Advances in the study of POAG-related genes and central nervous system diseases / 国际眼科杂志(Guoji Yanke Zazhi)

@#In recent years, considerable progress has been made in the study of glaucoma, especially primary open angle glaucoma(POAG). A series of POAG genes has been identified through genetic linkage analysis and genome-wide association studies(GWAS), which significantly advanced the study of glaucoma genetics. The latest perspective suggests that glaucoma is a disease of the central nervous system(CNS). A large number of basic clinical studies have demonstrated the close association between CNS disease and glaucoma. Among these studies, discoveries related to genetics are of prominence.

Genetic study of cardiovascular disease subtypes defined by International Classification of Diseases / 北京大学学报(医学版)

OBJECTIVE@#To study the molecular connection among cardiovascular diseases (CVD) subtypes defined by the International Classification of Diseases (ICD) version 10 (ICD-10).@*METHODS@#Both phenotypic data and genotypic data used in this study were obtained from the UK Biobank. A total of 380 083 participants aged between 40 and 69 years were included. Those without any cardiovascular disease (either no ICD-10 code at all or no ICD-10 code containing letter I) were assigned to the control group. The five CVD subtypes were: ischaemic heart diseases (IHD), pulmonary heart disease and diseases of pulmonary circulation (PHD), cerebrovascular diseases (CRB), diseases of arteries, arterioles and capillaries (AAC), diseases of veins, lymphatic vessels and lymph nodes, and diseases not elsewhere classified (VLL). We first performed a genome-wide association study (GWAS) for each of the five subtypes. We summarized novel loci using genome-wide significance threshold P=5×10-8. Next, we used linkage disequilibrium score regression (LDSC) method to assess genetic correlation among the five subtypes. Lastly, we applied mendelian randomization (MR) approach to assess the causal relationship among the subtypes. The particular software that we used was generalised summary-data-based mendelian randomisation (GSMR).@*RESULTS@#Through GWAS, we identified hundreds of genome-wide significant SNPs: 672 for IHD, 241 for PHD, 31 for CRB, 48 for AAC, and 193 for VLL. By comparing with published literature, we found 28 novel loci, for PHD (n=14), CRB (n =7) and AAC (n =7). Eight of these 28 loci were rare, where the lead SNP had minor allele frequency (MAF) less than 1%. LDSC analyses indicated IHD had significant genetic correlation with VLL (P=2.52×10-7), PHD (P=3.77×10-3) and AAC (P=4.90×10-3), respectively. Bidrectional GSMR analyses showed that IHD had a positive causal relationship with VLL (P=7.40×10-5) and AAC (P=1.50×10-3), while reverse causality was not supported.@*CONCLUSION@#This study adopted an innovative approach to study the molecular connection among CVD subtypes that are defined by ICD. We identified potentially positive genetic correlation and causal effects among some of these subtypes. Research along this line will provide scientific insights and serve as a guidance for future ICD standards.

Obesity subtypes, related biomarkers & heterogeneity

Obesity is a serious medical condition worldwide, which needs new approaches and recognized international consensus in treating diseases leading to morbidity. The aim of this review was to examine heterogeneous links among the various phenotypes of obesity in adults. Proteins and associated genes in each group were analysed to differentiate between biomarkers. A variety of terms for classification and characterization within this pathology are currently in use; however, there is no clear consensus in terminology. The most significant groups reviewed include metabolically healthy obese, metabolically abnormal obese, metabolically abnormal, normal weight and sarcopenic obese. These phenotypes do not define particular genotypes or epigenetic gene regulation, or proteins related to inflammation. There are many other genes linked to obesity, though the value of screening all of those for diagnosis has low predictive results, as there are no significant biomarkers. It is important to establish a consensus in the terminology used and the characteristics attributed to obesity subtypes. The identification of specific molecular biomarkers is also required for better diagnosis in subtypes of obesity.

Evaluating the effect of WNT pathway genes considering interactions on the risk of non-syndromic oral clefts among Chinese populations / 北京大学学报(医学版)

OBJECTIVE@#In this study, we used genome-wide association study (GWAS) data to explore whether WNT pathway genes were associated with non-syndromic oral clefts (NSOC) considering gene-gene interaction and gene-environment interaction.@*METHODS@#We conducted the analysis using 806 non-syndromic cleft lip with or without cleft palate (NSCL/P) case-parent trios and 202 non-syndromic cleft palate (NSCP) case-parent trios among Chinese populations selected from an international consortium established for a GWAS of non-syndromic oral clefts. Genotype data and maternal environmental exposures were collected through DNA samples and questionnaires. Conditional Logistic regression models were adopted to explore gene-gene interaction and gene-environment in teraction using trio package in R software. The threshold of significance level was set as 3.47×10-4 using Bonferroni correction.@*RESULTS@#A total of 144 single nucleotide polymorphisms (SNPs) in seven genes passed the quality control process in NSCL/P trios and NSCP trios, respectively. Totally six pairs of SNPs interactions showed statistically significant SNP-SNP interaction (P < 3.47×10-4) after Bonferroni correction, which were rs7618735 (WNT5A) and rs10848543 (WNT5B), rs631948 (WNT11) and rs556874 (WNT5A), and rs631948 (WNT11) and rs472631 (WNT5A) among NSCL/P trios; rs589149 (WNT11) and rs4765834 (WNT5B), rs1402704 (WNT11) and rs358792 (WNT5A), and rs1402704 (WNT11) and rs358793 (WNT5A) among NSCP trios, respectively. In addition, no significant result was found for gene-environment interaction analysis in both of the NSCL/P trios and NSCP trios.@*CONCLUSION@#Though this study failed to detect significant association based on gene-environment interactions of seven WNT pathway genes and the risk of NSOC, WNT pathway genes may influence the risk of NSOC through potential gene-gene interaction.

Lipoprotein(a): An independent, genetic, and causal factor for cardiovascular disease and acute myocardial infarction

Lipoprotein(a) [Lp(a)] is a circulating lipoprotein, and its level is largely determined by variation in the Lp(a) gene (LPA) locus encoding apo(a). Genetic variation in the LPA gene that increases Lp(a) level also increases coronary artery disease (CAD) risk, suggesting that Lp(a) is a causal factor for CAD risk. Lp(a) is the preferential lipoprotein carrier for oxidized phospholipids (OxPL), a proatherogenic and proinflammatory biomarker. Lp(a) adversely affects endothelial function, inflammation, oxidative stress, fibrinolysis, and plaque stability, leading to accelerated atherothrombosis and premature CAD. The INTER-HEART Study has established the usefulness of Lp(a) in assessing the risk of acute myocardial infarction in ethnically diverse populations with South Asians having the highest risk and population attributable risk. The 2018 Cholesterol Clinical Practice Guideline have recognized elevated Lp(a) as an atherosclerotic cardiovascular disease risk enhancer for initiating or intensifying statin therapy.

Genome-Wide Association Studies Associated with Backfat Thickness in Landrace and Yorkshire Pigs

Although pork quality traits are important commercially, genome-wide association studies (GWASs) have not well considered Landrace and Yorkshire pigs worldwide. Landrace and Yorkshire pigs are important pork-providing breeds. Although quantitative trait loci of pigs are well-developed, significant genes in GWASs of pigs in Korea must be studied. Through a GWAS using the PLINK program, study of the significant genes in Korean pigs was performed. We conducted a GWAS and surveyed the gene ontology (GO) terms associated with the backfat thickness (BF) trait of these pigs. We included the breed information (Yorkshire and Landrace pigs) as a covariate. The significant genes after false discovery rate (<0.01) correction were AFG1L, SCAI, RIMS1, and SPDEF. The major GO terms for the top 5% of genes were related to neuronal genes, cell morphogenesis and actin cytoskeleton organization. The neuronal genes were previously reported as being associated with backfat thickness. However, the genes in our results were novel, and they included ZNF280D, BAIAP2, LRTM2, GABRA5, PCDH15, HERC1, DTNBP1, SLIT2, TRAPPC9, NGFR, APBB2, RBPJ, and ABL2. These novel genes might have roles in important cellular and physiological functions related to BF accumulation. The genes related to cell morphogenesis were NOX4, MKLN1, ZNF280D, BAIAP2, DNAAF1, LRTM2, PCDH15, NGFR, RBPJ, MYH9, APBB2, DTNBP1, TRIM62, and SLIT2. The genes that belonged to actin cytoskeleton organization were MKLN1, BAIAP2, PCDH15, BCAS3, MYH9, DTNBP1, ABL2, ADD2, and SLIT2.

Advances in the research of genome-wide association studies on healthy adult height and missing heritability / 中国法医学杂志

Human height, a complex trait with over 80% heritability, is determined by genetic and environment factors. Currently, a certain amount of specific variants about human height have been found, especially with the widely used of genome-wide association studies (GWAS) in genetics research, making it a great progress for the discovering of height associated genes. However, single nucleotide polymorphisms (SNPs) found by GWAS can only explain a minority of the heritable. This article reviews the progress of GWAS about height associated genes and missing heritability domestic and overseas.

Genetics of rheumatoid arthritis: a new boost is needed in Latin American populations / Genética da artrite reumatoide: é necessário um novo impulso em populações latino-americanas

ABSTRACT Rheumatoid Arthritis (RA) is an autoimmune inflammatory rheumatic disease which affects several organs and tissue, predominantly the synovial joints. Like many other autoimmune diseases, RA is a complex disease, where genetic variants, environmental factors and random events interact to trigger pathological pathways. Genetic implication in RA is evident, and recent advances have expanded our knowledge about the genetic factors that contribute to RA. An exponential increment in the number of genes associated with the disease has been described, mainly through gene wide screen studies (GWAS) involving international consortia with large patient cohorts. However, there are a few studies on Latin American populations. This article describes what is known about the RA genetics, the future that is emerging, and how this will develop a more personalized approach for the treatment of the disease. Latin American RA patients cannot be excluded from this final aim, and a higher collaboration with the international consortia may be needed for a better knowledge of the genetic profile of patients from this origin.

RESUMO A artrite reumatoide (AR) é uma doença reumática inflamatória autoimune que afeta vários órgãos e tecidos, predominantemente as articulações sinoviais. Como muitas outras doenças autoimunes, a AR é uma doença complexa, em que variantes genéticas, fatores ambientais e eventos aleatórios interagem e desencadeiam vias patológicas. A implicação genética na AR é evidente e avanços recentes têm expandido nosso conhecimento sobre os fatores genéticos que contribuem para a doença. Houve um incremento exponencial na quantidade de genes associados à doença descritos, principalmente por estudos de associação genômica ampla (GWAS) que envolveram consórcios internacionais com grandes grupos de pacientes. No entanto, há poucos estudos em populações latino-americanas. Este artigo descreve o que é conhecido sobre a genética na AR, o que vem a seguir e como isso vai desenvolver uma abordagem mais personalizada para o tratamento da doença. Os pacientes latino-americanos com AR não podem ser excluídos desse objetivo final e pode ser necessária uma maior colaboração com os consórcios internacionais para se obter um melhor conhecimento do perfil genético dos pacientes provenientes dessa região.

Pathway Analysis of Metabolic Syndrome Using a Genome-Wide Association Study of Korea Associated Resource (KARE) Cohorts

Metabolic syndrome (MetS) is a complex disorder related to insulin resistance, obesity, and inflammation. Genetic and environmental factors also contribute to the development of MetS, and through genome-wide association studies (GWASs), important susceptibility loci have been identified. However, GWASs focus more on individual single-nucleotide polymorphisms (SNPs), explaining only a small portion of genetic heritability. To overcome this limitation, pathway analyses are being applied to GWAS datasets. The aim of this study is to elucidate the biological pathways involved in the pathogenesis of MetS through pathway analysis. Cohort data from the Korea Associated Resource (KARE) was used for analysis, which include 8,842 individuals (age, 52.2 +/- 8.9 years; body mass index, 24.6 +/- 3.2 kg/m2). A total of 312,121 autosomal SNPs were obtained after quality control. Pathway analysis was conducted using Meta-analysis Gene-Set Enrichment of Variant Associations (MAGENTA) to discover the biological pathways associated with MetS. In the discovery phase, SNPs from chromosome 12, including rs11066280, rs2074356, and rs12229654, were associated with MetS (p < 5 x 10(-6)), and rs11066280 satisfied the Bonferroni-corrected cutoff (unadjusted p < 1.38 x 10(-7), Bonferroni-adjusted p < 0.05). Through pathway analysis, biological pathways, including electron carrier activity, signaling by platelet-derived growth factor (PDGF), the mitogen-activated protein kinase kinase kinase cascade, PDGF binding, peroxisome proliferator-activated receptor (PPAR) signaling, and DNA repair, were associated with MetS. Through pathway analysis of MetS, pathways related with PDGF, mitogen-activated protein kinase, and PPAR signaling, as well as nucleic acid binding, protein secretion, and DNA repair, were identified. Further studies will be needed to clarify the genetic pathogenesis leading to MetS.

Role of histone acetylation in diabetes mellitus / 中华内分泌代谢杂志

Histone acetylation is a crucial part of histone modifications in epigenetics.Histone acetylation is involved in the onset of diabetes and diabetic complications,through the mechanism of inducing hyperglycemia by means of metabolic memory effect,interfering islet development and regulating the expression of inflammatory factors and pathogenic genes.Genome-wide association studies are gradually unveilling the pathogenesis of diabetes and preclinical studies are rapidly elucidating that histone deacetylase should be considered as a new target for the treatment of diabetes.

Progress in single nucleotide polymorphism with cancer susceptibility and its clinical application / 中华检验医学杂志

Single nueleotide polymorphisms (SNPs) are the most common genetic variants in human genome.Candidate gene,genome-wide association studies (GWASs) and exome sequencing which base on SNPs have made a great progress in identifying cancer susceptibility.The development and application of high resolutions in SNPs has played an important role in clarifying the mechanism,prevention,diagnosis and targeted therapy in cancers.

Drug resistance in epilepsy and the ABCB1 gene: The clinical perspective.

Multidrug resistance is one of the most serious problems in the treatment of epilepsy that is likely to have a complex genetic and acquired basis. Various experimental data support the hypothesis that over-expression of antiepileptic drug (AED) transporters may play a pivotal role in drug resistance. Hyyt 6however, key questions concerning their functionality remain unanswered. The idea that P-glycoprotein, encoded by the ABCB1 gene, might mediate at least part of the drug resistance was met with both enthusiasm and skepticism. As in oncology, initial optimism has been clouded subsequently by conflicting results. The first study reporting a positive association between genetic variation in the P-glycoprotein and multidrug-resistant epilepsy was published in 2003. Since then, several other genetic association studies have attempted to verify this result. However, taken overall, the role of P-glycoprotein in drug resistance in epilepsy still remains uncertain. We intend to critically review the inherent problems associated with epilepsy pharmacogenetic studies in general and with ABCB1 polymorphisms studies in particular. The lessons learnt from the ABCB1 studies can help us to guide future association genetics studies to investigate AED resistance, and thereby taking us closer to the cherished dream of personalized AED therapy.

Hipertrigliceridemias de origen genético / Hypertriglyceridemias of genetic origen

Hypertriglyceridemia (HTG) is defined as plasma triglycerides (TG) > 150 mg/dL, and it is a frequent disease in the general population. When plasma TG reach concentrations > 500 mg/dL (severe HTG), there is usually a genetic defect involved. This defect can involve a single gene or be of polygenic inheritance. In polygenic HTG, the phenotypic expression of the disease is usually associated to the presence of certain diseases such as diabetes, obesity or insulin resistance. The most common known genes associated with monogenic hypertriglyceridemia are LPL and APOC2, but in recent years a few cases caused by mutant APOA5, GPIHBP1 and LMF1, have been identified. Furthermore, genome wide association studies (GWA) have brought up new genes that are related to discrete changes in triglyceride plasma levels of the general population. Among them, it is worth mentioning GCKR, TRIB1, MLXIPL, GALNT2, APOB, APOC2, APOA5, APOE, LPL, ANGPTL3 and NCAN. It is remarkable that most severe hypertriglyceridemias are of polygenic origin, and they could involve a major susceptibility gene. Only in a few cases of severe or very severe HTG (TG > 2.000 mg/dL) the genetic cause is known.

Sulwon Lecture 2009: The Search for Genetic Risk Factors of Type 2 Diabetes Mellitus

Type 2 diabetes mellitus (T2DM) is caused by complex interplay between multiple genetic and environmental factors. The three major approaches used to identify the genetic susceptibility include candidate gene approach, familial linkage analysis and genome- wide association analysis. Recent advance in genome-wide association studies have greatly improved our understanding of the pathophysiology of T2DM. As of the end of 2010, there are more than 40 confirmed T2DM-associated genetic loci. Most of the T2DM susceptibility genes were implicated in decreased beta-cell function. However, these genetic variations have a modest effect and their combination only explains less than 10% of the T2DM heritability. With the advent of the next-generation sequencing technology, we will soon identify rare variants of larger effect as well as causal variants. These advances in understanding the genetics of T2DM will lead to the development of new therapeutic and preventive strategies and individualized medicine.

Genome-wide Association Analysis Based on Copy Number Variations / 生物化学与生物物理进展

Copy number variations (CNVs) refer as a DNA segment that is 1 kb or larger and is presented at a variable copy number in comparison with a reference genome. Classes of CNVs include insertions, deletions, duplications and their complex combinations. Because they widely distributed in the genome with some important characteristics, such as heritable, relative stable and heterogeneity, CNVs are considered as novel genomic polymorphism markers. And the alteration of gene dosage which resulted from CNVs could change phenotype, so a novel CNV genome-wide association analysis (CNV-GWAS) strategy appeared recently and began to used for identifying susceptible genes of complex diseases. It was approved that it could complement the tranditional genome-wide association studies based on single nucleotide polymorphisms. Therefore, genomic structure variances are favorable for revealing the molecular mechanisms and genetic foundation of complex diseases.