Information requirements and regulatory approaches for heritable genetic risk assessment and risk communication

With the evolution of genetic toxicology as a scientific discipline and the formation of the Environmental Mutagen Society (EMS), much thought was given to the study of chemicals in the human environment for their mutagenic effects. The Society's goal was to promote scientific investigation and dissemination of information related to genetic toxicology. Subsequently, the concern for chemically induced genetic damage in human germ cells and its potential impact on genetic diseases was detailed in the Committee 17 Report (1975). With new information on the involvement of genetic alterations in disease and on the ramifications of possible effects of exposures to environmental mutagens, it is becoming increasingly necessary to again focus our attention on the assessment of heritable genetic effects. Clearly, strategies for communication of genetic hazard/risk assessments to exposed individuals and to those charged with regulating environmental agents need to be developed.     

Quantifying introgression risk with realistic population genetics

Introgression is the permanent incorporation of genes from the genome of one population into another. This can have severe consequences, such as extinction of endemic species, or the spread of transgenes. Quantification of the risk of introgression is an important component of genetically modified crop regulation. Most theoretical introgression studies aimed at such quantification disregard one or more of the most important factors concerning introgression: realistic genetical mechanisms, repeated invasions and stochasticity. In addition, the use of linkage as a risk mitigation strategy has not been studied properly yet with genetic introgression models. Current genetic introgression studies fail to take repeated invasions and demographic stochasticity into account properly, and use incorrect measures of introgression risk that can be manipulated by arbitrary choices. In this study, we present proper methods for risk quantification that overcome these difficulties. We generalize a probabilistic risk measure, the so-called hazard rate of introgression, for application to introgression models with complex genetics and small natural population sizes. We illustrate the method by studying the effects of linkage and recombination on transgene introgression risk at different population sizes.     

Managing the risk of comparing estimated breeding values across flocks or herds through connectedness: a review and application

Comparing predicted breeding values (BV) among animals in different management units (e.g. flocks, herds) is challenging if units have different genetic means. Unbiased estimates of differences in BV may be obtained by assigning base animals to genetic groups according to their unit of origin, but units must be connected to estimate group effects. If many small groups exist, error of BV prediction may be increased. Alternatively, genetic groups can be excluded from the statistical model, which may bias BV predictions. If adequate genetic connections exist among units, bias is reduced. Several measures of connectedness have been proposed, but their relationships to potential bias in BV predictions are not well defined. This study compares alternative strategies to connect small units and assesses the ability of different connectedness statistics to quantify potential bias in BV prediction. Connections established using common sires across units were most effective in reducing bias. The coefficient of determination of the mean difference in predicted BV was a perfect indicator of potential bias remaining when comparing individuals in separate units. However, this measure is difficult to calculate; correlated measures such as prediction errors of differences in unit means and correlations among prediction errors are suggested as practical alternatives.     

Pregnancy and the risk of torsades de pointes in congenital long-QT syndrome

Patients with congenital long-QT syndrome (LQTS) are at increased risk of ventricular arrhythmias during stressful situations. Large-scale studies have pointed out that affected individuals are particularly at risk in the period following pregnancy (post-partum). This is recognised especially for women with an LQTS type 2. Here, we describe two cases of young women with LQTS type 2, both admitted to our institution with symptomatic torsades de pointes a few weeks after delivery. Both patients carried a mutation in the KCNH2 gene. One patient was nullipara, while the other had had an uneventful previous pregnancy. In both cases treatment with a β-blocker did not prevent life-threatening cardiac arrhythmias. The risk of arrhythmias is thought to gradually decrease to pre-pregnancy values in the nine months after delivery. Considering the difficulties related to continuous monitoring of a patient for such a long period and the desire of these patients to have more children in the foreseeable future, ICD implantation was performed. (Neth Heart J 2008;16:422-5.)     

Adiposity significantly modifies genetic risk for dyslipidemia

Recent genome-wide association studies have identified multiple loci robustly associated with plasma lipids, which also contribute to extreme lipid phenotypes. However, these common genetic variants explain <12% of variation in lipid traits. Adiposity is also an important determinant of plasma lipoproteins, particularly plasma TGs and HDL cholesterol (HDLc) concentrations. Thus, interactions between genes and clinical phenotypes may contribute to this unexplained heritability. We have applied a weighted genetic risk score (GRS) for both plasma TGs and HDLc in two large cohorts at the extremes of BMI. Both BMI and GRS were strongly associated with these lipid traits. A significant interaction between obese/lean status and GRS was noted for each of TG (P_Interaction = 2.87 × 10⁻⁴) and HDLc (P_Interaction = 1.05 × 10⁻³). These interactions were largely driven by SNPs tagging APOA5, glucokinase receptor (GCKR), and LPL for TG, and cholesteryl ester transfer protein (CETP), GalNAc-transferase (GALNT2), endothelial lipase (LIPG), and phospholipid transfer protein (PLTP) for HDLc. In contrast, the GRS_{LDL cholesterol} × adiposity interaction was not significant. Sexual dimorphism was evident for the GRS_HDL on HDLc in obese (P_Interaction = 0.016) but not lean subjects. SNP by BMI interactions may provide biological insight into specific genetic associations and missing heritability.     

Evolutionary constraints mediate extinction risk under climate change

Mounting evidence suggests that rapid evolutionary adaptation may rescue some organisms from the impacts of climate change. However, evolutionary constraints might hinder this process, especially when different aspects of environmental change generate antagonistic selection on genetically correlated traits. Here, we use individual-based simulations to explore how genetic correlations underlying the thermal physiology of ectotherms might influence their responses to the two major components of climate change—increases in mean temperature and thermal variability. We found that genetic correlations can influence population dynamics under climate change, with declines in population size varying three-fold depending on the type of correlation present. Surprisingly, populations whose thermal performance curves were constrained by genetic correlations often declined less rapidly than unconstrained populations. Our results suggest that accurate forecasts of the impact of climate change on ectotherms will require an understanding of the genetic architecture of the traits under selection.     

Association between lncRNA-H19 polymorphisms and hepatoblastoma risk in an ethic Chinese population

H19 polymorphisms are associated with increased susceptibility to several cancers; however, their role in hepatoblastoma remains unclear. In this study, we investigated the association between three H19 polymorphisms (rs2839698 G>A, rs3024270 C>G, rs217727 G>A) and hepatoblastoma susceptibility in 213 hepatoblastoma patients. The rs2839698 and rs3024270 polymorphisms were associated with significantly increased hepatoblastoma risk, with the GG genotype associated with a higher risk of hepatoblastoma than the CC genotype at the rs3024270 locus. The rs217727 polymorphism was associated with significantly decreased hepatoblastoma risk, with the AG genotype associated with a lower risk of hepatoblastoma than the GG genotype. These findings were confirmed by combined analysis, and stratification analysis revealed that age, gender and clinical stage were associated with increased hepatoblastoma susceptibility. The GGG and AGG haplotypes were significantly associated with increased hepatoblastoma risk compared with the GCA reference (rs2839698, rs3024270, rs217727). The rs2839698 and rs3024270 polymorphisms correlated with decreased MRPL23-AS1 expression, whereas the rs217727 polymorphism was associated with increased MRPL23-AS1 expression. Overall, the H19 rs2839698, rs3024270 and rs217727 polymorphisms were associated with hepatoblastoma susceptibility in a Chinese Han population.     

Genetically engineered trees for plantation forests: key considerations for environmental risk assessment

Forests are vital to the world's ecological, social, cultural and economic well‐being yet sustainable provision of goods and services from forests is increasingly challenged by pressures such as growing demand for wood and other forest products, land conversion and degradation, and climate change. Intensively managed, highly productive forestry incorporating the most advanced methods for tree breeding, including the application of genetic engineering (GE), has tremendous potential for producing more wood on less land. However, the deployment of GE trees in plantation forests is a controversial topic and concerns have been particularly expressed about potential harms to the environment. This paper, prepared by an international group of experts in silviculture, forest tree breeding, forest biotechnology and environmental risk assessment (ERA) that met in April 2012, examines how the ERA paradigm used for GE crop plants may be applied to GE trees for use in plantation forests. It emphasizes the importance of differentiating between ERA for confined field trials of GE trees, and ERA for unconfined or commercial‐scale releases. In the case of the latter, particular attention is paid to characteristics of forest trees that distinguish them from shorter‐lived plant species, the temporal and spatial scale of forests, and the biodiversity of the plantation forest as a receiving environment.     

Association between polymorphisms in IL21 gene and risk for sepsis

Context: Sepsis is now the leading cause of death in the noncardiovascular intensive care unit (ICU).

Objective: To investigate whether polymorphisms in IL21 gene contribute to sepsis susceptibility.

Materials and methods: Three single-nucleotide polymorphisms of IL21 (rs907715, rs2055979, rs12508721) were genotyped by TaqMan assay in patients with sepsis and control subjects.

Results: Polymorphisms rs2055979 and rs12508721 in IL21 were more frequent in sepsis patients compared to general population. But allele frequency of rs907715 was not significantly different between sepsis patients and control subjects.

Conclusion: Polymorphisms in IL21 may be associated with sepsis risk.     

Sire coloration influences offspring survival under predation risk in the moorfrog

When breeding, male moor frogs Rana arvalis develop a bright blue dorsal coloration which varies in intensity between males. We tested whether this colour acts as a potential signal of a male's genetic quality to female moor frogs by artificially crossing pairs of males differing in the extent of the blue coloration to the same female. Maternal half-sibships provide a powerful means to detect paternal genetic effects on offspring as they control for other potentially confounding variables. We assayed the ability of offspring to survive an ecologically realistic test of fitness by exposing them to predation by the larvae of the predatory water beetle Dytiscus marginalis. Although sire's coloration did not influence tadpole body size, it did affect their ability to survive the predation trial. Offspring of bright blue males had higher survival than those of dull males when exposed to large predators, which were more voracious predators than smaller ones. Our results indicate that paternal secondary sexual traits provide information about genetic effects on offspring fitness in this species, but suggest that these effects may be context-dependent. Variable selection caused by contextual dependence may have important consequences for the evolution of female choice rules, and for the maintenance of genetic variation for both male trait and female preference.     

Genetic risk of domestication in artificial fish stocking and its possible reduction

Genetic hazards associated with the stocking of fish juveniles produced in hatcheries were studied with simple mathematical models. Domestication is the process of acquiring a genetic characteristics that are advantageous in a hatchery environment but that are disadvantageous in a natural environment due to the selection pressure in the hatchery differing from that in the natural environment. Conditions for the propagation of mutants enhancing domestication were obtained for a variety of stocking strategies specified by parameters related to hatchery productivity and kind of brood stock used. By using this, the possibility of reducing the risk of domestication was studied. As a means of reducing the risk, selective use of wild-born individuals for brood stock was considered. The effectiveness of this was analyzed for both the cases where all brood stock is collected from the wild, and the male brood stock is collected from the wild and the female brood stock is born and reared in a hatchery. We also estimate how much hatchery release can be increased without increasing the risk by employing these means. It is concluded that the use of only male brood stock from the wild is not very effective in reducing the risk of domestication. Further, it is concluded that selective use of the wild-born individuals of both sexes for brood stock is highly desirable if the contribution of released individuals to the natural reproduction is high. In other words, substantial increase of hatchery release may be possible while keeping risk at a level comparable to that under moderate hatchery release, if it is accompanied by the selective use of wild-born individuals for brood stock.     

Seeing and knowing in twenty-first century genetic medicine: the clinical pedigree as epistemological tool and hybrid risk technique

This paper explores the clinical pedigree as a risk technique within the context of the predictive genetic testing (PGT) clinic. We situate the PGT clinic as a site of genetic governance in that it is a site both for the production of knowledge about genetic risk and for intervening in the everyday lives of individuals and their families who learn to cultivate their relations with themselves and their biological relatives in relation to genetic risk knowledge. Drawing on literature of the pedigree as socially constructed and on notions of risk governance, we suggest that the pedigree operates as an epistemological tool and risk technique – that is, as a visual device that assists in organizing the social relations of knowledge production and aids in effecting shifts in patient subjectivity in ways that are consistent with neoliberal notions of active citizenship.     

遗传风险评分在复杂疾病遗传学研究中的应用

心血管疾病、2型糖尿病、原发性高血压、哮喘、肥胖、肿瘤等复杂疾病在全球范围内流行,并成为人类死亡的主要原因。越来越多的人开始关注遗传易感性在复杂疾病发病机制中的作用。至今,与复杂疾病相关的易感基因和基因序列变异仍未完全清楚。人们希望通过遗传关联研究来阐明复杂疾病的遗传基础。近年来,全基因组关联研究和候选基因研究发现了大量与复杂疾病有关的基因序列变异。这些与复杂疾病有因果和(或)关联关系的基因序列变异的发现促进了复杂疾病预测和防治方法的产生和发展。遗传风险评分(Genetic risk score,GRS)作为探索单核苷酸多态(Single nucleotide polymorphisms,SNPs)与复杂疾病临床表型之间关系的新兴方法,综合了若干SNPs的微弱效应,使基因多态对疾病的预测性大幅度提升。该方法在许多复杂疾病遗传学研究中得到成功应用。本文重点介绍了GRS的计算方法和评价标准,简要列举了运用GRS取得的系列成果,并对运用过程中所存在的局限性进行了探讨,最后对遗传风险评分的未来发展方向进行了展望。     

Genetic risk for earlier menarche also influences peripubertal body mass index

It is unclear whether earlier age at menarche is associated with higher body mass index (BMI) because they share a common genetic underpinning. We investigated the impact of single nucleotide polymorphisms (SNPs) influencing menarche timing on peripubertal BMI. For 556 Fels Longitudinal Study children (277 boys/279 girls) born 1928–1992, a genetic risk score (GRS₄₂) was computed as the sum of the number of risk alleles in 42 putative menarche SNPs. Serial BMI Z‐scores within ±6.99 years from each individual's age at peak height velocity (Age@PHV) were grouped into seven time points (?6 years, ?4 years, –2 years, Age@PHV, +2 years, +4years, and +6 years). Heritability of BMI ranged from 0.53 to 0.85 across the time points. The effect of GRS₄₂ on BMI Z‐scores at each time point was modeled using variance components‐based procedures. GRS₄₂ had a significant (P < 0.05) effect at every time point; an increase of one risk allele was associated with an increase of 0.03–0.08 BMI Z‐scores. A separate score (GRS₂₉) was computed that excluded 13 of the menarche SNPs previously documented to also influence adiposity; significant main effects were observed at Age@PHV+4 and +6 years. This finding supports a causal effect of advanced sexual development on post‐Age@PHV BMI. Significant positive GRS₄₂ (or GRS₂₉)‐by‐birth year interactions indicate that some genetic influences on BMI have amplified over the 20th century. This gene‐by‐environment interaction also suggests that children with a genetic predisposition to earlier sexual development might avoid elevated BMI through alteration of their nutritional environment. Am J Phys Anthropol, 2013. © 2012 Wiley Periodicals, Inc.     

Life-history decisions under predation risk: Importance of a game perspective

We model ontogenetic shifts (e.g. in food or habitat use) during development under predation risk. We ask whether inclusion of state and frequency dependence will provide new insights when compared with game-free life-history theory. We model a simple biological scenario in which a prey animal must switch from a low-predation, low-growth habitat to a high-predation, high-growth habitat. To assess the importance of frequency dependence, we compare the results of four scenarios of increasing complexity: (1) no predation; (2) constant predation; (3) frequency-dependent predation (predation risk diluted at high prey density); and (4) frequency-dependent predation as in (3) but with predators allowed to respond adaptively to prey behaviour. State dependence is included in all scenarios through initial size, assumed to be environmental. A genetic algorithm is used to search for optimal solutions to the scenarios. We find substantially different results in the four different scenarios and suggest a decision tree by which biological systems could be tested to ascertain which scenario is most applicable.     

SNP rs2243828 in MPO associated with myeloperoxidase level and atrial fibrillation risk in Chinese Han population

Previous studies shown that myeloperoxidase (MPO) level is higher in patients with atrial fibrillation (AF); however, no genetic evidence between MPO and AF risk in human population was observed. Therefore, the present study was aimed to investigate the association between rs2243828, a variant in promoter region of MPO and the risk of AF in Chinese GeneID population. The results demonstrated that the minor G allele of rs2243828 showed a significant association with AF in two independent population (GeneID‐north population with 694 AF cases and 710 controls, adjusted P_‐adj = 6.25 × 10^?3 with an odds ratio was 0.77, GeneID‐central population with 1106 cases and 1501 controls, P_‐adj = 9.88 × 10^?5 with an odds ratio was 0.75). The results also showed G allele was significantly associated with lower plasma concentration of myeloperoxidase in general population. We also observed a significant difference of odds ratio between subgroups of hypertension and non‐hypertension. Therefore, our findings identified variant in MPO associated with risk of AF and it may give strong evidence to link the inflammation with the incidence of AF.     

Genetic risk variants for dyslexia on chromosome 18 in a German cohort

Dyslexia is characterized by impaired reading and spelling. The disorder has a prevalence of about 5% in Germany, and a strong hereditary component. Several loci are thought to be involved in the development of dyslexia. Scerri et al. identified eight potential dyslexia‐associated single nucleotide polymorphisms (SNPs) in seven genes on chromosome 18 in an English‐speaking population. Here, we present an association analysis that explores the relevance of these SNPs in a German population comprising 388 dyslexia cases and 364 control cases. In case–control analysis, three nominal SNP associations were replicated. The major alleles of NEDD4L‐rs12606138 and NEDD4L‐rs8094327 were risk associated [odds ratio (OR) = 1.35, 95% confidence interval (CI) = 1.0–1.7, P‐value = 0.017 and OR = 1.39, 95% CI = 1.1–1.7, P‐value = 0.007, respectively], and both SNPs were in strong linkage disequilibrium (r² = 0.95). For MYO5B‐rs555879, the minor allele was risk associated (OR = 1.31, 95% CI = 1.1–1.6, P‐value = 0.011). The combined analysis of SNP sets using set enrichment analysis revealed a study‐wide significant association for three SNPs with susceptibility for dyslexia. In summary, our results substantiate genetic markers in NEDD4L and MYO5B as risk factors for dyslexia and provide first evidence that the relevance of these markers is not restricted to the English language .     

Multiple cholinergic nicotinic receptor genes affect nicotine dependence risk in African and European Americans

Several independent studies show that the chromosome 15q25.1 region, which contains the CHRNA5–CHRNA3–CHRNB4 gene cluster, harbors variants strongly associated with nicotine dependence, other smoking behaviors, lung cancer and chronic obstructive pulmonary disease. We investigated whether variants in other cholinergic nicotinic receptor subunit (CHRN) genes affect the risk of nicotine dependence in a new sample of African Americans (AAs) (N = 710). We also analyzed this AA sample together with a European American (EA) sample (N = 2062, 1608 of which have been previously studied), allowing for differing effects in the two populations. Cases are current nicotine‐dependent smokers and controls are non‐dependent smokers. Variants in or near CHRND–CHRNG, CHRNA7 and CHRNA10 show modest association with nicotine dependence risk in the AA sample. In addition, CHRNA4, CHRNB3–CHRNA6 and CHRNB1 show association in at least one population. CHRNG and CHRNA4 harbor single nucleotide polymorphisms (SNPs) that have opposite directions of effect in the two populations. In each of the population samples, these loci substantially increase the trait variation explained, although no loci meet Bonferroni‐corrected significance in the AA sample alone. The trait variation explained by three key associated SNPs in CHRNA5–CHRNA3–CHRNB4 is 1.9% in EAs and also 1.9% in AAs; this increases to 4.5% in EAs and 7.3% in AAs when we add six variants representing associations at other CHRN genes. Multiple nicotinic receptor subunit genes outside chromosome 15q25 are likely to be important in the biological processes and development of nicotine dependence, and some of these risks may be shared across diverse populations.