Multiple testing in large-scale genetic studies

Interactions between Polygenic Risk of Obesity and Dietary Factors on Anthropometric Outcomes: A Systematic Review and Meta-Analysis of Observational Studies

BACKGROUND

Diet is an important determinant of health and may moderate genetic susceptibility to obesity, but meta-analyses of available evidence are lacking.

OBJECTIVES

This study aimed to systematically review and meta-analyze evidence on the moderating effect of diet on genetic susceptibility to obesity, assessed with polygenic risk scores (PRS).

METHODS

A systematic search was conducted using MEDLINE, EMBASE, Web of Science, and the Cochrane Library to retrieve observational studies that examined PRS-diet interactions on obesity-related outcomes. Dietary exposures of interest included diet quality/dietary patterns and consumption of specific food and beverage groups. Random-effects meta-analyses were performed for pooled PRS- healthy eating index (HEI) interaction coefficients on body mass index (BMI) (on the basis of data from 4 cohort studies) and waist circumference (WC) (on the basis of data from 3 cohort studies).

RESULTS

Out of 36 retrieved studies, 78% were conducted among European samples. Twelve out of 21 articles examining dietary indices/patterns, and 16 out of 21 articles examining food/beverage groups observed some significant PRS-diet interactions. However, within many articles, findings are inconsistent when testing different combinations of obesity PRS-dietary factors and outcomes. Nevertheless, higher HEI scores and adherence to plant-based dietary patterns emerged as the more prominent diet quality/patterns that moderated genetic susceptibility to obesity, whereas higher consumption of fruits and vegetables, and lower consumption of fried foods and sugar-sweetened beverages emerged as individual food/beverage moderators. Results from the meta-analysis suggest that a higher HEI attenuates genetic susceptibility on BMI (pooled PRS∗HEI coefficient: -0.08; 95% confidence interval (CI): -0.15, 0.00; P = 0.0392) and WC (-0.37; 95% CI: -0.60, -0.15; P = 0.0013).

CONCLUSIONS

Current observational evidence suggests a moderating role of overall diet quality in polygenic risk of obesity. Future research should aim to identify genetic loci that interact with dietary exposures on anthropometric outcomes and conduct analyses among diverse ethnic groups.

TRIAL REGISTRATION NUMBER

This study was registered at the International Prospective Register of Systematic Reviews as CRD42022312289.

In the context of the triple burden of malnutrition: A systematic review of gene-diet interactions and nutritional status

Genetic background interacts with dietary components to modulate nutritional health status. This study aimed to review the evidence for gene-diet interactions in all forms of malnutrition. A comprehensive systematic literature search was conducted through April 2021 to identify observational and intervention studies reporting the effects of gene-diet interactions in over-nutrition, under-nutrition and micronutrient status. Risk of publication bias was assessed using the Quality Criteria Checklist and a tool specifically designed for gene-diet interaction research. 167 studies from 27 populations were included. The majority of studies investigated single nucleotide polymorphisms (SNPs) in overnutrition (n = 158). Diets rich in whole grains, vegetables, fruits and low in total and saturated fats, such as Mediterranean and DASH diets, showed promising effects for reducing obesity risk among individuals who had higher genetic risk scores for obesity, particularly the risk alleles carriers of FTO rs9939609, rs1121980 and rs1421085. Other SNPs in MC4R, PPARG and APOA5 genes were also commonly studied for interaction with diet on overnutrition though findings were inconclusive. Only limited data were found related to undernutrition (n = 1) and micronutrient status (n = 9). The findings on gene-diet interactions in this review highlight the importance of personalized nutrition, and more research on undernutrition and micronutrient status is warranted.

Combinational Drug Repurposing from Genetic Networks Applied to Alzheimer’s Disease

Background: Human diseases are multi-factorial biological phenomena resulting from perturbations of numerous functional networks. The complex nature of human diseases explains frequently observed marginal or transitory efficacy of mono-therapeutic interventions. For this reason, combination therapy is being increasingly evaluated as a biologically plausible strategy for reversing disease state, fostering the development of dedicated methodological and experimental approaches. In parallel, genome-wide association studies (GWAS) provide a prominent opportunity for disclosing human-specific therapeutic targets and rational drug repurposing. Objective: In this context, our objective was to elaborate an integrated computational platform to accelerate discovery and experimental validation of synergistic combinations of repurposed drugs for treatment of common human diseases. Methods: The proposed approach combines adapted statistical analysis of GWAS data, pathway-based functional annotation of genetic findings using gene set enrichment technique, computational reconstruction of signaling networks enriched in disease-associated genes, selection of candidate repurposed drugs and proof-of-concept combinational experimental screening. Results: It enables robust identification of signaling pathways enriched in disease susceptibility loci. Therapeutic targeting of the disease-associated signaling networks provides a reliable way for rational drug repurposing and rapid development of synergistic drug combinations for common human diseases. Conclusion: Here we demonstrate the feasibility and efficacy of the proposed approach with an experiment application to Alzheimer’s disease.

MultipleTesting.com: A tool for life science researchers for multiple hypothesis testing correction

Scientists from nearly all disciplines face the problem of simultaneously evaluating many hypotheses. Conducting multiple comparisons increases the likelihood that a non-negligible proportion of associations will be false positives, clouding real discoveries. Drawing valid conclusions require taking into account the number of performed statistical tests and adjusting the statistical confidence measures. Several strategies exist to overcome the problem of multiple hypothesis testing. We aim to summarize critical statistical concepts and widely used correction approaches while also draw attention to frequently misinterpreted notions of statistical inference. We provide a step-by-step description of each multiple-testing correction method with clear examples and present an easy-to-follow guide for selecting the most suitable correction technique. To facilitate multiple-testing corrections, we developed a fully automated solution not requiring programming skills or the use of a command line. Our registration free online tool is available at www.multipletesting.com and compiles the five most frequently used adjustment tools, including the Bonferroni, the Holm (step-down), the Hochberg (step-up) corrections, allows to calculate False Discovery Rates (FDR) and q-values. The current summary provides a much needed practical synthesis of basic statistical concepts regarding multiple hypothesis testing in a comprehensible language with well-illustrated examples. The web tool will fill the gap for life science researchers by providing a user-friendly substitute for command-line alternatives.

Adaptive markers distinguish North and South Pacific Albacore amid low population differentiation

Albacore (Thunnus alalunga) support an economically valuable global fishery, but surprisingly little is known about the population structure of this highly migratory species. Physical tagging data suggest that Albacore from the North and South Pacific Ocean are separate stocks, but results from previous genetic studies did not support this two stock hypothesis. In addition, observed biological differences among juveniles suggest that there may be population substructure in the North Pacific. We used double-digest restriction site-associated DNA sequencing to assess population structure among 308 Albacore caught in 12 sample areas across the Pacific Ocean (10 North, 2 South). Since Albacore are highly migratory and spawning areas are unknown, sample groups were not assumed to be equivalent to populations and the genetic data were analyzed iteratively. We tested for putatively adaptive differences among groups and for genetic variation associated with sex. Results indicated that Albacore in the North and South Pacific can be distinguished using 84 putatively adaptive loci, but not using the remaining 12,788 presumed neutral sites. However, two individuals likely represent F1 hybrids between the North and South Pacific populations, and 43 Albacore potentially exhibit lower degrees of mixed ancestry. In addition, four or five cross-hemisphere migrants were potentially identified. No genetic evidence was found for population substructure within the North Pacific, and no loci appeared to distinguish males from females. Potential functions for the putatively adaptive loci were identified, but an annotated Albacore genome is required for further exploration. Future research should try to locate spawning areas so that life history, demography, and genetic population structure can be linked and spatiotemporal patterns can be investigated.

Sex matters: Otolith shape and genomic variation in deacon rockfish (Sebastes diaconus)

Little is known about intraspecific variation within the deacon rockfish (Sebastes diaconus), a recently described species found in the northeast Pacific Ocean. We investigated population structure among fish sampled from two nearshore reefs (Siletz Reef and Seal Rock) and one offshore site (Stonewall Bank) within a <50-km2 area off the Oregon coast. Fish from the three sample sites exhibited small but statistically significant differences based on genetic variation at >15,000 neutral loci, whether analyzed independently or classified into nearshore and offshore groups. Male and females were readily distinguished using genetic data and 92 outlier loci were associated with sex, potentially indicating differential selection between males and females. Morphometric results indicated that there was significant secondary sexual dimorphism in otolith shape, but further sampling is required to disentangle potential confounding influence of age. This study is the first step toward understanding intraspecific variation within the deacon rockfish and the potential management implications. Since differentiation among the three sample sites was small, we consider the results to be suggestive of a single stock. However, future studies should evaluate how the stock is affected by differences in sex, age, and gene flow between the nearshore and offshore environments.

The impact of age-related cataracts on colour perception, postoperative recovery and related spectra derived from test of hue perception

Background

Cataract patients were always excluded from studies on ageing of colour vision; thus, effect of age-related cataracts on deterioration of colour perception has not been analysed. In present study, impacts of age-related cataracts on colour discrimination, postoperative recovery and related spectra were investigated.

Methods

In this cohort study, thirty age-related cataract patients scheduled for binocular surgery and 30 elderly volunteers were enrolled. Colour discrimination under photopic (1000 lx) and mesopic (40 lx) conditions was evaluated with Farnsworth-Munsell 100-hue test. The total error score (TES) and partial error score (PES) were calculated.

Results

Preoperatively, the TES in the patient group was 129.7 ± 59.5 at 1000 lx and 194.6 ± 74.5 at 40 lx, exhibiting worse discrimination than the volunteer group (TES_1000lux = 71.5 ± 37.5 and TES_40lux = 113.1 ± 38.8, p ≤ 0.001). Inferior perception were detected in the yellow to green-yellow (Y-GY), green-yellow to green (GY-G), green to blue-green (G-BG) and blue-green to blue (BG-B) colour bands (p ≤ 0.003), corresponding to the 470 nm–580 nm range of the visible light spectrum. Under mesopic conditions, the impact expanded to all colour bands except for yellow-red to yellow (YR-Y). Postoperatively, the TES in the patient group were 80.4 ± 62.4 at 1000 lx and 112.0 ± 85.2 at 40 lx, which were lower than those of the preoperative phase (p ≤ 0.001) but similar to those of the volunteer group (p ≥ 0.505). Postoperative improvement occurred in the Y-GY, GY-G and G-BG colour bands (490 nm to 580 nm) at 1000 lx (p ≤ 0.001) and shifted to the Y-GY, GY-G, G-BG and BG-B colour bands (470 nm to 580 nm) at 40 lx (p ≤ 0.001). Deterioration of hue perception for decrement of illumination was detected in the red to yellow-red (R-YR), Y-GY, G-BG, BG-B, blue to purple-blue (B-PB) and red-purple to red (RP-R) colour bands (450 nm to 500 nm) in the volunteer group (p ≤ 0.002) and the R-YR, G-BG, BG-B, B-PB, PB-P and red-purple to red (RP-R) colour bands (from the short-wavelength end to 500 nm) in the patient group preoperatively (p ≤ 0.001).

Conclusions

Phacoemulsification could effectively rebuild colour perception in patients with age-related cataract. The postoperative benefits were most significant in colour bands corresponding with spectrum from 470 nm to 580 nm.

Electronic supplementary material

The online version of this article (10.1186/s12886-019-1057-6) contains supplementary material, which is available to authorized users.

Cumulus cell transcriptome profiling is not predictive of live birth after in vitro fertilization: a paired analysis of euploid sibling blastocysts

OBJECTIVE

To compare the transcriptome of cumulus cells associated with a euploid embryo that resulted in live birth with that of a sibling euploid embryo without sustained implantation.

DESIGN

Paired analysis.

SETTING

Academic institution.

PATIENT(S)

Couples undergoing in vitro fertilization (IVF)/intracytoplasmic sperm injection with preimplantation genetic screening with female age ≤42 years and normal ovarian reserve.

INTERVENTION(S)

Transcriptome profiling of cumulus cells from sibling oocytes for correlation with live birth after euploid blastocyst transfer. Embryos were individually cultured to facilitate association with clinical outcomes. The cumulus cell transcriptome from the embryo resulting in live birth was compared with that of its sibling embryo without sustained implantation to investigate potential biomarkers that may aid in embryo selection.

MAIN OUTCOME MEASURE(S)

Differential gene expression in cumulus cells associated with a euploid embryo resulting in live birth and its sibling euploid embryo without sustained implantation using next-generation RNA sequencing (RNAseq).

RESULT(S)

Cumulus cell RNAseq of 34 samples (from 17 patients) generated an average of 10.4 ± 4 × 10⁶ reads per sample. A total of 132 differentially expressed genes between sibling embryos that resulted in a live birth and those that did not were identified (P<.05). However, after correcting for multiple testing none of the genes remained significantly differentially expressed (false discovery rate <.05).

CONCLUSION(S)

The RNAseq profiles were similar between cumulus cells associated with a euploid embryo resulting in live birth and its sibling embryo that did not sustain implantation. The cumulus cell transcriptome is not predictive of live birth within an individual patient's cohort of euploid embryos.

Multiple Testing in the Context of Gene Discovery in Sickle Cell Disease Using Genome-Wide Association Studies

The issue of multiple testing, also termed multiplicity, is ubiquitous in studies where multiple hypotheses are tested simultaneously. Genome-wide association study (GWAS), a type of genetic association study that has gained popularity in the past decade, is most susceptible to the issue of multiple testing. Different methodologies have been employed to address the issue of multiple testing in GWAS. The purpose of the review is to examine the methodologies employed in dealing with multiple testing in the context of gene discovery using GWAS in sickle cell disease complications.

A Multi-Marker Genetic Association Test Based on the Rasch Model Applied to Alzheimer's Disease

Results from Genome-Wide Association Studies (GWAS) have shown that the genetic basis of complex traits often include many genetic variants with small to moderate effects whose identification remains a challenging problem. In this context multi-marker analysis at the gene and pathway level can complement traditional point-wise approaches that treat the genetic markers individually. In this paper we propose a novel statistical approach for multi-marker analysis based on the Rasch model. The method summarizes the categorical genotypes of SNPs by a generalized logistic function into a genetic score that can be used for association analysis. Through different sets of simulations, the false-positive rate and power of the proposed approach are compared to a set of existing methods, and shows good performances. The application of the Rasch model on Alzheimer's Disease (AD) ADNI GWAS dataset also allows a coherent interpretation of the results. Our analysis supports the idea that APOE is a major susceptibility gene for AD. In the top genes selected by proposed method, several could be functionally linked to AD. In particular, a pathway analysis of these genes also highlights the metabolism of cholesterol, that is known to play a key role in AD pathogenesis. Interestingly, many of these top genes can be integrated in a hypothetic signalling network.

Genetic variation in CD36, HBA, NOS3 and VCAM1 is associated with chronic haemolysis level in sickle cell anaemia: a longitudinal study

Chronic haemolysis stands out as one of the hallmarks of sickle cell anaemia, a clinically heterogeneous autosomal recessive monogenic anaemia. However, the genetic architecture of this sub-phenotype is still poorly understood. Here, we report the results of an association study between haemolysis biomarkers (serum LDH, total bilirubin and reticulocyte count) and the inheritance of 41 genetic variants of ten candidate genes in a series of 99 paediatric SS patients (median current age of 9.9 yr) followed up in two general hospitals in Greater Lisboa area (median follow-up per patient of 5.0 yr). Although in a large number of tests a seemingly significant (i.e. P < 0.05) association was observed, the following ones were confirmed upon correction for multiple comparisons: (i) an increased serum LDH level was associated with haplotype 7 within VCAM1 gene; (ii) a lower total bilirubin was associated with the 3.7-kb deletion at HBA gene, rs2070744_T allele at NOS3 gene, and haplotype 9 within VCAM1 promoter; and (iii) a diminished reticulocyte count was associated with the 3.7-kb deletion at HBA, whereas an increased count was associated with rs1984112_G allele at CD36 gene. On the whole, our findings suggest a complex genetic architecture for the sickle cell anaemia haemolysis process involving multiple pathways, namely control of vascular cell adhesion, NO synthesis and erythrocyte volume and haemoglobinisation.

Changes in school environment, awareness and actions regarding overweight prevention among Dutch secondary schools between 2006-2007 and 2010-2011

Background

Schools can be an important setting for the prevention of overweight. This nation-wide survey investigated changes in the obesogenity of the school environment, the awareness of schools regarding overweight, school health policy, and actions taken by schools to prevent overweight.

Methods

In 2006/2007 and 2010/2011, questionnaires were sent to all Dutch secondary schools, (n = 1250 and n = 1145, response rate 44% and 33% respectively, repeated data for 187 schools).

Results

The percentage of schools with vending machines for soft drinks (~90%) and sweets (~80%) remained fairly stable, whereas slightly more schools indicated to have a canteen (87%-91%). The food supply was reported to be healthier in 2010/2011 compared to 2006/2007. Canteens and/or vending machines offered more often fresh fruits (+8%), sandwiches (+11%), water (+11%) and salad (+7%) and less often sugar sweetened soft drinks (−10%). However, unfavorable changes such as an increase in the supply of pizza slices (+13%) and milk and yoghurt drinks with added sugar (+12%) were also reported. Between 2006/2007 and 2010/2011, the presence of water coolers increased (12% versus 33%) as well as facilities for physical activity (67% versus 77%). However, more schools had vending places of unhealthy foods in the vicinity (73% versus 85%). Compared to 2006/2007, a higher percentage of schools indicated that they have taken actions to stimulate healthy eating behavior (72% versus 80%) or to prevent overweight (34% versus 52%) in 2010/2011. Less schools indicated that they expect to pay more attention to overweight prevention in the near future (56% versus 43%), but none of them expected to pay less attention.

Conclusions

Several aspects of the school environment changed in a positive way. However, schools should be encouraged to contribute to the prevention of overweight, or to continue to do so.