Genetic studies of bipolar disorder and recurrent major depression in a large Scottish family

Bipolar disorder and recurrent major depression are complex psychiatric illnesses with a substantial, yet unknown genetic component. Genetic studies have identified linkage of bipolar disorder and recurrent major depression with markers on chromosome 4p15-p16 in a large Scottish family and three smaller families. To focus the search for genetic factors for susceptibility to illness two approaches were adopted: a chromosome 4p15-p16 candidate gene study and a whole-genome linkage scan. In the first instance, phosphatidylinositol 4-kinase type-II beta (PI4K2B) was selected as a candidate gene. Analysis of haplotypes in the four linked families identified two regions, both of which were shared by three families. PI4K2B lies within one of these regions. PI4K2B is also a worthy functional candidate as it is a member of the phosphatidylinositol pathway, which is targeted by lithium for therapeutic effect in bipolar disorder. Expression studies at the allele-specific mRNA and protein level were performed in lymphoblastoid cell lines from the large Scottish family. There was no evidence for expression differences between affected and non-affected family members. However, a case-control association study showed preliminary evidence for association of schizophrenia but not bipolar disorder, with tagging single nucleotide polymorphisms from the PI4K2B genomic region. Second, the linkage evidence for bipolar disorder and recurrent major depression in the large Scottish family was re-examined. This was important because additional family members had been recruited and advances in technology made it feasible to cover all chromosome regions more densely than had been possible ten years ago. Stringent genotyping and pedigree error checks were performed to ensure an optimised dataset for analysis. Furthermore, the large family was divided in an informative manner for ease of analysis using both parametric and non-parametric methods, supplemented by haplotype analysis. Genome-wide significant evidence for linkage was observed on chromosome 4p15- p16 and genome-wide suggestive evidence was observed on chromosomes 8p21 and 1p36. The analysis clearly supports the evidence for a susceptibility locus of bipolar disorder and recurrent major depression on chromosome 4p15-p16, while identifying other genetic loci that may confer risk to psychiatric illness

Genetic Dissection of Behavioral and Neurogenomic Responses to Acute Ethanol

Individual differences in initial sensitivity to ethanol are strongly related to the heritable risk of alcoholism in humans. To elucidate key molecular networks that modulate ethanol sensitivity we performed a systems genetics analysis of ethanol-responsive gene expression in brain regions of the mesocorticolimbic reward circuit (prefrontal cortex, nucleus accumbens and ventral midbrain) across the BXD RI panel, a highly diverse family of isogenic mouse strains before and after treatment with ethanol. Acute ethanol altered the expression of ~2,750 genes in one or more regions and 400 transcripts were jointly modulated in all three. Ethanol-responsive gene networks were extracted with a powerful graph theoretical method that efficiently summarized ethanol\u27s effects. These networks correlated with acute behavioral responses to ethanol and other drugs of abuse. As predicted, networks were heavily populated by genes controlling synaptic transmission and neuroplasticity. Several of the most densely interconnected network hubs, including Kcnma1 and Gsk3-beta, are known to influence behavioral or physiological responses to ethanol, validating our overall approach. Other major hub genes like Grm3 and Nrg3 represent novel targets of ethanol effects. Networks were under strong genetic control by variants that we mapped to a small number of chromosomal loci. Using a novel combination of genetic, bioinformatic and network-based approaches, we identified high priority cis-regulatory candidate genes, including Scn1b, Gria1, Sncb and Nell2. The ethanol-responsive gene networks identified here represent a previously uncharacterized intermediate phenotype between DNA variation and ethanol sensitivity in mice. Networks involved in synaptic transmission were strongly regulated by ethanol and could contribute to behavioral plasticity seen with chronic ethanol. Our novel finding that hub genes and a small number of loci exert major influence over the ethanol response of gene networks could have important implications for future studies regarding the mechanisms and treatment of alcohol use disorders

A systematic genome-wide association analysis for inflammatory bowel diseases (IBD)

Two independent and hypothesis-free genome-wide association studies were carried out to find novel susceptibility genes for Crohn’s disease (CD), which is a chronic inflammatory disorder of the bowel. In a first sequence-based and “direct” scan, approximately 20,000 nonsynonymous SNPs, which result in a change in protein sequence, were typed. The second “indirect” map-based scan comprised about 100,000 evenly distributed SNPs

Summaries of plenary, symposia, and oral sessions at the XXII World Congress of Psychiatric Genetics, Copenhagen, Denmark, 12-16 October 2014

The XXII World Congress of Psychiatric Genetics, sponsored by the International Society of Psychiatric Genetics, took place in Copenhagen, Denmark, on 12-16 October 2014. A total of 883 participants gathered to discuss the latest findings in the field. The following report was written by student and postdoctoral attendees. Each was assigned one or more sessions as a rapporteur. This manuscript represents topics covered in most, but not all of the oral presentations during the conference, and contains some of the major notable new findings reported

Computational analysis of innate and adaptive immune responses

Both innate and adaptive immune processes rely on the activation of differentiated haematopoietic stem cell lineages to affect an appropriate response to pathogens. This thesis employs a largely network biology focused approach to better understand the specificity of immune cell responses in two distinct cases of pathogenic challenge. In the context of adaptive immunity, I studied the transcriptional responses of T cells during Graft-versus-Host Disease (GvHD). GvHD represents one of the major complications to arise following allogeneic hematopoietic stem cell transplantation and yet why only particular organs are damaged as a result of this pathology is still unclear. To investigate whether key GvHD transcriptional signatures seen in effector CD8+ T cells compared to naïve T cells are triggered in target organs or the secondary lymphoid organs, a module-based association test was developed to combine the output of gene clustering algorithms with that of differential expression analysis. This methodology significantly aided the identification of skin specific effector T cell transcriptional programs believed to drive murine GvHD pathogenesis at this site. Turning to the innate immune response, I investigated the transcriptional profiles of resting and activated macrophages in the setting of Tuberculosis (TB), the second leading cause of death from infectious disease worldwide. Regression-based analyses and clustering of macrophage expression data provided insight into the variations in gene expression profiles of naïve macrophages compared to those infected with Mycobacterium tuberculosis (MTB) or a vaccine strain of mycobacteria (BCG). The availability of genotype data as part of the macrophage dataset facilitated an expression quantitative trait loci (eQTL) study which highlighted a novel association between the cytoskeleton gene BCAR1 and TB risk, together with a previously undescribed trans-eQTL module specific to MTB infected macrophages. Potential genetic variants impacting expression of the aforementioned GvHD specific T cell transcriptional signatures were additionally investigated using external trans-eQTL datasets

Forward vs. reverse genetics: a bovine perspective based on visible and hidden phenotypes of inherited disorders

In modern cattle production, we have seen a negative trend for decades in reproduction while productivity and performance have improved. Although considered genetically complex, part of these fecundity, fertility, and rearing success issues are caused by Mendelian monogenic disorders. Traditionally, such disorders are investigated opportunistically based on their sporadic occurrence and through subsequent targeted analysis of affected individuals. This approach is called the forward genetic approach (FGA). Modern genomic technologies, such as single nucleotide polymorphism (SNP) array genotyping and whole-genome sequencing (WGS), allow for straightforward locus mapping and the identification of candidate causal variants in affected individuals or families. Nevertheless, a major drawback is the arbitrary sampling and availability of well-phenotyped individuals for research, especially for mostly invisible defects affecting fecundity, early embryonic death, and abortions. Therefore, the reverse genetic approach (RGA) is applied to screen for underlying recessive lethal or sub-lethal variants. This approach requires the availability of massive population-wide genomic data. By applying a haplotype screen for a significant deviation of the Hardy-Weinberg equilibrium, genomic regions potentially harboring candidate causal variants are identified. The subsequent generation of WGS data of haplotype carriers allows for the mining for pathogenic variants potentially causing a reduction in homozygosity. In the first part of my thesis, I present 18 successful, 1 inconclusive example, and 1 example addressing co-dominant effects of a known disorder. These FGA analyzes include heritable skin (n=7), bone (n=7), neuromuscular (n=1), eye (n=2), as well as syndromic disorders (n=3) in various European cattle breeds. Missense and frameshift variants in the IL17RA, DSP, and FA2H genes were described in three recessive genodermatoses: immunodeficiency with psoriasis-like skin alterations, syndromic ichthyosis, and ichthyosis congenita, respectively. Hypohidrotic ectodermal dysplasia was described as X-linked disorder that is associated with a gross deletion in the EDA gene. In dominant genodermatoses, a missense variant in COL5A2 was shown to lead to classical Ehlers-Danlos syndrome, an in-frame deletion in KRT5 was shown to cause epidermolysis bullosa simplex, and results of a study using an individual case of juvenile angiomatosis remained inconclusive. A recessive disorder described as hemifacial macrosomia was associated with a missense variant in LAMB1. Chondrodysplasia in a single family was shown to be caused by a de novo mutation in the bull leading to a stop-loss of the gene FGFR3. De novo mutations (missense and large deletions) in the COL2A1 and COL1A1 genes were associated with achondrogenesis type II (bulldog calf syndrome), and osteogenesis imperfecta type II, respectively. Another mutation that we found to affect bone morphology was a trisomy in chromosome 29 leading to proportional dwarfism with facial dysplasia. Congenital neuromuscular channelopathy was for the first time associated with a missense variant in KCNG1. Furthermore, a de novo missense variant in ADAMTSL4 and a recessive missense variant in CNGB3 were shown to cause congenital cataract and achromatopsia, respectively. Additionally, cases of pulmonary hypoplasia and anasarca syndrome were analyzed and shown to be caused by trisomy 20 in two unrelated calves and a recessively inherited missense variant in ADAMTS3. Moreover, the fatal syndromic disorder skeletal-cardo-enteric dysplasia was described to be caused by a de novo missense variant in MAP2K2. Finally, I investigated the effects on blood cholesterol and triglyceride levels of heterozygous carriers of the previously described APOB-related cholesterol deficiency. In the second part of my thesis, I present the outcome of the RGA in four main Swiss populations, that was validated with the SWISScow custom array. In the Brown Swiss dairy population, 72 haplotype regions showed significant depletions in homozygosity. Four of these haplotypes (BH6, BH14, BH24, and BH34) were associated with missense and nonsense variants in different genes (MARS2, MRPL55, CPT1C, and ACSL5, respectively). In the Original Braunvieh population, eight haplotype regions were identified. Candidate causal variants included a missense variant in TUBGCP5 gene associated with haplotype OH2, and a splice site frameshift variant in LIG3 gene associated with haplotype OH4. In the Holstein population, 24 haplotype regions were identified with a significant reduction of homozygosity. Subsequently, four novel candidate variants were proposed: a nonsense variant in KIR2DS1 for haplotype HH13, in-frame deletion in the genes NOTCH3 for HH21 haplotype, and RIOX1 for HH25 haplotype, and finally, a missense variant in PCDH15 for HH35 haplotype. In the Simmental population, eleven haplotype regions were detected. The haplotype SH5 was associated with a frameshift variant in DIS3 gene and the haplotypes SH8 and SH9 with missense variants in the CYP2B6 and NUBPL genes, respectively. For the breeds Brown Swiss, Original Braunvieh, and Holstein, association studies were carried out including traits describing fertility, birth, growth, and survival. Thereby most of the described mentioned haplotypes show additive effects. Regardless of the approach, all the described candidate causal variants can be used as a tool of precision diagnostics and represent a step forward towards personalized medicine in cattle. Furthermore, these variants can be easily genotyped and allow for targeted breeding to reduce the number of risk matings, which would lead to a reduction of affected animals and significant improvement in animal health and welfare

구조 변이 기반 인간 게놈 특성 규명을 위한 생물정보학 연구

학위논문 (박사)-- 서울대학교 대학원 : 농생명공학부, 2014. 8. 김희발.지난 몇 년 동안 질병 관련 유전체 구조적 변이 (단일염기 다형성과 유전자 복제 수 변이) 연구에 대한 노력이 계속되고 있다. 단일염기 다형성은 참조유전체와 비교하여 DNA 염기서열에서 하나의 염기서열의 차이를 가지고 유전자 복제 수 변이는 1,000 개 이상의 구조적 변이이다. 전장유전체연관분석은 유전체 구조적 변이와 질병에 관한 후보유전자를 찾는데 많이 연구되고 있다. 데이터 마이닝은 복잡하고 많은 양의 정보를 통찰하는데 중요하다. 이러한 생물학적 네트워크는 연구자가 정보를 통하여 복잡한 문제에 대한 의미론적 해답을 찾는데 도움을 준다. 따라서, 이 논문의 목표는 한국인에서 간 질병과 관련된 유전적 변이를 찾고, 간 기능이나 인종 차이에 영향을 미치는 생물학적 네트워크를 구축하여 이에 대한 의미론적 해답을 찾고 유전체 구조적 변이에 대한 시각화 툴을 구축하는데 있다. 제 1 장에서는 유전자 복제 수 변이, 전장유전체연관분석과 생물학적 네트워크에 관하여 기술하였다. 1) 유전자 복제 수 변이에 대한 개요와 원천 및 찾는 방법을 기술하였고 연구동향과 질병에서의 역할을 정리하였다. 2) 전장유전체연관분석에 대한 개요와 배경을 정리하였고 방법 및 결과를 요약하였다. 3) 생물학적 네트워크에 관한 개요 및 연구동향을 정리하였다. 제 2 장에서는 한국인에 관한 간 형질과 유전자 복제 수 변이의 메타연관분석을 수행하였다. KARE1 파트에서는 1) 한국인 8,842 명에 대해 총 10,162 개의 유전자 복제 수 변이를 찾았고, 2) 간 형질에 대한 유전자 복제 수 변이의 영향을 보기 위하여 단일 선형 회귀 분석을 수행하였다. 그 결과, AST 와 ALT 에 대해서 각각 100 개와 16 개가 유의하게 나왔다. 3) 그 유의한 유전자 복제 수 변이의 지역에 39 개의 유전자가 위치해 있었고 4) 그 유전자에 대해 기능적 분류 분석 결과, 간 관련 후보유전자로서 인정이 되었다. KARE2 파트에서는 KARE1 파트의 반복 유전체연관분석을 수행하였다. 1) 한국인 407 명에 대해 총 3,046 개의 유전자 복제 수 변이를 찾았고, 2) 단일 선형 회귀 분석을 이용하여 유전자 복제 수 변이와 간 형질과의 연관분석을 수행하였다. 그 결과, AST 와 ALT 에 대해서 각각 32 개 (140 개의 유전자)와 42 개 (172 개의 유전자)가 유의하게 나왔다. 3) 반복분석결과, 한국인의 유전자 복제 수 변이와 간 관련하여 총 9 개의 유전자가 유의하게 나왔다. 제 3 장에서는 간 기능과 인종 차이를 나타내는 유전자 복제 수 관련 생물학적 네트워크를 구축하였다. 노드는 유전자, 질병, 대사, 화학물질, 약, 임상정보, 변이 등으로 구성되어있고, 연결은 유전자-질병, 유전자-변이, 유전자-화학물질, 대사-질병, 대사-화학물질, 화학물질-약, 질병-임상정보, 임상정보-약 등으로 구성되어있다. 생물학적 네트워크 분석을 통해 한국인 간 기능 유전자 복제 수 변이 관련 총 4 개의 질병과 1 개의 대사회로 및 7 개의 약을 밝혀내었고, 인종 차이 유전자 복제 수 변이 관련 총 3 개의 질병과 1 개의 약 및 5 개의 대사회로를 밝혀내었다. 제 4 장에서는 유전자 복제 수 변이와 단일염기다형성의 시각화를 위한 툴을 구축하였다. 총 6 개의 메뉴로 1) 유전자 복제 수 변이나 단일염기다형성의 위치에 풍부한 요소 검사와 2) 염색체상의 변이 위치 분포 3) log2 ratio 분포 4) binning 단위 당 변위 분포 5) homozygosity 분포 6) cytomapping 시각화로 구성되어있다. 이 툴은 값으로 나타나는 변이로부터 생물학적 의미를 쉽게 이해하는데 도움을 주고, 또한 어떤 설치나 다운로드 없이 쉽게 이용 가능하다. 전장유전체 연관분석을 통해 한국인의 유전자 복제 수 변이와 간 형질 관련 유력한 후보유전자를 찾을 수 있었고, 간 질병과 인종차이 유전자 복제 수 변이관련 의미론적 생물학 네트워크를 구축할 수 있었다. 또한 다양한 유전자 복제 수 변이 연구를 함으로써 축적되어온 변이 시각화를 위한 총집합적 툴을 개발하였다. 이러한 네트워크와 시각화 툴은 질병이나 인종 관련 유전자 복제 수 변이의 의미론적 생물학 의미 발견이 가능하고 시각화 툴은 값으로 나타나는 유전자 복제 수 변이로부터 생물학적 해석에 도움이 된다.Over the past few years, efforts focused on investigating the effects of copy number variations (CNVs) in human disease have been continuing. Genetic differences are attributable in part to large-scale structural variations between individuals. CNV is a form of structural variation as a DNA segment ≥ 1 kb in size when compared to a reference genome. Therefore, CNV was used to identify what associated with susceptibility and resistance to diseases. Genome-wide association studies (GWAS) have been used to investigate novel candidate genes associated with complex traits. Many of studies have been reported the association between SNPs or CNVs and complex diseases. Also, several GWA studies have been applied to a personalized medicine. Data mining provided important insights into the data with complicated and huge quantity. These semantic networks have given researchers knowledgeable information answers to complex questions through integration of the available data. Therefore, this thesis is to identify the genetic variation associated with liver diseases between Koreans, construct biological networks to understand the semantic knowledge about liver functions or ethnic disparities, and develop the visualization tool to explain a biological meaning for CNVs or SNPs. In chapter 1, the general background of CNV, GWAS, and biological network were summarized. First, for CNV, the general overview, mechanism sources, identification methods, various researches in human, and associations with complex diseases were presented. Second, for GWAS, the general overview, biological background, various methods, result findings, clinical application, and limitations were presented. Third, for biological network, the general overview and biological network systems were presented. In chapter 2, two parts (KARE1 and KARE2) were constituted as replication studies of GWA (genome-wide association) for hepatic biochemical markers AST or ALT in Korean cohorts. In KARE1, the analysis of CNVs in 8,842 Koreans reveals thirty-nine genes associated with hepatic biochemical markers AST (aspartate aminotransferase) and/or ALT (alanine aminotransferase). I genotyped on Affymetrix Genome-Wide Human 5.0 arrays for all samples and identified 10,162 CNVs using HelixTree software (ver. 7.0). To explain the impact of CNVs on each quantitative trait (AST or ALT), univariate linear regression was performed. As the result, 100 CNVs were significant for AST and 16 were significant for ALT at the significance level of 5%. I identified thirty-nine genes located within the significant CNV regions. According to the functional annotation by using DAVID tool, the CNV-based genes are likely to be associated with liver diseases. In KARE2, a study of GWA for hepatic biomarkers was investigated in 407 Korean cohorts. Affymetrix Genome-Wide Human 6.0 array was genotyped for all samples and CNVs were identified using HelixTree software. By using univariate linear regression, 32 and 42 CNVs showed significance for AST and ALT, respectively (p-value < 0.05). To replication study of GWA for hepatic biomarker, CNV-based genes between KARE1 (AST-1885, ALT-773) and KARE2 (AST-140, ALT-172) were compared using NetBox software. As a result, nine genes (CIDEB, DFFA, PSMA3, PSMC5, PSMC6, PSMD12, PSMF1, SDC4, and SIAH1) were overlapped for AST, yet no overlapping genes were found for ALT. Structural variation analysis of CNV-based genes is useful to understand the biological phenotypes or diseases. In chapter 3, to identify knowledgeable biological meanings for complex big data, two biological networks were constructed on liver functions or ethnic disparities using BioXM software. These semantic networks contained entities (Gene, Disease, Pathway, Chemical, Drug, SNP, CNV, ClinicalTrials, GO, drug, and SomaticMutation) and relationships between two entities (Gene-GO, Gene-Pathway, Gene-Disease, Gene-Chemical, Gene-SNP, Gene-CNV, Gene-SomaticMutation, Pathway-Chemical, Pathway-Chemical, Pathway-Disease, Chemical-Drug, ClinicalTrials-Disease, and ClinicalTrials-Drug). The application of the semantic liver functions network using the KARE2 data are shown in three clusters, including four diseases, one pathway, and seven drugs. Ethnic disparities network was constructed using the ethnic specific SNP-based genes. By eliminating the overlapped SNPs from HapMap samples, ethnic specific SNPs were identified and the SNP-based genes were mapped to the UCSC RefGene lists (ver. hg18). As a result, ethnic specific 22, 25, and 332 genes were identified in the CEU (USA), JPT (Japan), and YRI (Africa) individuals, respectively. The application of ethnic disparities network showed interesting results in the three categories, including three diseases, one drug, and five pathways. The majority of these findings were consistent with the previous studies that an understanding of genetic variability explained ethnic disparities. In chapter 4, VCS (Visualization of CNVs or SNPs) tool was constructed to visualize CNVs or SNPs detected in animals such as mammals, vertebrates, insects, and worms. VCS can easily interpret a biological meaning from the numerical value of CNVs or SNPs. The VCS provides six visualization tools: (ⅰ) the enrichment of genome contents in CNV region(ⅱ) the physical distribution of CNV or SNP on chromosomes(ⅲ) the distribution of log2 ratio of CNVs with criteria of interested(ⅳ) the number distribution of CNVs or SNPs per binning unit (10 kb, 100 kb, 1Mb, and 10Mb)(ⅴ) the homozygosity distribution of SNP genotype on chromosomesand (ⅵ) cytomap of genes within CNVs or SNPs. By GWAS analyzing between CNVs and hepatic biochemical markers AST or ALT, a lot of biological meaning associated with liver diseases in Korean cohorts could be obtained. Also, semantic biological networks for liver functions or ethnic disparities could be obtained knowledgeable findings. Finally, VCS tool could be achieved by interpreting a biological meaning from the numerical value by graphical viewing, and offered more directly insertable tip-top figures in study. Therefore, in this thesis, I analyzed replication study of GWA for hepatic biomarkers AST or ALT (Chapter 2), constructed the semantic biological networks for liver functions or ethnic disparities (Chapter 3), and developed the VCS web-tool to visualize the CNVs or SNPs (Chapter 4).ABSTRACT I CONTENTS VI LIST OF TABLES VIII LIST OF FIGURES X GENERAL INTRODUCTION XIII CHAPTER 1. LITERATURE REVIEW 1 1.1 COPY NUMBER VARIATION (CNV) 2 1.2 GENOME-WIDE ASSOCIATION STUDY (GWAS) 7 1.3 BIOLOGICAL NETWORK 14 CHAPTER 2. A REPLICATION STUDY OF GWA BETWEEN CNVS AND HEPATIC BIOMARKERS AST OR ALT IN KOREAN COHORTS 16 2.1 ABSTRACT 17 2.2 INTRODUCTION 19 2.3 MATERIALS AND METHODS 23 2.4 RESULTS 27 2.5 DISCUSSION 45 CHAPTER 3. BIOLOGICAL NETWORKS TO IDENTIFY KNOWLEDGEABLE MEANINGS FOR LIVER FUNCTIONS OR ETHNIC DISPARITIES 52 3.1 ABSTRACT 53 3.2 INTRODUCTION 55 3.3 MATERIALS AND METHODS 57 3.4 RESULTS 60 3.5 DISCUSSION 81 CHAPTER 4. VCS: TOOL FOR VISUALIZING COPY NUMBER VARIATION AND SINGLE NUCLEOTIDE POLYMORPHISM 87 4.1 ABSTRACT 88 4.2 INTRODUCTION 90 4.3 PROGRAM OVERVIEW 92 4.4 IMPLEMENTATION 109 GENERAL DISCUSSION 111 REFERENCES 113 SUPPLEMENTARY MATERIALS 133 요약(국문초록) 176Docto