The purpose of this pilot study was to investigate a measure of motor sequencing deficit as a potential endophenotype of speech sound disorder (SSD) in a multigenerational family with evidence of familial SSD.
In a multigenerational family with evidence of a familial motor-based SSD, affectation status and a measure of motor sequencing during oral motor testing were obtained. To further investigate the role of motor sequencing as an endophenotype for genetic studies, parametric and nonparametric linkage analyses were conducted using a genome-wide panel of 404 microsatellites.
In seven of the ten family members with available data, SSD affectation status and motor sequencing status coincided. Linkage analysis revealed four regions of interest, 6p21, 7q32, 7q36, and 8q24, primarily identified with the measure of motor sequencing ability. The 6p21 region overlaps with a locus implicated in rapid alternating naming in a recent genome-wide dyslexia linkage study. The 7q32 locus contains a locus implicated in dyslexia. The 7q36 locus borders on a gene known to affect component traits of language impairment.
Results are consistent with a motor-based endophenotype of SSD that would be informative for genetic studies. The linkage results in this first genome-wide study in a multigenerational family with SSD warrant follow-up in additional families and with fine mapping or next-generation approaches to gene identification.
speech sound disorder; multigenerational family; genome-wide linkage analysis; sequential motor speech task; 6p21; 7q32; 7q36; 8q24
Epidemiological and clinical studies suggest that rates of antisocial behavior, depression, and impulsive substance use are increased among individuals diagnosed with alcohol dependence relative to those who are not. Thus, the present study conducted genome-wide linkage scans of antisocial behavior, depression, and impulsive substance use in the University of California at San Francisco Family Alcoholism Study.
Antisocial behavior, depressive symptoms, and impulsive substance use were assessed using three scales from the MMPI-2, the Antisocial Practices content scale (ASP), the Depression content scale (DEP), and the revised MacAndrew Alcoholism scale (MAC-R). Linkage analyses were conducted using a variance components approach.
Suggestive evidence of linkage to three genomic regions independent of alcohol and cannabis dependence diagnostic status was observed: the ASP scale showed evidence of linkage to chromosome 13 at 11 cM, the MAC-R scale showed evidence of linkage to chromosome 15 at 47 cM, and all 3 scales showed evidence of linkage to chromosome 17 at 57–58 cM.
Each of these regions has shown prior evidence of linkage and association to substance dependence as well as other psychiatric disorders such as mood and anxiety disorders, ADHD, and schizophrenia thus suggesting potentially broad relations between these regions and psychopathology.
Genetic Linkage; Depressive Symptoms; Antisocial Practices; Substance Use Disorders; MMPI-2
The choice of phenotype definitions for genetic studies of panic and phobic disorders is complicated by family, twin and neurobiological data indicating both distinct and shared risk factors as well as heterogeneity within categories. We previously reported a genome scan in 120 multiplex panic disorder (PD) families using a phenotype that closely adhered to the DSM IV PD definition. Here we extend this work by conducting exploratory linkage analyses in this same pedigree set using ten additional literature- based panic and phobia-related phenotypes that take into account aspects of these hypothesized complexities.
Multiply affected families (> 2 individuals with PD) were recruited from clinical and non-clinical sources, evaluated by clinician administered semi-structured interview and subsequent blind consensus best estimate procedure. Each phenotype was analyzed under dominant and recessive models using parametric 2-point (homogeneity and heterogeneity), multipoint, and non-parametric methods. Empirically based permutations were used to estimate model specific and global (across all phenotypes) p-values.
The highest score was a 2-point lod (4.27, global p < 0.08) on chromosome 13 (D13S793, 76cM) for the phenotype “specific or social phobia” under a recessive model and conditions of homogeneity. There was minimal support for linkage to any of the remaining nine phenotypes.
Though interpretation of findings is limited by sample size and the large number of phenotypes and models analyzed these data suggest a region on chromosome 13 as a potential site for further exploration in relation to risk for specific and social phobias.
panic; linkage; anxiety; specific phobia; social phobia; phenotype
STriatal-Enriched protein tyrosine Phosphatase (STEP) is a brain-specific member of the PTP family that has been implicated in learning and memory. In this study, we examined the association of the PTPN5 (protein-tyrosine-phosphatase non-receptor 5) gene, which encodes for STEP, with both schizophrenia and cognitive functioning in the Israeli Jewish population.
A 868 subjects schizophrenia (SZ) case-control study was performed (286 cases and 582 controls). Eleven STEP tagging SNPs were selected, and single markers and haplotypes association analyses were performed. A cognitive variability study included 437 healthy females who completed a computerized cognitive battery. We performed univariate associations between the SNPs and cognitive performance. The possible functional role of these variants was examined by studying their association with gene expression levels in the brain.
In the SZ study, we found nominal association in the whole sample between rs4075664 and SZ. SZ males showed a more significant association for 3 SNPs (rs4075664, rs2278732, rs4757710). Haplotypes of the studied SNPs were associated with SZ both in the overall sample and within the male sub-sample. Expression analysis provided some support for the effects of the associated SNPs on PTPN5 expression level. The cognitive variability study showed positive associations between PTPN5 SNPs and different cognitive subtests. Principal component analysis demonstrated an “Attention Index” neurocognitive component that was associated with two SNP pairs (rs10832983*rs10766504 and rs7932938*rs4757718).
The results imply a model in which PTPN5 may play a role in normal cognitive functioning and contributes to aspects of the neuropathology of schizophrenia.
schizophrenia; PTPN5; psychiatric genetics; cognitive function; association study
Childhood-onset schizophrenia (COS) is a rare severe form of schizophrenia that may have greater salient genetic risk. Despite evidence for high heritability, conclusive genetic causes of schizophrenia remain elusive. Recent genomic technologies in concert with large case-control cohorts, have led to several associations of highly penetrant rare copy number variants (CNVs) and schizophrenia. We previously reported two patients with COS who carried a microduplication disrupting the PXDN and MYT1L genes at 2p25.3. This is a significantly higher rate of duplications within our COS population (N=92) when compared to 2,026 healthy controls (p=0.002). As a replication, we report a meta-analysis of four recently published studies that together provide strong evidence for association between variably-sized microduplications involving the MYT1L gene and schizophrenia. None have reported this separately. Altogether, among 5,325 cases and 9,279 controls, 10 microduplications were observed; 9 in cases and 1 in a control (OR=15.7, p=0.001). Further, the 2% rate observed in our COS patients is also significantly higher than the rate in adult onset cases (0.14%, OR=16.6, p=0.01). This report adds to the growing body of literature implicating rare CNVs as risk factors for schizophrenia, and that some risk CNVs are more common among extreme early-onset cases.
CNV; childhood-onset schizophrenia; 2p25.3; MYT1L; PXDN; 1M Illumina SNP microarray
Slight perturbations in maternal sex steroid production and metabolism may interfere with normal fetal neurodevelopment. The balance of maternal estrogens and androgens may have direct fetal effects, may influence the fetal hypothalamic-pituitary-gonadal axis or may alter local hormonal activity within the fetal brain. We investigated maternal functional polymorphisms of CYP17, CYP19 and CYP1B1, which control three major enzymatic steps in sex steroid biosynthesis and metabolism, in relation to childhood behaviors.
The Mount Sinai Children’s Environmental Health Study enrolled a multiethnic urban pregnancy cohort from 1998–2002 (n = 404). DNA was obtained from maternal blood (n=149) and from neonatal cord blood (n=53). At each visit, mothers completed the Behavior Assessment System for Children (BASC), a parent-reported questionnaire used to evaluate children for behavior problems. We focused on problem behaviors more commonly associated with ADHD (hyperactivity, attention problems, externalizing behaviors, conduct disorder, poor adaptability) to see if maternal genetic variants in sex steroid production and metabolism influence sexually-dimorphic behaviors in offspring.
The more active gene variants were significantly associated with Attention Problems and poorer Adaptive Skills in male compared to female offspring. The CYP19 variant allele was also significantly associated with worse scores for boys on the Hyperactivity, Externalizing Problems Composite and Adaptive Skills Composite scales (p < 0.05).
We observed maladaptive behaviors in the male offspring of mothers who carried functional polymorphisms in the sex steroid pathway. The strongest associations were in domains commonly affected in Attention Deficit-Hyperactivity Disorder.
single nucleotide polymorphism; estradiol; androgen; BASC; attention deficit-hyperactivity disorder; 17-alpha-hydroxylase; aromatase; cytochrome P-450; CYP1B1
Recent work shows promising associations between schizophrenia and polymorphisms in Neuregulin-1 (NRG1) and a large literature also finds strong familial relationships between schizophrenia and cognitive deficits. Given the role of NRG1 in glutamate regulation and glutamate’s effect on cognition, we hypothesized that cognitive deficits may be related to variation within NRG1, providing a possible mechanism to increase risk for schizophrenia.
This study examined the associations between NRG1, cognition, and schizophrenia using a multigenerational multiplex family sample (total N = 419, 40 families), including 58 affected participants (schizophrenia or schizoaffective disorder-depressed type) and their 361 unaffected relatives. Participants were genotyped for 40 NRG1 single nucleotide polymorphisms (SNPs), chosen largely based on previous associations with schizophrenia. All participants completed structured diagnostic interviews and a computerized neurocognitive battery assessing eight cognitive domains. Variance component quantitative trait analyses tested for associations between individual NRG1 SNPs and cognitive performance in the total sample, a subsample of healthy participants with no DSM diagnosis, and using general intelligence as a covariate.
Effect sizes (within-family beta coefficients) ranged from 0.08 to 0.73, and 61 of these associations were nominally significant (p≤.05), with 12 associations at p≤.01, although none achieved the modified Bonferroni significance threshold of p<.0003. Attention was the most frequently nominally associated domain and rs10503929, a non-synonymous SNP, was the most frequently nominally associated SNP.
Although not significant experiment-wise, these findings suggest that further study of the associations between variation in NRG1 and cognition may be productive.
NRG1; attention; rs10503929
Animal and human studies have implicated oxytocin (OXT) in affiliative and prosocial behaviors. We tested whether genetic variation in the OXT receptor (OXTR) gene is associated with conduct disorder (CD).
Utilizing a family-based sample of adolescent probands recruited from an adolescent substance abuse treatment program, control probands and their families (total sample n=1,750), we conducted three tests of association with CD and 10 SNPs (single nucleotide polymorphisms) in the OXTR gene: (1) family-based comparison utilizing the entire sample; (2) within-Whites, case-control comparison of adolescent patients with CD and controls without CD; and (3) within-Whites case-control comparison of parents of patients and parents of controls.
Family-based association tests failed to show significant results (no results p<0.05). While strictly correcting for the number of tests (α=0.002), adolescent patients with CD did not differ significantly from adolescent controls in genotype frequency for the OXTR SNPs tested; similarly, comparison of OXTR genotype frequencies for parents failed to differentiate patient and control family type, except a trend association for rs237889 (p=0.004).
In this sample, 10 SNPs in the OXTR gene were not significantly associated with CD.
antisocial; delinquency; callousness; genetics
Developmental Dyslexia is a heritable condition, with genetic factors accounting for 44%–75% of the variance in performance tests of reading component subphenotypes. Compelling genetic linkage and association evidence supports a quantitative trait locus in the 6p21.3 region, which encodes a gene called DCDC2. In the present study, we explored the contribution of two DCDC2 markers to dyslexia, related reading and memory phenotypes in nuclear families of Italian origin.
303 nuclear families recruited on the basis of having a proband with Developmental Dyslexia have been studied with 6p21.3 markers, BV677278 and rs793862. Marker-trait association was investigated by the quantitative transmission disequilibrium test (QTDT, version 2.5.1) as modelled by Abecasis et al. (2000), which allows for the analyses of quantitative traits. Seven phenotypes were used in association analyses, i.e. word and non-word reading, word and non-word spelling, orthographic choice, memory and the affected status based on inclusion criteria.
QTDT analyses yielded evidence for association between reading skills and the BV677278 deletion (empirical p-values= .025–.029) and between memory and BV677278 allele 10 (empirical p-value= .0001).
Our result adds further evidence in support of DCDC2 contributing to the deficits in Developmental Dyslexia. More specifically, our data support the view that DCDC2 influences both reading and memory impairments thus shedding further light into the etiologic basis and the phenotypic complexity of Developmental Dyslexia.
DCDC2; Developmental Dyslexia; Transmission Disequilibrium Test; association study
Borderline personality disorder (BPD) is a severe disorder with high morbidity and mortality, but unknown etiology. Childhood abuse has been proposed as an etiological factor, but the mechanism by which an abuse history could influence risk for BPD has not been determined. The aim of this study was to determine whether the Tryptophan Hydroxylase 1 gene is related to BPD in a clinical sample, and whether TPH1 genotypes or haplotypes moderate the relationship between abuse history and BPD.
Three hundred ninety-eight patients diagnosed with mood disorders were genotyped for TPH1 G-6526A promoter polymorphism (rs4537731) and the A218C intron 7 polymorphism (rs1800532) and a set of ancestry informative markers, assessed for DSM IV diagnoses, and assessed for a history of physical and/or sexual abuse.
Patients with a diagnosis of BPD were more likely to be risk allele carriers (A alleles at both loci) than the non-BPD group. Logistic regression analysis predicting BPD diagnosis with both single SNPs and haplotypes showed significant interaction effects between genotype and abuse history. Poisson regression predicting the number of BPD diagnostic criteria met with the same predictor set also included a significant interaction term. Risk allele carriers with a history of abuse had an increased likelihood of a BPD diagnosis.
Variation in TPH1may increase risk for developing BPD as a result of childhood abuse. Elements of BPD pathology may be due in part to a genetically influenced serotonergic dysfunction, which in turn may lead to a differential response to environmental stressors.
TPH1; tryptophan hydroxylase; A218C; G-6526A; Borderline Personality Disorder; Childhood Abuse; Suicide; Impulsivity; Impulsiveness
Depression and alcohol dependence are common psychiatric disorders that often co-occur. Both disorders are genetically influenced, with heritability estimates in the range of 35–60%. In addition, evidence from twin studies suggests that alcohol dependence and depression are genetically correlated. Here we report results from a genome-wide association study (GWAS) of a comorbid phenotype in which cases meet the DSM-IV symptom threshold for major depressive symptomatology and DSM-IV criteria for alcohol dependence.
Samples (N=467 cases and N=407 controls) were of European-American descent, and were genotyped using the Illumina Human 1M BeadChip array.
Although no SNP meets genome-wide significance criteria, we identify ten markers with p-values < 1 × 10−5, seven of which are located in known genes, which have not been previously implicated in either disorder. Genes harboring SNPs yielding p<1 × 10−3 are functionally enriched for a number of gene ontology categories, notably several related to glutamatergic function. Investigation of expression localization using online resources suggests that these genes are expressed across a variety of tissues, including behaviorally relevant brain regions. Genes that have been previously associated with depression, alcohol dependence, or other addiction-related phenotypes – such as CDH13, CSMD2, GRID1, and HTR1B – were implicated by nominally significant SNPs. Finally, the degree of overlap of significant SNPs between a comorbid phenotype and an alcohol dependence-only phenotype is modest.
These results underscore the complex genomic influences on psychiatric phenotypes, and suggest that a comorbid phenotype is partially influenced by genetic variants that do not affect alcohol dependence alone.
genetics of alcoholism; comorbidity; genetic risk; depressive syndrome
Recent research implicates the COMT Val108/158Met polymorphism in stress-sensitivity, via modulation of hypothalamic-pituitary-adrenal (HPA) function. In healthy samples, Met-homozygosity has been associated with greater HPA activity (i.e., cortisol) and stress sensitivity, though findings are mixed among clinical samples. To date, there are no reports examining baseline or longitudinal changes in HPA activity as a function of COMT genotype in youth. This study examined the association of COMT with salivary cortisol across a one-year period in healthy and at-risk adolescents with DSM-IV-TR Axis II diagnoses. Results indicated higher cortisol levels for Met-homozygotes (compared to heterozygotes and Val homozygotes) at the one-year follow-up, and increased mean cortisol levels across a one-year period among Met-carriers, suggesting that COMT associates with differences in cortisol secretion during adolescence. Findings are discussed with respect to COMT genotype as a potential genetic indicator of psychiatric risk that modulates developmental changes in HPA activity.
genetic; COMT; catechol-o-methyltransferase; psychosis; schizophrenia; stress; risk; cortisol; hypothalamic-pituitary-adrenal axis; HPA
In previous analyses of non-Hispanic white women we found a stronger relation between abuse history and mid-pregnancy elevated depressive symptoms in women with the serotonin transporter (5-HTTLPR) S/S genotype. Here we focus on African-American women (N=698). Our inquiry is motivated by racial differences in depression diagnosis/treatment, stressors and frequency of major 5-HTTLPR alleles (S, LA, LG).
Stressful life events (lifetime) and depressive symptoms (current) were ascertained at 15–27 weeks gestation. A Center for Epidemiological Studies Depression score of ≥18 was considered “elevated”. Life events were scored together and separated into six sub-constructs. 5-HTTLPR genotypes were grouped as follows: 1) L and S alleles, 2) S-LG equivalence (“tri- to biallelic”) and 3) LA/LA, all others, S/S (“high/intermediate/low”). Odds ratios (OR) for “elevated” depressive symptoms-life events (total and sub-constructs) relations were calculated for each genotype grouping.
The prevalence of “elevated” depressive symptoms did not vary by genotype. The relation between stressful life events and “elevated” depressive symptoms was stronger in S/S compared to LA/LA genotype (interaction P=0.11). Of the six sub-constructs, only abuse showed a statistically significant gene-environment interaction. The OR for the abuse- “elevated” depressive symptoms association was greater for S/S vs. LA/LA (interaction P= 0.03) and in the “tri- to biallelic” grouping (interaction P=0.04). In the “high/intermediate/low” grouping, “low” (S/S) had a higher OR (5.5) than both “intermediate” and “high” (ORs≤2.3) (interaction P=0.10).
These results show the importance of examining racial groups, specific stressful events and different 5-HTTLPR genotype groupings when exploring gene-environment interactions in depression.
5-HTTLPR; African American; depressive symptoms; gender; gene-environment interaction; stressful life events; pregnancy; women
Autism is a neurodevelopmental disorder with a strong genetic component to susceptibility. Here, we report the molecular characterization of an apparent de novo 281 kb duplication of Chromosome 2p25.3 in two male half-siblings with autism.
The 2p25.3 duplication was first identified through a low-density microarray, validated with FISH, and duplication breakpoints were delineated using an Affymetrix 6.0 SNP microarray.
FISH results validated the novel copy number variant and revealed the mother to be mosaic, with ~33% of her lymphoblast cells carrying the duplication. Therefore, the duplication was transmitted through the mechanism of germline mosaicism. Additionally, duplication breakpoints were refined and show that PXDN is fully duplicated, while seven exons of the terminal portion of the 25 exon gene MYT1L are within the duplicated region.
MYT1L, a gene predominately expressed in the brain, has recently been linked to other neuropsychiatric illness such as schizophrenia and depression. Results from this study indicate that the 2p25.3 duplication disrupting PXDN and MYT1L is a potential autism-causing variant in the pedigree reported here and should receive further consideration as a candidate gene for autism.
MYT1L; autistic disorder; DNA copy number variations; mosaicism; genetics
Antisocial personality disorder (ASPD) frequently co-occurs with substance dependence (SD). A functional polymorphism (5-HTTLPR) in the serotonin transporter gene has been widely studied as a risk factor for a variety of psychopathologic conditions, including aggressive/violent behavior. Childhood abuse is an important predictor of ASPD. We examined 5-HTTLPR genotype and adverse childhood events (ACEs) as risk factors for ASPD in a SD sample.
Study participants [602 European Americans (EAs) and 779 African Americans (AAs)] were interviewed to obtain lifetime diagnoses of ASPD and SD and information on ACEs. Tri-allelic genotypes for 5-HTTLPR were obtained using standard methods. We used logistic generalized estimating equations (GEE) regression to examine ACEs and 5-HTTLPR genotype and their interaction as predictors of ASPD, separately by population group.
There were 203 (14.7%) participants diagnosed with ASPD. The frequency of the low-activity 5-HTTLPR S’ allele did not differ by ASPD diagnosis, and there was no overall 5-HTTLPR × ACE interaction. However, among EAs, male sex (OR=3.36; p<0.001) and ACE history (OR=1.47; p=0.002) were significant predictors of ASPD. Among AAs, there was a significant interaction of sex × 5-HTTLPR genotype × ACEs (χ2=13.92, p<0.001). Among AA men, each additional ACE significantly increased the odds of ASPD irrespective of genotype, while among AA women, the effect of ACEs on ASPD was significant only among S’ homozygotes. However, these results are limited by the small sample size in each subgroup, (particularly AA women with S’S’ genotype; N=7) and require replication.
Childhood maltreatment contributes to the risk of antisocial personality disorder, an effect for which there is preliminary evidence of moderation by 5-HTTLPR genotype in AA women.
Serotonin Transporter Gene; SLC6A4; Child Abuse; Antisocial Personality Disorder; gene × environment
A recent study in a sample of Plains Indians showed association between eight SNPs located in the SGIP1 gene and resting theta electroencephalogram (EEG) power (Hodgkinson et al., 2010). This association appeared to generalize to alcohol use disorders, for which EEG power is a potential endophenotype.
We analyzed a large, diverse sample for replication of the association of these implicated SGIP1 SNPs (genotyped on the Illumina 1M platform) with alcohol dependence (N = 3988) and theta EEG power (N = 1066).
We found no evidence of association of the previously implicated SGIP1 SNPs with either alcohol dependence or theta EEG power (all p > 0.15) in the current sample.
The previously implicated SNPs located in SGIP1 showed no association with alcohol dependence or theta EEG power in the present sample of individuals with European and/or African ancestry. This failure to replicate may be the result of differences in ancestry between the current and original samples.
alcoholism; electroencephalogram; candidate gene association study
Alcoholism and affective disorders are both strongly comorbid and heritable. We have investigated the genetic comorbidity between bipolar affective disorder and alcoholism.
A genome-wide allelic association study of 506 patients from the University College London (UCL) bipolar disorder case control sample and 510 ancestrally-matched supernormal controls. 143 of the bipolar subjects fulfilled the research diagnostic criteria (RDC) diagnosis of alcoholism. 372,193 single nucleotide polymorphisms (SNPs) were genotyped. Genes previously shown to be associated with alcoholism and addiction phenotypes were then tested for association in the bipolar alcoholic sample using gene wise permutation tests of all SNPs genotyped within a 50kb region flanking each gene.
Several CNS genes showed significant (p<0.05) gene wise evidence of association with bipolar alcoholism. The genes implicated which replicated previously identified associations with alcoholism were: cadherin 11 (CDH11), collagen type XI alpha 2 (COL11A2), neuromedin U receptor 2 (NMUR2), exportin7 (XP07) and semaphorin associated protein 5A (SEMA5A). The SNPs most strongly implicated in bipolar alcoholism, but which did not meet conventional genome-wide significance criteria were the insulin-like growth factor binding protein 7 (IGFBP7), carboxypeptidase O (CPO), cerebellin 2 (CBLN2), and the cadherin 12 (CDH12) genes.
We have confirmed the role of some genes previously shown to be associated with alcoholism in the comorbid bipolar alcoholism subgroup. In this subgroup bipolar disorder may lower the threshold for the phenotypic expression of these alcoholism susceptibility genes. We also show that some genes may independently increase susceptibility to affective disorder and alcoholism.
Bipolar; alcoholism; genome wide association; comorbid; gene wise
Research implicates the A1 allele of the dopamine D2 receptor gene (DRD2) Taq1A polymorphism in the development of depression and anxiety.
Furthermore, recent papers suggest that children with A1 allele of this gene may receive less positive parenting, and that the effects of this gene on child symptoms may be moderated by parenting. We sought to replicate and extend these findings using behavioral measures in a nonclinical sample of young children.
In a sample of 473 preschool-aged children and their mothers, structured clinical interview measures and maternal reports of child symptoms were collected, and standardized observations of parent–child interactions were conducted.
An association was detected between the DRD2 A1 allele and symptoms of depression and anxiety indexed using interview and parent report methods. As found in previous reports, children with the DRD2 A1 allele received less supportive parenting and displayed higher levels of negative emotionality during parent–child interactions. Tests of mediation and moderation were conducted.
We found associations between the DRD2 A1 allele and early-emerging anxious and depressive symptoms in a community sample of preschool-aged children, and evidence of a gene–environment correlation and moderation of the main effect of child genotype on child symptoms by parenting.
anxiety; depression; dopamine D2 receptor gene; parenting
Mood disorders are highly heritable forms of major mental illness. A major breakthrough in elucidating the genetic architecture of mood disorders was anticipated with the advent of genome-wide association studies (GWAS). However, to date few susceptibility loci have been conclusively identified. The genetic etiology of mood disorders appears to be quite complex, and as a result, alternative approaches for analyzing GWAS data are needed. Recently, a polygenic scoring approach that captures the effects of alleles across multiple loci was successfully applied to the analysis of GWAS data in schizophrenia and bipolar disorder (BP). However, this method may be overly simplistic in its approach to the complexity of genetic effects. Data mining methods are available that may be applied to analyze the high dimensional data generated by GWAS of complex psychiatric disorders. We sought to compare the performance of five data mining methods, namely, Bayesian Networks (BN), Support Vector Machine (SVM), Random Forest (RF), Radial Basis Function network (RBF), and Logistic Regression (LR), against the polygenic scoring approach in the analysis of GWAS data on BP. The different classification methods were trained on GWAS datasets from the Bipolar Genome Study (2,191 cases with BP and 1,434 controls) and their ability to accurately classify case/control status was tested on a GWAS dataset from the Wellcome Trust Case Control Consortium. The performance of the classifiers in the test dataset was evaluated by comparing area under the receiver operating characteristic curves (AUC). BN performed the best of all the data mining classifiers, but none of these did significantly better than the polygenic score approach. We further examined a subset of SNPs in genes that are expressed in the brain, under the hypothesis that these might be most relevant to BP susceptibility, but all the classifiers performed worse with this reduced set of SNPs. The discriminative accuracy of all of these methods is unlikely to be of diagnostic or clinical utility at the present time. Further research is needed to develop strategies for selecting sets of SNPs likely to be relevant to disease susceptibility and to determine if other data mining classifiers that utilize other algorithms for inferring relationships among the sets of SNPs may perform better.
data mining; Genome-Wide Association; Mood Disorders
A recent genome-wide association study and follow-up shows significant association with the protocadherin 11 X-linked (PCDH11X) gene. Carrasquillo et al. (2009) show statistical association with four PCDH11X polymorphisms (rs5984894, rs2573905, rs5941047, rs4568761) in five of seven cohorts. The combined analysis of 2,356 cases and 2,384 controls showed the strongest association with a p-value of 2.2 × 10-7 with an allele specific odds ratio of 1.30 (95% CI, 1.18–1.43) at the rs5984894 polymorphism. We tested for association at these four SNPs in two independent datasets and then performed a joint analysis. Though we had adequate power to detect effects sizes with the reported odds ratios, we did not detect association between LOAD and the PCDH11X polymorphisms in our dataset of 889 cases and 850 controls, indicating that the PCDH11X association, if not a false positive, is not as strong or generalized as previously hypothesized.
Alzheimer disease; genetic association study; PCDH11X
This study’s aims were to map loci linked to self-rating of the effects of alcohol and to determine if there was overlap with loci previously mapped for other substance dependence phenotypes in an American Indian community at high risk for substance dependence.
Each participant gave a blood sample and completed a structured diagnostic interview using the Semi Structured Assessment for the Genetics of Alcoholism (SSAGA). Retrospective report of responses to alcohol during the FIRST FIVE TIMES they had ever drank alcohol was estimated from the Self-Rating of the Effects of Alcohol (SRE) questionnaire for each participant. Genotypes were determined for a panel of 791 micro-satellite polymorphisms in 381 members of multiplex families using SOLAR.
Analyses of multipoint variance component LOD scores, for the FIRST FIVE TIMES phenotype, revealed two loci that had a LOD score greater than 3.0 on chromosomes 6 and 9. Additionally, 3 locations were identified with LOD scores above 2.0 on chromosomes 10, 12, 17.
These results corroborate the importance of regions on chromosome 6 and 9 highlighted in prior segregation studies in this and other populations for substance dependence-related phenotypes, as well as an area on chromosome 10 previously identified for the FIRST FIVE TIMES phenotype in the collaborative study on the genetics of alcoholism. These studies additionally lend further support the construct that the SRE may represent an important endophenotype associated with alcohol and other substance dependence.
American Indians; alcohol dependence; linkage studies; SRE
Conduct disorder is a serious, relatively common disorder of childhood and adolescence. Findings from genetic association studies searching for genetic determinants of the liability toward such behaviors have been inconsistent. One possible explanation for differential results is that most studies define phenotype from a single assessment; for many adolescents conduct problems decrease in severity over time, while for others such behaviors persist. Therefore, longitudinal datasets offer the opportunity to refine phenotype.
We utilized Caucasians first assessed during adolescence from the National Youth Survey Family Study. Nine waves of data were utilized to create latent growth trajectories and test for associations between trajectory class and 5HTTLPR genotype.
For the full sample, 5HTTLPR was not associated with conduct problem phenotypes. However, the short (s) allele was associated with chronic conduct problems in females; a nominally significant gender by 5HTTLPR genotype interaction was noted.
Longitudinal studies provide unique opportunities for phenotypic refinement and such techniques, with large samples, may be useful for phenotypic definition with other study designs, such as whole genome association studies.
delinquency; antisocial; genetic association; aggression; serotonin