The impact of population heterogeneity on risk estimation in genetic counseling

Impact of Genetic Risk Score and Dietary Protein Intake on Vitamin D Status in Young Adults from Brazil

Given the relationship between vitamin D deficiency (VDD) and adverse outcomes of metabolic diseases, we investigated the interplay of dietary and genetic components on vitamin D levels and metabolic traits in young adults from Brazil. Genetic analysis, dietary intake, and anthropometric and biochemical measurements were performed in 187 healthy young adults (19−24 years). Genetic risk scores (GRS) from six genetic variants associated with vitamin D (vitamin D-GRS) and 10 genetic variants associated with metabolic disease (metabolic-GRS) were constructed. High vitamin D-GRS showed a significant association with low 25(OH)D concentrations (p = 0.001) and high metabolic-GRS showed a significant association with high fasting insulin concentrations (p = 0.045). A significant interaction was found between vitamin D-GRS and total protein intake (g/day) (adjusted for non-animal protein) on 25(OH)D (pinteraction = 0.006), where individuals consuming a high protein diet (≥73 g/d) and carrying >4 risk alleles for VDD had significantly lower 25(OH)D (p = 0.002) compared to individuals carrying ≤4 risk alleles. Even though our study did not support a link between metabolic-GRS and vitamin D status, our study has demonstrated a novel interaction, where participants with high vitamin D-GRS and consuming ≥73 g of protein/day had significantly lower 25(OH)D levels. Further research is necessary to evaluate the role of animal protein consumption on VDD in Brazilians.

Evaluation of the relationships of the WBP1L gene with schizophrenia and the general psychopathology scale based on a case-control study

WBP1L is a target of microRNA 137 (miR-137) and has been considered a candidate gene for schizophrenia (SCZ). To investigate the relationships between WBP1L and SCZ and its related symptom scales, a total of 5,993 Chinese Han subjects, including 2,128 SCZ patients and 3,865 controls, were enrolled. In addition, an independent sample set for replication study including 1,052 SCZ patients and 2,124 controls were also recruited. Thirty-two tag single nucleotide polymorphisms (SNPs) located within gene region of WBP1L were selected for genotyping and analyzing. The expression quantitative trait loci (eQTL) effects for the targeted SNPs were investigated with gene expression data from multiple human tissues. Rs4147157 (OR = 0.84, p = 1.51 × 10^-5 ) and rs284854 (OR = 1.14, p = 7.00 × 10^-4 ) were significantly associated with SCZ disease status and these association signals were replicated in our replication sample. A significant association was identified between rs4147157 and the general (β = -.66, p = .001) and total (β = -.8, p = .0042) scores of positive and negative syndrome scale scores in SCZ patients. Both SNPs were significant eQTL for genes around WBP1L in human brain tissues including ARL3 and AS3MT. To conclude, SNPs rs4147157 and rs284854 were associated with SCZ in the Chinese Han population. Additionally, rs4147157 was significantly associated with specific symptom features of SCZ.

Analyzing heterogeneous complexity in complementary and alternative medicine research: a systems biology solution via parsimony phylogenetics

Systems biology offers cutting-edge tools for the study of complementary and alternative medicine (CAM). The advent of 'omics' techniques and the resulting avalanche of scientific data have introduced an unprecedented level of complexity and heterogeneous data to biomedical research, leading to the development of novel research approaches. Statistical averaging has its limitations and is unsuitable for the analysis of heterogeneity, as it masks diversity by homogenizing otherwise heterogeneous populations. Unfortunately, most researchers are unaware of alternative methods of analysis capable of accounting for individual variability. This paper describes a systems biology solution to data complexity through the application of parsimony phylogenetic analysis. Maximum parsimony (MP) provides a data-based modeling paradigm that will permit a priori stratification of the study cohort(s), better assessment of early diagnosis, prognosis, and treatment efficacy within each stratum, and a method that could be used to explore, identify and describe complex human patterning.

Uneventful clinical courses of Korean patients with methylcrotonylglycinuria and their common mutations

Methylcrotonylglycinuria (MCG) is an inborn error of leucine catabolism and results from the deficiency of 3-methylcrotonyl-CoA carboxylase. Patients with MCG show a highly variable clinical phenotype, ranging from asymptomatic to severe. With the introduction of newborn screening using tandem mass spectrometry, most patients with MCG are identified in their asymptomatic neonatal periods. Owing to their fair clinical outcomes, there exists a controversy over the need for aggressive medical intervention or even for newborn screening for MCG. Our study, reporting 11 Korean MCG patients from nine unrelated families, who were identified by newborn screening or family member testing and normally developed without experiencing an metabolic crisis during the follow-up period of 2.6±1.96 years (range, 1-10 years), indicates that the aggressive medical intervention might not be needed at least for the MCG patients identified by screening program in asymptomatic period. A total of six MCCC2 mutations, but no MCCC1 mutation, were identified in 17 of 18 alleles (94.4%). p.D280Y was identified in the 12/18 alleles (66.7%), indicating a founder effect. Moreover, the rest five variants, p.S342K, p.Q496H, p.P552S, p.T556A and p.P459S, were all previously unreported. The results of our study indicate that the distinct molecular genetic characteristics exist in Korean MCG patients.

Assessing Environmental Modifiers of Disease Risk Associated with Rare Mutations

OBJECTIVE

As disease-predisposing mutations are increasingly identified, there is growing need to assess the effects of lifestyle and environmental factors on disease risks in mutation carriers. Such assessment is difficult when the mutations are rare and evaluating them in large population samples is costly.

METHODS

This paper describes four study designs for evaluating the effects of environmental exposures in carriers of rare disease-predisposing mutations.

RESULTS

The strengths and weaknesses of the designs are assessed, and strategies for analyzing the data obtained from such designs are considered.

CONCLUSIONS

When exposure effects in noncarriers are well-established and exposure is independent of carrier status in the population of disease-free controls, the case-only design provides a feasible and efficient method for inferring effects in carriers. When exposure effects in noncarriers are not well established, the most feasible design options are those that compare exposures in carrier cases to either untyped controls or to carrier controls. These two designs have complementary strengths and weaknesses; thus inferences are stronger when measures of association estimated using the two designs are consistent.

Prognostic DNA testing and counselling for dominant optic atrophy due to a novel OPA1 mutation

CASE REPORT

To report the case of a 26-year-old woman with a family history of dominant optic atrophy who requested DNA testing and counselling. Ophthalmologic examination showed her affected father had bilateral temporal papillary pallor. Direct genomic sequencing of the OPA1 gene revealed a novel heterozygous nonsense mutation (Arg879stop). Because no mutation in OPA1 was detected in the daughter, we could counsel her that the possibility was very low that she was a carrier or would pass the disease-causing gene to her children.

COMMENTS

Our study provides evidence of the apparent value of molecular genetic analysis of OPA1 gene as predictive DNA testing, although the exact risk and benefit of this type of analysis awaits further study.

Newborn screening for 3-methylcrotonyl-CoA carboxylase deficiency: population heterogeneity ofMCCA andMCCB mutations and impact on risk assessment

New technology enables expansion of newborn screening (NBS) of inborn errors aimed to prevent adverse outcome. In conditions with a large share of asymptomatic phenotypes, the potential harm created by NBS must carefully be weighed against benefit. Policies vary throughout the United States, Australia, and Europe due to limited data on outcome and treatability of candidate screening conditions. We elaborated the rationale for decision making in 3-methylcrotonyl-coenzyme A (CoA) carboxylase deficiency (MCCD), which afflicts leucine catabolism, with reported outcomes ranging from asymptomatic to death. In Bavaria, we screened 677,852 neonates for 25 conditions, including MCCD, based on elevated concentrations of 3-hydroxyisovalerylcarnitine (3-HIVA-C). Genotypes of MCCA (MCCC1) and MCCB (MCCC2) were assessed in identified newborns, their relatives, and in individuals (n = 17) from other regions, and correlated to biochemical and clinical phenotypes. NBS revealed eight newborns and six relatives with MCCD, suggesting a higher frequency than previously assumed (1:84,700). We found a strikingly heterogeneous spectrum of 22 novel and eight reported mutations. Allelic variants were neither related to biochemical nor anamnestic data of our probands showing all asymptomatic or benign phenotypes. Comparative analysis of case reports with NBS data implied that only few individuals (< 10%) develop symptoms. In addition, none of the symptoms reported so far can clearly be attributed to MCCD. MCCD is a genetic condition with low clinical expressivity and penetrance. It largely represents as nondisease. So far, there are no genetic or biochemical markers that would identify the few individuals potentially at risk for harmful clinical expression. The low ratio of benefit to harm was pivotal to the decision to exclude MCCD from NBS in Germany. MCCD may be regarded as exemplary of the ongoing controversy arising from the inclusion of potentially asymptomatic conditions, which generates a psychological burden for afflicted families and a financial burden for health care systems.

Modelling clinical trials in heterogeneous samples

Individual variation in genetic, phenotypic and environmental factors could lead to significant differences in rates of drug metabolism, in clinical responses to drugs, and in drug side effects. The impact of population heterogeneity on treatment effect estimation and on assessment and application of clinical trial findings has been less than fully studied. In this paper, we studied the properties of models that reflect population heterogeneity of clinical trial samples by unmeasured covariates such as genetic susceptibility. The impact of heterogeneity on the estimation of treatment effect in a two-armed placebo or active-controlled clinical trial was quantified using logistic regression models. We also proposed a two-stage clinical trial, where the effects of individual drug-response-related covariates were estimated in a 'training data set' in the first stage of the trial. In the second stage of the trial, a subgroup of individuals with enhanced (or reduced) sensitivity to drug treatments in a heterogeneous risk cohort was identified based on information about their drug-related characteristics. Only these 'responders' were included in the subsequent efficacy test. Our simulation results showed that population heterogeneity could lead to biased estimation of treatment effect not only in the contaminated groups but also in the uncontaminated groups. A two-stage trial could greatly increase the power of an efficacy test over a 'full trial' even with fewer individuals enrolled in the trial; results would apply to a more highly specified population. The bigger the covariate effects, the more efficient the two-stage trial is compared to a 'full trial'.