Protein molecular function influences mutation rates in human genetic diseases with allelic heterogeneity

Molecular epidemiology studies have used the counts of different mutational types like transitions, transversions, etc. to identify putative mutagens, with little reference to gene organization and structure–function of the translated product. Moreover, geographical variation in the mutational spectrum is not limited to the mutational types at the nucleotide level but also have a bearing at the functional level. Here, we developed a novel measure to estimate the rate of spontaneous detrimental mutations called “mutation index” for comparing the mutational spectra consisting of all single base, missense, and non-missense changes. We have analyzed 1609 mutations occurring in 38 exons in 24 populations in three diseases viz. hemophilia B (F9 gene – 420 mutations in 9 populations across 8 exons), hemophilia A (F8 gene – 650, 8 and 26, respectively) and ovarian carcinoma (TP53 gene – 539, 7 and 4, respectively). We considered exons as units of evolution instead of the entire gene and observed feeble differences among populations implying lack of a mutagen-specific effect and the possibility of mutation causing endogenous factors. In all the three genes we observed elevated rates of detrimental mutations in exons encoding regions of significance for the molecular function of the protein. We propose that this can be extended to the entire exome with implications in exon-shuffling and complex human diseases.     

Investigation of genetic risk factors for chronic adult diseases for association with preterm birth

Preterm birth (PTB) is the leading cause of infant mortality. PTB pathophysiology overlaps with those of adult cardiovascular, immune and metabolic disorders (CIMD), with mechanisms including inflammation, immunotolerance, thrombosis, and nutrient metabolism. Whereas many genetic factors for CIMD have been identified, progress in PTB has lagged. We hypothesized that highly validated genetic risk factors for CIMD may also be associated with PTB. We conducted case–control study of four female cohorts with spontaneous PTB (n = 673) versus term (n = 1119). Of 35 SNPs genotyped, there were 13 statistically significant associations (P < 0.05), which were more than expected (binomial test; P = 0.02). In US White (307 cases/342 controls), the G allele of HLA-DQA1 (A/G) rs9272346 was protective for PTB in the initial discovery cohort (P = 0.02; OR = 0.65; 95 % CI 0.46, 0.94). This protective association replicated (P = 0.02; OR = 0.85; 95 % CI 0.75, 0.97) nominally in the Danish Cohort (883 cases, 959 controls), but lost significance upon multiple testing correction. We observed more statistically significant associations than expected, suggesting that chance is an unlikely explanation for one or more of the associations. Particularly, a protective association of the G allele of HLA-DQA1 was found in two independent cohorts, and in previous studies, this same allele was found to protect against type-1-diabetes (meta-analysis P value 5.52 × 10^–219). Previous investigations have implicated HLA phenotypic variation in recurrent fetal loss and in chronic chorioamnionitis. Given the limited sample size in his study, we suggest larger studies to further investigate possible HLA genetic involvement in PTB.     

Referral and experience with genetic testing among women with early onset breast cancer

The purpose of this study was to determine whether physicians refer women with early onset breast cancer for genetic testing for BRCA1 and BRCA2, and how women respond to being offered testing and use the results. A web-based survey was distributed to 1221 women with early onset breast cancer. The survey included 158 questions divided into the following sections: demographics, family history of cancer, medical history, treatment history, and experience with genetic testing. Of 551 women diagnosed since 1993 who responded to the survey (45.1%), less than half (45%, n = 246) had ever discussed genetic testing with their physician and/or been referred to see a genetic counselor. Women with a family history of cancer (53%) and Ashkenazi Jewish women (81%) were more likely to have been referred. Of those who had discussed testing, 60% had undergone or were interested in testing. Overall 92 women were tested and 19 (20.6%) of these tested positive for a deleterious BRCA1 or BRCA2 mutation. Fourteen (74%) who tested positive subsequently underwent prophylactic surgery. Satisfaction with counseling and the decision to be tested was high. Among women who were not offered testing, the fact that the test had not been offered by their physician (89%), and fear of discrimination (83%) were the two most frequently cited factors for lack of interest in testing. A substantial number of women are not being referred to genetic counseling and/or testing after a diagnosis of early onset breast cancer. Among those who were tested, there was high interest in prophylactic surgery after confirmation of a BRCA1/2 mutation.     

A system for studying genetic changes in Candida albicans during infection

Candida albicans is a diploid yeast with a dimorphic life history. It exists commensally in many healthy humans but becomes a potent pathogen in immunocompromised hosts. The underlying genetic mechanisms by which C. albicans switches from a commensal to a pathogenic form in the host are not well understood. To study the evolution of virulence in mammalian hosts, we used GAL1 as selectable marker system that allows for both positive and negative selection in selective media. We show that the deletion of one or both copies of GAL1 in the C. albicans genome does not change virulence in a systemic mouse model. We obtained estimates for the frequency of mitotic recombination at the GAL1 locus during systemic infection. Our observations suggest that genetic changes such as mitotic recombination and gene conversion occur at a high enough frequency to be important in the transition of C. albicans from a commensal to a pathogenic organism.     

Linkage analysis for diseases with variable age of onset

We present a method for the multivariate linkage analysis of the age of onset of a disease. The approach allows the incorporation of covariates for the study of gene by environment interactions. It is applicable to general pedigrees. The likelihood of the data is expressed as a function of the number of alleles identical by descent at a marker, the censored ages of onset and disease status, and environmental exposures. In a simulation study, we compare the power to detect linkage under different sampling schemes for either a dominant or recessive trait when approximately 10% of individuals are gene carriers. The majority of the linkage information from a sample of randomly selected sib pairs was retained when the analyses were limited to sibships with one sibling having early-onset disease (<59 years old). Incorporating parental phenotypes could improve the power to detect the gene. When the sample consists of affected sib pairs (ASPs) having variable age of onset, the likelihood ratio (LR) test had higher power than the means (t(2)) test for detecting a locus with a large genetic relative risk (R(g) = 20). However, the power of the two tests was similar when ASPs are selected so that the proband has an early onset of disease. Lastly, the LR test had more power than the t(2) test to detect linkage in the presence of gene by environment interactions.     

A hybrid likelihood algorithm for risk modelling

The risk of radiation-induced cancer is assessed through the follow-up of large cohorts, such as atomic bomb survivors or underground miners who have been occupationally exposed to radon and its decay products. The models relate to the dose, age and time dependence of the excess tumour rates, and they contain parameters that are estimated in terms of maximum likelihood computations. The computations are performed with the software package EPICURE, which contains the two main options of person-by person regression or of Poisson regression with grouped data. The Poisson regression is most frequently employed, but there are certain models that require an excessive number of cells when grouped data are used. One example involves computations that account explicitly for the temporal distribution of continuous exposures, as they occur with underground miners. In past work such models had to be approximated, but it is shown here that they can be treated explicitly in a suitably reformulated person-by person computation of the likelihood. The algorithm uses the familiar partitioning of the log-likelihood into two terms,L ₁ andL ₀. The first term,L ₁, represents the contribution of the events (tumours). It needs to be evaluated in the usual way, but constitutes no computational problem. The second term,L ₀, represents the event-free periods of observation. It is, in its usual form, unmanageable for large cohorts. However, it can be reduced to a simple form, in which the number of computational steps is independent of cohort size. The method requires less computing time and computer memory, but more importantly it leads to more stable numerical results by obviating the need for grouping the data. The algorithm may be most relevant to radiation risk modelling, but it can facilitate the modelling of failure-time data in general.     

A hybrid life cycle assessment model for comparison with conventional methodologies in Australia

Background, aim, and scope  

One barrier to the further implementation of LCA as a quantitative decision-support tool is the uncertainty created by the diversity of available analytical approaches. This paper compares conventional (‘process analysis’) and alternative (‘input–output analysis’) approaches to LCA, and presents a hybrid LCA model for Australia that overcomes the methodological limitations of process and input–output analysis and enables a comparison between the results achieved using each method. A case study from the water industry illustrates this comparison.     

A genetic model for age at onset in Huntington disease.

Although numerous investigators have confirmed excess paternal transmission among juvenile-onset cases of Huntington disease (HD), there are conflicting reports that the late-onset form is inherited more often from the mother than from the father. Results from a survey of age at onset and age at death in 569 patients corroborate earlier findings of delayed onset of HD among offspring of affected mothers at both ends of the onset-age spectrum: 23 of 28 juvenile-onset offspring had affected fathers, and there were 1.6 times more late-onset offspring born to affected mothers than to affected fathers. These patterns, together with data that link age-at-onset variability to familial longevity trends, suggest a model where age at onset is governed, generally, by a set of independently inherited aging genes, but expression of the HD gene may be significantly delayed in individuals who possess a particular maternally transmitted factor.     

A theoretical psychological perspective on predictive testing for late onset hereditary diseases

Because of the burden of serious late onset hereditary diseases, psychological counselling is commonly included in the predictive testing procedure. We discuss the components of psychological counselling in the context of neurodegenerative disorders such as Huntington's disease, some hereditary cancers and some hereditary heart diseases. Psychological counselling should be tailored to the specific characteristics of the disease: penetrance and expression of the mutation, variability of the age at onset and efficacy of prevention and treatment, if available. Finally theories that have already been used for the psychological framing of counselling in the context of predictive testing or to formulate research hypotheses (e.g. Transactional Model of Stress and Coping, Common Sense Model of Self-regulation) are discussed.     

Genetic risk factors for myocardial infarction more clearly manifest for early age of first onset

Epidemiological genetics established that heritability in determining the risk of myocardial infarction (MI) is substantially greater when MI occurs early in life. However, the genetic architecture of early-onset and late-onset MI was not compared. We analyzed genotype frequencies of SNPs in/near 20 genes whose protein products are involved in the pathogenesis of atherosclerosis in two groups of Russian patients with MI: the first group included patients with age of first MI onset <60 years (N?=?230) and the second group with onset ≥60 years (N?=?174). The control group of corresponding ethnicity consisted of 193 unrelated volunteers without cardiovascular diseases (93 individuals were over 60 years). We found that in the group of patients with age of onset <60 years, SNPs FGB rs1800788*T, TGFB1 rs1982073*T/T, ENOS rs2070744*C and CRP rs1130864*T/T were associated with risk of MI, whereas in patients with age of onset ≥60 years, only TGFB1 rs1982073*T/T was associated with risk of MI. Using APSampler software, we found composite markers associated with MI only in patients with early onset: FGB rs1800788*T?+?TGFB1 rs1982073*T; FGB rs1800788*T?+?LPL rs328*C?+?IL4 rs2243250*C; FGB rs1800788*T?+?ENOS rs2070744*C (Fisher p values of 1.4?×?10^?6 to 2.2?×?10^?5; the permutation p values of 1.1?×?10^?5 to 3.0?×?10^?4; ORs?=?2.67–2.54). Alleles included in the combinations were associated with MI less significantly and with lower ORs than the combinations themselves. The result showed a substantially greater contribution of the genetic component in the development of MI if it occurs early in life, and demonstrated the usefulness of genetic testing for young people.     

A new semi-determinate tomato hybrid for early production

By using the knowledge of the genetic constitution and the characteristics of the available tomato lines for selection, there were created several dozens of hybrid combinations characterised by semi-determinate habit, with large fruits and early maturing. These hybrids were tested in preliminary and comparative trials with the hybrids Balkan F₁, Balca F₁, Žar F₁, and some others as standard varieties. These tomato hybrids were grown earlier but they are grown even today in the early production, for the market in green houses and in the open field. The hybrid Marco F₁ was the best of all. Its yield was 25 t/ha in the plastic-house (the same as in the standard), up to 32 t/ha in the open field (5 % more than in the standard). This hybrid was a few days later than Balkan, with the fruits weighting 200 grams (fruits were approximately 60 % heavier than in the standard). It possess the genetic V, F and Tm resistance.     

Effect of genetic and environmental influences on cardiometabolic risk factors: a twin study

Background

Patients with the metabolic syndrome are more likely to develop type 2 diabetes and may have an increased risk of cardiovascular disease (CVD) events.We aimed to establish whether CVD event rates were influenced by the metabolic syndrome as defined by the World Health Organisation (WHO), the National Cholesterol Education Program (NCEP) Adult Treatment Panel III (ATP III) and the International Diabetes Federation (IDF) and to determine which component(s) of the metabolic syndrome (MS) conferred the highest cardiovascular risk in in 4900 patients with type 2 diabetes allocated to placebo in the Fenofibrate Intervention and Event Lowering in Diabetes (FIELD) trial.

Research design and methods

We determined the influence of MS variables, as defined by NCEP ATPIII, IDF and WHO, on CVD risk over 5 years, after adjustment for CVD, sex, HbA_1c, creatinine, and age, and interactions between the MS variables in a Cox proportional-hazards model.

Results

About 80% had hypertension, and about half had other features of the metabolic syndrome (IDF, ATPIII). There was no difference in the prevalence of metabolic syndrome variables between those with and without CVD at study entry. The WHO definition identified those at higher CVD risk across both sexes, all ages, and in those without prior CVD, while the ATPIII definition predicted risk only in those aged over 65 years and in men but not in women. Patients meeting the IDF definition did not have higher risk than those without IDF MS. CVD risk was strongly influenced by prior CVD, sex, age (particularly in women), baseline HbA1_c, renal dysfunction, hypertension, and dyslipidemia (low HDL-c, triglycerides > 1.7 mmol/L). The combination of low HDL-c and marked hypertriglyceridemia (> 2.3 mmol/L) increased CVD risk by 41%. Baseline systolic blood pressure increased risk by 16% per 10 mmHg in those with no prior CVD, but had no effect in those with CVD. In those without prior CVD, increasing numbers of metabolic syndrome variables (excluding waist) escalated risk.

Conclusion

Absence of the metabolic syndrome (by the WHO definition) identifies diabetes patients without prior CVD, who have a lower risk of future CVD events. Hypertension and dyslipidemia increase risk.     

A twin study of genetic influences on epilepsy outcome.

The identification of genetic factors that confer susceptibility to the epilepsies has to date been the focus of genetic efforts in this field. Few studies have assessed the genetic contribution to disease course in epilepsy, yet an understanding of the genetic influences on epilepsy outcome is key to developing new therapeutic strategies. The aim of this study was to assess the genetic contributions to epilepsy outcome in twin pairs concordant for epilepsy. We studied 37 epilepsy concordant twin pairs (27 monozygotic, 10 dizygotic) in whom there were no recognized environmental contributions (e.g., acquired brain injury) to epilepsy, and in whom the most likely cause for epilepsy was a shared genetic susceptibility. Clinical outcome was determined using the binary measure of Seizure Status (seizure remission or recurrence) and on a six-category ordinal Outcome Scale. Epilepsy outcome was independent of age of seizure onset, age at assessment and major epilepsy syndrome diagnosis. The proportion of twin pairs concordant for Seizure Status was 0.81 (22/27) for monozygous and 1.0 (10/10) for dizygous pairs, p = 0.3. Within-pair correlation in outcome (Outcome Scale) was 0.60 (95% CI: 0.32, 0.78) in monozygous and 0.78 (0.48, 0.92) in dizygous pairs. These data provide no evidence for genetic influences on epilepsy outcome independent of those that contribute to disease susceptibility. The observed high correlations for outcome suggest that, for epilepsy, susceptibility genes also have a major influence on outcome.     

A common genetic variant (97906C>A) of DAB2IP/AIP1 is associated with an increased risk and early onset of lung cancer in Chinese males

DOC-2/DAB2 interactive protein (DAB2IP) is a novel identified tumor suppressor gene that inhibits cell growth and facilitates cell apoptosis. One genetic variant in DAB2IP gene was reported to be associated with an increased risk of aggressive prostate cancer recently. Since DAB2IP involves in the development of lung cancer and low expression of DAB2IP are observed in lung cancer, we hypothesized that the variations in DAB2IP gene can increase the genetic susceptibility to lung cancer. In a case-control study of 1056 lung cancer cases and 1056 sex and age frequency-matched cancer-free controls, we investigated the association between two common polymorphisms in DAB2IP gene (-1420T>G, rs7042542; 97906C>A, rs1571801) and the risk of lung cancer. We found that compared with the 97906CC genotypes, carriers of variant genotypes (97906AC+AA) had a significant increased risk of lung cancer (adjusted odds ratio [OR] = 1.33, 95%CI = 1.04-1.70, P = 0.023) and the number of variant (risk) allele worked in a dose-response manner (P(trend) = 0.0158). Further stratification analysis showed that the risk association was more pronounced in subjects aged less than 60 years old, males, non-smokers, non-drinkers, overweight groups and in those with family cancer history in first or second-degree relatives, and the 97906A interacted with overweight on lung cancer risk. We further found the number of risk alleles (97906A allele) were negatively correlated with early diagnosis age of lung cancer in male patients (P = 0.003). However, no significant association was observed on the -1420T>G polymorphism. Our data suggested that the 97906A variant genotypes are associated with the increased risk and early onset of lung cancer, particularly in males.     

Pdha-2: A model for studying transcriptional regulation in early spermatocytes

Precise temporal and tissue-specific expression of genes during spermatocyte differentiation is crucial for the formation of functional spermatozoa. However, the mechanisms that regulate gene expression during spermatogenesis are poorly understood. One testisspecific gene, Pdha-2, is beginning to emerge as a potentially important model for the study of these events. This review focuses on our current understanding of the expression and regulation of Pdha-2 during spermatogenesis. © 1994 Wiley-Liss, Inc.     

Population programs for the detection of couples at risk for severe monogenic genetic diseases

Population genetic screening programs for carrier detection of severe genetic disorders exist worldwide, mainly for beta-thalassemia. These screening programs are either mandatory or voluntary. In several Arab countries and Iran, the state has made thalassemia carrier detection mandatory, while tests for detecting carriers are required by the religious authorities in Cyprus. In all the existing mandatory genetic screening programs, the couples have to get the information about the tests before marriage, but the decision whether or not to marry is left to them. Voluntary programs exist for instance in several Mediterranean countries for the prevention of thalassemia and for several genetic diseases among Jews. While voluntary programs leave the decision to be screened or not to the individual, a major problem is that in many cases awareness about the existence of screening tests is very sparse. Some programs, for instance in Canada or Australia, therefore provide education about genetic tests and screening at school in order to allow the individuals to be able to make an informed decision about their reproductive choices. This article represents the opinions of the author and not necessarily those of the Ministry.     

A new methodology for studying parasite specificity and life cycles of trematodes

A new approach to the genome characterization of trematode sporocysts is described to investigate the life cycles of three species of Helicometra and to compare their degree of specificity for mollusc and teleost hosts.