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We created an online platform to record clinical and genetic information of patients with epilepsy. The platform is helping a stablished community of neurologists to integrate their findings and to share information across borders. The application is designed in such way that it will allow scalability and maintainability in the future.

EFHC1 variants are the most common mutations in inherited myoclonic and grand mal clonic-tonic-clonic (CTC) convulsions of juvenile myoclonic epilepsy (JME). We reanalyzed 54 EFHC1 variants associated with epilepsy from 17 cohorts based on National Human Genome Research Institute (NHGRI) and American College of Medical Genetics and Genomics (ACMG) guidelines for interpretation of sequence variants. We calculated Bayesian LOD scores for variants in coinheritance, unconditional exact tests and odds ratios (OR) in case–control associations, allele frequencies in genome databases, and predictions for conservation/pathogenicity. We reviewed whether variants damage EFHC1 functions, whether efhc1−/− KO mice recapitulate CTC convulsions and “microdysgenesis” neuropathology, and whether supernumerary synaptic and dendritic phenotypes can be rescued in the fly model when EFHC1 is overexpressed. We rated strengths of evidence and applied ACMG combinatorial criteria for classifying variants. Nine variants were classified as “pathogenic,” 14 as “likely pathogenic,” 9 as “benign,” and 2 as “likely benign.” Twenty variants of unknown significance had an insufficient number of ancestry-matched controls, but ORs exceeded 5 when compared with racial/ethnic-matched Exome Aggregation Consortium (ExAC) controls. NHGRI gene-level evidence and variant-level evidence establish EFHC1 as the first non–ion channel microtubule–associated protein whose mutations disturb R-type VDCC and TRPM2 calcium currents in overgrown synapses and dendrites within abnormally migrated dislocated neurons, thus explaining CTC convulsions and “microdysgenesis” neuropathology of JME. Genet Med 19 2, 144–156.

GAW20 provided a platform for developing and evaluating statistical methods to analyze human lipid-related phenotypes, DNA methylation, and single-nucleotide markers in a study involving a pharmaceutical intervention. In this article, we present an overview of the data sets and the contributions analyzing these data. The data, donated by the Genetics of Lipid Lowering Drugs and Diet Network (GOLDN) investigators, included data from 188 families (N = 1105) which included genome-wide DNA methylation data before and after a 3-week treatment with fenofibrate, single-nucleotide polymorphisms, metabolic syndrome components before and after treatment, and a variety of covariates. The contributions from individual research groups were extensively discussed prior, during, and after the Workshop in groups based on discussion themes, before being submitted for publication.

In juvenile myoclonic epilepsy, data are limited on the genetic basis of networks promoting convulsions with diffuse polyspikes on electroencephalography (EEG) and the subtle microscopic brain dysplasia called microdysgenesis.Using Sanger sequencing, we sequenced the exomes of six members of a large family affected with juvenile myoclonic epilepsy and confirmed cosegregation in all 37 family members. We screened an additional 310 patients with this disorder for variants on DNA melting-curve analysis and targeted real-time DNA sequencing of the gene encoding intestinal-cell kinase ( ICK). We calculated Bayesian logarithm of the odds (LOD) scores for cosegregating variants, odds ratios in case-control associations, and allele frequencies in the Genome Aggregation Database. We performed functional tests of the effects of variants on mitosis, apoptosis, and radial neuroblast migration in vitro and conducted video-EEG studies in mice lacking a copy of Ick.A variant, K305T (c.914A→C), cosegregated with epilepsy or polyspikes on EEG in 12 members of the family affected with juvenile myoclonic epilepsy. We identified 21 pathogenic ICK variants in 22 of 310 additional patients (7%). Four strongly linked variants (K220E, K305T, A615T, and R632X) impaired mitosis, cell-cycle exit, and radial neuroblast migration while promoting apoptosis. Tonic-clonic convulsions and polyspikes on EEG resembling seizures in human juvenile myoclonic epilepsy occurred more often in knockout heterozygous mice than in wild-type mice (P=0.02) during light sleep with isoflurane anesthesia.Our data provide evidence that heterozygous variants in ICK caused juvenile myoclonic epilepsy in 7% of the patients included in our analysis. Variant ICK affects cell processes that help explain microdysgenesis and polyspike networks observed on EEG in juvenile myoclonic epilepsy. (Funded by the National Institutes of Health and others.).

Juvenile myoclonic epilepsy (JME), the most common genetic epilepsy, remains enigmatic because it is considered one disease instead of several diseases. We ascertained three large multigenerational/multiplex JME pedigrees from Honduras with differing JME subsyndromes, including Childhood Absence Epilepsy evolving to JME (CAE/JME; pedigree 1), JME with adolescent onset pyknoleptic absence (JME/pA; pedigree 2), and classic JME (cJME; pedigree 3). All phenotypes were validated, including symptomatic persons with various epilepsies, asymptomatic persons with EEG 3.5–6.0 Hz polyspike waves, and asymptomatic persons with normal EEGs. Two‐point parametric linkage analyses were performed with 5185 single‐nucleotide polymorphisms on individual pedigrees and pooled pedigrees using four diagnostic models based on epilepsy/EEG diagnoses. Haplotype analyses of the entire genome were also performed for each individual. In pedigree 1, haplotyping identified a 34 cM region in 2q21.2–q31.1 cosegregating with all affected members, an area close to 2q14.3 identified by linkage (Z max = 1.77; pedigree 1). In pedigree 2, linkage and haplotyping identified a 44 cM cosegregating region in 13q13.3–q31.2 (Z max = 3.50 at 13q31.1; pooled pedigrees). In pedigree 3, haplotyping identified a 6 cM cosegregating region in 17q12. Possible cosegregation was also identified in 13q14.2 and 1q32 in pedigree 3, although this could not be definitively confirmed due to the presence of uninformative markers in key individuals. Differing chromosome regions identified in specific JME subsyndromes may contain separate JME disease‐causing genes, favoring the concept of JME as several distinct diseases. Whole‐exome sequencing will likely identify a CAE/JME gene in 2q21.2–2q31.1, a JME/pA gene in 13q13.3–q31.2, and a cJME gene in 17q12.

Dopaminergic and serotonergic systems have been implicated in PTSD. The present study evaluated the association of four catechol-O-methyltransferase (COMT) gene loci, and the joint effect of COMT and tryptophan hydroxylase 2 (TPH2) genes on PTSD symptoms.Subjects included 200 Caucasian Armenian adults exposed to the 1988 Spitak earthquake from 12 multigenerational (3-5 generations) families. Instruments used included the UCLA PTSD Reaction Index based on DSM-5 criteria, and the Beck Depression Inventory.The adjusted heritabilitiy of vulnerability to DSM-5 based PTSD symptoms was 0.60 (p10(-4)). There was a significant association of the COMT allele rs4633C with total PTSD (p0.03), and D category (p0.04) (negative alterations in cognitions and mood) severity scores, but not with C category (avoidance) scores. There was no genetic correlation between C and D category severity scores. COMT allele rs4633C and the TPH-2 allele rs11178997T together accounted for 7% of the variance in PTSD severity scores (p0.001). None of the COMT alleles were associated with depression.The ratings of earthquake exposure and prior trauma may have been subject to recall bias. The findings may not be generalizable to other ethnic/racial populations.COMT allele rs4633C may be causally related and/or is in linkage disequilibrium with gene(s) that are causally related to PTSD symptoms. Carriers of these COMT and the TPH-2 alleles may be at increased risk for PTSD. The findings provide biological support for dividing DSM-IV category C symptoms into DSM-5 categories C and D.

With the advance of next-generation sequencing technologies in recent years, rare genetic variant data have now become available for genetic epidemiology studies. For family samples, however, only a few statistical methods for association analysis of rare genetic variants have been developed. Rare variant approaches are of great interest, particularly for family data, because samples enriched for trait-relevant variants can be ascertained and rare variants are putatively enriched through segregation. To facilitate the evaluation of existing and new rare variant testing approaches for analyzing family data, Genetic Analysis Workshop 18 (GAW18) provided genotype and next-generation sequencing data and longitudinal blood pressure traits from extended pedigrees of Mexican American families from the San Antonio Family Study. Our GAW18 group members analyzed real and simulated phenotype data from GAW18 by using generalized linear mixed-effects models or principal components to adjust for familial correlation or by testing binary traits using a correction factor for familial effects. With one exception, approaches dealt with the extended pedigrees in their original state using information based on the kinship matrix or alternative genetic similarity measures. For simulated data our group demonstrated that the family-based kernel machine score test is superior in power to family-based single-marker or burden tests, except in a few specific scenarios. For real data three contributions identified significant associations. They substantially reduced the number of tests before performing the association analysis. We conclude from our real data analyses that further development of strategies for targeted testing or more focused screening of genetic variants is strongly desirable.

Introduced into a specific population, a juvenile myoclonic epilepsy (JME) mutation generates linkage disequilibrium (LD). Linkage disequilibrium is strongest when the JME mutation is of recent origin, still “hitchhiking” alleles surrounding it, as a haplotype into the next thousands of generations. Recombinations decay LD over tens of thousands of generations causing JME alleles to produce smaller genetic displacements, requiring other genes or environment to produce an epilepsy phenotype. Family-based linkage analysis captures rare epilepsy alleles and their “hitchhiking” haplotypes, transmitted as Mendelian traits, supporting the common disease/multiple rare allele model. Genome-wide association studies identify JME alleles whose linkage disequilibrium has decayed through thousands of generations and are sorting out the common disease/common allele versus rare allele models. Five Mendelian JME genes have been identified, namely, CACNB4 , CASR , GABRa1 , GABRD , and Myoclonin1/EFHC1. Three SNP alleles in BRD2, Cx-36, and ME2 and microdeletions in 15q13.3, 15q11.2, and 16p13.11 also contribute risk to JME. This article is part of a supplemental special issue entitled Juvenile Myoclonic Epilepsy: What is it Really?

Genetic Analysis Workshop 19 provided a platform for developing and evaluating statistical methods to analyze whole-genome sequence and gene expression data from a pedigree-based sample, as well as whole-exome sequence data from a large cohort of unrelated individuals. In this article we present an overview of the data sets, the GAW experience, and summaries of the contributions arranged into nine methodological themes.

Summary Purpose: The β3 subunit of the γ-aminobutyric acid type A receptors (GABAA–Rs) is an essential component of GABAA–Rs in fetal, perinatal, and adult mammalian brain. Various transcripts of the β3 subunit gene (GABRB3) produce various proteins with different N-termini. Rare variants in this N-terminus (exon 1A and exon 2) of GABRB3 protein segregate in affected family members of two multigeneration-multiplex families with remitting childhood absence epilepsy (rCAE), suggesting GABRB3 is a major Mendelian epilepsy gene for rare families with CAE. Therefore, the N-terminus of GABRB3 could be important for GABRB3 regulation in development, and its alteration could produce rCAE. Herein we determine if single nucleotide polymorphisms (SNPs) within the 1,148-bp region upstream from exon 1A influence the expression of GABRB3. Methods: We studied luciferase reporter expression for promoter activity, 1,148-bp upstream from exon 1A, using human embryonic kidney 293 cells. We generated constructs of the promoter region and compared different SNP haplotypes in 48 patients with rCAE. Next, we compared frequencies of rs20317, located in the core promoter region, and rs4906902, located in the enhancer region between 48 patients with rCAE and >500 healthy controls matched for ethnicity and ancestral origin. Key Findings: Highest luciferase expression occurred 230-bp upstream of exon 1A. The construct that excluded this region lost luciferase activity. Therefore, this region contains the core promoter of exon 1A. Allele C but not allele G (rs20317) significantly increased luciferase expression activity. Allele C creates binding motifs for cMYB and EGR-3. Longer constructs overlapping this region have a binding motif for REST (RE1-silencing transcription factor), a critical epigenetic modulator for neuronal genes. REST represses expression of neuronal genes in nonneuronal tissues, resulting in reduced luciferase expression activity. Even in the suppressed condition, the longer construct enhanced luciferase expression activity of the shorter construct, which excluded the distal end containing rs4906902. However, allele frequencies of rs20317 and rs4906902 were not significantly associated with 48 rCAE patients in comparison to >500 controls matched for ethnicity and ancestral origin. Significance: Common SNPs in the promoter region increase luciferase expression activity. An epigenetic modulator, REST, specifically alters expression of GABRB3 exon 1A transcripts, suggesting epigenetic regulation by REST dominantly controls the expression of GABRB3 variant 2 transcript in early life GABAA signaling. Abnormal epigenetic regulation could be involved in absence seizures.

Genotyping of rare variants on a large scale is now possible using next-generation sequencing. Sample selection is a crucial step in designing the genetic study of a complex disease, and knowledge of the efficiency and limitations of population-based and family-based designs can help researchers make the appropriate choice. The nine contributions to Group 5 of Genetic Analysis Workshop 17 evaluate population-based and family-based designs by comparing the results obtained with various methods applied to the mini-exome simulations. These simulations consisted of 200 replicates composed of unrelated individuals and eight extended pedigrees with genotypes and various phenotypes. The methods tested for association with a population-based and/or a family-based design, tested for linkage with a family-based design, or estimated heritability. We summarize the strengths and weaknesses of both designs. Although population-based designs seem more suitable for detecting the effect of multiple rare variants, family-based designs can potentially enrich the sample in rare variants, for which the effect would be concealed at the population level. However, as of today, the main limitation is still the high cost of next-generation sequencing. Genet. Epidemiol. 35:S41–S47, 2011. © 2011 Wiley Periodicals, Inc.

Juvenile myoclonic epilepsy (JME) is the most common cause of primary grand mal seizures and accounts for at least 3 to 12% of all epilepsies. JME can be inherited as a Mendelian autosomal dominant or autosomal recessive trait or as a non-Mendelian complex genetic trait. Three mutation-harboring Mendelian genes for JME have been reported. Mutations in α1 subunit of γ-aminobutyric acid receptor subtype A on chromosome 5q34 segregated with nine affected individuals of a three-generation French Canadian family with JME (Cossette et al., 2002). Mutations in a chloride-channel gene, CLCN2 on chromosome 3q26 segregated with five affected members of a three-generation German family with JME (Haug et al., 2003). Our group first mapped a JME locus in chromosome 6p12 (Liu et al., 1995, 1996; Serratosa et al., 1996; Bai et al., 2002) and identified a mutation-harboring Mendelian gene that encodes a protein with one EF-hand motif. Hence, we called the gene EFHC1. We reported one doubly heterozygous and three heterozygous missense mutations segregated in 21 clinical and electroencephalography (EEG) affected members of six unrelated two- to four-generation JME Hispanic families from California (U.S.A.) and Mexico (Suzuki et al., 2004). The 6p12 JME locus was again mapped independently by two separate groups; first, by a genome-wide linkage study of JME families from various countries of Europe (Hempelmann et al., 2006) and second by a chromosome 6p12 replication genetic linkage study in a smaller cohort of 18 Dutch families (Pinto et al., 2004). Similar and novel missense mutations in EFHC1 were reported in Caucasian JME patients from Tennessee (U.S.A.), Italy, and Austria (Ma et al., 2006; Stogmann et al., 2006; Annesi et al., 2007). Therefore the causality of the gene in a Mendelian JME has been established, but the influence of common functional single nucleotide polymorphisms (SNPs) in JME with complex genetics has not been established. Pinto et al. (2006) reported three SNPs of EFHC1 that were not associated with JME in a case-control study of 112 unrelated patients and 180 controls. In our present study, we chose the most common four coding SNPs of EFHC1 and performed both case-control and family-based association studies to determine if they contribute to the complex genetics of JME.

High-density genetic marker data, especially sequence data, imply an immense multiple testing burden. This can be ameliorated by filtering genetic variants, exploiting or accounting for correlations between variants, jointly testing variants, and by incorporating informative priors. Priors can be based on biological knowledge or predicted variant function, or even be used to integrate gene expression or other omics data. Based on Genetic Analysis Workshop (GAW) 19 data, this article discusses diversity and usefulness of functional variant scores provided, for example, by PolyPhen2, SIFT, or RegulomeDB annotations. Incorporating functional scores into variant filters or weights and adjusting the significance level for correlations between variants yielded significant associations with blood pressure traits in a large family study of Mexican Americans (GAW19 data set). Marker rs218966 in gene PHF14 and rs9836027 in MAP4 significantly associated with hypertension; additionally, rare variants in SNUPN significantly associated with systolic blood pressure. Variant weights strongly influenced the power of kernel methods and burden tests. Apart from variant weights in test statistics, prior weights may also be used when combining test statistics or to informatively weight p values while controlling false discovery rate (FDR). Indeed, power improved when gene expression data for FDR-controlled informative weighting of association test p values of genes was used. Finally, approaches exploiting variant correlations included identity-by-descent mapping and the optimal strategy for joint testing rare and common variants, which was observed to depend on linkage disequilibrium structure. peerReviewed

Non-human primates (NHP) provide crucial research models. Their strong similarities to humans make them particularly valuable for understanding complex behavioral traits and brain structure and function. We report here the genetic mapping of an NHP nervous system biologic trait, the cerebrospinal fluid (CSF) concentration of the dopamine metabolite homovanillic acid (HVA), in an extended inbred vervet monkey ( Chlorocebus aethiops sabaeus ) pedigree. CSF HVA is an index of CNS dopamine activity, which is hypothesized to contribute substantially to behavioral variations in NHP and humans. For quantitative trait locus (QTL) mapping, we carried out a two-stage procedure. We first scanned the genome using a first-generation genetic map of short tandem repeat markers. Subsequently, using >100 SNPs within the most promising region identified by the genome scan, we mapped a QTL for CSF HVA at a genome-wide level of significance (peak logarithm of odds score >4) to a narrow well delineated interval (

The 2001 classification subcommittee of the International League Against Epilepsy (ILAE) proposed to 'group JME, juvenile absence epilepsy, and epilepsy with tonic clonic seizures only under the sole heading of idiopathic generalized epilepsies (IGE) with variable phenotype'. The implication is that juvenile myoclonic epilepsy (JME) does not exist as the sole phenotype of family members and that it should no longer be classified by itself or considered a distinct disease entity. Although recognized as a common form of epilepsy and presumed to be a lifelong trait, a long-term follow-up of JME has not been performed. To address these two issues, we studied 257 prospectively ascertained JME patients and encountered four groups: (i) classic JME (72%), (ii) CAE (childhood absence epilepsy) evolving to JME (18%), (iii) JME with adolescent absence (7%), and (iv) JME with astatic seizures (3%). We examined clinical and EEG phenotypes of family members and assessed clinical course over a mean of 11 +/- 6 years and as long as 52 years. Forty per cent of JME families had JME as their sole clinical phenotype. Amongst relatives of classic JME families, JME was most common (40%) followed by grand mal (GM) only (35%). In contrast, 66% of families with CAE evolving to JME expressed the various phenotypes of IGE in family members. Absence seizures were more common in family members of CAE evolving to JME than in those of classic JME families (P < 0.001). Female preponderance, maternal transmission and poor response to treatment further characterized CAE evolving to JME. Only 7% of those with CAE evolving to JME were seizure-free compared with 58% of those with classic JME (P < 0.001), 56% with JME plus adolescent pyknoleptic absence and 62% with JME plus astatic seizures. Long-term follow-up (1-40 years for classic JME; 5-52 years for CAE evolving to JME, 5-26 years for JME with adolescent absence and 3-18 years for JME with astatic seizures) indicates that all subsyndromes are chronic and perhaps lifelong. Seven chromosome loci, three epilepsy-causing mutations and two genes with single nucleotide polymorphisms (SNPs) associating with JME reported in literature provide further evidence for JME as a distinct group of diseases.

Summary: Idiopathic generalized epilepsies (IGEs) comprise at least 40% of epilepsies in the United States, 20% in Mexico, and 8% in Central America. Here, we review seizure phenotypes across IGE syndromes, their response to treatment and advances in molecular genetics that influence nosology. Our review included the Medline database from 1945 to 2005 and our prospectively collected Genetic Epilepsy Studies (GENESS) Consortium database. Generalized seizures occur with different and similar semiologies, frequencies, and patterns, ages at onset, and outcomes in different IGEs, suggesting common neuroanatomical pathways for seizure phenotypes. However, the same seizure phenotypes respond differently to the same treatments in different IGEs, suggesting different molecular defects across syndromes. De novo mutations in SCN1A in sporadic Dravet syndrome and germline mutations in SCN1A, SCN1B, and SCN2A in generalized epilepsies with febrile seizures plus have unraveled the heterogenous myoclonic epilepsies of infancy and early childhood. Mutations in GABRA1, GABRG2, and GABRB3 are associated with absence seizures, while mutations in CLCN2 and myoclonin/EFHC1 substantiate juvenile myoclonic epilepsy as a clinical entity. Refined understanding of seizure phenotypes, their semiology, frequencies, and patterns together with the identification of molecular lesions in IGEs continue to accelerate the development of molecular epileptology.

Understanding the latest advances in the molecular genetics of the epilepsies is important, as it provides a basis for comprehending the new practice of epileptology. Epilepsies have traditionally been classified and subtyped on the basis of clinical and neurophysiologic concepts. However, the complexity and variability of phenotypes and overlapping clinical features limit the resolution of phenotype-based classification and confound epilepsy nosology. Identification of tightly linked epilepsy DNA markers and discovery of epilepsy-causing mutations provide a basis for refining the classification of epilepsies. Recent discoveries regarding the genetics surrounding certain epilepsy types (including Lafora's progressive myoclonic epilepsy, the severe myoclonic epilepsy of infancy of Dravet, and idiopathic generalized epilepsies) may be the beginning of a better understanding of how rare Mendelian epilepsy genes and their genetic architecture can explain some complexities of the common epilepsies.

Current studies of genetic influences on behavior in nonhuman primates have both expanded and confirmed studies on genetic influences on human behaviors. Many behaviors have been shown to be heritable. Most of the genetic methods have focused on candidate gene approaches, looking at associations and linkages of candidate genes identified through the human literature, with particular focus on genes in the serotonin and dopaminergic systems. An advantage of studying these systems in nonhuman primates is that it is possible to get repeated measures of expression levels of these neurotransmitters, allowing for more accurate evaluation of the effects genetic variation have on neurotransmitter activity.

To assess the prevalence of macrocephaly (head circumference [ges ]1.88 standard deviations above normative data for age and sex or >97th centile) in autism and other pervasive developmental disorders, 41 children with autism, and a comparison group of 21 children with tuberous sclerosis complex (TSC) or an unspecified seizure disorder were studied. Familiality of head circumference was also assessed from measurements of 133 first-degree relatives. Significantly higher rates of macrocephaly were found in probands with autism (12.2%) and their first-degree relatives (15.5%) when compared against a published normative sample. The incidence of macrocephaly in the comparison group of probands with TSC and seizure disorder (9.5%) and their first-degree relatives (8.3%) was higher than normative data as well, although the relation between macrocephaly and autism was more pronounced. Head circumference and extreme scores reflecting macrocephaly were moderately heritable in the present sample (H2=0.47). The increased prevalence of macrocephaly in relatives of children with autism compared with control children suggests that this characteristic may be a familial risk factor in the pathogenesis of autism.

We developed a method to identify gene x environment interactions (G x Es). To test this method in the simulated data (Problem 2, GAW11), we first identified an environmental factor (E1) that was associated with the simulated disorder. We stratified affected sibling pairs (ASPs) into two groups, those concordant for the presence of E1 and those concordant for the absence of E1. We then localized genes on chromosomes 3 and 5 using identity-by-descent (IBD) sharing rates among ASPs. Because the stratified IBD sharing rates are independent of the environmental factor if there is no G x E, we inferred the existence of a G x E near loci 3G44 and 3G45 by testing whether the proportion of ASPs sharing no alleles IBD differed among the two groups.

Evidence that the dopamine D4 receptor is a susceptibility gene in attention deficit hyperactivity disorder

Genetic Analysis Workshop 18 provided a platform for developing and evaluating statistical methods to analyze whole-genome sequence data from a pedigree-based sample. In this article we present an overview of the data sets and the contributions that analyzed these data. The family data, donated by the Type 2 Diabetes Genetic Exploration by Next-Generation Sequencing in Ethnic Samples Consortium, included sequence-level genotypes based on sequencing and imputation, genome-wide association genotypes from prior genotyping arrays, and phenotypes from longitudinal assessments. The contributions from individual research groups were extensively discussed before, during, and after the workshop in theme-based discussion groups before being submitted for publication.

A multivariate approach to affected-sib-pair analyses was performed to localize disease-susceptibility genes with a minimum number of type I errors (false positives). Using 1,155 independent affected sib pairs extracted from Problem 2A of the GAW10 data set, we were able to localize major genes (MG) 1 and 2. Using 30% of the affected-sib-pair sample (N = 337) we were able to localize MG1. False positives were not detected in either of these samples.

Specific genetic hypotheses about the mode of transmission of bipolar affective disorders were examined by performing complex segregation analyses of Old Order Amish families. The analyses were performed on 1) the total set of 42 families including 689 relatives, 2) a subset of 19 families consisting of those kindreds sharing common ancestors within three generations that contained 333 relatives, and 3) a subset of 23 more distantly related families with 356 relatives. When all 42 families were included in the analyses, the specific mode of transmission that could be distinguished was dependent upon the diagnostic scheme used in the analysis. An autosomal dominant mode of inheritance could be rejected when relatives with bipolar I, atypical bipolar, major depressive disorder, and hypomania were included as affected. When analyses included only the subset of families more closely related, an autosomal dominant inheritance model was found to be consistent with transmission of BP I disorder. It was not possible to distinguish between other transmission models with broader diagnostic schemes in this subset of families. Finally, results of analyses on the subset of more distantly related families suggest that there is a significant proportion of Old Order Amish families in which the genetic factors contributing to the expression of bipolar illness are either polygenic or oligogenic.

The effect of dichotomizing a continuous phenotype in linkage analysis of a simulated oligogenic trait is explored. We conclude that dichotomization does not in itself preclude the detection of loci which account for as little as 16% of the genetic variance of the disease. The effects of inclusion of known covariates and quantitative trait linkage analysis are also discussed. © 1995 Wiley-Liss, Inc.

The merging of psychological and genetic methodologies has led to an increasing appreciation of environmental moderators of the relationships between genotype and phenotype. Here we used a nonhuman-primate model to study the moderating effect of the mother’s genotype on the association of a dopamine D4 receptor (DRD4) gene polymorphism with juvenile impulsivity, assessed in a standardized social-challenge test. The results showed that juvenile carriers of the rare 5-repeat variant of the exon III 48-base-pair repeat polymorphism scored significantly higher in social impulsivity than juveniles homozygous for the common 6-repeat allele. In addition, juvenile genotype interacted with maternal genotype to influence impulsivity, with the highest rates of impulsivity found in variant offspring with variant mothers. These results highlight the importance of considering the genotype of the parents in studies of early experience and vulnerability genes for impulsivity-related traits.

To examine the potential contribution of the serotonin hydroxylase (TPH1 and TPH2) genes, and the serotonin transporter promoter polymorphism (5HTTLPR) to the unique and pleiotropic risk of PTSD symptoms and depressive symptoms.Participants included 200 adults exposed to the 1988 Spitak earthquake from 12 multigenerational families (3 to 5 generations). Severity of trauma exposure, PTSD, and depressive symptoms were assessed using standard psychometric instruments. Pedigree-based variance component analysis was used to assess the association between select genes and the phenotypes.After adjusting for age, sex, exposure and environmental variables, there was a significant association of PTSD symptoms with the 't' allele of TPH1 SNP rs2108977 (p0.004), explaining 3% of the phenotypic variance. This allele also showed a non-significant trend for an association with depressive symptoms (p=0.08). Also, there was a significant association of PTSD symptoms and the 't' allele of TPH2 SNP rs11178997 (p=0.03), explaining 4% of the variance. Depressive symptoms were significantly associated with the 's' allele of 5HTTLPR (p=0.03), explaining 4% of the variance.Retrospective rating of exposure may have been subject to memory failure leading to misestimation of symptom severities. Second, findings may not be generalizable to other ethnic/racial populations.To our knowledge, this is the first published report showing that variants in TPH1 and TPH2 genes constitute risk factors for PTSD symptoms. Additionally, the TPH1 gene may be associated pleiotropically with PTSD and depressive symptoms. The association of the 's' allele of 5HTTLPR polymorphism with depression adds to similar findings from case/case-control studies.

Genetic Analysis Workshop 17 (GAW17) provided a platform for evaluating existing statistical genetic methods and for developing novel methods to analyze rare variants that modulate complex traits. In this article, we present an overview of the 1000 Genomes Project exome data and simulated phenotype data that were distributed to GAW17 participants for analyses, the different issues addressed by the participants, and the process of preparation of manuscripts resulting from the discussions during the workshop.

Considerable attention has been paid to identifying genetic influences and gene-environment interactions that increase vulnerability to environmental stressors, with promising but inconsistent results. A nonhuman primate model is presented here that allows assessment of genetic influences in response to a stressful life event for a behavioural trait with relevance for psychopathology. Genetic and environmental influences on free-choice novelty seeking behaviour were assessed in a pedigreed colony of vervet monkeys before and after relocation from a low stress to a higher stress environment. Heritability of novelty seeking scores, and genetic correlations within and between environments were conducted using variance components analysis. The results showed that novelty seeking was markedly inhibited in the higher stress environment, with effects persisting across a 2-year period for adults but not for juveniles. There were significant genetic contributions to novelty seeking scores in each year (h(2) = 0.35-0.43), with high genetic correlations within each environment (rhoG > 0.80) and a lower genetic correlation (rhoG = 0.35, non-significant) between environments. There were also significant genetic contributions to individual change scores from before to after the move (h(2) = 0.48). These results indicate that genetic regulation of novelty seeking was modified by the level of environmental stress, and they support a role for gene-environment interactions in a behavioural trait with relevance for mental health.

Chronic activation of the hypothalamic-pituitary adrenal (HPA) system is a risk factor for a variety of physical and mental disorders, and yet the complexity of the system has made it difficult to define the role of genetic and environmental factors in producing long term individual differences in HPA activity. Cortisol levels in hair have been suggested as a marker of total HPA activation over a period of several months. This study takes advantage of a pedigreed nonhuman primate colony to investigate genetic and environmental influences on hair cortisol levels before and after an environmental change. A sample of 226 adult female vervet monkeys (age 3–18) living in multigenerational, matrilineal social groups at the Vervet Research Colony were sampled in a stable low stress baseline environment and 6 months after the entire colony was moved to a new facility with more frequent handling and group disturbances (higher stress environment). Variance components analysis using the extended colony pedigree was applied to determine heritability of hair cortisol levels in the two environments. Bivariate genetic correlation assessed degree of overlap in genes influencing hair cortisol levels in the low and higher stress environments. The results showed that levels of cortisol in hair of female vervets increased significantly from the baseline to the post-move environment. Hair cortisol levels were heritable in both environments (h2 = 0.31), and there was a high genetic correlation across environments (rhoG = 0.79), indicating substantial overlap in the genes affecting HPA activity in low and higher stress environments. This is the first study to demonstrate that the level of cortisol in hair is a heritable trait. It shows the utility of hair cortisol as a marker for HPA activation, and a useful tool for identifying genetic influences on long term individual differences in HPA activity. The results provide support for an additive model of the effects of genes and environment on this measure of long term HPA activity.

The objective of this study was to assess the generality of the association of DRD2 and DAT genes and Post-Traumatic Stress Disorder (PTSD) diagnosis/symptom severity. Two hundred ethnic Armenians from 12 multigenerational families exposed to the catastrophic 1988 Spitak earthquake were studied. Common polymorphisms A1/A2 alleles of the DRD2 and '9' repeat allele of DAT gene were genotyped. Heritability, association and linkage were assessed using variance component genetic analyses. After adjusting for the covariates, the heritabilities of PTSD diagnosis and B and C category symptoms were: 0.37, 0.75 and 0.39 respectively. Category D symptoms were not heritable. Neither the DRD2 nor the DAT polymorphisms explained the variation seen in PTSD diagnosis, total PTSD symptom severity, and categories B and C symptom severities. These findings contradict prior reports of positive associations between both DRD2 and DAT, and PTSD.

Mutation-containing Mendelian genes that cause monogenic epilepsies can be found by the power of large scale genome scans and linkage analyses that use large multigeneration, multiplex families, positional cloning, and high throughput sequencing. Linkage disequilibrium-based case control association studies, powered to a sufficiently large cohort (perhaps 5000–10 000 syndromically defined epilepsy cases and an equal number of controls), executed in two stages (for replication), can be performed in the future if the United States, Canadian, Mexican, South America, Central American, and European epilepsy consortia pool their cohorts. With success, antiepileptic drugs can be designed against the specific molecular defects of ‘epileptic’ Mendelian genes, as well as against single nucleotide polymorphisms (SNP)-susceptibility alleles that increase risks for non-Mendelian epilepsies.

To examine the heritabilities of symptoms of posttraumatic stress disorder (PTSD), anxiety, depression, and the shared genetic component of these symptoms among family members exposed to the 1988 Spitak earthquake in Armenia.Two hundred members of 12 multigenerational families exposed to the Spitak earthquake were studied using a battery that assessed earthquake exposure and symptoms of PTSD, anxiety, and depression. Heritabilities of these phenotypes were determined using variance component analyses and shared genetic vulnerabilities between these phenotypes were determined using bivariate analyses.Heritabilities were as follows: PTSD symptoms 41% (P0.001), anxiety symptoms 61% (P0.001), and depressive symptoms 66% (P0.001). The genetic correlation (rhog0) of PTSD symptoms with anxiety symptoms was 0.75 (P0.001) and with depressive symptoms it was 0.71 (P0.001). The genetic correlation of anxiety with depressive symptoms was 0.54 (P0.001).The heritabilities found in this multigenerational family study indicate that the genetic make-up of some individuals renders them substantially more vulnerable than others to develop symptoms of PTSD, anxiety, and depression. A large proportion of the genetic liability for PTSD, anxiety, and depression are shared. The findings offer promise for identifying susceptibility genes for these phenotypes.

KAVANAGH, KYLIE, LYNN A. FAIRBANKS, JULIA N. BAILEY, MATTHEW J. JORGENSEN, MARTHA WILSON, LI ZHANG, LAWRENCE L. RUDEL, AND JANICE D. WAGNER. Characterization and heritability of obesity and associated risk factors in vervet monkeys. Obesity. 2007;15:1666–1674. Objective: The objective was to determine the prevalence and heritability of obesity and risk factors associated with metabolic syndrome (MS) in a pedigreed colony of vervet monkeys. Design: A cross-sectional study of plasma lipid and lipoprotein concentrations, glycemic indices, and morphometric measures with heritability calculated from pedigree analysis. A selected population of females was additionally assessed for insulin sensitivity and glucose tolerance. Subjects: All mature male (n 98), pregnant (n 40) and non-pregnant female (n 157) vervet monkeys were included in the study. Seven non-pregnant females were selected on the basis of high or average glycated hemoglobin (GHb) for further characterization of carbohydrate metabolism. Measurements: Morphometric measurements included body weight, length, waist circumference, and calculated BMI. Plasma lipids [total cholesterol (TC), triglycerides (TG), high-density lipoprotein cholesterol (HDL-C)] and glycemic measures (fasting blood glucose, insulin, and GHb) were measured. A homeostasis model assessment index was further reported. Glucose tolerance testing and hyperinsulinemic-euglycemic clamps were performed on 7 selected females. Conclusion: Vervet monkeys demonstrate obesity, insulin resistance, and associated changes in plasma lipids even while consuming a low-fat (chow) diet. Furthermore, these parameters are heritable. Females are at particular risk for central obesity and an unfavorable lipid profile (higher TG, TC, and no estrogen-related increase in HDL-C). Selection of females by elevated GHb indicated impaired glucose tolerance and was associated with central obesity. This colony provides a unique opportunity to study the development of obesity-related disorders, including both genetic and environmental influences, across all life stages.

The spectacular progress in genomics increasingly highlights the importance of comparative biology in biomedical research. In particular, nonhuman primates, as model systems, provide a crucial intermediate between humans and mice. The close similarities between humans and other primates are stimulating primate studies in virtually every area of biomedical research, including development, anatomy, physiology, immunology, and behavior. The vervet monkey (Chlorocebus aethiops sabaeus) is an important model for studying human diseases and complex traits, especially behavior. We have developed a vervet genetic linkage map to enable mapping complex traits in this model organism and facilitate comparative genomic analysis between vervet and other primates. Here we report construction of an initial genetic map built with about 360 human orthologous short tandem repeats (STRs) that were genotyped in 434 members of an extended vervet pedigree. The map includes 226 markers mapped in a unique order with a resolution of 9.8 Kosambi centimorgans (cM) in the vervet monkey genome, and with a total length (including all 360 markers) of 2726 cM. At least one complex and 11 simple rearrangements in marker order distinguish vervet chromosomes from human homologs. While inversions and insertions can explain a similar number of changes in marker order between vervet and rhesus homologs, mostly inversions are observed when vervet chromosome organization is compared to that in human and chimpanzee. Our results support the notion that large inversions played a less prominent role in the evolution within the group of the Old World monkeys compared to the human and chimpanzee lineages.

The association of novelty seeking with a repeat polymorphism in the coding region of the dopamine D4 receptor gene (DRD4) has been demonstrated in several human populations, but not in others. The objective of this study was to test the generality of the association in a captive nonhuman primate population of known history, using objective methods for assessing novelty seeking and a pedigree-based association design.Four hundred and fifty two socially-living vervet monkeys (Cercopithecus aethiops) from a large multigenerational pedigree at the UCLA-VA Vervet Research Colony were studied. Two variants in the 48 base pair repeat in exon III of the DRD4 gene have been found in this population, a six-repeat (92%) and a less common five-repeat (8%). Novelty seeking was measured by the latency to approach a large and potentially threatening novel object placed in the home enclosure. Heritability of novelty seeking and the association of novelty seeking with the DRD4 polymorphism were assessed using variance component modeling as implemented in Sequential Oligogenic Linkage Analysis Routines.The variance component analysis indicated that the DRD4 variant explained a significant portion of the total variance in novelty seeking. The final model included a significant effect of the DRD4 polymorphism (P=0.03), which explained 13% of the phenotypic variance, and a significant remaining genetic effect (h=0. 467+/-0.095, P0.0001).The association of DRD4 with novelty seeking has now been replicated in a nonhuman primate species, the vervet monkey.

Juvenile myoclonic epilepsy (JME) is a distinct form of idiopathic generalized epilepsy (IGE). One of the candidate regions for human JME has been mapped on chromosome band 6p11-p12 by linkage analyses and is termed EJM1 (MIM 254770). Recently, we reported the reduction of the EJM1 region to 3.5cM that contains 18 genes, the exclusion of three genes (LRRC1, GCLC, KIAA0057) by mutation analyses, and the identification of Myoclonin1/EFHC1 as the EJM1 gene. Here, we describe detailed physical and transcriptome maps of the 3.5cM EJM1 region, and detailed results of mutation analyses for the remained 14 genes (HELO1, GCMA, KIAA0936, FBXO9, GSTA3, GSTA4, PTD011, KIAA0576, LMPB1, IL17F, MCM3, PKHD1, KIAA0105, TFAP2B) in patients with JME. We identified 49 single nucleotide changes in eight genes. Twelve amino acid substitutions occurred in two genes, 11 silent mutations in seven genes, and 26 in the non-coding or intronic regions of seven genes. Twelve amino acid substitutions in the two genes (IL17F, PKHD1) were also observed in healthy control individuals or did not co-segregate with the disease phenotypes in other family members. Thus, the absence of significant and potentially functional mutations in the remaining 14 genes further supports the concept that Myoclonin1/EFHC1 is the EJM1 gene in chromosome 6p12.

The purpose of these analyses was to determine if incorporating or adjusting for covariates in genetic analyses helped or hindered in genetic analyses, specifically heritability and linkage analyses. To study this question, two types of covariate models were used in the simulated Genetic Analysis Workshop 14 dataset in which the true gene locations are known. All four populations of one replicate were combined for the analyses. The first model included typical covariates of sex and cohort (population) and the second included the typical covariates and also those related endophenotypes that are thought to be associated with the trait (phenotypes A, B, C, D, E, F, G, H, I, J, K, and L). A final best fit model produced in the heritability analyses was used for linkage. Linkage for disease genes D1, D3, and D4 were localized using models with and without the covariates. The use of inclusion of covariates did not appear to have any consistent advantage or disadvantage for the different phenotypes in regards to gene localization or false positive rate.

Juvenile myoclonic epilepsy (JME) is the most frequent cause of hereditary grand mal seizures. We previously mapped and narrowed a region associated with JME on chromosome 6p12-p11 (EJM1). Here, we describe a new gene in this region, EFHC1, which encodes a protein with an EF-hand motif. Mutation analyses identified five missense mutations in EFHC1 that cosegregated with epilepsy or EEG polyspike wave in affected members of six unrelated families with JME and did not occur in 382 control individuals. Overexpression of EFHC1 in mouse hippocampal primary culture neurons induced apoptosis that was significantly lowered by the mutations. Apoptosis was specifically suppressed by SNX-482, an antagonist of R-type voltage-dependent Ca(2+) channel (Ca(v)2.3). EFHC1 and Ca(v)2.3 immunomaterials overlapped in mouse brain, and EFHC1 coimmunoprecipitated with the Ca(v)2.3 C terminus. In patch-clamp analysis, EFHC1 specifically increased R-type Ca(2+) currents that were reversed by the mutations associated with JME.

Background Impulsivity contributes to multiple psychiatric disorders and sociobehavioral problems, and the more serious consequences of impulsivity are typically manifest in social situations. This study assessed the genetic contribution to impulsivity and aggressiveness in a social context using a nonhuman primate model. Methods Subjects were 352 adolescent and adult vervet monkeys from an extended multigenerational pedigree. Behavior was assessed in the Intruder Challenge Test, a standardized test that measures impulsivity and aggressiveness toward a stranger. Genetic and maternal contributions to variation in the Social Impulsivity Index and its two subscales, impulsive approach and aggression, were estimated using variance components analyses. Results The results found significant genetic contributions to social impulsivity (h 2 = .35 ± .11) and to each of the subscales, with no significant influence of maternal environment. There was a high genetic correlation between the impulsive approach and aggression subscales (rho = .78 ± .12). Conclusions This is the first study to demonstrate heritability of social impulsivity in adolescents and adults for any nonhuman primate species. The high genetic correlation suggests the same genes may influence variation in both impulsive approach and aggression. These results provide a promising basis for identification of susceptibility loci for impulsivity and aggressiveness.

Juvenile myoclonic epilepsy is a common subtype of idiopathic epilepsy accounting for 4-11% of all epilepsies. We reported previously significant evidence of linkage between chromosome 6p12-11 microsatellites and the clinical epilepsy and EEG traits of JME families from Belize and Los Angeles. To narrow the JME region, we ascertained and genotyped 31 new JME families from Mexico using a later generation of Genethon microsatellites. Two point linkage analyses obtained significant Z(max) values of 3.70 for D6S1573 and 2.65 for D6S1714 at theta(m = f) = 0.10, and 3.49 for D6S465, 2.11 for D6S1960 at theta(m = f) = 0.05 assuming autosomal dominant inheritance with 70% age-dependent penetrance. Multipoint LOD score curve peaked at 4.21 for D6S1573. Haplotype and recombination analysis reduced the JME region to 3.5 cM flanked by D6S272 and D6S1573. These results provide confirmatory evidence that a major susceptibility gene for JME exists in chromosome 6p12 in Spanish-Amerinds of Mexico.

We develop regression methodology to identify subsets of single nucleotide polymorphisms (SNPs) within candidate genes related to quantitative traits and apply our methods to the simulated Genetic Analysis Workshop (GAW) 12 data set. In the data set we find 694 SNP loci with minimum allele frequencies of at least 0.01. We assume an additive casual model between these SNPs and all five quantitative traits. After initial screening using one-way analysis of variance, we employ a computationally efficient, simulated annealing algorithm to select among all possible subsets of SNP loci, using a generalization of Mallows' Cp as our optimality criterion. The simple transition kernel we develop evaluates new subsets in O(1), by requiring just three arithmetic operations to calculate the proposed RSS based on the Gauss-Jordan pivot. We identify an SNP loci located at 6-5782 related to traits 2 and 3 and several sites on gene 2 related to trait 5 using a subsample of 1,000 individuals and the full data set (n = 8,250) for comparison.

Tuberous sclerosis complex (TSC) is an autosomal dominant disorder (OMIM 191092) characterised by autism, seizures, mental retardation, benign tumours of the brain, heart, kidney, lung, and skin, and malignant tumours of the kidney.1 TSC has a wide range of phenotypic variability, with some subjects severely affected and others only mildly affected. There are two TSC genes, TSC1 on chromosome 9q342 and TSC2 on chromosome 16p13.3Approximately two thirds of cases of TSC appear to result from de novo germline mutations. In 1994, an extended four generation family with 19 affected members was reported in which 34 members (17 affected with TSC and 17 unaffected) underwent both physical and psychiatric assessments.4 The majority of the affected subjects had mild physical expression of TSC, but there was significant clustering of neuropsychiatric disorders among affected subjects compared with their unaffected relatives. The disorders that were over-represented included mood disorder, anxiety disorder, and autism. The largest difference was observed in anxiety disorder, which was seen in 10 of the affected subjects and in two of the unaffected subjects (p=0.016). One affected child had pervasive developmental disorder and one had autism. Analysis of this family suggested that TSC could present phenotypically with mild physical signs and symptoms, but with significant neuropsychiatric disease. Linkage to the TSC2 gene locus on chromosome 16p13.3 was shown with a lod score of over 3.4 We report here the identification of a missense mutation in exon 34 of the TSC2 gene in affected members of this family. We also examined a second four generation family5from the same geographical area as the …

many of the milder forms of epilepsy, the genetic contribution is made up of many factors that each contributes little to the disease risk. This is called multifactorial inheritance. Juvenile myoclonic epilepsy (JME) is thought to be inherited in amultifactorial mode. So, while genetic factors are largely to blame for the condition, we encountermany sporadic cases, in addition to families with multiple affected members with JME and families with both JME and other forms of epilepsy. Genetic research is aimed at finding genetic factors that contribute to disease risk. If the genetic factor has a large effect, genetic testing can be used for diagnosis and prognosis and, maybe, for treatment. In multifactorial disorders, such as JME, the aims are more fundamental: understanding the biology of the disorder by placing the genes that contribute in a network that makes sense. The quality of the research into multifactorial traits depends on many factors: first, a correct diagnosis; next, knowledge of ethnicity of the patients and the healthy people we used to compare them with; and, finally, the quality of the lab work and the statistical analysis. In this talk, I will discuss what is known about the multifactorial genetics of JME and what is done to move forward. I will dedicate time to the question as to why knowledge of ethnicity is important in this type of studies.

ss Open Acce Introduction Genetic Analysis Workshop 14: microsatellite and single-nucleotide polymorphism marker loci for genome-wide scans Joan E Bailey-Wilson*1, Laura Almasy2, Mariza de Andrade3, Julia Bailey4, Heike Bickeboller5, Heather J Cordell6, E Warwick Daw7, Lynn Goldin8, Ellen L Goode9, Courtney Gray-McGuire10, Wayne Hening11, Gail Jarvik12, Brion S Maher13, Nancy Mendell14, Andrew D Paterson15, John Rice16, Glen Satten17, Brian Suarez16, Veronica Vieland18, Marsha Wilcox19, Heping Zhang20, Andreas Ziegler21 and Jean W MacCluer2

Amongst idiopathic generalized epilepsies, juvenile myoclonic epilepsy (JME) is the most common, accounting for 12 to 30% of all epilepsies in the Western world. 'Classic' JME consists of awakening myoclonias, grand mal convulsions and EEG 4 to 6 Hz polyspike waves that appear in adolescence. Probands and affected family members do not have pyknoleptic 3Hz spike and wave absences. However, in 10 to 30% of patients, rare or spanioleptic polyspike wave absences appear. In 1988, 1995 and 1996, we mapped 'classic' JME to a 7 cM locus in chromosome 6p12-11, called EJM1, using families from Los Angeles and Belize. In 2001, we studied one large family from Belize and 21 new families from Los Angeles and Mexico cities, aided by a BAC/PAC based physical map and six new dinucleotide repeats, to narrow EJM1 to an interval between D6S272 and D6S1573. In 2002, we found myoclonin, the putative gene for typical JME in 6p12. At the congress, we will reveal the identity of the myoclonin gene, its putative function and discuss the significance of this discovery in the JME population at large.