Use of multivariate linkage analysis for dissection of a complex cognitive trait

A bivariate genome-wide association study identifies ADAM12 as a novel susceptibility gene for Kashin-Beck disease

Kashin-Beck disease (KBD) is a chronic osteoarthropathy, which manifests as joint deformities and growth retardation. Only a few genetic studies of growth retardation associated with the KBD have been carried out by now. In this study, we conducted a two-stage bivariate genome-wide association study (BGWAS) of the KBD using joint deformities and body height as study phenotypes, totally involving 2,417 study subjects. Articular cartilage specimens from 8 subjects were collected for immunohistochemistry. In the BGWAS, ADAM12 gene achieved the most significant association (rs1278300 p-value = 9.25 × 10⁻⁹) with the KBD. Replication study observed significant association signal at rs1278300 (p-value = 0.007) and rs1710287 (p-value = 0.002) of ADAM12 after Bonferroni correction. Immunohistochemistry revealed significantly decreased expression level of ADAM12 protein in the KBD articular cartilage (average positive chondrocyte rate = 47.59 ± 7.79%) compared to healthy articular cartilage (average positive chondrocyte rate = 64.73 ± 5.05%). Our results suggest that ADAM12 gene is a novel susceptibility gene underlying both joint destruction and growth retardation of the KBD.

Genome scan for cognitive trait loci of dyslexia: Rapid naming and rapid switching of letters, numbers, and colors

Dyslexia, or specific reading disability, is a common developmental disorder that affects 5-12% of school-aged children. Dyslexia and its component phenotypes, assessed categorically or quantitatively, have complex genetic bases. The ability to rapidly name letters, numbers, and colors from rows presented visually correlates strongly with reading in multiple languages and is a valid predictor of reading and spelling impairment. Performance on measures of rapid naming and switching, RAN and RAS, is stable throughout elementary school years, with slowed performance persisting in adults who still manifest dyslexia. Targeted analyses of dyslexia candidate regions have included RAN measures, but only one other genome-wide linkage study has been reported. As part of a broad effort to identify genetic contributors to dyslexia, we performed combined oligogenic segregation and linkage analyses of measures of RAN and RAS in a family-based cohort ascertained through probands with dyslexia. We obtained strong evidence for linkage of RAN letters to the DYX3 locus on chromosome 2p and RAN colors to chromosome 10q, but were unable to confirm the chromosome 6p21 linkage detected for a composite measure of RAN colors and objects in the previous genome-wide study.

Genetic risk variants for dyslexia on chromosome 18 in a German cohort

Dyslexia is characterized by impaired reading and spelling. The disorder has a prevalence of about 5% in Germany, and a strong hereditary component. Several loci are thought to be involved in the development of dyslexia. Scerri et al. identified eight potential dyslexia-associated single nucleotide polymorphisms (SNPs) in seven genes on chromosome 18 in an English-speaking population. Here, we present an association analysis that explores the relevance of these SNPs in a German population comprising 388 dyslexia cases and 364 control cases. In case-control analysis, three nominal SNP associations were replicated. The major alleles of NEDD4L-rs12606138 and NEDD4L-rs8094327 were risk associated [odds ratio (OR) = 1.35, 95% confidence interval (CI) = 1.0-1.7, P-value = 0.017 and OR = 1.39, 95% CI = 1.1-1.7, P-value = 0.007, respectively], and both SNPs were in strong linkage disequilibrium (r(2)  = 0.95). For MYO5B-rs555879, the minor allele was risk associated (OR = 1.31, 95% CI = 1.1-1.6, P-value = 0.011). The combined analysis of SNP sets using set enrichment analysis revealed a study-wide significant association for three SNPs with susceptibility for dyslexia. In summary, our results substantiate genetic markers in NEDD4L and MYO5B as risk factors for dyslexia and provide first evidence that the relevance of these markers is not restricted to the English language.

Identification of a major locus, TNF1, that controls BCG-triggered tumor necrosis factor production by leukocytes in an area hyperendemic for tuberculosis

BACKGROUND

Tumor necrosis factor (TNF) is a key immune regulator of tuberculosis resistance, as exemplified by the highly increased risk of tuberculosis disease among individuals receiving TNF-blocker therapy.

METHODS

We determined the extent of TNF production after stimulation with BCG or BCG plus interferon gamma (IFN-γ) using a whole blood assay in 392 children belonging to 135 nuclear families from an area hyperendemic for tuberculosis in South Africa. We conducted classical univariate and bivariate genome-wide linkage analysis of TNF production using the data from both stimulation protocols by means of an extension of the maximum-likelihood-binomial method for quantitative trait loci to multivariate analysis.

RESULTS

Stimulation of whole blood by either BCG or BCG plus IFN-γ resulted in a range of TNF release across subjects. Extent of TNF production following both stimulation protocols was highly correlated (r = 0.81). We failed to identify genetic linkage of TNF release when considering each stimulus separately. However, using a multivariate approach, we detected a major pleiotropic locus (P < 10(-5)) on chromosome region 11p15, termed TNF locus 1 (TNF1), that controlled TNF production after stimulation by both BCG alone and BCG plus IFN-γ.

CONCLUSIONS

The TNF1 locus was mapped in the vicinity of the TST1 locus, previously identified in the same family sample, that controls tuberculin skin test (TST) negativity per se, that is, T-cell-independent resistance to Mycobacterium tuberculosis infection. This suggested that there is a connection between TST negativity per se and TNF production.

The genetics of reading disabilities: from phenotypes to candidate genes

This article provides an overview of (a) issues in definition and diagnosis of specific reading disabilities at the behavioral level that may occur in different constellations of developmental and phenotypic profiles (patterns); (b) rapidly expanding research on genetic heterogeneity and gene candidates for dyslexia and other reading disabilities; (c) emerging research on gene-brain relationships; and (d) current understanding of epigenetic mechanisms whereby environmental events may alter behavioral expression of genetic variations. A glossary of genetic terms (denoted by bold font) is provided for readers not familiar with the technical terms.

A Note on the Asymptotic Distribution of Likelihood Ratio Tests to Test Variance Components

When using maximum likelihood methods to estimate genetic and environmental components of (co)variance, it is common to test hypotheses using likelihood ratio tests, since such tests have desirable asymptotic properties. In particular, the standard likelihood ratio test statistic is assumed asymptotically to follow a χ2distribution with degrees of freedom equal to the number of parameters tested. Using the relationship between least squares and maximum likelihood estimators for balanced designs, it is shown why the asymptotic distribution of the likelihood ratio test for variance components does not follow a χ2distribution with degrees of freedom equal to the number of parameters tested when the null hypothesis is true. Instead, the distribution of the likelihood ratio test is a mixture of χ2distributions with different degrees of freedom. Implications for testing variance components in twin designs and for quantitative trait loci mapping are discussed. The appropriate distribution of the likelihood ratio test statistic should be used in hypothesis testing and model selection.

In search of the perfect phenotype: an analysis of linkage and association studies of reading and reading-related processes

Reading ability and specific reading disability (SRD) are complex traits involving several cognitive processes and are shaped by a complex interplay of genetic and environmental forces. Linkage studies of these traits have identified several susceptibility loci. Association studies have gone further in detecting candidate genes that might underlie these signals. These results have been obtained in samples of mainly European ancestry, which vary in their languages, inclusion criteria, and phenotype assessments. Such phenotypic heterogeneity across samples makes understanding the relationship between reading (dis)ability and reading-related processes and the genetic factors difficult; in addition, it may negatively influence attempts at replication. In moving forward, the identification of preferable phenotypes for future sample collection may improve the replicability of findings. This review of all published linkage and association results from the past 15 years was conducted to determine if certain phenotypes produce more replicable and consistent results than others.

Dyslexia and DYX1C1: deficits in reading and spelling associated with a missense mutation

The status of DYX1C1 (C15q21.3) as a susceptibility gene for dyslexia is unclear. We report the association of this gene with reading and spelling ability in a sample of adolescent twins and their siblings. Family-based association analyses were carried out on 13 single-nucleotide polymorphisms (SNPs) in DYX1C1, typed in 790 families with up to 5 offspring and tested on 6 validated measures of lexical processing (irregular word) and grapheme-phoneme decoding (pseudo-word) reading- and spelling-based measures of dyslexia, as well as a short-term memory measure. Significant association was observed at the misssense mutation rs17819126 for all reading measures and for spelling of lexical processing words, and at rs3743204 for both irregular and nonword reading. Verbal short-term memory was associated with rs685935. Support for association was not found at rs3743205 and rs61761345 as previously reported by Taipale et al., but these SNPs had very low (0.002 for rs3743205) minor allele frequencies in this sample. These results suggest that DYX1C1 influences reading and spelling ability with additional effects on short-term information storage or rehearsal. Missense mutation rs17819126 is a potential functional basis for the association of DYX1C1 with dyslexia.

Identification of candidate genes for dyslexia susceptibility on chromosome 18

BACKGROUND

Six independent studies have identified linkage to chromosome 18 for developmental dyslexia or general reading ability. Until now, no candidate genes have been identified to explain this linkage. Here, we set out to identify the gene(s) conferring susceptibility by a two stage strategy of linkage and association analysis.

METHODOLOGY/PRINCIPAL FINDINGS

Linkage analysis: 264 UK families and 155 US families each containing at least one child diagnosed with dyslexia were genotyped with a dense set of microsatellite markers on chromosome 18. Association analysis: Using a discovery sample of 187 UK families, nearly 3000 SNPs were genotyped across the chromosome 18 dyslexia susceptibility candidate region. Following association analysis, the top ranking SNPs were then genotyped in the remaining samples. The linkage analysis revealed a broad signal that spans approximately 40 Mb from 18p11.2 to 18q12.2. Following the association analysis and subsequent replication attempts, we observed consistent association with the same SNPs in three genes; melanocortin 5 receptor (MC5R), dymeclin (DYM) and neural precursor cell expressed, developmentally down-regulated 4-like (NEDD4L).

CONCLUSIONS

Along with already published biological evidence, MC5R, DYM and NEDD4L make attractive candidates for dyslexia susceptibility genes. However, further replication and functional studies are still required.

Genetics of white matter development: a DTI study of 705 twins and their siblings aged 12 to 29

White matter microstructure is under strong genetic control, yet it is largely unknown how genetic influences change from childhood into adulthood. In one of the largest brain mapping studies ever performed, we determined whether the genetic control over white matter architecture depends on age, sex, socioeconomic status (SES), and intelligence quotient (IQ). We assessed white matter integrity voxelwise using diffusion tensor imaging at high magnetic field (4-Tesla), in 705 twins and their siblings (age range 12-29; 290 M/415 F). White matter integrity was quantified using a widely accepted measure, fractional anisotropy (FA). We fitted gene-environment interaction models pointwise, to visualize brain regions where age, sex, SES and IQ modulate heritability of fiber integrity. We hypothesized that environmental factors would start to outweigh genetic factors during late childhood and adolescence. Genetic influences were greater in adolescence versus adulthood, and greater in males than in females. Socioeconomic status significantly interacted with genes that affect fiber integrity: heritability was higher in those with higher SES. In people with above-average IQ, genetic factors explained over 80% of the observed FA variability in the thalamus, genu, posterior internal capsule, and superior corona radiata. In those with below-average IQ, however, only around 40% FA variability in the same regions was attributable to genetic factors. Genes affect fiber integrity, but their effects vary with age, sex, SES and IQ. Gene-environment interactions are vital to consider in the search for specific genetic polymorphisms that affect brain integrity and connectivity.

Association of reading disabilities with regions marked by acetylated H3 histones in KIAA0319

Reading disabilities (RDs) have been associated with chromosome 6p with recent studies pointing to two genes, DCDC2 and KIAA0319. In this study, markers across the 6p region were tested for association with RD. Our strongest findings were for association with markers in KIAA0319, although with the opposite alleles compared with a previous study. We also found association with markers in VMP, but not with DCDC2. Current evidence indicates that differential regulation of KIAA0319 and DCDC2 contributes to RD, thus we used chromatin immunoprecipitation coupled with genomic tiling arrays (ChIP-chip) to map acetylated histones, a molecular marker for regulatory elements, across a 500 kb genomic region covering the RD locus on 6p. This approach identified several regions marked by acetylated histones that mapped near associated markers, including intron 7 of DCDC2 and the 5' region of KIAA0319. The latter is located within the 70 kb region previously associated with differential expression of KIAA0319. Interestingly, five markers associated with RD in independent studies were also located within the 2.7 kb acetylated region, and six additional associated markers, including the most significant one in this study, were located within a 22 kb haplotype block that encompassed this region. Our data indicates that this putative regulatory region is a likely site of genetic variation contributing to RD in our sample, further narrowing the candidate region.

Genetics of developmental dyslexia

Developmental dyslexia is a highly heritable disorder with a prevalence of at least 5% in school-aged children. Linkage studies have identified numerous loci throughout the genome that are likely to harbour candidate dyslexia susceptibility genes. Association studies and the refinement of chromosomal translocation break points in individuals with dyslexia have resulted in the discovery of candidate genes at some of these loci. A key function of many of these genes is their involvement in neuronal migration. This complements anatomical abnormalities discovered in dyslexic brains, such as ectopias, that may be the result of irregular neuronal migration.

Dyslexia and DCDC2: normal variation in reading and spelling is associated with DCDC2 polymorphisms in an Australian population sample

The 6p21-p22 chromosomal region has been identified as a developmental dyslexia locus both in linkage and association studies, the latter generating evidence for the doublecortin domain containing 2 (DCDC2) as a candidate gene at this locus (and also for KIAA0319). Here, we report an association between DCDC2 and reading and spelling ability in 522 families of adolescent twins unselected for reading impairment. Family-based association was conducted on 21 single nucleotide polymorphisms (SNPs) in DCDC2 using quantitative measures of lexical processing (irregular-word reading), phonological decoding (non-word reading) and spelling-based measures of dyslexia derived from the Components of Reading Examination test. Significant support for association was found for rs1419228 with regular-word reading and spelling (P=0.002) as well as irregular-word reading (P=0.004), whereas rs1091047 was significantly associated (P=0.003) with irregular-word reading (a measure of lexical storage). Four additional SNPs (rs9467075, rs9467076, rs7765678 and rs6922023) were nominally associated with reading and spelling. This study provides support for DCDC2 as a risk gene for reading disorder, and suggests that this risk factor acts on normally varying reading skill in the general population.

Reconsidering the asymptotic null distribution of likelihood ratio tests for genetic linkage in multivariate variance components models under complete pleiotropy

Accurate knowledge of the null distribution of hypothesis tests is important for valid application of the tests. In previous papers and software, the asymptotic null distribution of likelihood ratio tests for detecting genetic linkage in multivariate variance components models has been stated to be a mixture of chi-square distributions with binomial mixing probabilities. For variance components models under the complete pleiotropy assumption, we show by simulation and by theoretical arguments based on the geometry of the parameter space that all aspects of the previously stated asymptotic null distribution are incorrect-both the binomial mixing probabilities and the chi-square components. Correcting the null distribution gives more conservative critical values than previously stated, yielding P values that can easily be 10 times larger. The true mixing probabilities give the highest probability to the case where all variance parameters are estimated positive, and the mixing components show severe departures from chi-square distributions. Thus, the asymptotic null distribution has complex features that raise challenges for the assessment of significance of multivariate linkage findings. We propose a method to generate an asymptotic null distribution that is much faster than other empirical methods such as permutation, enabling us to obtain P values with higher precision more efficiently.

Multivariate association analysis of the components of metabolic syndrome from the Framingham Heart Study

Metabolic syndrome, by definition, is the manifestation of multiple, correlated metabolic impairments. It is known to have both strong environmental and genetic contributions. However, isolating genetic variants predisposing to such a complex trait has limitations. Using pedigree data, when available, may well lead to increased ability to detect variants associated with such complex traits. The ability to incorporate multiple correlated traits into a joint analysis may also allow increased detection of associated genes. Therefore, to demonstrate the utility of both univariate and multivariate family-based association analysis and to identify possible genetic variants associated with metabolic syndrome, we performed a scan of the Affymetrix 50 k Human Gene Panel data using 1) each of the traits comprising metabolic syndrome: triglycerides, high-density lipoprotein, systolic blood pressure, diastolic blood pressure, blood glucose, and body mass index, and 2) a composite trait including all of the above, jointly. Two single-nucleotide polymorphisms within the cholesterol ester transfer protein (CETP) gene remained significant even after correcting for multiple testing in both the univariate (p < 5 x 10-7) and multivariate (p < 5 x 10-9) association analysis. Three genes met significance for multiple traits after correction for multiple testing in the univariate analysis, while five genes remained significant in the multivariate association. We conclude that while both univariate and multivariate family-based association analysis can identify genes of interest, our multivariate approach is less affected by multiple testing correction and yields more significant results.

Comparison of univariate and multivariate linkage analysis of traits related to hypertension

Complex traits are often manifested by multiple correlated traits. One example of this is hypertension (HTN), which is measured on a continuous scale by systolic blood pressure (SBP). Predisposition to HTN is predicted by hyperlipidemia, characterized by elevated triglycerides (TG), low-density lipids (LDL), and high-density lipids (HDL). We hypothesized that the multivariate analysis of TG, LDL, and HDL would be more powerful for detecting HTN genes via linkage analysis compared with univariate analysis of SBP. We conducted linkage analysis of four chromosomal regions known to contain genes associated with HTN using SBP as a measure of HTN in univariate Haseman-Elston regression and using the correlated traits TG, LDL, and HDL in multivariate Haseman-Elston regression. All analyses were conducted using the Framingham Heart Study data. We found that multivariate linkage analysis was better able to detect chromosomal regions in which the angiotensinogen, angiotensin receptor, guanine nucleotide-binding protein 3, and prostaglandin I2 synthase genes reside. Univariate linkage analysis only detected the AGT gene. We conclude that multivariate analysis is appropriate for the analysis of multiple correlated phenotypes, and our findings suggest that it may yield new linkage signals undetected by univariate analysis.

Calculating asymptotic significance levels of the constrained likelihood ratio test with application to multivariate genetic linkage analysis

The asymptotic distribution of the multivariate variance component linkage analysis likelihood ratio test has provoked some contradictory accounts in the literature. In this paper we confirm that some previous results are not correct by deriving the asymptotic distribution in one special case. It is shown that this special case is a good approximation to the distribution in many situations. We also introduce a new approach to simulating from the asymptotic distribution of the likelihood ratio test statistic in constrained testing problems. It is shown that this method is very efficient for small p-values, and is applicable even when the constraints are not convex. The method is related to a multivariate integration problem. We illustrate how the approach can be applied to multivariate linkage analysis in a simulation study. Some more philosophical issues relating to one-sided tests in variance components linkage analysis are discussed.

Two functions of early language experience

The unique human ability of linguistic communication, defined as the ability to produce a practically infinite number of meaningful messages using a finite number of lexical items, is determined by an array of "linguistic" genes, which are expressed in neurons forming domain-specific linguistic centers in the brain. In this review, I discuss the idea that infants' early language experience performs two complementary functions. In addition to allowing infants to assimilate the words and grammar rules of their mother language, early language experience initiates genetic programs underlying language production and comprehension. This hypothesis explains many puzzling characteristics of language acquisition, such as the existence of a critical period for acquiring the first language and the absence of a critical period for the acquisition of additional language(s), a similar timetable for language acquisition in children belonging to families of different social and cultural status, the strikingly similar timetables in the acquisition of oral and sign languages, and the surprisingly small correlation between individuals' final linguistic competence and the intensity of their training. Based on the studies of microcephalic individuals, I argue that genetic factors determine not only the number of neurons and organization of interneural connections within linguistic centers, but also the putative internal properties of neurons that are not limited to their electrophysiological and synaptic properties.

Sex-specific effect of IL9 polymorphisms on lung function and polysensitization

Sex differences in asthma-associated phenotypes are well known but the genetic factors that may account for these differences have received little attention. This study aimed to characterize sex-specific and pleiotropic genetic factors underlying four quantitative phenotypes involved in the main asthma physiopathological pathways: immunoglobulin E levels, a measure of polysensitization (SPTQ), eosinophil counts and a measure of lung function FEV(1)/H(2) (forced expiratory volume in one second divided by height square). Sex-stratified univariate and bivariate linkage analyses were conducted in 295 families from the Epidemiological study on the Genetics and Environment of Asthma study. We found genome-wide significant evidence for a male-specific pleiotropic QTL (quantitative trait loci) on 5q31 (P=7 x 10(-9)) influencing both FEV(1)/H(2) and SPTQ and for a female-specific pleiotropic QTL on 11q23 underlying SPTQ and immunoglobulin E (P=2 x 10(-5)). Three other sex-specific regions of linkage were detected for eosinophil: 4q24 and 22q13 in females, and 3p25 in males. Further, bivariate association analysis of FEV(1)/H(2) and SPTQ with 5q31 candidate genes in males showed a significant association with two single-nucleotide polymorphisms within IL9 gene, rs2069885 and rs2069882 (P=0.02 and P=0.002, respectively, after Bonferroni's correction). This study underlies the importance of taking into account complex mechanisms, such as heterogeneity according to sex and pleiotropy to unravel the genes involved in asthma phenotypes.

Multivariate association test using haplotype trend regression

Genetic association analyses with haplotypes may be more powerful than analyses with single markers, under certain conditions. Furthermore, simultaneously considering multiple correlated traits may make use of additional information that would not be considered when analyzing individual traits. In this study, we propose a haplotype based test of association for multivariate quantitative traits in unrelated samples. Specifically, we extend a population based haplotype trend regression (HTR) approach to multivariate scenarios. We mainly focused on bivariate HTR, and the simulation results showed that the proposed method had correct pre-specified type-I error rates. The power of the proposed method was largely influenced by the size and source of correlation between variables, being greatest when correlation of a specific gene was opposite in sign to the residual correlation.

A genome-wide scan for Eysenckian personality dimensions in adolescent twin sibships: psychoticism, extraversion, neuroticism, and lie

We report the first genome-wide scan of adolescent personality. We conducted a genome-wide scan to detect linkage for measures of adolescent Psychoticism, Extraversion, Neuroticism, and Lie from the Junior Eysenck Personality Questionnaire. Data are based on 1,280 genotyped Australian adolescent twins and their siblings. The highest linkage peaks were found on chromosomes 16 and 19 for Neuroticism, on chromosomes 1, 7, 10, 13 m, and 18 for Psychoticism, and on chromosomes 2 and 3 for Extraversion.

The power of linkage analysis of a disease-related endophenotype using asymmetrically ascertained sib pairs

A linkage study of a qualitative disease endophenotype in a sample of sib pairs, consisting of one disease affected proband and one sibling is considered. The linkage statistic compares marker allele sharing with the proband in siblings with an abnormal endophenotype to siblings with the normal endophenotype. Expressions for the distribution of this linkage statistic, in terms of the recombination fraction are derived and (1) the genetic parameter values (allele frequency and endophenotype and disease penetrance) and (2) the abnormal endophenotype rates in the population and in classes of relatives of disease affected probands. It is then shown that when either the disease or the abnormal endophenotype has additive penetrance, the expressions simplify to a monotonic function of the difference between abnormal endophenotype rates in siblings and in the population. Thought disorder is considered as a putative schizophrenia endophenotype. Forty sets of genetic parameter values that correspond to the known prevalence values for thought disorder in schizophrenic patients, siblings of schizophrenics and the general population are evaluated. For these genetic parameter values, numerical results show that the test statistic has>70% power (α = 0.0001) in general with a sample of 200 or more proband-sibling pairs to detect the linkage between a marker (θ = 0.01), and a locus pleiotropic for schizophrenia and thought disorder.

Multivariate genomewide linkage scan of neurocognitive traits and ADHD symptoms: suggestive linkage to 3q13

Family and twin studies suggest that a range of neurocognitive traits index the inherited liability to ADHD; however, the utility of such measures as endophenotypes in molecular genetic studies remains largely untested. The current article examined whether the inclusion of neurocognitive measures in a genomewide linkage analysis of ADHD could aid in identifying QTL linked to the behavioral symptoms of the condition. Data were from an affected sibling pair linkage study of DSM-IV ADHD conducted at Massachusetts General Hospital. The sample included 1,212 individuals from 271 families. ADHD symptoms were assessed with the K-SADS-E. The neurocognitive battery included Wechsler Intelligence Scales subtests, the Stroop, the Wisconsin Card Sorting Test (WCST), the Rey-Osterreith Complex Figure, a working memory CPT, the CVLT and WRAT-III subscales. Evidence for linkage was assessed using a simulation-based method that combines information from univariate analyses into the equivalent of a multivariate test. After correction for multiple trait testing, a region on chromosome 3q13 showed suggestive linkage to all neurocognitive traits examined and inattention symptoms of ADHD. The second highest peak occurred on 22q12 but showed linkage to a single subscale of the WCST. In univariate analysis, this region retained criteria for suggestive linkage to this measure after correction for multiple trait testing. Our primary findings raise the possibility that one or more genes on 3q13 influence neurocognitive functions and behavioral symptoms of inattention. Overall, these data support the utility of neurocognitive traits as ADHD endophenotypes, but also highlight their limited genetic overlap with the disorder.

A bivariate whole genome linkage study identified genomic regions influencing both BMD and bone structure

Areal BMD (aBMD) and areal bone size (ABS) are biologically correlated traits and are each important determinants of bone strength and risk of fractures. Studies showed that aBMD and ABS are genetically correlated, indicating that they may share some common genetic factors, which, however, are largely unknown. To study the genetic factors influencing both aBMD and ABS, bivariate whole genome linkage analyses were conducted for aBMD-ABS at the femoral neck (FN), lumbar spine (LS), and ultradistal (UD)-forearm in a large sample of 451 white pedigrees made up of 4498 individuals. We detected significant linkage on chromosome Xq27 (LOD = 4.89) for LS aBMD-ABS. In addition, we detected suggestive linkages at 20q11 (LOD = 3.65) and Xp11 (LOD = 2.96) for FN aBMD-ABS; at 12p11 (LOD = 3.39) and 17q21 (LOD = 2.94) for LS aBMD-ABS; and at 5q23 (LOD = 3.54), 7p15 (LOD = 3.45), Xq27 (LOD = 2.93), and 12p11 (LOD = 2.92) for UD-forearm aBMD-ABS. Subsequent discrimination analyses indicated that quantitative trait loci (QTLs) at 12p11 and 17q21 may have pleiotropic effects on aBMD and ABS. This study identified several genomic regions that may contain QTLs important for both aBMD and ABS. Further endeavors are necessary to follow these regions to eventually pinpoint the genetic variants affecting bone strength and risk of fractures.

Enhanced detection of genetic association of hypertensive heart disease by analysis of latent phenotypes

Hypertension and hypertensive heart disease (HHD) are inter-related phenotypes frequently observed with other comorbidities such as diabetes, obesity, and dyslipidemia, which probably reflect the complex gene-gene and/or gene-environment interactions resulting in HHD. The complexity of HHD led us to examine intermediate phenotypes (e.g., echocardiographically-derived measures) for simpler clues to the genetic underpinnings of the disease. We applied the method of independent component analysis to a prospective study of the metabolic predictors of left ventricular hypertrophy and extracted latent traits of HHD from panels of multi-dimensional anthropomorphic, hemodynamic echocardiographic and metabolic data. Based on the latent trait values, classification of subjects into different risk groups for HHD captured meaningful subtypes of the disease as reflected in the distributions of primary clinical indicators. Furthermore, we detected genetic associations of the latent HHD traits with single nucleotide polymorphisms in three candidate genes in the peroxisome proliferator-activated receptors complex, for which no significant association was found with the original clinical indicators of HHD. Consensus analysis of the results from repeated independent component analysis runs showed satisfactory robustness and estimated about 3-4 separate unseen sources for the observed HHD-related outcomes.

Linkage to chromosome 1p36 for attention-deficit/hyperactivity disorder traits in school and home settings

BACKGROUND

Limited success has been achieved through previous attention-deficit/hyperactivity disorder (ADHD) linkage scans, which were all designed to map genes underlying the dichotomous phenotype. The International Multi-centre ADHD Genetics (IMAGE) project performed a whole genome linkage scan specifically designed to map ADHD quantitative trait loci (QTL).

METHODS

A set of 1094 single selected Caucasian ADHD nuclear families was genotyped on a highly accurate and informative single nucleotide polymorphism (SNP) panel. Two quantitative traits measuring the children's symptoms in home and school settings were collected and standardized according to a population sample of 8000 children to reflect the developmental nature and gender prevalence difference of ADHD. Univariate linkage test was performed on both traits and their mean score.

RESULTS

A significant common linkage locus was found at chromosome 1p36 with a locus-specific heritability of 5.1% and a genomewide empirical p < .04. Setting-specific suggestive linkage signals were also found: logarithm of odds (LOD) = 2.2 at 9p23 for home trait and LOD = 2.6 at 11q21 for school trait.

CONCLUSIONS

These results indicate that given large samples with proper phenotypic measures, searching for ADHD genes with a QTL strategy is an important alternative to using the clinical diagnosis. The fact that our linkage region 1p36 overlaps with the dyslexia QTL DYX8 further suggests it is potentially a pleiotropic locus for ADHD and dyslexia.

Bivariate genome linkage analysis suggests pleiotropic effects on chromosomes 20p and 3p for body fat mass and lean mass

Total body fat mass (TBFM) and total body lean mass (TBLM) are the major components of the human body. Although these highly correlated phenotypic traits are frequently used to characterize obesity, the specific shared genetic factors that influence both traits remain largely unknown. Our study was aimed at identifying common quantitative trait loci (QTLs) contributing to both TBFM and TBLM. We performed a whole genome-linkage scan study in a large sample of 3255 subjects from 420 Caucasian pedigrees. Bivariate linkage analysis was carried out in both the entire sample and gender-specific subsamples. Several potentially important genomic regions that may harbour QTLs important for TBFM and TBLM were identified. For example, 20p12-11 achieved a LOD score of 2.04 in the entire sample and, in the male subsample, two genomic regions, 20p12 (LOD=2.08) and 3p26-25 (LOD=1.92), showed suggestive linkage. In addition, two-point linkage analyses for chromosome X showed suggestive linkages on Xp22 in the entire sample (LOD=2.14) and significant linkage on Xp22 in the female subsample (LOD=3.05). Complete pleiotropy was suggested for 20p12 and 3p26-25 in males. Our results suggest that QTLs on chromosomes 20p12, 3p26-25 and Xp22 may jointly influence TBFM and TBLM. Further fine mapping and gene identification studies for these pleiotropic effects are needed.

QTLs identified for P3 amplitude in a non-clinical sample: importance of neurodevelopmental and neurotransmitter genes

BACKGROUND

The P3(00) event-related potential is an index of processing capacity (P3 amplitude) and stimulus evaluation (P3 latency) as well as a phenotypic marker of various forms of psychopathology where P3 abnormalities have been reported.

METHODS

A genome-wide linkage scan of 400-761 autosomal markers, at an average spacing of 5-10 centimorgans (cM), was completed in 647 twins/siblings (306 families mostly comprising dizygotic twins), mean age 16.3, range 15.4-20.1 years, for whom P3 amplitude and latency data were available.

RESULTS

Significant linkage for P3 amplitude was observed on chromosome 7q for the central recording site (logarithm-of-odds [LOD] = 3.88, p = .00002) and in the same region for both frontal (LOD = 2.19, p = .0015) and parietal (LOD = 1.67, p = .0053) sites, with multivariate analysis also identifying linkage in this region (LOD = 2.14, p = .0017). Suggestive linkage was also identified on 6p (LOD(max) = 2.49) and 12q (LOD(max) = 2.24), with other promising regions identified on 9q (LOD(max) = 2.14) and 10p (LOD(max) = 2.18). Less striking were the results for P3 latency; LOD > 1.5 were found on chromosomes 1q, 9q, 10q, 12q, and 19p.

CONCLUSIONS

This is a first step in the identification of genes for normal variation in the P3. Loci identified here for P3 amplitude suggest the possible importance of neurodevelopmental genes in addition to those influencing neurotransmitters, fitting with the evidence that P3 amplitude is sensitive to diverse types of brain abnormalities.

Validating endophenotypes for schizophrenia using statistical modeling of twin data

The use of endophenotypes (intermediate quantitative traits) is one strategy that may provide valuable information about the neural mechanisms underlying disease etiology and facilitate discovery of susceptibility genes. For a trait to be an appropriate endophenotype, several key features should exist. In this article we discuss validating potential electrophysiological endophenotypes for schizophrenia based on conventionally accepted criteria. We focus on applying a twin study design and model fitting techniques to evaluate whether three event-related potential paradigms (P300, P50, and MMN) meet criteria as valid endophenotypes of schizophrenia.

Evidence for linkage of a new region (11p14) to eczema and allergic diseases

Asthma, allergic rhinitis (AR) and atopic dermatitis also called eczema are allergic co-morbidites, which are likely to depend on pleiotropic genetic effects as well as on specific genetic factors. After a previous genome-wide linkage screen conducted for asthma and AR in a sample of 295 French EGEA families ascertained through asthmatic subjects, the aim here was to search for genetic factors involved in eczema and more particularly the ones shared by the three allergic diseases using the same EGEA data. In this sake, eczema and phenotypes of "allergic disease" accounting for the joint information on the presence/absence of the three diseases were examined by linkage analyses using the maximum likelihood binomial method. A fine mapping was carried out in regions detected for potential linkage, followed by association studies using the family-based association test (FBAT). Evidence for linkage to 11p14 region was shown for "allergic disease" and eczema. Linkage was also indicated between eczema and 5q13 and between "allergic disease" and both 5p15 and 17q21 regions. Fine mapping supported the evidence of linkage to 11p14 and FBAT analyses showed the association between "allergic disease" and a marker located at the linkage peak on 11p14. Further investigations in this region will allow identifying genetic factor(s) which could have pleiotropic effect in the three allergic diseases.

A review of association and linkage studies for genetical analyses of learning disorders

Learning disorders (LD) commonly comprise of a heterogeneous group of disorders manifested by unexpected problems in some children's experiences in the academic performance arena. These problems especially comprise of a variety of disorders which may be subclassified to attention-deficit hyperactivity disorder (ADHD), reading disability (RD), specific language impairment (SLI), speech-sound disorder (SSD), and dyspraxia. The aim of this review is to summarize the current molecular studies and some of the most exciting recent developments in molecular genetic research on LD. The findings for the association and linkage of LD with candidate genes will help to set the research agendas for future studies to follow.

Evidence for a pleiotropic QTL on chromosome 5q13 influencing both time to asthma onset and asthma score in French EGEA families

Although many genome screens have been conducted for asthma as a binary trait, there is limited information regarding the genetic factors underlying variation of asthma expression. Phenotypes related to variable disease expression include time to asthma onset and variation in clinical expression as measured by an asthma score built from EGEA data. A recent genome scan conducted for this score led to detection of a new region (18p11) not revealed by analysis of dichotomous asthma. Our goal was to characterize chromosomal regions harboring genes underlying time to asthma onset and to search for pleiotropic QTL influencing both time to asthma onset and the asthma score. We conducted a genome-wide linkage screen for time to asthma onset, modeled by martingale residuals from Cox survival model, in EGEA families with at least two asthmatic sibs. This was followed by a bivariate linkage scan of these residuals and asthma score. Univariate linkage analysis was performed using the Maximum Likelihood Binomial method that we extended to bivariate analysis. This screen revealed two regions potentially linked to time to asthma onset, 1p31 (LOD = 1.70, P = 0.003) and 5q13 (LOD = 1.87, P = 0.002). Bivariate linkage analysis led to a substantial improvement of the linkage signal on 5q13 (P = 0.00007), providing evidence for a pleiotropic QTL influencing both variation of time to asthma onset and of clinical expression. Use of quantitative phenotypes of variable disease expression and suitable statistical methodology can improve the power to detect new regions harboring genes which may play an important role in onset and course of disease.

Multivariate linkage analysis of specific language impairment (SLI)

Specific language impairment (SLI) is defined as an inability to develop appropriate language skills without explanatory medical conditions, low intelligence or lack of opportunity. Previously, a genome scan of 98 families affected by SLI was completed by the SLI Consortium, resulting in the identification of two quantitative trait loci (QTL) on chromosomes 16q (SLI1) and 19q (SLI2). This was followed by a replication of both regions in an additional 86 families. Both these studies applied linkage methods to one phenotypic trait at a time. However, investigations have suggested that simultaneous analysis of several traits may offer more power. The current study therefore applied a multivariate variance-components approach to the SLI Consortium dataset using additional phenotypic data. A multivariate genome scan was completed and supported the importance of the SLI1 and SLI2 loci, whilst highlighting a possible novel QTL on chromosome 10. Further investigation implied that the effect of SLI1 on non-word repetition was equally as strong on reading and spelling phenotypes. In contrast, SLI2 appeared to have influences on a selection of expressive and receptive language phenotypes in addition to non-word repetition, but did not show linkage to literacy phenotypes.

Regression-based multivariate linkage analysis with an application to blood pressure and body mass index

Multivariate linkage analysis has been suggested for the analysis of correlated traits, such as blood pressure (BP) and body mass index (BMI), because it may offer greater power and provide clearer results than univariate analyses. Currently, the most commonly used multivariate linkage methods are extensions of the univariate variance component model. One concern about those methods is their inherent sensitivity to the assumption of multivariate normality which cannot be easily guaranteed in practice. Another problem possibly related to all multivariate linkage analysis methods is the difficulty in interpreting nominal p-values, because the asymptotic distribution of the test statistic has not been well characterized. Here we propose a regression-based multivariate linkage method in which a robust score statistic is used to detect linkage. The p-value of the statistic is evaluated by a simple and rapid simulation procedure. Theoretically, this method can be used for any number and type of traits and for general pedigree data. We apply this approach to a genome linkage analysis of blood pressure and body mass index data from the Beaver Dam Eye Study.

Interrelationship and Familiality of Dyslexia Related Quantitative Measures

Dyslexia is a complex gene-environment disorder with poorly understood etiology that affects about 5% of school-age children. Dyslexia occurs in all languages and is associated with a high level of social and psychological morbidity for the individual and their family; approximately 40-50% have persistent disability into adulthood. The core symptoms are word reading and spelling deficits, but several other cognitive components influence the core phenotype. A broad spectrum of dyslexia related phenotypes, including phonological decoding, phoneme awareness, orthographic processing, short-term memory, rapid naming and basic mathematical abilities, were investigated in large sample of 287 German dyslexia families. We explored the interrelationship between the component phenotypes using correlation and principal component analyses (PCA). In addition, we estimated familiality for phenotypes as well as for the factors suggested by PCA. The correlation between the component phenotypes varied between -0.1 and 0.7. The PCA resulted in three factors: a general dyslexia factor, a speed of processing factor and a mathematical abilities factor. The familiality estimates of single components and factors ranged between 0.25 and 0.63. Instead of analyzing single dyslexia-related components, multivariate analyses including factor analytic approaches may help in the identification of susceptibility genes.

Genetics of dyslexia: the evolving landscape

Dyslexia is among the most common neurodevelopmental disorders, with a prevalence of 5-12%. At the phenotypic level, various cognitive components that enable reading and spelling and that are disturbed in affected individuals can be distinguished. Depending on the phenotype dimension investigated, inherited factors are estimated to account for up to 80%. Linkage findings in dyslexia are relatively consistent across studies in comparison to findings for other neuropsychiatric disorders. This is particularly true for chromosome regions 1p34-p36, 6p21-p22, 15q21 and 18q11. Four candidate genes have recently been identified through systematic linkage disequilibrium studies in linkage region 6p21-p22, and through cloning approaches at chromosomal breakpoints. Results indicate that a disturbance in neuronal migration is a pathological correlate of dyslexia at the functional level. This review presents a summary of the latest insights into the genetics of dyslexia and an overview of anticipated future developments.

Genomewide scans of red cell indices suggest linkage on chromosome 6q23

BACKGROUND

The red cell indices quantify the size, number and oxygen-carrying ability of erythrocytes. Although the genetic basis of many monogenic forms of anaemia is well understood, comparatively little is known about the genes responsible for variation in the red cell indices among healthy participants.

OBJECTIVE

To identify quantitative trait loci (QTLs) responsible for normal variation in the red cell indices of 391 pairs of dizygotic twins who were measured longitudinally at 12, 14 and 16 years of age.

RESULTS

Evidence suggesting linkage of red cell indices to haemoglobin concentration (LOD = 3.03) and haematocrit (LOD = 2.95) on chromosome 6q23, a region previously identified as possibly harbouring a QTL for haematocrit, was found. Evidence for linkage to several other regions of the genome, including chromosome 4q32 for red cell count and 7q for mean cell volume, was also found. In contrast, there was little evidence of linkage to the chromosomal regions containing the genes for erythropoietin (7q21) and its receptor (19p13.2), nor to the regions containing the genes for the haemoglobin alpha (16p13.3) and beta chains (11p15.5).

CONCLUSION

Findings provide additional evidence for a QTL affecting haemoglobin and haematocrit on chromosome 6q23. In contrast, polymorphisms in the genes coding for erythropoietin, its receptor and the haemoglobin alpha and beta chains do not appear to contribute substantially to variation in the red cell indices between healthy persons.

Genes, language development, and language disorders

Genetic factors are important contributors to language and learning disorders, and discovery of the underlying genes can help delineate the basic neurological pathways that are involved. This information, in turn, can help define disorders and their perceptual and processing deficits. Initial molecular genetic studies of dyslexia, for example, appear to converge on defects in neuronal and axonal migration. Further study of individuals with abnormalities of these genes may lead to the recognition of characteristic cognitive deficits attributable to the neurological dysfunction. Such abnormalities may affect other disorders as well, and studies of co-morbidity of dyslexia with attention deficit disorder and speech sound disorder are helping to define the scope of these genes and show the etiological and cognitive commonalities between these conditions. The genetic contributions to specific language impairment (SLI) are not as well defined at this time, but similar molecular approaches are being applied to identify genes that influence SLI and comorbid disorders. While there is co-morbidity of SLI with dyslexia, it appears that most of the common genetic effects may be with the language characteristics of autism spectrum disorders rather than with dyslexia and related disorders. Identification of these genes and their neurological and cognitive effects should lay out a functional network of interacting genes and pathways that subserve language development. Understanding these processes can form the basis for refined procedures for diagnosis and treatment.

Further evidence that the KIAA0319 gene confers susceptibility to developmental dyslexia

The DYX2 locus on chromosome 6p22.2 is the most replicated region of linkage to developmental dyslexia (DD). Two candidate genes within this region have recently been implicated in the disorder: KIAA0319 and DCDC2. Variants within DCDC2 have shown association with DD in a US and a German sample. However, when we genotyped these specific variants in two large, independent UK samples, we obtained only weak, inconsistent evidence for their involvement in DD. Having previously found evidence that variation in the KIAA0319 gene confers susceptibility to DD, we sought to refine this genetic association by genotyping 36 additional SNPs in the gene. Nine SNPs, predominantly clustered around the first exon, showed the most significant association with DD in one or both UK samples, including rs3212236 in the 5' flanking region (P = 0.00003) and rs761100 in intron 1 (P = 0.0004). We have thus refined the region of association with developmental dyslexia to putative regulatory sequences around the first exon of the KIAA0319 gene, supporting the presence of functional mutations that could affect gene expression. Our data also suggests a possible interaction between KIAA0319 and DCDC2, which requires further testing.

Genes, environment, and dyslexia. The 2005 Norman Geschwind Memorial Lecture

This article presents an overview of some methods and results from our continuing studies of genetic and environmental influences on dyslexia, and on individual differences across the normal range that have been conducted over the past 25 years in the Colorado Learning Disabilities Research Center (CLDRC) and in related projects. CLDRC investigators compare the similarities of identical twin pairs who share all their genes and fraternal twins who share half their segregating genes to assess the balance of genetic, shared family environment, and nonshared environment influences on dyslexia and on individual differences across the normal range. We have learned that among the children we have studied in Colorado, group deficits in reading (dyslexia) and individual differences in reading across the normal range are primarily due to genetic influences, and these genetic influences are often shared with some of the same genetic influences on deficits and individual differences in language and ADHD. We have also learned from our molecular-genetic linkage studies that there are regions on several chromosomes likely to contain genes that influence dyslexia. Several specific genes within these regions have been tentatively identified through molecular-genetic association analyses, but much more research is needed to understand the pathways among specific genes, regions of noncoding DNA that regulate the activity of those genes, the brain, and dyslexia. I conclude with a discussion of our research on individual differences in early reading development, on the role of early learning constraints in dyslexia, and on how genetic influences are expressed through their interaction and correlation with the environment.

The genetic bases of speech sound disorders: evidence from spoken and written language

The purpose of this article is to review recent findings suggesting a genetic susceptibility for speech sound disorders (SSD), the most prevalent communication disorder in early childhood. The importance of genetic studies of SSD and the hypothetical underpinnings of these genetic findings are reviewed, as well as genetic associations of SSD with other language and reading disabilities. The authors propose that many genes contribute to SSD. They further hypothesize that some genes contribute to SSD disorders alone, whereas other genes influence both SSD and other written and spoken language disorders. The authors postulate that underlying common cognitive traits, or endophenotypes, are responsible for shared genetic influences of spoken and written language. They review findings from their genetic linkage study and from the literature to illustrate recent developments in this area. Finally, they discuss challenges for identifying genetic influence on SSD and propose a conceptual framework for study of the genetic basis of SSD.

Replication of reported linkages for dyslexia and spelling and suggestive evidence for novel regions on chromosomes 4 and 17

We report the first genome-wide linkage analysis for reading and spelling in a sample of 403 families of twins, aged between 12 and 25 years taken from the normal population and unselected for reading ability. These traits showed heritabilities of 0.52-0.73, and support for linkage exceeded replication levels (lod > 1.44) of seven of the 11 linkages reported in dyslexic samples, namely: 2q22.3, 3p12-q13, 6q11.2, 7q32, 15q21.1, 18p21, and Xq27.3. For five of these (2q22.3, 6q11.2, 7q32, 18p21, and Xq27), this study provides the first independent replication. 1p34-36 and 2p15-16 received some support, with lods of 1.2 and 0.83, respectively, whereas two regions received little support (6p23-21.3 and 11p15.5). This study also identified two novel linkages at 4p15.33-16.1 and 17p13.3, which received suggestive support (max. lod 2.08 and 1.99, respectively).

Developmental dyslexia: an update

Dyslexia is the most common and carefully studied of the learning disabilities in school-age children. It is characterized by a marked impairment in the development of reading skills, and affects a large number of people (5-10%). Reading difficulties may also arise from poor vision, emotional problems, decreased hearing ability, and behavioral disorders, such as attention-deficit hyperactivity (ADHD). Although many areas of the brain are involved in reading, analysis of postmortem brain specimens by a variety of imaging techniques most consistently suggests that deficiency within a specific component of the language system - the phonologic module - in the temporo-parietal-occipital brain region underlies dyslexia. It is a highly familial and heritable disorder with susceptibility loci on chromosomes 1, 2, 3, 6, 11, 13, 15 and 18. Recently, four candidate genes (KIAA 0319, DYX1C1, DCDC2 and ROBO1) are shown to be associated with dyslexia. Although some of these results are controversial because of the genetic heterogeneity of the disorder, the available evidence suggests that dyslexia could be due to the abnormal migration and maturation of neurons during early development. Interestingly, in spite of genetic heterogeneity, the pathology appears to involve common phonological coding deficits. The condition can be managed by a highly structured educational training exercise.