Power evaluations for family-based tests of association with incomplete parental genotypes

While a variety of methods have been developed to deal with incomplete parental genotype information in family-based association tests, sampling design issues with incomplete parental genotype data still have not received much attention. In this article, we present simulation studies with four genetic models and various sampling designs and evaluate power in family-based association studies. Efficiency depends heavily on disease prevalence. With rare diseases, sampling affecteds and their parents is preferred, and three sibs will be required to have close power if parents are unavailable. With more common diseases, sampling affecteds and two sibs will generally be more efficient than trios. When parents are unavailable, siblings need not be phenotyped if the disease is rare, but a loss of power will result with common diseases. Finally, for a class of complex traits where other genetic and environmental factors also cause phenotypic correlation among siblings, little loss of efficiency occurs to rare disease, but substantial loss of efficiency occurs to common disease.     

Potenzial und Herausforderungen der personalisierten Genomik und des 1000-Genom-Projekts

The ability to sequence entire individual human genomes has heralded a new era in human genetics. Such advances in sequencing technologies make it possible to address new questions such as the generation of a comprehensive map of common and rare genetic variants in humans. The 1000 Genome Project will analyze 2500 genomes and is expected to greatly expand our knowledge about genomic variation, both on single nucleotide polymorphisms and genomic structural variants in a number of human ethnic populations. Furthermore, the possibility to use these new sequencing technologies for such large scale projects will be evaluated. Finally, new bioinformatics solutions will be developed to efficiently store and process such large volumes of data for the scientific community. This catalogue of common and rare variations will facilitate the development of better methods for phenotype-genotype associations and help uncover the molecular bases for a variety of diseases in the near future.     

Methods for detecting associations with rare variants for common diseases: application to analysis of sequence data

Although whole-genome association studies using tagSNPs are a powerful approach for detecting common variants, they are underpowered for detecting associations with rare variants. Recent studies have demonstrated that common diseases can be due to functional variants with a wide spectrum of allele frequencies, ranging from rare to common. An effective way to identify rare variants is through direct sequencing. The development of cost-effective sequencing technologies enables association studies to use sequence data from candidate genes and, in the future, from the entire genome. Although methods used for analysis of common variants are applicable to sequence data, their performance might not be optimal. In this study, it is shown that the collapsing method, which involves collapsing genotypes across variants and applying a univariate test, is powerful for analyzing rare variants, whereas multivariate analysis is robust against inclusion of noncausal variants. Both methods are superior to analyzing each variant individually with univariate tests. In order to unify the advantages of both collapsing and multiple-marker tests, we developed the Combined Multivariate and Collapsing (CMC) method and demonstrated that the CMC method is both powerful and robust. The CMC method can be applied to either candidate-gene or whole-genome sequence data.     

Protein microarrays: from serodiagnosis to whole proteome scale analysis of the immune response against pathogenic microorganisms

Microbial diseases remain the most common cause of global mortality and morbidity. Scientific and technical achievements have dramatically improved the possibilities of investigating the humoral immune response against the whole proteome of microbial organisms. A number of genomes of microbial organisms responsible for diseases of worldwide medical importance such as Plasmodium, Toxoplasma, Mycobacterium, Streptococcus, Neisseria, Salmonella, Borrelia, and Rickettsia species have already been sequenced or will be available in the very near future. High-throughput assays such as protein microarrays have been clinically validated in serum for detecting the presence of antibodies directed against microbial antigens. Computational technologies for processing large sets of data are rapidly being developed. Such a powerful combination of genomic information and assays now offers the opportunity to identify the microbial antigens that, either alone or in combination, function as targets of natural acquired immunity against infectious diseases. This information will prove invaluable for developing vaccines against a series of microorganisms of medical relevance that are urgently needed, e.g., malaria. Additional applications of these technologies include the development of a microbial antigen array for the early serodiagnosis of both common and rare infectious diseases. This review will focus on technical and scientific issues concerning the use of antigen microarrays for vaccine development and the serodiagnosis of infectious diseases.     

Nutrigenomics and nutrigenetics

PURPOSE OF REVIEW: Nutritional genomics has tremendous potential to change the future of dietary guidelines and personal recommendations. Nutritional genomics covers nutrigenomics, which explores the effects of nutrients on the genome, proteome and metabolome, and nutrigenetics, the major goal of which is to elucidate the effect of genetic variation on the interaction between diet and disease. Nutrigenetics has been used for decades in certain rare monogenic diseases such as phenylketonuria, and it has the potential to provide a basis for personalized dietary recommendations based on the individual's genetic makeup in order to prevent common multifactorial disorders decades before their clinical manifestation. RECENT FINDINGS: Preliminary results regarding gene-diet interactions in cardiovascular diseases are for the most part inconclusive because of the limitations of current experimental designs. Success in this area will require the integration of various disciplines, and will require investigators to work on large population studies that are designed to investigate gene-environment interactions. SUMMARY: Based on the current knowledge, we anticipate that in the future we will be able to harness the information contained in our genomes to achieve successful aging using behavioral changes, with nutrition being the cornerstone of this endeavor.     

Elicitation of Expert Prior Opinion: Application to the MYPAN Trial in Childhood Polyarteritis Nodosa

Objectives

Definitive sample sizes for clinical trials in rare diseases are usually infeasible. Bayesian methodology can be used to maximise what is learnt from clinical trials in these circumstances. We elicited expert prior opinion for a future Bayesian randomised controlled trial for a rare inflammatory paediatric disease, polyarteritis nodosa (MYPAN, Mycophenolate mofetil for polyarteritis nodosa).

Methods

A Bayesian prior elicitation meeting was convened. Opinion was sought on the probability that a patient in the MYPAN trial treated with cyclophosphamide would achieve disease remission within 6-months, and on the relative efficacies of mycophenolate mofetil and cyclophosphamide. Expert opinion was combined with previously unseen data from a recently completed randomised controlled trial in ANCA associated vasculitis.

Results

A pan-European group of fifteen experts participated in the elicitation meeting. Consensus expert prior opinion was that the most likely rates of disease remission within 6 months on cyclophosphamide or mycophenolate mofetil were 74% and 71%, respectively. This prior opinion will now be taken forward and will be modified to formulate a Bayesian posterior opinion once the MYPAN trial data from 40 patients randomised 1:1 to either CYC or MMF become available.

Conclusions

We suggest that the methodological template we propose could be applied to trial design for other rare diseases.     

A Statistical Approach for Rare-Variant Association Testing in Affected Sibships

Sequencing and exome-chip technologies have motivated development of novel statistical tests to identify rare genetic variation that influences complex diseases. Although many rare-variant association tests exist for case-control or cross-sectional studies, far fewer methods exist for testing association in families. This is unfortunate, because cosegregation of rare variation and disease status in families can amplify association signals for rare variants. Many researchers have begun sequencing (or genotyping via exome chips) familial samples that were either recently collected or previously collected for linkage studies. Because many linkage studies of complex diseases sampled affected sibships, we propose a strategy for association testing of rare variants for use in this study design. The logic behind our approach is that rare susceptibility variants should be found more often on regions shared identical by descent by affected sibling pairs than on regions not shared identical by descent. We propose both burden and variance-component tests of rare variation that are applicable to affected sibships of arbitrary size and that do not require genotype information from unaffected siblings or independent controls. Our approaches are robust to population stratification and produce analytic p values, thereby enabling our approach to scale easily to genome-wide studies of rare variation. We illustrate our methods by using simulated data and exome chip data from sibships ascertained for hypertension collected as part of the Genetic Epidemiology Network of Arteriopathy (GENOA) study.     

Histamine: an undercover agent in multiple rare diseases?

Histamine is a biogenic amine performing pleiotropic effects in humans, involving tasks within the immune and neuroendocrine systems, neurotransmission, gastric secretion, cell life and death, and development. It is the product of the histidine decarboxylase activity, and its effects are mainly mediated through four different G-protein coupled receptors. Thus, histamine-related effects are the results of highly interconnected and tissue-specific signalling networks. Consequently, alterations in histamine-related factors could be an important part in the cause of multiple rare/orphan diseases. Bearing this hypothesis in mind, more than 25 rare diseases related to histamine physiopathology have been identified using a computationally assisted text mining approach. These newly integrated data will provide insight to elucidate the molecular causes of these rare diseases. The data can also help in devising new intervention strategies for personalized medicine for multiple rare diseases.     

Lycopene and heart health

Cardiovascular diseases (CVDs) are the leading causes of human morbidity and mortality in developed countries. Specific biomarkers in this context are markers of inflammation, lipid status, thrombosis and oxidative stress. One recommendation for CVD prevention is to increase consumption of fruits and vegetables as good sources of secondary plant products, e.g. carotenoids. This review aimed to show linkages between lycopene, one main carotenoid in the human diet, and prevention of heart diseases by looking for epidemiological data, results from in vitro experiments and results from in vivo studies (animal studies and human intervention trials). In addition, patents and products within the context of lycopene and CVD prevention will be discussed with a special emphasis on health claims. Epidemiological data, in vitro data and results from animal experiments partly showed promising preventive mechanisms of lycopene. In contrast, until now, human intervention studies mostly failed to show any CVD prevention. However, there is still an encouraging situation, giving hints for antioxidant as well as anti-inflammatory effects of lycopene. These mechanisms could be the background for cardio-protective effects of tomatoes and tomato products. In summary, there are a lot of investigations needed in the future to give reliable results to establish these CVD-preventive effects.     

Blood pressure follows the kidney

Epidemiological and experimental data strongly suggest that cardiovascular diseases can originate from an aberrant environment during fetal development, a phenomenon referred to as perinatal programming. This review will focus on the role of the kidneys in determining blood pressure, and how (re)programming the renal development can persistently ameliorate hereditary hypertension. By combining physiologic and genomic studies we have discovered some candidate pathways suited for (re)programming the development of hypertension. This sets the stage for mechanistic analysis in future studies.     

Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms

Currently, single-nucleotide polymorphisms (SNPs) with minor allele frequency (MAF) of >5% are preferentially used in case-control association studies of common human diseases. Recent technological developments enable inexpensive and accurate genotyping of a large number of SNPs in thousands of cases and controls, which can provide adequate statistical power to analyze SNPs with MAF <5%. Our purpose was to determine whether evaluating rare SNPs in case-control association studies could help identify causal SNPs for common diseases. We suggest that slightly deleterious SNPs (sdSNPs) subjected to weak purifying selection are major players in genetic control of susceptibility to common diseases. We compared the distribution of MAFs of synonymous SNPs with that of nonsynonymous SNPs (1) predicted to be benign, (2) predicted to be possibly damaging, and (3) predicted to be probably damaging by PolyPhen. Our sources of data were the International HapMap Project, ENCODE, and the SeattleSNPs project. We found that the MAF distribution of possibly and probably damaging SNPs was shifted toward rare SNPs compared with the MAF distribution of benign and synonymous SNPs that are not likely to be functional. We also found an inverse relationship between MAF and the proportion of nsSNPs predicted to be protein disturbing. On the basis of this relationship, we estimated the joint probability that a SNP is functional and would be detected as significant in a case-control study. Our analysis suggests that including rare SNPs in genotyping platforms will advance identification of causal SNPs in case-control association studies, particularly as sample sizes increase.     

Rare variants regulate expression of nearby individual genes in multiple tissues

The rapid decrease in sequencing cost has enabled genetic studies to discover rare variants associated with complex diseases and traits. Once this association is identified, the next step is to understand the genetic mechanism of rare variants on how the variants influence diseases. Similar to the hypothesis of common variants, rare variants may affect diseases by regulating gene expression, and recently, several studies have identified the effects of rare variants on gene expression using heritability and expression outlier analyses. However, identifying individual genes whose expression is regulated by rare variants has been challenging due to the relatively small sample size of expression quantitative trait loci studies and statistical approaches not optimized to detect the effects of rare variants. In this study, we analyze whole-genome sequencing and RNA-seq data of 681 European individuals collected for the Genotype-Tissue Expression (GTEx) project (v8) to identify individual genes in 49 human tissues whose expression is regulated by rare variants. To improve statistical power, we develop an approach based on a likelihood ratio test that combines effects of multiple rare variants in a nonlinear manner and has higher power than previous approaches. Using GTEx data, we identify many genes regulated by rare variants, and some of them are only regulated by rare variants and not by common variants. We also find that genes regulated by rare variants are enriched for expression outliers and disease-causing genes. These results suggest the regulatory effects of rare variants, which would be important in interpreting associations of rare variants with complex traits.     

Field immobilization for treatment of an unknown illness in a wild chimpanzee (Pan troglodytes schweinfurthii) at Gombe National Park, Tanzania: findings, challenges, and lessons learned

Infectious diseases are widely presumed to be one of the greatest threats to ape conservation in the wild. Human diseases are of particular concern, and the costs and benefits of human presence in protected areas with apes are regularly debated. While numerous syndromes with fatal outcomes have recently been described, precise identification of pathogens remains difficult. These diagnostic difficulties are compounded by the fact that direct veterinary intervention on wild apes is quite rare. Here we present the unique case of a wild chimpanzee at Gombe National Park that was observed with a severe illness and was subsequently examined and treated in the field. Multiple specimens were collected and tested with the aim of identifying the pathogen responsible for the illness. Our findings represent the first extensive screening of a living wild chimpanzee, yet despite our efforts, the cause and source of illness remain unknown. Nevertheless, our findings represent valuable baseline data for the ape conservation community and for comparison with other recent findings. In addition, we present the case here to demonstrate the planning required and multiple types of expertise necessary to maximize the amount of data obtained from such a rare intervention, and to provide lessons learned for future studies.     

RAMEDIS

The RAMEDIS system is a platform-independent, web-based information system for rare diseases based on individual case reports. It was developed in close cooperation with clinical partners and collects information on rare metabolic diseases in extensive detail (e.g. symptoms, laboratory findings, therapy and genetic data). This combination of clinical and genetic data enables the analysis of genotype-phenotype correlations. By using largely standardised medical terms and conditions, the contents of the database are easy to compare and analyse. In addition, a convenient graphical user interface is provided by every common web browser. RAMEDIS supports an extendable number of different genetic diseases and enables cooperative studies. Furthermore, use of RAMEDIS should lead to advances in epidemiology, integration of molecular and clinical data, and generation of rules for therapeutic intervention and identification of new diseases.     

Network analysis of genome-wide association studies for drug target prioritisation

Over the past decades, genome-wide association studies (GWAS) have led to a dramatic expansion of genetic variants implicated with human traits and diseases. These advances are expected to result in new drug targets but the identification of causal genes and the cell biology underlying human diseases from GWAS remains challenging. Here, we review protein interaction network-based methods to analyse GWAS data. These approaches can rank candidate drug targets at GWAS-associated loci or among interactors of disease genes without direct genetic support. These methods identify the cell biology affected in common across diseases, offering opportunities for drug repurposing, as well as be combined with expression data to identify focal tissues and cell types. Going forward, we expect that these methods will further improve from advances in the characterisation of context specific interaction networks and the joint analysis of rare and common genetic signals.     

Genetic determinants of cholangiopathies: Molecular and systems genetics

Familial cholangiopathies are rare but potentially severe diseases. Their spectrum ranges from fairly benign conditions as, for example, benign recurrent intrahepatic cholestasis to low-phospholipid associated cholelithiasis and progressive familial intrahepatic cholestasis (PFIC). Many cholangiopathies such as primary biliary cholangitis (PBC) or primary sclerosing cholangitis (PSC) affect first the bile ducts (“ascending pathophysiology”) but others, such as PFIC, start upstream in hepatocytes and cause progressive damage “descending” down the biliary tree and leading to end-stage liver disease. In recent years our understanding of cholestatic diseases has improved, since we have been able to pinpoint numerous disease-causing mutations that cause familial cholangiopathies. Accordingly, six PFIC subtypes (PFIC type 1–6) have now been defined. Given the availability of genotyping resources, these findings can be introduced in the diagnostic work-up of patients with peculiar cholestasis. In addition, functional studies have defined the pathophysiological consequences of some of the detected variants. Furthermore, ABCB4 variants do not only cause PFIC type 3 but confer an increased risk for chronic liver disease in general. In the near future these findings will serve to develop new therapeutic strategies for patients with liver diseases. Here we present the latest data on the genetic background of familial cholangiopathies and discuss their application in clinical practice for the differential diagnosis of cholestasis of unknown aetiology. As look in the future we present “system genetics” as a novel experimental tool for the study of cholangiopathies and disease-modifying genes. This article is part of a Special Issue entitled: Cholangiocytes in Health and Disease edited by Jesus Banales, Marco Marzioni, Nicholas LaRusso and Peter Jansen.     

Immunomodulatory properties of human adult and fetal multipotent mesenchymal stem cells

In recent years, a large number of studies have contributed to our understanding of the immunomodulatory mechanisms used by multipotent mesenchymal stem cells (MSCs). Initially isolated from the bone marrow (BM), MSCs have been found in many tissues but the strong immunomodulatory properties are best studied in BM MSCs. The immunomodulatory effects of BM MSCs are wide, extending to T lymphocytes and dendritic cells, and are therapeutically useful for treatment of immune-related diseases including graft-versus-host disease as well as possibly autoimmune diseases. However, BM MSCs are very rare cells and require an invasive procedure for procurement. Recently, MSCs have also been found in fetal-stage embryo-proper and extra-embryonic tissues, and these human fetal MSCs (F-MSCs) have a higher proliferative profile, and are capable of multilineage differentiation as well as exert strong immunomodulatory effects. As such, these F-MSCs can be viewed as alternative sources of MSCs. We review here the current understanding of the mechanisms behind the immunomodulatory properties of BM MSCs and F-MSCs. An increase in our understanding of MSC suppressor mechanisms will offer insights for prevalent clinical use of these versatile adult stem cells in the near future.     

Big Data and Health Research—The Governance Challenges in a Mixed Data Economy

Denmark is a society that has already moved towards Big Data and a Learning Health Care System. Data from routine healthcare has been registered centrally for years, there is a nationwide tissue bank, and there are numerous other available registries about education, employment, housing, pollution, etcetera. This has allowed Danish researchers to study the link between exposures, genetics and diseases in a large population. This use of public registries for scientific research has been relatively uncontroversial and has been supported by facilitative regulation that allows data to be used without the consent of data subjects. However, in the future much of the data will not be held by public authorities but by private companies. What are the implications of this shift for the governance of the research use of the data? This paper will argue that increased involvement of Research Ethics Committees and better training of researchers are necessary; and that some form of consent will have to be re-introduced. Four different consent models will be discussed: Opt-Out, Broad/Blanket consent, Dynamic consent, and Meta consent. It will be argued that a governance model including a possibility for citizens to make meta-choices strikes the best balance between individual and public interests.     

Regulation of intestinal protein metabolism by amino acids

Gut homeostasis plays a major role in health and may be regulated by quantitative and qualitative food intake. In the intestinal mucosa, an intense renewal of proteins occurs, at approximately 50 % per day in humans. In some pathophysiological conditions, protein turnover is altered and may contribute to intestinal or systemic diseases. Amino acids are key effectors of gut protein turnover, both as constituents of proteins and as regulatory molecules limiting intestinal injury and maintaining intestinal functions. Many studies have focused on two amino acids: glutamine, known as the preferential substrate of rapidly dividing cells, and arginine, another conditionally essential amino acid. The effects of glutamine and arginine on protein synthesis appear to be model and condition dependent, as are the involved signaling pathways. The regulation of gut protein degradation by amino acids has been minimally documented until now. This review will examine recent data, helping to better understand how amino acids regulate intestinal protein metabolism, and will explore perspectives for future studies.