Genetic analysis of a candidate region for psychiatric illness on chromosone 4p

Psychiatric illnesses are debilitating conditions for those affected and place a significant burden on the National Health Service, the social services and the family. Here I describe genetic analysis, physical mapping and transcript mapping of a region of chromosome 4p that is linked to psychiatric illness, including bipolar and unipolar affective disorders and schizophrenia.I have studied four families that show linkage of psychiatric illness to chromosome 4p. Linkage was first observed in a large family, F22, segregating bipolar affective disorder (BPAD) and recurrent major depression (RMD). Subsequently, a smaller family, F59, segregating affective disorders (Blackwood et al, 1996a), and two families (F50 & F48) segregating schizophrenia (SCZ), schizoaffective disorder and BPAD confirmed this linkage.Previously, comparison of the haplotypes inherited with illness in each family allowed prioritisation of two sub-regions for detailed study. Minimal Region One (MR1) is defined by overlap of the disease chromosomes from three Celtic families (F22, F59 & F50). Minimal Region Two (MR2) is defined by the two largest families F22 and F48, as well as F50. The sequence available from the human genome sequencing project for these two regions is largely complete. Here, I describe an extension to the BAC map in the repetitive telomeric end of MR1. The telomeric end of MR1 is defined by a recombination event in an individual from F50. I mapped clones, designed markers and refined the position of the recombination breakpoint. I also refined the position of the recombination breakpoint at the centromeric end of MR1, as defined by a member of F59.I describe construction of a transcript map of MR land 2 using bioinformatics methods, RT-PCR and cDNA library screening. I then selected two candidate genes from this region: orphan g-protein-coupled receptor 78 (GPR78) and superoxide dismutase 3 (SOD3), for further study. Firstly, I identified SNPs in the genes from the linked families, and then carried out a preliminary association study on 95 SCZ in patients, 93 BPAD patients 95 controls. The linkage disequilibrium (LD) between the markers was measured and, using a low stringency significant p-value cut off, revealed a positive association in GPR78. SNPs were then tested on a larger population for association. This work adds to the case for studying the role of chromosome 4 in the genetic susceptibility to affective disorder

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

The XVth World Congress of Psychiatric Genetics, October 7–11, 2007: Rapporteur summaries of oral presentations

The World Congress of Psychiatric Genetics (WCPG) has become an annual event since the early 1990's sponsored by the International Society of Psychiatric Genetics (ISPG). Each year the latest published and unpublished findings are aired for discussion by representatives of the majority of research programs on this topic world-wide. The 2007 congress was held in New York City and attracted over 1000 researchers. The topics emphasized included results from whole genome association studies, the significance of copy number variation and the important contributions of epigenetic events to psychiatric disorders. There were over 20 oral sessions devoted to these and other topics of interest. Young investigator recipients of travel awards served as rapporteurs to summarize sessions and these summaries follow.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/58040/1/30711_ftp.pd

Investigating genome-wide transcriptional and methylomic consequences of a balanced t(1;11) translocation linked to major mental illness

Schizophrenia, bipolar disorder and major depressive disorder are devastating psychiatric conditions with a complex, overlapping genetic and environmental architecture. Previously, a family has been reported where a balanced chromosomal translocation between chromosomes 1 and 11 [t(1;11)] shows significant linkage to these disorders. This translocation transects three genes: Disrupted in schizophrenia- 1 (DISC1) on chromosome 1, a non-coding RNA, Disrupted in schizophrenia-2 (DISC2) antisense to DISC1, and a non-coding transcript, DISC1 fusion partner-1 (DISC1FP1) on chromosome 11, all of which could result in pathogenic properties in the context of the translocation. This thesis focuses on the genome-wide effects of the t(1;11) translocation, primarily examining differences in gene expression and DNA methylation, using various biological samples from the t(1;11) family. To assess the genome-wide effects of the t(1;11) translocation on methylation, DNA methylation was profiled in whole-blood from 41 family members using the Infinium HumanMethylation450 BeadChip. Significant differential methylation was observed within the translocation breakpoint regions on chromosomes 1 and 11. Downstream analysis identified additional regions of differential methylation outwith these chromosomes, while pathway analysis showed terms related to psychiatric disorders and neurodevelopment were enriched amongst differentially methylated genes, in addition to more general terms pertaining to cellular function. Using induced pluripotent stem cell (iPSC) technology, neuronal samples were developed from fibroblasts in a subset of individuals profiled for genome-wide methylation in whole blood (N = 6) with an aim to replicate the significant findings around the breakpoint regions. Here, methylation was profiled using the Infinium HumanMethylation450 BeadChip’s successor: the Infinium MethylationEPIC BeadChip. The results from the blood-based study failed to replicate in the neuronal samples, which could be attributed to low statistical power or tissue-specific factors such as methylation quantitative trait loci. The differences in methylation in the most significantly differentially methylated loci were found to be driven by a single individual, rendering further interpretation of the findings from this analysis difficult without additional samples. Cross-tissue analyses of DNA methylation were performed on blood and neuronal DNA from these six individuals, revealing little correlation between cell types. DISC1 is central to a network of interacting protein partners, including the transcription factor ATF4, and PDE4; both of which are associated with the cAMP signalling pathway. Haploinsufficiency of DISC1 due to the translocation may therefore be disruptive to cAMP-mediated gene expression. In order to identify transcriptomic effects which may be related to the t(1;11) translocation, genome-wide expression profiling was performed in lymphoblastoid cell line RNA from 13 family members. No transcripts were found to be differentially expressed at the genome-wide significant level. A post-hoc power analysis suggested that more samples would be required in order to detect genome-wide significant differential expression. However, imposing a fold-change cut-off to the data identified a number of candidate genes for follow-up analysis, including SORL1: a member of the brain-expressed Sortilin gene family. Sortilin genes have been linked to multiple psychiatric disorders including schizophrenia, bipolar disorder and Alzheimer’s disease. Follow-up analyses of Sortilin family members were performed in a Disc1 mouse model of schizophrenia, containing an amino acid substitution (L100P). Here, developmental gene expression profiling was performed with an additional aim to optimise and validate work performed by others using this mouse model. However, results from these experiments were variable between two independent batches mice tested. Additional investigation of Sortilin family genes was performed using GWAS data from human samples, using machine learning techniques to identify epistatic interactions linked to depression and brain function, revealing no statistically significant interactions. The results presented in this thesis suggest a potential mechanism for differential DNA methylation in the context of chromosomal translocations, and suggests mechanisms whereby increased risk of illness is conferred upon translocation carriers through dysregulation of transcription and DNA methylation

Design and application of SuRFR: an R package to prioritise candidate functional DNA sequence variants

Genetic analyses such as linkage and genome wide association studies (GWAS) have been extremely successful at identifying genomic regions that harbour genetic variants contributing to complex disorders. Over 90% of disease-associated variants from GWAS fall within non-coding regions (Maurano et al., 2012). However, pinpointing the causal variants has proven a major bottleneck to genetic research. To address this I have developed SuRFR, an R package for the ranked prioritisation of candidate causal variants by predicted function. SuRFR produces rank orderings of variants based upon functional genomic annotations, including DNase hypersensitivity signal, chromatin state, minor allele frequency, and conservation. The ranks for each annotation are combined into a final prioritisation rank using a weighting system that has been parametrised and tested through ten-fold cross-validation. SuRFR has been tested extensively upon a combination of synthetic and real datasets and has been shown to perform with high sensitivity and specificity. These analyses have provided insight into the extent to which different classes of functional annotation are most useful for the identification of known regulatory variants: the most important factor for identifying a true variant across all classes of regulatory variants is position relative to genes. I have also shown that SuRFR performs at least as well as its nearest competitors whilst benefiting from the advantages that come from being part of the R environment. I have applied SuRFR to several genomics projects, particularly the study of psychiatric illness, including genome sequencing of a large Scottish family with bipolar disorder. This has resulted in the prioritisation of such variants for future study

Role of the Y chromosome in sex differences in ADHD and schizophrenia

ADHD and schizophrenia are neurodevelopmental disorders that are more prevalent in males and show sex differences in age of onset or severity. The Y chromosome is potentially an important influence on male susceptibility to neuropsychiatric disorders. The way the Y chromosome could increase risk to neuropsychiatric disorders is directly or indirectly by interacting with autosomal genes expressed in the brain. In addition, it could modify the disease phenotype. However, due to difficulties arising from the lack of recombination and widely accepted nomenclature, the Y chromosome has been largely excluded from genetic and genomic studies of neuropsychiatric disorders. To overcome this lack of knowledge, 9 Y chromosome markers were selected to represent the main Y chromosome haplogroups that are present in the U.K. and they were genotyped in a sample of 210 cases with ADHD, 313 cases with schizophrenia and 637 U.K. controls. Statistical analysis of Y chromosome haplogroups revealed that although there was no significantly increased representation of any haplogroup in cases with ADHD or schizophrenia compared to controls, there was evidence of a possible modifying effect on the phenotype of ADHD and schizophrenia. Y chromosome haplogroup 3 was associated with higher performance and full scale IQ within the sample of patients with ADHD. Haplogroup 1 was associated with better outcome and higher educational level within the sample of patients with schizophrenia. There was no association of Y chromosome haplogroups with IQ in a population sample of 3,749 individuals. Y chromosome haplogroups were also tested for interaction with tyrosine hydroxylase SNPs because animal studies suggest this is biologically plausible. Although there was no evidence of interaction, three tyrosine hydroxylase SNPs showed nominally significant association in the sample of male patients with schizophrenia. This study is one of the largest Y chromosome studies in the UK. It suggests that although Y chromosome variation does not appear to be associated with ADHD or schizophrenia, it may modify cognitive performance and clinical features

Genetic Heterogeneity in Autism Spectrum Disorders in a Population Isolate

Positional cloning has enabled hypothesis-free, genome-wide scans for genetic factors contributing to disorders or traits. Traditionally linkage analysis has been used to identify regions of interest, followed by meticulous fine mapping and candidate gene screening using association methods and finally sequencing of regions of interest. More recently, genome-wide association analysis has enabled a more direct approach to identify specific genetic variants explaining a part of the variance of the phenotype of interest. Autism spectrum disorders (ASDs) are a group of childhood onset neuropsychiatric disorders with shared core symptoms but varying severity. Although a strong genetic component has been established in ASDs, genetic susceptibility factors have largely eluded characterization. Here, we have utilized modern molecular genetic methods combined with the advantages provided by the special population structure in Finland to identify genetic risk factors for ASDs. The results of this study show that numerous genetic risk factors exist for ASDs even within a population isolate. Stratification based on clinical phenotype resulted in encouraging results, as previously identified linkage to 3p14-p24 was replicated in an independent family set of families with Asperger syndrome, but no other ASDs. Fine-mapping of the previously identified linkage peak for ASDs at 3q25-q27 revealed association between autism and a subunit of the 5-hydroxytryptamine receptor 3C (HTR3C). We also used dense, genome-wide single nucleotide polymorphism (SNP) data to characterize the population structure of Finns. We observed significant population substructure which correlates with the known history of multiple consecutive bottle-necks experienced by the Finnish population. We used this information to ascertain a genetically homogenous subset of autism families to identify possible rare, enriched risk variants using genome-wide SNP data. No rare enriched genetic risk factors were identified in this dataset, although a subset of families could be genealogically linked to form two extended pedigrees. The lack of founder mutations in this isolated population suggests that the majority of genetic risk factors are rare, de novo mutations unique to individual nuclear families. The results of this study are consistent with others in the field. The underlying genetic architecture for this group of disorders appears highly heterogeneous, with common variants accounting for only a subset of genetic risk. The majority of identified risk factors have turned out to be exceedingly rare, and only explain a subset of the genetic risk in the general population in spite of their high penetrance within individual families. The results of this study, together with other results obtained in this field, indicate that family specific linkage, homozygosity mapping and resequencing efforts are needed to identify these rare genetic risk factors.Paikkaan perustuva geenitunnistus eli positionaalinen kloonaus on mahdollistanut hypoteesittomat, koko perimän kattavat tutkimukset joilla voidaan kartoittaa tauteihin ja ominaisuuksiin vaikuttavia perinnöllisiä tekijöitä vaikka tautia aiheuttavia biologisia prosesseja ei tunneta. Modernit molekyyligenetiikan menetelmät ovat mahdollistaneet tiheät, jopa miljoonan geenimerkin kattavat tutkimukset, joilla voidaan tutkia perimän vaihtelua yksilötasolla tarkemmin kuin koskaan aikaisemmin. Suomalainen väestö on geneettisesti yhtenäinen, ja sitä ovat muokanneet perustajavaikutus, genettiset pullonkaulat ja sattuma. Suomalaisen väestön erityispiirteitä voidaan käyttää hyväksi tunnistettaessa riskigeenejä sairauksille. Verrattuna sekaväestöihin tautien riskigeenen kirjo on Suomessa mahdollisesti suppeampi, sillä maamme alkuperäiset asuttajat toivat mukanaan vain osan kaikista mahdollisista geneettisistä riskitekijöistä. Autismikirjon sairaudet ovat ryhmä vakavuudeltaan vaihtelevia, lapsuudessa alkavia neuropsykiatrisia sairauksia. Vaikka perintötekijöiden on todettu vaikuttavan vahvasti autismikirjon sairauksien syntyyn, aktiivisesta tutkimuksesta huolimatta ei sairauksille altistavia geenimuotoja vielä ole tunnistettu kuin kourallinen. Autismikirjon sairauksien tiedetään kuitenkin olevan ns. monitekijäisiä tauteja, eli niille altistavat sekä lukuisat geenivirheet että vielä tuntemattomat ympäristötekijät. Tässä tutkimuksessa olemme käyttääneet molekyyligenetiikan uusimpia menetelmiä hyödyntäen samalla suomalaisen väestön erityispiirteitä tunnistaaksemme näille sairauksille altistavia perinnöllisiä tekijöitä. Tämän väitöskirjatutkimuksen tulokset osoittavat, että autismikirjon sairauksille altistavat useat eri geenimuodot jopa Suomen kaltaisessa väestöisolaatissa. Vaikka tutkimuksessa löydettiin viitteitä myös yleisten geenimuotojen, kuten serotoniinreseptorin alayksikön HTR3C:n roolista autismin synnyssä, perustajamutaatioiden puute väestössämme osoittaa vahvasti, että autismikirjon perinnöllisistä riskitekijöistä suurin osa on uusia mutaatioita. Nämä harvinaiset mutaatiot selittävät vain pienen osan riskiä väestötasolla, mutta vaikuttavat merkittävästi yksittäisten perheiden riskiin. Autismin geneettisten riskitekijöiden tutkimuksissa tulisi jatkossa pääasiallisesti hyödyntää kytkentä-, homozygotiakartoitus- ja sekvenssianalyysiin perustuvia menetelmiä, joilla voidaan tutkia yksittäisten perheiden alttiusgeenejä, eikä pyrkiä tutkimaan väestössä yleisesti esiintyviä geenimuotoja

Autism Spectrum Disorders

Estimated prevalence rates of autism spectrum disorders (ASDs) have increased at an alarming rate over the past decade; current estimates stand as high as 1 in 110 persons in the population with a higher ratio of affected males to females. In addition to their emotional impact on the affected persons and their family members (in fact, the latter are often unrecognized unaffected “patients†themselves), the economic and social impacts of ASDs on society are staggering. Persons with ASDs will need interdisciplinary approaches to complex treatment and life planning, including, but not limited to, special education, speech and language therapy, vocational skills training and rehabilitation, social skills training and cognitive remediation, in addition to pharmacotherapy. The current book highlights some of the recent research on nosology, etiology, and pathophysiology. Additionally, the book touches on the implications of new research for treatment and genetic counseling. Importantly, because the field is advancing rapidly, no book can be considered the final word or finished product; thus, the availability of open access rapid publication is a mechanism that will help to assure that readers remain current and up-to-date