Candidate gene association studies: a comprehensive guide to useful in silico tools

Role of TNF-α in the Pathogenesis of Migraine

Background

Neurogenic neuroinflammation has a wide role in migraine pathogenesis including the transition from episodic migraine to chronic one. The seed molecule of neurogenic neuroinflammation, i.e., the TNF-α proinflammatory molecule, has gathered a lot of attention. This pleiotropic cytokine is a classical component of inflammatory soup, secreted by the microglial cell, and promotes a wide range of inflammatory reactions.

Aim

In this review, we aimed to provide a culminating and comprehending glimpse into the TNF-α in association with the migraine.

Method

A systematic literature survey method with a mixture of keywords was utilized to grasp the different elements that represent the association between TNF-α and migraine. Discussion. Highlighted the probable involvement of the TNF-α with migraine, the complexity of the matter such as activation of NF-KB signaling cascade, autoactivation, sensitization, and increased likelihood of transition cannot be neglected. Being TNF-α as a core node, it becomes the factor for linking diseases such as chronic inflammatory disorders, including COVID-19, and also interaction with other genes to develop severe conditions.

Conclusion

To this end, TNF-α plays a critical role in chronification, and inhibiting its signaling would likely be a crucial strategy for migraine therapy.

Schizophrenia in the genetic era: a review from development history, clinical features and genomic research approaches to insights of susceptibility genes

Schizophrenia is a devastating neuropsychiatric disorder affecting 1% of the world population and ranks as one of the disorders providing the most severe burden for society. Schizophrenia etiology remains obscure involving multi-risk factors, such as genetic, environmental, nutritional, and developmental factors. Complex interactions of genetic and environmental factors have been implicated in the etiology of schizophrenia. This review provides an overview of the historical origins, pathophysiological mechanisms, diagnosis, clinical symptoms and corresponding treatment of schizophrenia. In addition, as schizophrenia is a polygenic, genetic disorder caused by the combined action of multiple micro-effective genes, we further detail several approaches, such as candidate gene association study (CGAS) and genome-wide association study (GWAS), which are commonly used in schizophrenia genomics studies. A number of GWASs about schizophrenia have been performed with the hope to identify novel, consistent and influential risk genetic factors. Finally, some schizophrenia susceptibility genes have been identified and reported in recent years and their biological functions are also listed. This review may serve as a summary of past research on schizophrenia genomics and susceptibility genes (NRG1, DISC1, RELN, BDNF, MSI2), which may point the way to future schizophrenia genetics research. In addition, depending on the above discovery of susceptibility genes and their exact function, the development and application of antipsychotic drugs will be promoted in the future.

Genetics of bronchopulmonary dysplasia: An update

Bronchopulmonary dysplasia (BPD) is a multi-factorial disease that results from multiple clinical factors, including lung immaturity, mechanical ventilation, oxidative stress, pulmonary congestion due to increasing cardiac blood shunting, nutritional and immunological factors. Twin studies have indicated that susceptibility to BPD can be strongly inherited in some settings. Studies have reported associations between common genetic variants and BPD in preterm infants. Recent genomic studies have highlighted a potential role for molecular pathways involved in inflammation and lung development in affected infants. Rare mutations in genes encoding the lipid transporter ATP-binding cassette, sub-family A, member 3 (ABCA3 gene) which is involved in surfactant synthesis in alveolar type II cells, as well as surfactant protein B (SFTPB) and C (SFTPC) can also result in severe form of neonatal-onset interstitial lung diseases and may also potentially affect the course of BPD. This chapter summarizes the current state of knowledge on the genetics of BPD.

A Pilot Genome-Wide Association Study Identifies Novel Markers of Metabolic Syndrome in Patients with Psoriasis

BACKGROUND

Recent studies have reported that psoriasis is associated with the development of metabolic syndrome. Genome-wide association studies have been used to discover gene variant markers that occur frequently in case group in relation to specific diseases.

OBJECTIVE

The aim of the present study was to investigate the variants of specific genes involved in metabolic syndrome associated with psoriasis.

METHODS

A total of 95 psoriasis patients were recruited and divided into two groups: one with metabolic syndrome (38 patients) and the other without (57 patients). After genotyping, imputation, and quality checking, the association between the several single nucleotide polymorphisms and metabolic syndrome in psoriasis was tested, followed by gene set enrichment analysis.

RESULTS

We found 76 gene polymorphisms that conferred an increased risk for metabolic syndrome in patients with psoriasis. Four single nucleotide polymorphisms (rs17154774 of FRMD4A, rs77498336 of GPR116, rs75949580 and rs187682251 of MAPK4) showed the strongest association between metabolic syndrome and psoriasis. The epidermal growth factor receptor protein was located at the center of the protein interactions for the gene polymorphisms.

CONCLUSION

This study identified several previously unknown polymorphisms associated with metabolic syndrome in psoriasis. These results highlight the potential for future genetic studies to elucidate the development, and ultimately prevent the onset, of metabolic syndrome in patients with psoriasis.

Genetic Influences on the Developing Young Brain and Risk for Neuropsychiatric Disorders

Imaging genetics provides an opportunity to discern associations between genetic variants and brain imaging phenotypes. Historically, the field has focused on adults and adolescents; very few imaging genetics studies have focused on brain development in infancy and early childhood (from birth to age 6 years). This is an important knowledge gap because developmental changes in the brain during the prenatal and early postnatal period are regulated by dynamic gene expression patterns that likely play an important role in establishing an individual's risk for later psychiatric illness and neurodevelopmental disabilities. In this review, we summarize findings from imaging genetics studies spanning from early infancy to early childhood, with a focus on studies examining genetic risk for neuropsychiatric disorders. We also introduce the Organization for Imaging Genomics in Infancy (ORIGINs), a working group of the ENIGMA (Enhancing NeuroImaging Genetics through Meta-Analysis) consortium, which was established to facilitate large-scale imaging genetics studies in infancy and early childhood.

Methodological quality assessment of genetic studies on brain arteriovenous malformation related hemorrhage: A cross-sectional study

Objectives: Rupture of a brain arteriovenous malformation (bAVM) can cause intracranial hemorrhage and severe clinical outcomes. At present, the mechanisms of bAVM-related hemorrhage are poorly understood. This study aimed to summarize the potential genetic risk factors for bAVM-related hemorrhage and appraise the methodological quality of existing genetic studies on bAVM-related hemorrhage using a cross-sectional design. Methods: A systematic literature search was conducted on genetic studies associated with bAVM-related hemorrhage published in PubMed, Embase, Web of Science, China National Knowledge Internet, and Wangfang databases, up to November 2022. Subsequently, a cross-sectional study was performed to describe the potential candidate genetic variants of bAVM associated with risk of hemorrhage and to evaluate the methodological quality of the identified studies using the Newcastle-Ottawa quality assessment scale and Q-genie tool. Results: Of the 1811 records identified in the initial search, nine studies met the filtering criteria and were included. Twelve single nucleotide polymorphisms (SNPs), including IL6 rs1800795, IL17A rs2275913, MMP9 rs9509, VEGFA rs1547651, and EPHB4 rs314353, rs314308, and rs314313, were associated with bAVM-related hemorrhage. However, only 12.5% of the evaluated SNPs showed statistical power> 0.80 (α = 0.05). Methodological quality assessment revealed significant flaws in the designs of the included studies, such as less reliable representativeness of recruited individuals, short follow-up periods in cohort studies, and less comparability between groups of hemorrhagic and non-hemorrhagic patients. Conclusion: IL1B, IL6, IL17A, APOE, MMP9, VEGFA and EPHB4 were potentially associated with bAVM-related hemorrhage. The methodological designs of the analyzed studies required improvement in order to obtain more reliable results. Regional alliances and rare disease banks need to be established to recruit large numbers of bAVM patients (especially familial and extreme-trait cases) in a multicenter, prospective cohort study with an adequate follow-up period. Furthermore, it is important to use advanced sequencing techniques and efficient measures to filter candidate genetic variants.

A variant rs6214 within IGF-1 confers risk for ulcerative colitis in Chinese Han populations

Insulin growth factor-1 (IGF-1) has been found to correlate with various diseases such as cancer and cardiovascular diseases including ulcerative colitis (UC). The present study aimed to investigate the plausible association of rs6214 (C > T) within IGF-1 and UC susceptibility in Chinese Han populations. A total of 977 UC patients and 1029 healthy controls were enrolled, and rs6214 was genotyped with PCR and direct sequencing on the ABI 3730XL DNA analyzer platform. Logistic regression analysis was applied for the correlation of rs6214 and UC susceptibility via calculation of odds ratio (OR) with a 95% confidence interval (95% CI) adjusted for age and sex under different genetic models. The difference of clinical parameters between genotypes was measured by one-way analysis of variance (ANOVA). Additional functional assays were conducted to establish the probable relationship. The results indicated that the T allele of rs6214 showed roughly 37% greater risk for UC risk in the additive model (OR = 1.37, 95% CI = 1.21-1.55, P < 0.000001) when compared with C allele carriers, and the pattern was similar in other three genetic models. Further stratified analysis suggested that the association was particularly noteworthy in UC patients with extensive colitis and severe condition. Moreover, the blood level of IGF-1 was downregulated in UC patients, and the mRNA level was lower in T allele carriers in rectal tissues of UC cases. Additional luciferase assay demonstrated that rs6214 regulates IGF-1 expression via promoting miR-2053. Collectively, rs6214 increased UC susceptibility and suppresses IGF-1 expression by enhancing miR-2053 binding. The current findings provided evidence that rs6214 is a promising biomarker for UC prediction and prognosis.

Risky Early Family Environment and Genetic Associations with Adult Metabolic Dysregulation

Growing up in a family environment characterized by neglectful parenting, overt conflict, and unsupportive relationships is associated with poor health in adulthood. A risky early family environment may also be associated with obesity in adulthood, likely through the activation of the HPA axis. Likewise, the GABAergic (gamma-aminobutyric acid) T>C single nucleotide polymorphism in the 1519 nucleotide position of the GABAAα6 receptor subunit gene has been associated with a predisposition to a higher body mass index and a larger waist circumference. Participants (n = 213, Mage = 30.13 years, SD = 10.85; 57.7% men) from the Pittsburgh Cold Study 3 completed a demographic questionnaire, the Risky Families Questionnaire (RFQ) and had their height, weight, and waist circumference measured during a physical exam. Participant DNA was recovered from buccal swabs and genotyped for the various allelic types of the SNP according to published protocols. In secondary data analyses, we tested the hypothesis that early family environment and GABRA6 would be positively associated with body mass index and waist circumference. We also examined diurnal cortisol as a mechanism linking both early risky family environment and GABRA6 to metabolic outcomes. The findings provide evidence that a risky early family environment may exert more influence than genetic predisposition when determining the indices of metabolic health in adulthood.

The Role of Pharmacogenomics in Opioid Prescribing

Pharmacogenomics is increasingly important to guide objective, safe, and effective individualised prescribing. Personalised prescribing has revolutionised treatments in the past decade, allowing clinicians to maximise drug efficacy and minimise adverse effects based on a person’s genetic profile. Opioids, the gold standard for cancer pain relief, are among the commonest medications prescribed in palliative care practice. This narrative review examines the literature surrounding opioid pharmacogenomics and its applicability to the palliative care cancer population. There is currently limited intersection between the fields of palliative care and pharmacogenomics, but growing evidence presents a need to build linkages between the two disciplines. Pharmacogenomic evidence guiding opioid prescribing is currently available for codeine and tramadol, which relates to CYP2D6 gene variants. However, these medications are prescribed less commonly for pain in palliative care. Research is accelerating with other opioids, where oxycodone (CYP2D6) and methadone (CYP2B6, ABCB1) already have moderate evidence of an association in terms of drug metabolism and downstream analgesic response and side effects. OPRM1 and COMT are receiving increasing attention and have implications for all opioids, with changes in opioid dosage requirements observed but they have not yet been studied widely enough to be considered clinically actionable. Current evidence indicates that incorporation of pharmacogenomic testing into opioid prescribing practice should focus on the CYP2D6 gene and its actionable variants. Although opioid pharmacogenomic tests are not widely used in clinical practice, the progressively reducing costs and rapid turnover means greater accessibility and affordability to patients, and thus, clinicians will be increasingly asked to provide guidance in this area. The upsurge in pharmacogenomic research will likely discover more actionable gene variants to expand international guidelines to impact opioid prescribing. This rapidly expanding area requires consideration and monitoring by clinicians in order for key findings with clinical implications to be accessible, meaningfully interpretable and communicated.

Computational Analysis of Deleterious SNPs in NRAS to Assess Their Potential Correlation With Carcinogenesis

The NRAS gene is a well-known oncogene that acts as a major player in carcinogenesis. Mutations in the NRAS gene have been linked to multiple types of human tumors. Therefore, the identification of the most deleterious single nucleotide polymorphisms (SNPs) in the NRAS gene is necessary to understand the key factors of tumor pathogenesis and therapy. We aimed to retrieve NRAS missense SNPs and analyze them comprehensively using sequence and structure approaches to determine the most deleterious SNPs that could increase the risk of carcinogenesis. We also adopted structural biology methods and docking tools to investigate the behavior of the filtered SNPs. After retrieving missense SNPs and analyzing them using six in silico tools, 17 mutations were found to be the most deleterious mutations in NRAS. All SNPs except S145L were found to decrease NRAS stability, and all SNPs were found on highly conserved residues and important functional domains, except R164C. In addition, all mutations except G60E and S145L showed a higher binding affinity to GTP, implicating an increase in malignancy tendency. As a consequence, all other 14 mutations were expected to increase the risk of carcinogenesis, with 5 mutations (G13R, G13C, G13V, P34R, and V152F) expected to have the highest risk. Thermodynamic stability was ensured for these SNP models through molecular dynamics simulation based on trajectory analysis. Free binding affinity toward the natural substrate, GTP, was higher for these models as compared to the native NRAS protein. The Gly13 SNP proteins depict a differential conformational state that could favor nucleotide exchange and catalytic potentiality. A further application of experimental methods with all these 14 mutations could reveal new insights into the pathogenesis and management of different types of tumors.

Genetic variation in the ovine KAP22-1 gene and its effect on wool traits in Egyptian sheep

The objective of this study was to investigate the genetic polymorphisms in the keratin-associated protein (KAP22-1) gene in Barki (n=206), Rahmani (n=28) and Ossimi (n=28) as the three major sheep breeds in Egypt. Subsequently, the detected variants were correlated with important wool traits. The traits included greasy fleece weight (GFW, g), staple length (SL, cm), prickle factor (PF, %), medullated fiber (MF, %), fiber diameter (FD, µm), crimp percentage (CR, %) and the standard deviation of FD (SDfd, µm), as well as the subjectively assessed traits of kemp score (KS), handle grade (HG), greasy color grade (GCG), bulk grade (BG), luster grade (LG) and staple structure (SST). Animals were genotyped by polymerase chain reaction (PCR) – single strand conformation polymorphism (SSCP). Five SSCP banding patterns representing three different nucleotide variants (A, B and C) were detected. DNA sequencing confirmed three single nucleotide polymorphisms (SNPs). Animal age significantly affected GFW (P=0.007), SDfd (P=0.006), SL (P=0.002), CR (P=0.006), KS (P=0.001), LG (P=0.006) and SST (P=0.013). Likewise, the breed had a significant effect on all studied traits except HG and BG, which was not significant. Results showed significant associations between the KAP22-1 variants and CR (P=0.01), SL (P=0.012), KS (P<0.001) and GCG (P=0.01). Interestingly, animals with BB genotypes tended to produce more wool yield (1163.63±65.91 g) with high SL (8.38±0.20 cm), CR (8.38±0.21 %) and KS (1.98±1.88). Results of this study strongly recommend the KAP22-1 gene as a candidate gene for wool production traits in Egyptian sheep, with new useful insights into the visually assessed wool traits. The identified genetic markers may be incorporated into breeding strategies and genetic improvement programs of wool traits in Egyptian sheep.

Genomic Medicine in Periodontal Disease: Old Issue, New Insights

Genetic variability is the main cause of phenotypic variation. Some variants may be associated with several diseases and can be used as risk biomarkers, identifying animals with higher susceptibility to develop the pathology. Genomic medicine uses this genetic information for risk calculation, clinical diagnosis and prognosis, allowing the implementation of more effective preventive strategies and/or personalized therapies. Periodontal disease (PD) is the inflammation of the periodontium induced mainly by bacterial plaque and is the leading cause of tooth loss. Microbial factors are responsible for the PD initiation; however, several studies support the genetic influence on the PD progression. The main purpose of the present publication is to highlight the main steps involved in the genomic medicine applied to veterinary patients, describing the flowchart from the characterization of the genetic variants to the identification of potential associations with specific clinical data. After investigating which genes might potentially be implicated in canine PD, the RANK gene, involved in the regulation of osteoclastogenesis, was selected to illustrate this approach. A case-control study was performed using DNA samples from a population of 90 dogs – 50 being healthy and 40 with PD. This analysis allowed for the discovery of four new intronic variations that were banked in GenBank (g.85A>G, g.151G>T, g.268A>G and g.492T>C). The results of this study are not intended to be applied exclusively to PD. On the contrary, this genetic information is intended to be used by other researchers as a foundation for the development of multiple applications in the veterinary clinical field.

Effect of Genetic Polymorphism Including NUP153 and SVEP1 on the Pharmacokinetics and Pharmacodynamics of Ticagrelor in Healthy Chinese Subjects

BACKGROUND AND OBJECTIVE

The search for potential gene loci that affect the pharmacodynamics and pharmacokinetics of ticagrelor is a matter of broad clinical interest. The objective of this study was to investigate the effect of genetic polymorphisms on the pharmacokinetics and pharmacodynamics of ticagrelor in healthy Chinese subjects.

METHODS

This is a multi-center study in China, including three hospitals from Beijing, Nanchang, and Changsha. Healthy Chinese subjects aged 18-45 years with unknown genotypes were included. All subjects received a single oral dose of 90 mg of ticagrelor. Platelet aggregation and the area under the concentration-time curve for ticagrelor and its major active metabolite in plasma samples were assessed. Genome-wide association studies and candidate gene association analysis related to ticagrelor were performed.

RESULTS

One hundred and seventy-five native Chinese subjects were enrolled and completed the study. According to the p value, the threshold of ticagrelor population was 6.57 × 10^-7 (0.05/76106), one single-nucleotide polymorphism chr6:17616513 of gene NUP153 (p = 2.03 × 10^-7) related to the area under the concentration-time curve for plasma concentration at time zero versus the last measurable timepoint, and one single nucleotide polymorphism rs17204533 of gene SVEP1 (p = 3.96 × 10^-7) related to P2Y12 reaction unit_12h of ticagrelor was identified. In addition, L1TD1, CETP, CLEC2A, CHSY1, PDZRN3, CTU2, PIEZO1, APOBEC1, SEMA6A, KAZN, and FASN polymorphisms might influence the pharmacokinetics of ticagrelor, while PARP10, TRIB1, CYP2C19, and UGT2B7 might affected its pharmacodynamics.

CONCLUSIONS

Genetic variation affects the pharmacokinetics and pharmacodynamics of ticagrelor in healthy individuals. The detection of NUP153, SVEP1 gene variation will be helpful for pharmacodynamic prediction and evaluation, and the regulation of these genes may be the target of new drug development. Further studies are required to confirm the results and explore whether these single-nucleotide polymorphisms are associated only with platelet activity or also with cardiovascular events and all-cause mortality.

CLINICAL TRIAL REGISTRATION

NCT03161002.

Genomics and Epigenomics of Gestational Diabetes Mellitus: Understanding the Molecular Pathways of the Disease Pathogenesis

One of the most common complications during pregnancy is gestational diabetes mellitus (GDM), hyperglycemia that occurs for the first time during pregnancy. The condition is multifactorial, caused by an interaction between genetic, epigenetic, and environmental factors. However, the underlying mechanisms responsible for its pathogenesis remain elusive. Moreover, in contrast to several common metabolic disorders, molecular research in GDM is lagging. It is important to recognize that GDM is still commonly diagnosed during the second trimester of pregnancy using the oral glucose tolerance test (OGGT), at a time when both a fetal and maternal pathophysiology is already present, demonstrating the increased blood glucose levels associated with exacerbated insulin resistance. Therefore, early detection of metabolic changes and associated epigenetic and genetic factors that can lead to an improved prediction of adverse pregnancy outcomes and future cardio-metabolic pathologies in GDM women and their children is imperative. Several genomic and epigenetic approaches have been used to identify the genes, genetic variants, metabolic pathways, and epigenetic modifications involved in GDM to determine its etiology. In this article, we explore these factors as well as how their functional effects may contribute to immediate and future pathologies in women with GDM and their offspring from birth to adulthood. We also discuss how these approaches contribute to the changes in different molecular pathways that contribute to the GDM pathogenesis, with a special focus on the development of insulin resistance.

Elucidation of Cellular Contributions to Heparin-Induced Thrombocytopenia Using Omic Approaches

Heparin-induced thrombocytopenia (HIT) is an unpredictable, complex, immune-mediated adverse drug reaction associated with a high mortality. Despite decades of research into HIT, fundamental knowledge gaps persist regarding HIT likely due to the complex and unusual nature of the HIT immune response. Such knowledge gaps include the identity of a HIT immunogen, the intrinsic roles of various cell types and their interactions, and the molecular basis that distinguishes pathogenic and non-pathogenic PF4/heparin antibodies. While a key feature of HIT, thrombocytopenia, implicates platelets as a seminal cell fragment in HIT pathogenesis, strong evidence exists for critical roles of multiple cell types. The rise in omic technologies over the last decade has resulted in a number of agnostic, whole system approaches for biological research that may be especially informative for complex phenotypes. Applying multi-omics techniques to HIT has the potential to bring new insights into HIT pathophysiology and identify biomarkers with clinical utility. In this review, we review the clinical, immunological, and molecular features of HIT with emphasis on key cell types and their roles. We then address the applicability of several omic techniques underutilized in HIT, which have the potential to fill knowledge gaps related to HIT biology.

GABAA subunit single nucleotide polymorphisms show sex-specific association to alcohol consumption and mental distress in a Norwegian population-based sample

Little is known about genetic influences on the relationship between alcohol consumption and mental distress in the general population, where the majority report consumption and distress far below diagnostic thresholds. This study investigated single nucleotide polymorphisms (SNPs) from candidate gene studies on alcohol use disorder and depressive disorders, for association with alcohol consumption and with mental distress in a population-based sample from the Cohort of Norway (n = 1978, 49% women). The relationship between alcohol consumption and mental distress was further examined for genotype modification. There was a positive correlation between mental distress and alcohol consumption in men, as well as an association between SNPs and mental distress in men (GABRG1, GABRA2, DRD2, ANKK1, MTHFR) and women (CHRM2, MTHFR) and between SNPs and alcohol consumption in women (GABRA2, MTHFR). No modification by SNP genotype was found on the relationship between alcohol consumption and mental distress. The association between mental distress and GABRG1 in men remained significant after correcting for multiple comparisons. The results indicate that alcohol consumption and mental distress are associated in the general population even at levels below clinical thresholds and point to SNPs in genes related to GABAergic signalling for level of mental distress in men.

Where the genome meets the connectome: Understanding how genes shape human brain connectivity

The integration of modern neuroimaging methods with genetically informative designs and data can shed light on the molecular mechanisms underlying the structural and functional organization of the human connectome. Here, we review studies that have investigated the genetic basis of human brain network structure and function through three complementary frameworks: (1) the quantification of phenotypic heritability through classical twin designs; (2) the identification of specific DNA variants linked to phenotypic variation through association and related studies; and (3) the analysis of correlations between spatial variations in imaging phenotypes and gene expression profiles through the integration of neuroimaging and transcriptional atlas data. We consider the basic foundations, strengths, limitations, and discoveries associated with each approach. We present converging evidence to indicate that anatomical connectivity is under stronger genetic influence than functional connectivity and that genetic influences are not uniformly distributed throughout the brain, with phenotypic variation in certain regions and connections being under stronger genetic control than others. We also consider how the combination of imaging and genetics can be used to understand the ways in which genes may drive brain dysfunction in different clinical disorders.

Diets, nutrients, genes and the microbiome: recent advances in personalised nutrition

As individuals seek increasingly individualised nutrition and lifestyle guidance, numerous apps and nutrition programmes have emerged. However, complex individual variations in dietary behaviours, genotypes, gene expression and composition of the microbiome are increasingly recognised. Advances in digital tools and artificial intelligence can help individuals more easily track nutrient intakes and identify nutritional gaps. However, the influence of these nutrients on health outcomes can vary widely among individuals depending upon life stage, genetics and microbial composition. For example, folate may elicit favourable epigenetic effects on brain development during a critical developmental time window of pregnancy. Genes affecting vitamin B12 metabolism may lead to cardiometabolic traits that play an essential role in the context of obesity. Finally, an individual's gut microbial composition can determine their response to dietary fibre interventions during weight loss. These recent advances in understanding can lead to a more complete and integrated approach to promoting optimal health through personalised nutrition, in clinical practice settings and for individuals in their daily lives. The purpose of this review is to summarise presentations made during the DSM Science and Technology Award Symposium at the 13th European Nutrition Conference, which focused on personalised nutrition and novel technologies for health in the modern world.

Oxytocin Receptor Gene Polymorphism in Lactating Dogs

Simple Summary

Oxytocin is commonly known for its role in mammalian bonding. Several studies have proved that polymorphisms of the oxytocin receptor gene are related to complex social behaviors in humans, but studies on the possible correlation between canine social behavior and oxytocin are mainly focused on the human–dog bond, and there are no data on the possible correlation between oxytocin receptor gene polymorphism and the maternal behavior of this species. Since mother–litter interactions could have a severe impact in determining later behavior in domestic dogs, the aim of this work was to investigate the possible correlation between salivary oxytocin, maternal care and the one known single-nucleotide polymorphism (rs8679684) located in the untranslated regulatory region of the oxytocin receptor gene in 19 lactating Labrador Retriever dogs. A significant correlation between oxytocin receptor gene polymorphism, peripheral oxytocin and maternal behavior in dogs was found. This implies that a more functional oxytocinergic system would lead to better mothering in dogs.

Abstract

Genetic variations in the oxytocinergic system, known to regulate social behavior throughout the evolution of mammals, are believed to account for differences in mammalian social behavior. Particularly, polymorphic variants of the oxytocin receptor (OXTR) gene have been associated with behavioral variations in both humans and dogs. In this study, we offered evidence of the correlation between levels of salivary oxytocin (sOXT), maternal behavior and a single-nucleotide gene variant in OXTR (rs8679684) in nineteen lactating Labrador Retriever dogs. Carriers of at least one copy of the minor A allele showed higher levels of sOXT and maternal care in comparison with the homozygous T allele carriers. Considering the relevance of mother care in newborn development, these findings could help us to better understand the possible impact of variants in the OXTR gene in selecting dams.

A current guide to candidate gene association studies

Important factors contribute to a gained momentum in candidate gene association studies (CGASs), including the generalized use of next-generation sequencing (NGS), growing opportunities for hospital-based research, and the availability of open-source databases and bioinformatics tools. This article summarizes the general principles and analytical methods as a guide to CGASs in today's favorable context.

Approach to genetic diagnosis of inborn errors of immunity through next-generation sequencing

Patients with inborn errors of immunity (IEI) present with a heterogeneous clinical and immunological phenotype, therefore a correct molecular diagnosis is crucial for the classification and subsequent therapeutic management. On the other hand, IEI are a group of rare congenital diseases with highly diverse features and, in most cases, an as yet unknown genetic etiology. Next generation sequencing has facilitated genetic examinations of rare inherited disorders during the recent years, thus allowing a suitable molecular diagnosis in the IEI patients. This review aimed to investigate the current findings about these techniques in the field of IEI, suggesting an efficient stepwise approach to molecular diagnosis of inborn errors of immunity.

Genome Wide Prediction, Mapping and Development of Genomic Resources of Mastitis Associated Genes in Water Buffalo

Water buffalo (Bubalus bubalis) are an important animal resource that contributes milk, meat, leather, dairy products, and power for plowing and transport. However, mastitis, a bacterial disease affecting milk production and reproduction efficiency, is most prevalent in populations having intensive selection for higher milk yield, especially where the inbreeding level is also high. Climate change and poor hygiene management practices further complicate the issue. The management of this disease faces major challenges, like antibiotic resistance, maximum residue level, horizontal gene transfer, and limited success in resistance breeding. Bovine mastitis genome wide association studies have had limited success due to breed differences, sample sizes, and minor allele frequency, lowering the power to detect the diseases associated with SNPs. In this work, we focused on the application of targeted gene panels (TGPs) in screening for candidate gene association analysis, and how this approach overcomes the limitation of genome wide association studies. This work will facilitate the targeted sequencing of buffalo genomic regions with high depth coverage required to mine the extremely rare variants potentially associated with buffalo mastitis. Although the whole genome assembly of water buffalo is available, neither mastitis genes are predicted nor TGP in the form of web-genomic resources are available for future variant mining and association studies. Out of the 129 mastitis associated genes of cattle, 101 were completely mapped on the buffalo genome to make TGP. This further helped in identifying rare variants in water buffalo. Eighty-five genes were validated in the buffalo gene expression atlas, with the RNA-Seq data of 50 tissues. The functions of 97 genes were predicted, revealing 225 pathways. The mastitis proteins were used for protein-protein interaction network analysis to obtain additional cross-talking proteins. A total of 1,306 SNPs and 152 indels were identified from 101 genes. Water Buffalo-MSTdb was developed with 3-tier architecture to retrieve mastitis associated genes having genomic coordinates with chromosomal details for TGP sequencing for mining of minor alleles for further association studies. Lastly, a web-genomic resource was made available to mine variants of targeted gene panels in buffalo for mastitis resistance breeding in an endeavor to ensure improved productivity and the reproductive efficiency of water buffalo.

The emergent phenomenon of aspirin resistance: insights from genetic association studies

Despite the clinical benefits of aspirin, the interindividual variation in response to this antiplatelet drug is considerable. The manifestation of aspirin resistance (AR) is frequently observed, although this complex process remains poorly understood. While AR etiology is likely to be multifactorial, genetic factors appear to be preponderant. According to several genetic association studies, both genome-wide and candidate gene studies, numerous SNPs in cyclooxygenase, thromboxane and platelet receptors-related genes have been identified as capable of negatively affecting aspirin action. Thus, it is essential to understand the clinical relevance of AR-related SNPs as potential predictive and prognostic biomarkers as they may be essential to defining the AR phenotype.

A brief guide to the science and art of writing manuscripts in biomedicine

Publishing articles in international scientific journals is the primary method for the communication of validated research findings and ideas. Journal articles are commonly used as a major input for evaluations of researchers and institutions. Few articles have been published previously about the different aspects needed for writing high-quality articles. In this manuscript, we provide an updated and brief guide for the multiple dimensions needed for writing manuscripts in the health and biological sciences, from current, international and interdisciplinary perspectives and from our expertise as authors, peer reviewers and editors. We provide key suggestions for writing major sections of the manuscript (e.g. title, abstract, introduction, methods, results and discussion), for submitting the manuscript and bring an overview of the peer review process and  of the post-publication impact of the articles.

Genetics and erectile dysfunction: leveraging early foundations for new discoveries

There is considerable interest in understanding the genetics of erectile dysfunction (ED). Since early twin studies that suggested a genetic component to ED, multiple candidate gene studies have identified genetic variants that may be associated with ED. Genome-wide association studies (GWAS) have overcome some of the criticism of the candidate gene approach. Two recent GWAS studies have identified loci near SIM1 that may be associated with ED and have renewed interest in the leptin melanocortin signaling pathway. We review the current literature on the genetic basis of ED by highlighting several candidate genes and genetic variants associated with ED.

Unraveling the susceptibility of paracoccidioidomycosis: Insights towards the pathogen-immune interplay and immunogenetics

Paracoccidioidomycosis (PCM) is a life-threatening systemic mycosis caused by Paracoccidioides spp. This disease comprises three clinical forms: symptomatic acute and chronic forms (PCM disease) and PCM infection, a latent form without clinical symptoms. PCM disease differs markedly according to severity, clinical manifestations, and host immune response. Fungal virulence factors and adhesion molecules are determinants for entry, latency, immune escape and invasion, and dissemination in the host. Neutrophils and macrophages play a paramount role in first-line defense against the fungus through the recognition of antigens by pattern recognition receptors (PRRs), activating their microbicidal machinery. Furthermore, the clinical outcome of the PCM is strongly associated with the variability of cytokines and immunoglobulins produced by T and B cells. While the mechanisms that mediate susceptibility or resistance to infection are dictated by the immune system, some genetic factors may alter gene expression and its final products and, hence, modulate how the organism responds to infection and injury. This review outlines the main findings relative to this topic, addressing the complexity of the immune response triggered by Paracoccidioides spp. infection from preclinical investigations to studies in humans. Here, we focus on mechanisms of fungal pathogenesis, the patterns of innate and adaptive immunity, and the genetic and molecular basis related to immune response and susceptibility to the development of the PCM and its clinical forms. Immunogenetic features such as HLA system, cytokines/cytokines receptors genes and other immune-related genes, and miRNAs are likewise discussed. Finally, we point out the occurrence of PCM in patients with primary immunodeficiencies and call attention to the research gaps and challenges faced by the PCM field.

Exploiting strain diversity and rational engineering strategies to enhance recombinant cellulase secretion by Saccharomyces cerevisiae

Consolidated bioprocessing (CBP) of lignocellulosic material into bioethanol has progressed in the past decades; however, several challenges still exist which impede the industrial application of this technology. Identifying the challenges that exist in all unit operations is crucial and needs to be optimised, but only the barriers related to the secretion of recombinant cellulolytic enzymes in Saccharomyces cerevisiae will be addressed in this review. Fundamental principles surrounding CBP as a biomass conversion platform have been established through the successful expression of core cellulolytic enzymes, namely β-glucosidases, endoglucanases, and exoglucanases (cellobiohydrolases) in S. cerevisiae. This review will briefly address the challenges involved in the construction of an efficient cellulolytic yeast, with particular focus on the secretion efficiency of cellulases from this host. Additionally, strategies for studying enhanced cellulolytic enzyme secretion, which include both rational and reverse engineering approaches, will be discussed. One such technique includes bio-engineering within genetically diverse strains, combining the strengths of both natural strain diversity and rational strain development. Furthermore, with the advancement in next-generation sequencing, studies that utilise this method of exploiting intra-strain diversity for industrially relevant traits will be reviewed. Finally, future prospects are discussed for the creation of ideal CBP strains with high enzyme production levels.Key Points• Several challenges are involved in the construction of efficient cellulolytic yeast, in particular, the secretion efficiency of cellulases from the hosts.• Strategies for enhancing cellulolytic enzyme secretion, a core requirement for CBP host microorganism development, include both rational and reverse engineering approaches.• One such technique includes bio-engineering within genetically diverse strains, combining the strengths of both natural strain diversity and rational strain development.

Loci associated with conception rate in crossbred beef heifers

The inability of beef cattle to maintain full term pregnancies has become an economic concern for the beef industry. Herd management and nutritional improvements have alleviated environmental impacts on embryonic and fetal loss, yet additional gains can be made through genomic selection. The objectives of this study were to identify loci and gene-sets in crossbred beef heifers associated with the number of services required to become pregnant (TBRD) and heifer conception rate at first service (HCR1). Heifers (n = 709) from a commercial beef operation underwent one round of artificial insemination, before exposure to bulls for natural service for 50 days. Pregnancy and time of conception was determined by ultrasound 35 days after the breeding season. Heifers were genotyped using the GeneSeek (Lincoln, NE) Bovine GGP50K BeadChip prior to genome-wide association analyses (GWAA) conducted using an EIGENSTRAT-like model to identify loci associated (P < 1 × 10⁻⁵) with TBRD and HCR1. One locus was associated (P = 8.97 × 10⁻⁶) with TBRD on BTA19 and included the positional candidate gene ASIC2, which is differentially expressed in the endometrium of fertility classified heifers, and the positional candidate gene, SPACA3. Gene-set enrichment analyses using SNP (GSEA-SNP) data, was performed and identified one gene-set, oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen as enriched (NES = 3.15) with TBRD and contained nine leading edge genes that contributed to the enrichment of the gene set. The enriched gene-set is involved in catalyzing oxidation-reduction reactions, which have been associated with oxidative stressors impacting pregnancy success. No loci were associated nor gene-sets enriched with HCR1. Identification of loci, positional candidate genes, gene-sets and leading edge genes enriched for fertility facilitate genomic selection that allows producers to select for reproductively superior cattle, reduce costs associated with infertility, and increase percent calf crop.

Periodontal inflammation: Integrating genes and dysbiosis

Biofilm bacteria co‐evolve and reach a symbiosis with the host on the gingival surface. The disruption of the homeostatic relationship between plaque bacteria and the host can initiate and promote periodontal disease progression. Recent advances in sequencing technologies allow researchers to profile disease‐associated microbial communities and quantify microbial metabolic activities and host transcriptional responses. In addition to confirming the findings from previous studies, new putative pathogens and novel genes that have not previously been associated with periodontitis, emerge. For example, multiple studies have reported that Synergistetes bacteria are associated with periodontitis. Genes involved in epithelial barrier defense were downregulated in periodontitis, while excessive expression of interleukin‐17 was associated with a hyperinflammatory response in periodontitis and with a unique microbial community. Bioinformatics‐enabled gene ontology pathway analyses provide a panoramic view of the bacterial and host activities as they shift from periodontal health to disease. Additionally, host innate factors, such as genetic variants identified by either a candidate‐gene approach or genome‐wide association analyses, have an impact on subgingival bacterial colonization. Transgenic mice carrying candidate genetic variants, or with the deletion of candidate genes mimicking the deleterious loss‐of‐function variant effect, provide experimental evidence validating the biologic relevance of the novel markers associated with the microbial phenotype identified through a statistical approach. Further refinement in bioinformatics, data management approaches, or statistical tools, are required to gain insight into host‐microbe interactions by harmonizing the multidimensional “big” data at the genomic, transcriptional, and proteomic levels.

Association between a TCF4 Polymorphism and Susceptibility to Schizophrenia

The basic helix-loop-helix (bHLH) transcription factor 4 (TCF4) had been identified as a susceptibility gene associated with schizophrenia (SCZ) by GWAS, but inconsistent results have been found in other studies. To validate these findings and to reveal the effects of different inheritance models, rs2958182, rs1261085, rs8766, and rs12966547 of the TCF4 gene were genotyped in the Northwest Han Chinese population (448 cases and 628 controls) via a multiplex polymerase chain reaction SNPscan assay. Single SNP, genotype, and association analyses with three different models were performed. We observed genotype and allele distributions of four SNPs that showed nonsignificant associations in the Northwest Han Chinese population. However, published datasets (51,892 cases and 68,498 controls) were collected and combined with our experimental results to ascertain the association of the TCF4 gene SNPs and SCZ, which demonstrated that rs2958182 (P=0.003) was a significant signal based on a systematic meta-analysis. To clarify the biological role of rs2958182, it is important to improve the understanding of the pathophysiology of SCZ.

Genetic influence on ageing-related changes in resting-state brain functional networks in healthy adults: A systematic review

This systematic review examines the genetic and epigenetic factors associated with resting-state functional connectivity (RSFC) in healthy human adult brains across the lifespan, with a focus on genes associated with Alzheimer's disease (AD). There were 58 studies included. The key findings are: (i) genetic factors have a low to moderate contribution; (ii) the apolipoprotein E ε2/3/4 polymorphism was the most studied genetic variant, with the APOE-ε4 allele most consistently associated with deficits of the default mode network, but there were insufficient studies to determine the relationships with other AD candidate risk genes; (iii) a single genome-wide association study identified several variants related to RSFC; (iv) two epigenetic independent studies showed a positive relationship between blood DNA methylation of the SLC6A4 promoter and RSFC measures. Thus, there is emerging evidence that genetic and epigenetic variation influence the brain's functional organisation and connectivity over the adult lifespan. However, more studies are required to elucidate the roles genetic and epigenetic factors play in RSFC measures across the adult lifespan.

Genetics of age-related hearing loss

Age-related hearing loss (ARHL) has recently been confirmed as a common complex trait, that is, it is heritable with many genetic variants each contributing a small amount of risk, as well as environmental determinants. Historically, attempts to identify the genetic variants underlying the ARHL have been of limited success, relying on the selection of candidate genes based on the limited knowledge of the pathophysiology of the condition, and linkage studies in samples comprising related individuals. More recently genome-wide association studies have been performed, but these require very large samples having consistent and reliable phenotyping for hearing loss (HL), and early attempts suffered from lack of reliable replication of their findings. Replicated variants shown associated with ARHL include those lying in genes GRM7, ISG20, TRIOBP, ILDR1, and EYA4. The availability of large biobanks and the development of collaborative consortia have led to a breakthrough over the last couple of years, and many new genetic variants associated with ARHL are becoming available, through the analysis publicly available bioresources and electronic health records. These findings along with immunohistochemistry and mouse models of HL look set to help disentangle the genetic architecture of ARHL, and highlight the need for standardization of phenotyping methods to facilitate data sharing and collaboration across research networks.

Delineating significant genome-wide associations of variants with antipsychotic and antidepressant treatment response: implications for clinical pharmacogenomics

Background

Genome-wide association studies (GWAS) have significantly contributed to the association of many clinical conditions and phenotypic characteristics with genomic variants. The majority of these genomic findings have been deposited to the GWAS catalog. So far, findings uncovering associations of single nucleotide polymorphisms (SNPs) with treatment efficacy in mood disorders are encouraging, but not adequate.

Methods

Statistical, genomic, and literature information was retrieved from EBI’s GWAS catalog, while we also searched for potential clinical information/clinical guidelines in well-established pharmacogenomics databases regarding the assessed drug-SNP correlations of the present study.

Results

Here, we provide an overview of significant genome-wide associations of SNPs with the response to commonly prescribed antipsychotics and antidepressants. Up to date, this is the first study providing novel insight in previously reported pharmacogenomics associations for antipsychotic/antidepressant treatment. We also show that although there are published CPIC guidelines for antidepressant agents, as well as the FDA labels include genome-based drug prescription information for both antipsychotic and antidepressant treatments, there are no specific clinical guidelines for the assessed drug-SNP correlations of this study.

Conclusions

Our present findings suggest that more effort should be implemented towards identifying GWA-significant antipsychotic and antidepressant pharmacogenomics correlations. Moreover, additional functional studies are required in order to characterise the potential role of the assessed SNPs as biomarkers for the response of patients to antipsychotic/antidepressant treatment.

Pharmacogenetics: Role of Single Nucleotide Polymorphisms

Genome sequencing methods have basically similar algorithms, although they show a few differences between the platforms. The human genome contains approximately three billion base pairs, and this amount is huge and therefore impossible to sequence at one step. However, this amount is not a problem for developed technology. Researchers break DNA into small random pieces and then sequence and reassemble. Library preparation, sequencing, bioinformatic approaches and reporting. High-quality library preparation is critical and the most important part of the next-generation sequencing workflow. Successful sequencing directly requires high-quality libraries. Sequencing is second step and all high-throughput sequencing approaches are generally based on conventional Sanger sequencing. After preparation of library and sequencing, later steps are completely computer-based (in silico) approaches called as bioinformatics.

A Nutrigenomics Approach Using RNA Sequencing Technology to Study Nutrient-Gene Interactions in Agricultural Animals

Thorough understanding of animal gene expression driven by dietary nutrients can be regarded as a bottom line of advanced animal nutrition research. Nutrigenomics (including transcriptomics) studies the effects of dietary nutrients on cellular gene expression and, ultimately, phenotypic changes in living organisms. Transcriptomics can be applied to investigate animal tissue transcriptomes at a defined nutritional state, which can provide a holistic view of intracellular RNA expression. As a novel transcriptomics approach, RNA sequencing (RNA-Seq) technology can monitor all gene expressions simultaneously in response to dietary intervention. The principle and history of RNA-Seq are briefly reviewed, and its 3 principal steps are described in this article. Application of RNA-Seq in different areas of animal nutrition research is summarized. Lastly, the application of RNA-Seq in swine science and nutrition is also reviewed. In short, RNA-Seq holds significant potential to be employed for better understanding the nutrient-gene interactions in agricultural animals.

Association of candidate genes with drought tolerance traits in zoysiagrass germplasm

Drought stress negatively influences the growth and physiology of perennial grasses. The objective of this study was to identify associations of candidate genes with drought tolerance traits in 96 zoysiagrass (Zoysia Willd.) accessions. Germplasm varied largely in leaf wilting, canopy and air temperature difference (CAD), leaf water content (LWC), chlorophyll fluorescence (Fv/Fm), leaf dry weight (LDW), stolon dry weight (SDW), rhizome dry weight (RZW), and root dry weight (RDW) under drought stress across the two experiments in 2014 and 2015 in a greenhouse. The population exhibited three subgroups based on molecular marker analysis and had minimum relative kinship. Associations between single nucleotide polymorphisms (SNPs) in BADH encoding betaine aldehyde dehydrogenase, DREB1 encoding DREB-like protein 1, Ndhf encoding NADH dehydrogenase subunit F, CAT encoding catalase, and VP1 encoding H⁺-pyrophosphatase were analyzed with trait under drought stress (D) and relative values compared to the control (R). Twenty-seven mark and trait associations were detected in year 2014, 2015, and a two-year combination across four genes, including 13 associations in 7 SNP loci in BADH, 9 associations in 5 SNP loci in DREB1, 3 associations in one SNP locus in Ndhf, and 2 associations in one SNP locus in CAT. Of them, one SNP in BADH was associated with D-RDW or D-SDW, three SNPs in DREB1 were associated with D-RZW, D-RDW, R-LWC, and D-CAD, and one SNP in CAT was associated with D-SDW. Nucleotide changes in these SNP loci caused non-synonymous amino acid substitutions. The results indicated that allelic diversity in genes involved in antioxidant metabolism, osmotic homeostasis, and dehydration responsive transcription factor could contribute to growth and physiological variations in zoysiagrass under drought stress.

Whole-genome resequencing from bulked-segregant analysis reveals gene set based association analyses for the Vibrio anguillarum resistance of turbot (Scophthalmus maximus)

Many achievements have been made to develop quantitative trait loci (QTLs) and gene-associated single nucleotide polymorphisms (SNPs) to facilitate practical marker-assisted selection (MAS) in aquatic animals. However, the systematic studies of SNPs associated with extreme threshold traits were poor in populations lacking of parental genomic information. Coupling next generation sequencing with bulked segregant analysis (BSA) should allow identification of numerous associated SNPs with extreme phenotypes. In the present study, using combination of SNP frequency difference and Euclidean distance, we conducted linkage analysis of SNPs located in genes involved in immune responses, and identified markers associated with Vibrio anguillarum resistance in turbot (Scophthalmus maximus). A total of 221 SNPs was found as candidate SNPs between resistant and susceptible individuals. Among these SNPs, 35 loci located in immune related genes were genotyped in verification population and 7 of them showed significant association with V. anguillarum resistance in both alleles and genotypes (P < 0.05). Among these 7 genes, PIK3CA-like, CYLD, VCAM1, RhoB and RhoGEF are involved in PI3K/Akt/mTOR pathway and NF-κB pathway, which influence the efficiency of bacteria entering the host and inflammation. SNP-SNP interaction analysis was performed by generalized multifactor dimensionality reduction (GMDR). The combination of SNP loci in RhoB, PIK3CA-like and ADCY3 showed a significant effect on V. anguillarum resistance with the verification rate in the sequencing population up to 70.8%. Taken all, our findings demonstrated the feasibility of BSA-seq approach in identifying genes responsible for the extreme phenotypes and will aid in performing MAS in turbot.

Advanced Genetic Approaches in Discovery and Characterization of Genes Involved With Osteoporosis in Mouse and Human

Osteoporosis is a complex condition with contributions from, and interactions between, multiple genetic loci and environmental factors. This review summarizes key advances in the application of genetic approaches for the identification of osteoporosis susceptibility genes. Genome-wide linkage analysis (GWLA) is the classical approach for identification of genes that cause monogenic diseases; however, it has shown limited success for complex diseases like osteoporosis. In contrast, genome-wide association studies (GWAS) have successfully identified over 200 osteoporosis susceptibility loci with genome-wide significance, and have provided most of the candidate genes identified to date. Phenome-wide association studies (PheWAS) apply a phenotype-to-genotype approach which can be used to complement GWAS. PheWAS is capable of characterizing the association between osteoporosis and uncommon and rare genetic variants. Another alternative approach, whole genome sequencing (WGS), will enable the discovery of uncommon and rare genetic variants in osteoporosis. Meta-analysis with increasing statistical power can offer greater confidence in gene searching through the analysis of combined results across genetic studies. Recently, new approaches to gene discovery include animal phenotype based models such as the Collaborative Cross and ENU mutagenesis. Site-directed mutagenesis and genome editing tools such as CRISPR/Cas9, TALENs and ZNFs have been used in functional analysis of candidate genes in vitro and in vivo. These resources are revolutionizing the identification of osteoporosis susceptibility genes through the use of genetically defined inbred mouse libraries, which are screened for bone phenotypes that are then correlated with known genetic variation. Identification of osteoporosis-related susceptibility genes by genetic approaches enables further characterization of gene function in animal models, with the ultimate aim being the identification of novel therapeutic targets for osteoporosis.

Risk Factor Genes in Patients with Dystonia: A Comprehensive Review

Background

Dystonia is a movement disorder with high heterogeneity regarding phenotypic appearance and etiology that occurs in both sporadic and familial forms. The etiology of the disease remains unknown. However, there is increasing evidence suggesting that a small number of gene alterations may lead to dystonia. Although pathogenic variants to the familial type of dystonia have been extensively reviewed and discussed, relatively little is known about the contribution of single-nucleotide polymorphisms (SNPs) to dystonia. This review focuses on the potential role of SNPs and other variants in dystonia susceptibility.

Methods

We searched the PubMed database for peer-reviewed articles published in English, from its inception through January 2018, that concerned human studies of dystonia and genetic variants. The following search terms were included: “dystonia” in combination with the following terms: 1) “polymorphisms” and 2) “SNPs” as free words.

Results

A total of 43 published studies regarding TOR1A, BDNF, DRD5, APOE, ARSG, NALC, OR4X2, COL4A1, TH, DDC, DBH, MAO, COMT, DAT, GCH1, PRKRA, MR-1, SGCE, ATP1A3, TAF1, THAP1, GNAL, DRD2, HLA-DRB, CBS, MTHFR, and MS genes, were included in the current review.

Discussion

To date, a few variants, which are possibly involved in several molecular pathways, have been related to dystonia. Large cohort studies are needed to determine robust associations between variants and dystonia with adjustment for other potential cofounders, in order to elucidate the pathogenic mechanisms of dystonia and the net effect of the genes.

Post-GWAS in prostate cancer: from genetic association to biological contribution

Genome-wide association studies (GWAS) have been successful in deciphering the genetic component of predisposition to many human complex diseases including prostate cancer. Germline variants identified by GWAS progressively unravelled the substantial knowledge gap concerning prostate cancer heritability. With the beginning of the post-GWAS era, more and more studies reveal that, in addition to their value as risk markers, germline variants can exert active roles in prostate oncogenesis. Consequently, current research efforts focus on exploring the biological mechanisms underlying specific susceptibility loci known as causal variants by applying novel and precise analytical methods to available GWAS data. Results obtained from these post-GWAS analyses have highlighted the potential of exploiting prostate cancer risk-associated germline variants to identify new gene networks and signalling pathways involved in prostate tumorigenesis. In this Review, we describe the molecular basis of several important prostate cancer-causal variants with an emphasis on using post-GWAS analysis to gain insight into cancer aetiology. In addition to discussing the current status of post-GWAS studies, we also summarize the main molecular mechanisms of potential causal variants at prostate cancer risk loci and explore the major challenges in moving from association to functional studies and their implication in clinical translation.

Wheat Resistances to Fusarium Root Rot and Head Blight Are Both Associated with Deoxynivalenol- and Jasmonate-Related Gene Expression

Fusarium graminearum is a major pathogen of wheat causing Fusarium head blight (FHB). Its ability to colonize wheat via seedling root infection has been reported recently. Our previous study on Fusarium root rot (FRR) has disclosed histological characteristics of pathogenesis and pathogen defense that mirror processes of spike infection. Therefore, it would be interesting to understand whether genes relevant for FHB resistance are induced in roots. The concept of similar-acting defense mechanisms provides a basis for research at broad Fusarium resistance in crop plants. However, molecular defense responses involved in FRR as well as their relation to spike resistance are unknown. To test the hypothesis of a conserved defense response, a candidate gene expression study was conducted to test the activity of selected prominent FHB defense-related genes in seedling roots, adult plant roots, spikes, and shoots. FRR was examined at seedling and adult plant stages to assess age-related pattern of disease and pathogen resistance. This study offers first evidence for a significant genetic overlap in root and spike defense responses, both in local and distant tissues. The results point to plant development-specific rather than organ-specific determinants of resistance, and suggest roots as an interesting model for studies on wheat-Fusarium interactions.

Pharmacogenetics of Adverse Drug Reactions

Adverse drug reactions (ADRs) are an important cause of morbidity and mortality. Genetic factors predispose to many ADRs, affecting susceptibility to both type A and type B reactions. The overall contribution of genetics will vary according to drug and ADR, and should be considered when attempting to predict and prevent ADRs. Genetic risk factors are considered in detail for a number of type A ADRs, especially those relating to warfarin and thiopurines, and type B ADRs affecting skin, the liver, and the heart. As the availability of whole genome sequencing increases, it is likely that prospective genotype for particular ADRs prior to drug prescription will become more common in the future. Current examples of genetic testing to prevent ADRs which have already been implemented and future prospects for developments in the field are discussed in detail.

Review on Pharmacogenetics and Pharmacogenomics Applied to the Study of Asthma

Nearly one-half of asthmatic patients do not respond to the most common therapies. Evidence suggests that genetic factors may be involved in the heterogeneity in therapeutic response and adverse events to asthma therapies. We focus on the three major classes of asthma medication: β-adrenergic receptor agonist, inhaled corticosteroids, and leukotriene modifiers. Pharmacogenetics and pharmacogenomics studies have identified several candidate genes associated with drug response.In this chapter, the main pharmacogenetic and pharmacogenomic studies in addition to the future perspectives in personalized medicine will be reviewed. The ideal treatment of asthma would be a tailored approach to health care in which adverse effects are minimized and the therapeutic benefit for an individual asthmatic is maximized leading to a more cost-effective care.

Genetic epidemiology of neural tube defects

It has been estimated that 60-70% of neural tube defects (NTDs) have a genetic component, but few causative genes have been identified. The lack of information on genes associated with non-syndromic NTDs in humans is especially notable as the "genomic revolution" has led to new tools (e.g., genome-wide genotyping arrays, next-generation sequencing) that are helping to elucidate the full spectrum of genetic variation (from common to rare) contributing to complex traits, including structural birth defects. However, the application of modern genomic approaches to the study of NTDs has lagged behind that of some other common structural birth defects. This may be due to the difficulty of assembling large study cohorts for anencephaly or spina bifida. The purpose of this review is to outline the evolution of genetic studies of NTDs, from studies of familial aggregation to candidate gene and genome-wide association studies, through whole-exome and whole-genome sequencing. Strategies for addressing gaps in NTD genetic research are also explored.