同效应。     

Estrogen receptor alpha single nucleotide polymorphism as predictor of diabetes type 2 risk in hypogonadal men

Abstract

Estradiol (E2) is, apart from its role as a reproductive hormone, also important for cardiac function and bone maturation in both genders. It has also been shown to play a role in insulin production, energy expenditure and in inducing lipolysis. The aim of the study was to investigate if low circulating testosterone or E2 levels in combination with variants in the estrogen receptor alpha (ESR1) and estrogen receptor beta (ESR2) genes were of importance for the risk of type-2 diabetes. The single nucleotide polymorphisms rs2207396 and rs1256049, in ESR1 and ESR2, respectively, were analysed by allele specific PCR in 172 elderly men from the population-based Tromsø study. The results were adjusted for age. In individuals with low total (≤11?nmol/L) or free testosterone (≤0.18?nmol/L) being carriers of the variant A-allele in ESR1 was associated with 7.3 and 15.9 times, respectively, increased odds ratio of being diagnosed with diabetes mellitus type 2 (p?=?0.025 and p?=?0.018, respectively). Lower concentrations of E2 did not seem to increase the risk of being diagnosed with diabetes. In conclusion, in hypogonadal men, the rs2207396 variant in ESR1 predicts the risk of type 2 diabetes.     

Risk Estimation and Value-of-Information Analysis for Three Proposed Genetic Screening Programs for Chronic Beryllium Disease Prevention

Genetic differences (polymorphisms) among members of a population are thought to influence susceptibility to various environmental exposures. In practice, however, this information is rarely incorporated into quantitative risk assessment and risk management. We describe an analytic framework for predicting the risk reduction and value-of-information (VOI) resulting from specific risk management applications of genetic biomarkers, and we apply the framework to the example of occupational chronic beryllium disease (CBD), an immune-mediated pulmonary granulomatous disease. One described Human Leukocyte Antigen gene variant, HLA-DP beta 1*0201, contains a substitution of glutamate for lysine at position 69 that appears to have high sensitivity (approximately 94%) but low specificity (approximately 70%) with respect to CBD among individuals occupationally exposed to respirable beryllium. The expected postintervention CBD prevalence rates for using the genetic variant (1) as a required job placement screen, (2) as a medical screen for semiannual in place of annual lymphocyte proliferation testing, or (3) as a voluntary job placement screen are 0.08%, 0.8%, and 0.6%, respectively, in a hypothetical cohort with 1% baseline CBD prevalence. VOI analysis is used to examine the reduction in total social cost, calculated as the net value of disease reduction and financial expenditures, expected for proposed CBD intervention programs based on the genetic susceptibility test. For the example cohort, the expected net VOI per beryllium worker for genetically based testing and intervention is $13,000, $1,800, and $5,100, respectively, based on a health valuation of $1.45 million per CBD case avoided. VOI results for alternative CBD evaluations are also presented. Despite large parameter uncertainty, probabilistic analysis predicts generally positive utility for each of the three evaluated programs when avoidance of a CBD case is valued at $1 million or higher. Although the utility of a proposed risk management program may be evaluated solely in terms of risk reduction and financial costs, decisions about genetic testing and program implementation must also consider serious social, legal, and ethical factors.     

浆细胞膜糖蛋白基因K121Q变异与老年人2型糖尿病的关联研究

目的探讨浆细胞膜糖蛋白基因(PC-1)4号外显子K121Q变异与老年人2型糖尿病的相关性。方法自2006年北京市社区2型糖尿病调查资料中选出有糖尿病家族史,且相互间无亲缘关系的老年2型糖尿病患者228例,同时选择非糖尿病健康老年对照人群308例。所有受试者均签署知情同意书,所有受试者均为汉族。应用聚合酶链反应-限制性片段长度多态性(PCR-RFLP)方法,检测PC-1基因K121Q的多态性分布情况。结果老年2型糖尿病患者中KK基因型177例(77.6%),KQ基因型46例(20.2%),QQ基因型5例(2.2%),K、Q等位基因频率分别是87.7%和12.3%;正常老年对照组中KK基因型239例(77.6%),KQ基因型63例(20.5%),QQ基因型6例(1.9%),K、Q等位基因频率分别是87.8%和12.2%;PC-1基因K121Q变异的基因型频率和等位基因频率在两组中的分布差异无显著性(P>0.05);PC-1基因K121Q变异的基因型频率和等位基因频率在男性和女性中的分布差异也无显著性(P>0.05);PC-1基因K121Q变异的KK基因型组与KQ QQ基因型组中的肥胖指标的特征差异也无显著性(P>0.05)。结论PC-1基因K121Q变异可能与老年人2型糖尿病的易感性无关联。     

Ant reproductive strategies

In contrast to what is generally believed, the reproductive strategies of ants are remarkably diverse and include such different phenomena, as wingless female and male sexuals, reproduction by mated workers, thelytokous parthenogenesis, and complete workerlessness. We review the various reproductive life histories and investigate them in the light of recent models on the evolution of dispersal strategies and multiple-queening. It appears that most deviations from “normal” colony propagation can be explained by a decreased success of dispersal and solitary founding by solitary queens in certain types of habitats. Consequently, alternative reproductive strategies are found especially in those species, in which environmental conditions or a highly specialized way of life are thought to make solitary founding costly. Among the key factors, which determine the success of reproductive strategies, appear to be spatial and temporal distribution of habitats and the availability of nest sites.     

Identification of quantitative trait loci for canine hip dysplasia by two sequential multipoint linkage analyses

Canine hip dysplasia (CHD) is characterized by hip laxity and subluxation that can lead to hip osteoarthritis. Studies have shown the involvement of multiple genetic regions in the expression of CHD. Although we have associated some variants in the region of fibrillin 2 with CHD in a subset of dogs, no major disease-associated gene has been identified. The focus of this study is to identify quantitative trait loci (QTL) associated with CHD. Two sequential multipoint linkage analyses based on a reversible jump Markov chain Monte Carlo approach were applied on a cross-breed pedigree of 366 dogs. Hip radiographic trait (Norberg Angle, NA) on both hips of each dog was tested for linkage to 21,455 single nucleotide polymorphisms across 39 chromosomes. Putative QTL for the NA was found on 11 chromosomes (1, 2, 3, 4, 7, 14, 19, 21, 32, 36, and 39). Identification of genes in the QTL region(s) can assist in identification of the aberrant genes and biochemical pathways involving hip dysplasia in both dogs and humans.     

Genetic variants in 5p13.2 and 7q21.1 are associated with treatment for benign prostatic hyperplasia with the α-adrenergic receptor antagonist

Background: The etiology of benign prostatic hyperplasia (BPH) has not been well established. The preferred medical treatment for many men with symptomatic benign prostatic hyperplasia is either an α-adrenergic receptor antagonist (α-blocker), or a 5α-reductase inhibitor. Single nucleotide polymorphism (SNP) is a powerful tool for successful implementation of individualized treatment.

Methods: Eighteen SNPs associated with drug efficacy in a Chinese population were genotyped in 790 BPH cases (330 aggressive and 460 non-aggressive BPH cases) and 1008 controls. All BPH patients were treated with α-adrenergic blockers for at least 9 months. We tested the associations between tagging single nucleotide polymorphism and BPH risk/aggressiveness, clinical characteristics at baseline, including the International Prostate Symptom Score (IPSS) and total prostate volume, and changes in clinical characteristics after treatment.

Results: There were nine SNPs associated with BPH risk, clinical progression and therapeutic effect. (1) There were nine tSNPs been chosen in CYP3A4, CYP3A5 and RANBP3L genes. (2) The SNP, rs16902947 in RANBP3L at 5p13.2 (p?=?.01), was significantly associated with BPH. (3) We found two SNPs, rs16902947 in RANBP3L at 5p13.2 (p?=?.0388) and rs4646437 in CYP3A4 at 7q21.1 (p?=?.0325), associated with drug effect. (4) Allele “G” for rs16902947 was found to be risk alleles for BPH risk (OR=?2.357, 95%CI 1.01–1.48). The “A” allele of rs4646437 was associated with lower IPSS at baseline (β=??0.4232, p=?.03255).

Conclusions: rs16902947, rs16902947 and rs4646437 single nucleotide polymorphisms are significantly associated with the clinical characteristics of benign prostatic hyperplasia and the efficacy of benign prostatic hyperplasia treatment.