Genome-wide association study of restless legs syndrome identifies common variants in three genomic regions

Batch effects in the BRLMM genotype calling algorithm influence GWAS results for the Affymetrix 500K array

The Affymetrix GeneChip Human Mapping 500K array is common for genome-wide association studies (GWASs). Recent findings highlight the importance of accurate genotype calling algorithms to reduce the inflation in Type I and Type II error rates. Differential results due to genotype calling errors can introduce severe bias in case-control association study results. Using data from the Wellcome Trust Case Control Consortium, 1991 individuals with coronary artery disease (CAD) and 1500 controls from the UK Blood Services (NBS) were genotyped on the Affymetrix 500K array. Different batch sizes and compositions were used in the Bayesian Robust Linear Model with Mahalanobis distance classifier (BRLMM) genotype calling algorithm to assess the batch effect on downstream association analysis. Results show that composition (cases and controls genotyped simultaneously or separate) and size (number of individuals processed by BRLMM at a time) can create 2-3% discordance in the results for quality control and statistical analysis and may contribute to the lack of reproducibility between GWASs. The changes in batch size are largely responsible for differential single-nucleotide polymorphism results, yet we observe evidence of an interactive effect of batch size and composition that contributes to discordant results in the list of significantly associated loci.

Evaluating variations of genotype calling: a potential source of spurious associations in genome-wide association studies

Genome-wide association studies (GWAS) examine the entire human genome with the goal of identifying genetic variants (usually single nucleotide polymorphisms (SNPs)) that are associated with phenotypic traits such as disease status and drug response. The discordance of significantly associated SNPs for the same disease identified from different GWAS indicates that false associations exist in such results. In addition to the possible sources of spurious associations that have been investigated and discussed intensively, such as sample size and population stratification, an accurate and reproducible genotype calling algorithm is required for concordant GWAS results from different studies. However, variations of genotype calling of an algorithm and their effects on significantly associated SNPs identified in downstream association analyses have not been systematically investigated. In this paper, the variations of genotype calling using the Bayesian Robust Linear Model with Mahalanobis distance classifier (BRLMM) algorithm and the resulting influence on the lists of significantly associated SNPs were evaluated using the raw data of 270 HapMap samples analysed with the Affymetrix Human Mapping 500K Array Set (Affy500K) by changing algorithmic parameters. Modified were the Dynamic Model (DM) call confidence threshold (threshold) and the number of randomly selected SNPs (size). Comparative analysis of the calling results and the corresponding lists of significantly associated SNPs identified through association analysis revealed that algorithmic parameters used in BRLMM affected the genotype calls and the significantly associated SNPs. Both the threshold and the size affected the called genotypes and the lists of significantly associated SNPs in association analysis. The effect of the threshold was much larger than the effect of the size. Moreover, the heterozygous calls had lower consistency compared to the homozygous calls.

Assessing sources of inconsistencies in genotypes and their effects on genome-wide association studies with HapMap samples

The discordance in results of independent genome-wide association studies (GWAS) indicates the potential for Type I and Type II errors. We assessed the repeatibility of current Affymetrix technologies that support GWAS. Reasonable reproducibility was observed for both raw intensity and the genotypes/copy number variants. We also assessed consistencies between different SNP arrays and between genotype calling algorithms. We observed that the inconsistency in genotypes was generally small at the specimen level. To further examine whether the differences from genotyping and genotype calling are possible sources of variation in GWAS results, an association analysis was applied to compare the associated SNPs. We observed that the inconsistency in genotypes not only propagated to the association analysis, but was amplified in the associated SNPs. Our studies show that inconsistencies between SNP arrays and between genotype calling algorithms are potential sources for the lack of reproducibility in GWAS results.

Association study between antipsychotic-induced restless legs syndrome and polymorphisms of monoamine oxidase genes in schizophrenia

OBJECTIVE

This study aimed to investigate whether the monoamine oxidase (MAO) A and B genes are associated with antipsychotic-induced restless legs syndrome (RLS) in schizophrenia.

METHODS

We assessed antipsychotic-induced RLS symptoms in 190 Korean schizophrenic patients and divided the subjects into two groups: those with RLS symptoms (n = 96) and those without RLS symptoms (n = 94). Genotyping was performed for the variable number of tandem repeat (VNTR) polymorphism of the MAOA gene and A644G polymorphism of the MAOB gene.

RESULTS

There was no significant difference in the genotype and allele frequencies of all polymorphisms investigated between these two groups. However, the result of global haplotype analysis showed a significant difference in haplotype frequencies between male subjects with and without RLS symptoms (p = 0.013). The interaction between two polymorphisms had a significant effect on the RLS scores of both male (p = 0.047) and female (p = 0.028) patients.

CONCLUSIONS

These data do not suggest that the MAOA gene VNTR and MAOB gene A644G polymorphisms are associated with antipsychotic-induced RLS symptoms in schizophrenia. However, we found that the haplotype frequencies differed between the male schizophrenic patients with and without RLS symptom and the interaction between the two polymorphisms had a significant influence on the RLS scores of patients with schizophrenia.

Genetic analysis of sleep

Almost 20 years ago, the gene underlying fatal familial insomnia was discovered, and first suggested the concept that a single gene can regulate sleep. In the two decades since, there have been many advances in the field of behavioral genetics, but it is only in the past 10 years that the genetic analysis of sleep has emerged as an important discipline. Major findings include the discovery of a single gene underlying the sleep disorder narcolepsy, and identification of loci that make quantitative contributions to sleep characteristics. The sleep field has also expanded its focus from mammalian model organisms to Drosophila, zebrafish, and worms, which is allowing the application of novel genetic approaches. Researchers have undertaken large-scale screens to identify new genes that regulate sleep, and are also probing questions of sleep circuitry and sleep function on a molecular level. As genetic tools continue to be refined in each model organism, the genes that support a specific function in sleep will become more apparent. Thus, while our understanding of sleep still remains rudimentary, rapid progress is expected from these recently initiated studies.

Identification of E74-like factor 1 (ELF1) as a transcriptional regulator of the Hox cofactor MEIS1

OBJECTIVE

Myeloid ectropic viral integration site 1 (MEIS1) is a Hox cofactor known for its role in development and is strongly linked to normal and leukemic hematopoiesis. Although previous studies have focused on identifying protein partners of MEIS1 and its transcriptionally regulated targets, little is known about the upstream transcriptional regulators of this tightly regulated gene. Understanding the regulation of MEIS1 is important to understanding normal hematopoiesis and leukemogenesis.

MATERIALS AND METHODS

Here we describe our studies focusing on the evolutionary conserved putative MEIS1 promoter region. Phylogenetic sequence analysis and reporter assays in MEIS1-expressing (K562) and nonexpressing (HL60) leukemic cell line models were used to identify key regulatory regions and potential transcription factor binding sites within the candidate promoter region followed by functional and expression studies of one identified regulator in both cell lines and primary human cord blood and leukemia samples.

RESULTS

Chromatin status of MEIS1 promoter region is associated with MEIS1 expression. Truncation and mutation studies coupled with reporter assays revealed that a conserved ETS family member binding site located 289 bp upstream of the annotated human MEIS1 transcription start site is required for promoter activity. Of the three ETS family members tested, only ELF1 was enriched on the MEIS1 promoter as assessed by both electrophoretic mobility shift assay and chromatin immunoprecipitation experiments in K562. This finding was confirmed in MEIS1-expressing primary human samples. Moreover, small interfering RNA-mediated knockdown of ELF1 in K562 cells was associated with a decreased MEIS1 expression.

CONCLUSIONS

We conclude that the ETS transcription factor ELF1 is an important positive regulator of MEIS1 expression.

Advances in the science of genomics in restless legs syndrome

Restless legs syndrome (RLS) is a sleep and movement disorder that affects up to 15% of the population across the lifespan. Many health care providers have doubted its validity as an illness and are uncertain as to the implications of health care outcomes. The cause of RLS is unknown. Common treatment options include dopaminergics, benzodiazepines, and opioids; however, the pharmacogenetic mechanisms of treatment are unknown. One of the greatest genetic discoveries in 2007 was the identification of genetic variance associated with RLS. There is, however, a lack of knowledge related to RLS and its genetic basis. Therefore, the purposes of this article are to (a) provide information about the science of clinical care related to RLS; (b) present a systematic review of the literature on the status of genetics/genomics of RLS, including the discovery of associated genetic variance; and (c) identify implications of the current state of the science for health care providers and biobehavioral researchers. With the continuing genetic discoveries in RLS, health care providers, specifically nurses who play a major role in research, genetic counseling, and education, need to understand the implications of this sleep and movement disorder for patients across the lifespan.

Low-risk variants FGFR2, TNRC9 and LSP1 in German familial breast cancer patients

To validate common low-risk variants predisposing for breast cancer (BC) in a large set of BRCA1/2 negative familial or genetically enriched cases from Germany, we genotyped 1,415 cases and 1,830 healthy women by MALDI-TOF in 105 candidate SNPs. Significantly higher ORs than previously reported for heterozygous unselected cases were found for the minor allele in FGFR2 (OR = 1.43, 95% CI 1.30-1.59, p-value = 1.24 x 10(-12)) and for TNRC9 (OR = 1.33, 95% CI 1.19-1.46, p-value = 1.54 x 10(-7)). Most intriguing, however, were the ORs for homozygous carriers from high-risk families for FGFR2 (OR = 2.05, 95% CI 1.68-2.51, LSP1 (OR = 0.49, 95% CI 0.28-0.86) and TNRC9 (OR = 1.62, 95% CI 1.27-2.07). Moreover, the additional validation of 99 CGEMS-SNPs identified putative novel susceptibility alleles within the LSP1 gene (OR = 0.73, 95% CI 0.61-0.87, p-value = 5.23 x 10(-4)). Finally, we provide evidence for the first time that a low-risk variant located at 6q22.33 (rs6569479) is associated with estrogen receptor negative BC in familial cases (OR = 1.33, 95% CI 1.06-1.66; p-value = 0.012). Our data confirm the impact of the previously identified susceptibility loci and provide preliminary evidence for novel susceptibility loci in familial BC cases and correlate them to specific histopathological subtypes defined by estrogen receptor status.

Whole genome association studies in complex diseases: where do we stand?

Hundreds of genome-wide association studies have been performed in recent years in order to try to identify common variants that associate with complex disease. These have met with varying success. Some of the strongest effects of common variants have been found in lateonset diseases and in drug response. The major histocompatibility complex has also shown very strong association with a variety of disorders. Although there have been some notable success stories in neuropsychiatric genetics, on the whole, common variation has explained little of the high heritability of these traits. In contrast, early studies of rare copy number variants have led rapidly to a number of genes and loci that strongly associate with neuropsychiatric disorders. It is likely that the use of whole-genome sequencing to extend the study of rare variation in neuropsychiatry will greatly advance our understanding of neuropsychiatric genetics.

Ropinirole in restless legs syndrome and periodic limb movement disorder

Restless legs syndrome and periodic limb movement disorder of sleep are now recognized as prevalent, distinct, yet overlapping disorders affecting all age groups. Although delineation of the mechanisms underlying these disorders continues to be the focus of very intense research efforts, it has become apparent that there is a prominent role for dopaminergic agents in the clinical management of these patients. Among the various dopaminergic drugs, ropinirole has undergone relatively intense and critical scrutiny, and appears to provide a safe and efficacious treatment option for patients with these two conditions. The more recent development of a controlled formulation for this drug is likely to yield additional benefits such as improved adherence and reduced fluctuations in daytime and nighttime symptoms. However, there is not enough evidence at this time to support such assumption.

Long non-coding RNAs in nervous system function and disease

Central nervous system (CNS) development, homeostasis, stress responses, and plasticity are all mediated by epigenetic mechanisms that modulate gene expression and promote selective deployment of functional gene networks in response to complex profiles of interoceptive and environmental signals. Thus, not surprisingly, disruptions of these epigenetic processes are implicated in the pathogenesis of a spectrum of neurological and psychiatric diseases. Epigenetic mechanisms involve chromatin remodeling by relatively generic complexes that catalyze DNA methylation and various types of histone modifications. There is increasing evidence that these complexes are directed to their sites of action by long non-protein-coding RNAs (lncRNAs), of which there are tens if not hundreds of thousands specified in the genome. LncRNAs are transcribed in complex intergenic, overlapping and antisense patterns relative to adjacent protein-coding genes, suggesting that many lncRNAs regulate the expression of these genes. LncRNAs also participate in a wide array of subcellular processes, including the formation and function of cellular organelles. Most lncRNAs are transcribed in a developmentally regulated and cell type specific manner, particularly in the CNS, wherein over half of all lncRNAs are expressed. While the numerous biological functions of lncRNAs are yet to be characterized fully, a number of recent studies suggest that lnRNAs are important for mediating cell identity. This function seems to be especially important for generating the enormous array of regional neuronal and glial cell subtypes that are present in the CNS. Further studies have also begun to elucidate additional roles played by lncRNAs in CNS processes, including homeostasis, stress responses and plasticity. Herein, we review emerging evidence that highlights the expression and function of lncRNAs in the CNS and suggests that lncRNA deregulation is an important factor in various CNS pathologies including neurodevelopmental, neurodegenerative and neuroimmunological disorders, primary brain tumors, and psychiatric diseases.

Intravenous iron dextran for severe refractory restless legs syndrome

Reduced brain iron is strongly associated with restless legs syndrome (RLS). Oral iron supplements are commonly recommended for RLS but are largely ineffective due to poor absorption and poor tolerability at required doses. Intravenous iron dextran has been shown to increase brain iron content. Surprisingly only a few reports have ever presented data on the clinical effect of high dose intravenous iron for RLS. We retrospectively identified 25 subjects (age 53.2+/-11.9, 7 male) that received intravenous iron for RLS refractory to conventional treatments. We infused 1g of high molecular weight iron dextran over five hours. The age of RLS onset was 32.6+/-13.0 years and 15 subjects had a positive family history of RLS. Patients attempted 7.5+/-2.7 medications for RLS prior to iron therapy. Baseline ferritins ranged from 5 to 248 ng/ml (mean 43.5+/-58.0) and 20/25 had ferritins of less than 50. Two subjects did not complete their entire infusion due to anaphylactic type symptoms but are included. Overall, 2 subjects reported complete amelioration of all RLS symptoms, 11 reported marked improvement, 2 moderate improvement, 3 mild improvement, and 6 reported no improvement. For those with improvement, the duration of effect was highly variable (mean 15.8+/-17.7 weeks, range 1-60 weeks). Twelve subjects had multiple infusions. Iron dextran can dramatically improve refractory RLS but results are inconsistent and not predicted by patient demographics. Although burdened by a higher rate of anaphylactic reactions, iron dextran may be superior to other IV iron preparations.

Approaches to unravel the genetics of sleep

Sleep and circadian rhythms are complex and inter-connected physiological processes. Relative to the remarkable progress made in identifying the genetic basis of circadian rhythms and some specific sleep disorders, efforts to identify genetic variants associated with normal variation in sleep have progressed more slowly. Two key issues concerning the design of such studies must be addressed in order to facilitate further progress. The first concerns the sleep related traits to be targeted. The second issue is the choice of the gene-mapping method (linkage, candidate gene association or genome-wide association). This paper discusses these issues, reviews published studies of sleep phenotypes, and recommends cost-effective methods to advance knowledge of the genetic determinants of normal sleep patterns.

Restless legs syndrome and erectile dysfunction

STUDY OBJECTIVES

Dopaminergic hypofunction in the central nervous system may contribute to restless legs syndrome (RLS) and erectile dysfunction (ED). We therefore examined whether men with RLS have higher prevalences of ED.

DESIGN

RLS was assessed using a set of standardized questions. Men were considered to have RLS if they met 4 RLS diagnostic criteria recommended by the International RLS Study Group, and had restless legs > or = 5 times/month. Erectile function was assessed by a questionnaire.

SETTING

Community-based.

PARTICIPANTS

23,119 men who participated in the Health Professional Follow-up Study free of diabetes and arthritis.

RESULTS

Multivariate-adjusted odds ratios for ED were 1.16 and 1.78 (95% confidence interval: 1.4, 2.3; P trend < 0.0001) for men with RLS symptoms 5-14 times/mo, and 15+ times/mo, respectively, relative to those without RLS, after adjusting for age, smoking, BMI, antidepressant use, and other covariates. The associations between RLS and ED persisted in subgroup analysis according to age, obesity, and smoking status.

CONCLUSIONS

Men with RLS had a higher likelihood of concurrent ED, and the magnitude of the observed association was increased with a higher frequency of RLS symptoms. These results suggest that ED and RLS share common determinants.

Restless legs syndrome and painful neuropathy-retrospective study. A role for nociceptive deafferentation?

OBJECTIVES

Restless legs syndrome (RLS) occurs in polyneuropathy with small fiber involvement, possibly as a peculiar form of neuropathic pain; however, the relationship between pain and RLS has been poorly investigated in polyneuropathy.

DESIGN, SETTING, AND PATIENTS

We evaluated retrospectively the occurrence of RLS in 102 consecutive patients with polyneuropathy manifesting with neuropathic pain or dysesthesia, referred to the Neuromuscular Center, using the National Institutes of Health criteria for RLS. The patients were classified in subgroups characterized respectively by allodynia (hyperphenomena), with reported unpleasant sensations evoked by tactile stimuli, and hypoalgesia (hypophenomena), with absent pain sensation to pinprick, according to putative mechanisms of pain.

RESULTS

RLS was present in 41/102 patients (40.2%). It was significantly more frequent in the "hypoalgesia" (23/37) than in the "allodynia" subgroup (9/31; P = 0.008) and in the not classifiable cases (9/34; P = 0.004).

CONCLUSIONS

RLS is frequent in painful polyneuropathy and is significantly associated with decreased small fiber input, thus nociceptive deafferentation may represent a factor interacting with RLS "generators," possibly at spinal level. We suggest that overactivity of the spinal structures implicated in RLS may be triggered by nociceptive deafferentation in a subgroup of patients with painful polyneuropathy. Our findings, prompting a mechanistic characterization of RLS associated with painful polyneuropathy, have to be confirmed in a prospective study.

Child and adolescent psychiatric genetics

The current status of child and adolescent psychiatric genetics appears promising in light of the initiation of genome-wide association studies (GWAS) for diverse polygenic disorders and the molecular elucidation of monogenic Rett syndrome, for which recent functional studies provide hope for pharmacological treatment strategies. Within the last 50 years, tremendous progress has been made in linking genetic variation to behavioral phenotypes and psychiatric disorders. We summarize the major findings of the Human Genome Project and dwell on largely unsuccessful candidate gene and linkage studies. GWAS for the first time offer the possibility to detect single nucleotide polymorphisms and copy number variants without a priori hypotheses as to their molecular etiology. At the same time it is becoming increasingly clear that very large sample sizes are required in order to enable genome wide significant findings, thus necessitating further large-scaled ascertainment schemes for the successful elucidation of the molecular genetics of childhood and adolescent psychiatric disorders. We conclude by reflecting on different scenarios for future research into the molecular basis of early onset psychiatric disorders. This review represents the introductory article of this special issue of the European Child and Adolescent Psychiatry.

Genotyping sleep disorders patients

OBJECTIVE

The genetic susceptibility factors underlying sleep disorders might help us predict prognoses and responses to treatment. Several candidate polymorphisms for sleep disorders have been proposed, but there has as yet inadequate replication or validation that the candidates may be useful in the clinical setting.

METHODS

To assess the validity of several candidate associations, we obtained saliva deoxyribonucleic acid (DNA) samples and clinical information from 360 consenting research participants who were undergoing clinical polysomnograms. Ten single nucleotide polymorphisms (SNPs) were genotyped. These were thought to be related to depression, circadian sleep disorders, sleep apnea, restless legs syndrome (RLS), excessive sleepiness, or to slow waves in sleep.

RESULTS

With multivariate generalized linear models, the association of TEF rs738499 with depressive symptoms was confirmed. Equivocal statistical evidence of association of rs1801260 (the C3111T SNP in the CLOCK gene) with morningness/eveningness and an association of Apolipoprotein E (APOE) rs429358 with the Epworth Sleepiness Scale (ESS) were obtained, but these associations were not strong enough to be of clinical value by themselves. Predicted association of SNPs with sleep apnea, RLS, and slow wave sleep were not confirmed.

CONCLUSION

The SNPs tested would not, by themselves, be of use for clinical genotyping in a sleep clinic.

No significance of the COMT val158met polymorphism in restless legs syndrome

The catechol-O-methyltransferase (COMT) val(158)met polymorphism, which codes for the substitution of valine (val) by methionine (met) leading to a reduced COMT activity in homo- or heterozygous individuals, is associated with individual pain sensitivity and dopaminergic responses in Parkinson's disease as well as with various chronic painful diseases. Recent investigations support the notion of an alteration of the medial pain pathway as well as of the descending inhibitory control system in restless legs syndrome (RLS), that both involve dopaminergic transmission as well. Thus, the distribution of the COMT val(158)met polymorphism was assessed in 298 RLS patients and compared with 135 healthy controls in relation to sex, age of onset and family history. The data revealed no significant differences in the distribution of the COMT val(158)met polymorphism in RLS patients compared with the control group, also when the heterozygous and the homozygous group containing the (158)met allele were combined. In addition, sex, age of onset and family history were not associated with the COMT val(158)met polymorphism in this German population of RLS patients. The present study adds to previous mostly negative investigations on the genetic determination of dopaminergic transmission in RLS, which have - so far - only detected an association of the MAO-A activity and RLS in females in a French-Canadian population. Further investigations assessing the different COMT haplotypes and experimental and clinical parameters are nevertheless warranted.

Genome-wide association studies: a powerful tool for neurogenomics

As their power and utility increase, genome-wide association (GWA) studies are poised to become an important element of the neurosurgeon's toolkit for diagnosing and treating disease. In this paper, the authors review recent findings and discuss issues associated with gathering and analyzing GWA data for the study of neurological diseases and disorders, including those of neurosurgical importance. Their goal is to provide neurosurgeons and other clinicians with a better understanding of the practical and theoretical issues associated with this line of research. A modern GWA study involves testing hundreds of thousands of genetic markers across an entire genome, often in thousands of individuals, for any significant association with a particular disease. The number of markers assayed in a study presents several practical and theoretical issues that must be considered when planning the study. Genome-wide association studies show great promise in our understanding of the genes underlying common neurological diseases and disorders, as well as in leading to a new generation of genetic tests for clinicians.

Depressive disorders in restless legs syndrome: epidemiology, pathophysiology and management

Epidemiological studies report a 2- to 4-fold risk of a depressive disorder in patients with restless legs syndrome (RLS) compared with healthy controls. The high prevalence rates of depression in RLS indicate an association between the two disorders. Severe sleep disturbance due to the nightly occurrence of RLS symptoms is a common complaint of patients with moderate or severe RLS and may substantially contribute to the emergence of depressive symptoms. Difficulty in the diagnosis of a depressive disorder in patients with RLS may arise from the overlap of symptoms in the two disorders, as sleep-related complaints are frequent both in RLS and depression. The treatment of depression in RLS has some unique aspects, as several antidepressants have been reported to trigger or worsen RLS. To date, no studies have been published regarding the course of depression in untreated and treated patients with RLS. On the other hand, the presence of co-morbid depression can have a substantial impact on the global treatment outcome. In patients with co-morbid moderate/severe depression, antidepressant therapy in parallel with or shortly after commencing RLS treatment is usually necessary. Data from recent trials with dopamine receptor agonists indicate that mild to moderate depressive symptoms are often relieved with improvement of RLS symptoms.

VALID: visualization of association study results and linkage disequilibrium

Promising findings from genetic association studies are commonly presented with two distinct figures: one gives the association study results and the other indicates linkage disequilibrium (LD) between genetic markers in the region(s) of interest. Fully interpreting the results of such studies requires synthesizing the information in these figures, which is generally done in a subjective and unsystematic manner. Here we present a method to formally combine association results and LD and display them in the same figure; we have developed a freely available web-based application that can be used to generate figures to display the combined data. To demonstrate this approach we apply it to fine mapping data from the prostate cancer 8q24 loci. Combining these two sources of information in a single figure allows one to more clearly assess patterns of association, facilitating the interpretation of genome-wide and fine mapping data and improving our ability to localize causal variants.

Parkin gene modifies the effect of RLS4 on the age at onset of restless legs syndrome (RLS)

A co-occurrence of restless legs syndrome (RLS) and Parkin mutations has been described. In South Tyrolean RLS patients, a novel RLS locus has been found (RLS4) and recurrent Parkin mutations have been reported. By a systematic screen we investigated the presence of founder Parkin mutations in South Tyrolean RLS patients with known carrier status at the RLS4 locus and assessed whether these mutations alone or in combination influence the RLS phenotype measured by three quantitative RLS traits (age at onset (AAO) and two severity measurements). The Parkin mutation alone showed no effect, whereas RLS4 had a significant effect on the AAO (P = 0.0096, decrease of AAO of 9.1 years), but did not influence severity. Carriers of both, a Parkin mutation and the RLS4 haplotype, showed an association with AAO (P = 0.0016), corresponding to an anticipation of RLS onset age of 16.9 years. However, there was no effect on the disease severity. Our results suggest that the occurrence of a heterozygous Parkin mutation works in tandem with the gene at the RLS4 locus to lower the AAO in RLS.

Kinase mutations in human disease: interpreting genotype-phenotype relationships

Protein kinases are one of the largest families of evolutionarily related proteins and comprise one of the most abundant gene families in humans. Here we survey kinase gene mutations from the perspective of human disease phenotypes and further analyse the structural features of mutant kinases, including mutational hotspots. Our evaluation of the genotype-phenotype relationship across 915 human kinase mutations - that underlie 67 single-gene diseases, mainly inherited developmental and metabolic disorders and also certain cancers - enhances our understanding of the role of kinases in development, kinase dysfunction in pathogenesis and kinases as potential targets for therapy.

Two-stage testing strategies for genome-wide association studies in family-based designs

The analysis of genome-wide association studies (GWAS) poses statistical hurdles that have to be handled efficiently in order for the study to be successful. The two largest impediments in the analysis phase of the study are the multiple comparisons problem and maintaining robustness against confounding due to population admixture and stratification. For quantitative traits in family-based designs, Van Steen (1) proposed a two-stage testing strategy that can be considered a hybrid approach between family-based and population-based analysis. By including the population-based component into the family-based analysis, the Van Steen algorithm maximizes the statistical power, while at the same time, maintains the original robustness of family-based association tests (FBATs) (2-4). The Van Steen approach consists of two statistically independent steps, a screening step and a testing step. For all genotyped single nucleotide polymorphisms (SNPs), the screening step examines the evidence for association at a population-based level. Based on support for a potential genetic association from the screening step, the SNPs are prioritized for testing in the next step, where they are analyzed with a FBAT (3). By exploiting population-based information in the screening step that is not utilized in family-based association testing step, the two steps are statistically independent. Therefore, the use of the population-based data for the purposes of screening does not bias the FBAT statistic calculated in the testing step. Depending on the trait type and the ascertainment conditions, Van Steen-type testing strategies can achieve statistical power levels that are comparable to those of population-based studies with the same number of probands. In this chapter, we review the original Van Steen algorithm, its numerous extensions, and discuss its advantages and disadvantages.

Update on the management of restless legs syndrome: existing and emerging treatment options

Restless legs syndrome (RLS) is a sensorimotor disorder, characterized by a circadian variation of symptoms involving an urge to move the limbs (usually the legs) as well as paresthesias. There is a primary (familial) and a secondary (acquired) form, which affects a wide variety of individuals, such as pregnant women, patients with end-stage renal disease, iron deficiency, rheumatic disease, and persons taking medications. The symptoms reflect a circadian fluctuation of dopamine in the substantia nigra. RLS patients have lower dopamine and iron levels in the substantia nigra and respond to both dopaminergic therapy and iron administration. Iron, as a cofactor of dopamine production and a regulator of the expression of dopamine type 2-receptor, has an important role in the RLS etiology. In the management of the disease, the first step is to investigate possible secondary causes and their treatment. Dopaminergic agents are considered as the first-line therapy for moderate to severe RLS. If dopaminergic drugs are contraindicated or not efficacious, or if symptoms are resistant and unremitting, gabapentin or other antiepileptic agents, benzodiazepines, or opioids can be used for RLS therapy. Undiagnosed, wrongly diagnosed, and untreated RLS is associated with a significant impairment of the quality of life.

Behavioral Sleep Medicine Interventions for Restless Legs Syndrome and Periodic Limb Movement Disorder

Restless Legs Syndrome (RLS) and Periodic Limb Movement Disorder (PLMD) are sleep disorders that are commonly seen in clinical practice. The standard treatment recommendations for these disorders are pharmacologic; most recently both conditions are most typically managed with pramipexole or ropinerole, which are FDA approved for the treatment of RLS. A mix of behavioral suggestions is included in treatment algorithms for providers as well as in patient education materials. While these suggestions have considerable merit, they are typically not delivered as an intervention, but instead provided as a series of helpful tips. There is emerging evidence for providing such suggestions as a more active and comprehensive intervention as part of a cognitive-behavioral package as well as for exercise therapy and cognitive behavioral therapy for insomnia to be delivered as active treatments for RLS and/or PLMD.

Restless legs syndrome

Restless legs syndrome (RLS) is a common neurological sensory-motor disorder that is characterized by intense restlessness and unpleasant creeping sensations deep inside the lower legs. Symptoms appear when the legs are at rest and are worst in the evening and at night. They force patients to keep moving their legs, and often to get out of bed and wander about. Periodic limb movements (PLMS) are also common during sleep amongst those suffering from RLS, and sleep efficiency is severely reduced. There are idiopathic as well as symptomatic forms of RLS, the latter being associated with e.g. pregnancy, iron deficiency and chronic renal failure. A family history of RLS is very common and pedigrees in these cases suggest an autosomal-dominant transmission with high penetrance. Genetic investigations have been performed in order to identify genes associated with RLS. Several loci have been found (on chromosomes 12q, 14q, 9p, 2q, 20p and 16p). Pathophysiology of RLS remains incompletely understood. However, advanced brain imaging studies and positive results of dopaminergic treatment suggest that RLS may be generated by dopamine dysfunction locally within the central nervous system. At present, there is a wide range of treatment options including levodopa, dopamine agonists, opioids, benzodiazepines, antiepileptic drugs and iron supplements.

The genetics of sleep disorders in humans: narcolepsy, restless legs syndrome, and obstructive sleep apnea syndrome

Sleep disorders are a group of neurological disorders known to cause public health problems associated with interference with daily activities including cognitive problems, poor job performance and reduced productivity. There is strong evidence emerging for the presence of genes influencing sleep disorders, such as narcolepsy (NRCLP), restless legs syndrome (RLS), and obstructive sleep apnea syndrome (OSAS). NRCLP is typically characterized by excessive daytime sleepiness, cataplexy, sleep paralysis and hallucinations. RLS is manifested by compelling need to move the legs and usually experienced when trying to sleep. OSAS is major sleep problem characterized by recurrent episodes of upper airway collapse and obstruction during sleep. In the recent years, many research groups have attempted to identify the susceptibility and candidate genes for NRCLP, RLS, and OSAS through the sequential analyses of genetic linkage and association. The purpose of this review is to summarize some of remarkable molecular advances in sleep and sleep disorders, thereby providing a greater understanding of the complex sleep processes, and a platform for future therapeutic interventions.

Age-related macular degeneration and functional promoter and coding variants of the apolipoprotein E gene

Age-related macular degeneration (AMD) is a frequent, multifactorial disease of the central retina and a major cause of irreversible vision loss in industrialized countries. Apolipoprotein E (APOE) has been consistently associated with AMD, particularly its two functional isoforms E2 (predisposing) and E4 (protective). The biological correlate of this association, however, is still unclear. In this study, we have defined an extended haplotype block encompassing the entire APOE gene locus, including known coding as well as cis-regulatory promoter variants. Of the five extended APOE haplotypes common in the general population, two were found to be significantly associated with AMD, namely G-G-G-G-epsilon2 (odds ratio [OR], 1.59; 95% confidence interval [CI], 1.19-2.12) and T-G-A-G-epsilon4 (OR, 0.76; 95% CI, 0.58-0.99). When analyzing common extended haplotype combinations, T-C-G-G-epsilon3/T-G-A-G-epsilon4 exhibited the most prominent effect (OR, 0.32; 95% CI, 0.20-0.51). Intriguingly, we also found one extended epsilon3-haplotype, G-G-G-A-epsilon3, to be protective in the homozygous state (OR, 0.65; 95% CI, 0.49-0.87). Since single nucleotide polymorphism (SNP) rs405509:G>T is a constituent of the extended epsilon-haplotype block and is known to significantly influence APOE promoter activity, we hypothesize that both the relative rate of APOE isoform expression in conjunction with established functional differences of the respective isoforms may be crucial in mediating AMD pathology. This would also imply that genotyping of the core epsilon-haplotypes alone is not sufficient to estimate AMD risk, but that determination of extended haplotype combinations, including the functional promoter SNP rs405509, is required instead.

Suicide neurobiology

In this review, we examine the history of the neurobiology of suicide, as well as the genetics, molecular and neurochemical findings in suicide research. Our analysis begins with a summary of family, twin, and adoption studies, which provide support for the investigation of genetic variation in suicide risk. This leads to an overview of neurochemical findings restricted to neurotransmitters and their receptors, including recent findings in whole genome gene expression studies. Next, we look at recent studies investigating lipid metabolism, cell signalling with a particular emphasis on growth factors, stress systems with a focus on the role of polyamines, and finally, glial cell pathology in suicide. We conclude with a description of new ideas to study the neurobiology of suicide, including subject-specific analysis, protein modification assessment, neuroarchitecture studies, and study design strategies to investigate the complex suicide phenotype.

Restless Legs Syndrome (RLS) and Parkinson's disease (PD)-related disorders or different entities?

The relationship between Restless Legs Syndrome (RLS) and Parkinson's disease (PD) is still controversial. Most genetic, pathological, and imaging data argue against a close association of these two disorders. Still, many studies reported an increased prevalence of RLS in PD patients. These studies are difficult to interpret because the current diagnostic criteria for RLS have not been validated in PD patients. Although many PD patients suffer from motor restlessness due to parkinsonism and may thus mimic RLS, the risk for (secondary) RLS in PD patients is probably slightly increased. This review provides an overview of the current pertinent literature and discusses the possible association between RLS and PD.

The genetic and molecular regulation of sleep: from fruit flies to humans

It has been known for a long time that genetic factors affect sleep quantity and quality. Genetic screens have identified several mutations that affect sleep across species, pointing to an evolutionary conserved regulation of sleep. Moreover, it has also been recognized that sleep affects gene expression. These findings have given valuable insights into the molecular underpinnings of sleep regulation and function that might lead the way to more efficient treatments for sleep disorders.

Factors contributing to the development of restless legs syndrome in patients with Parkinson disease

Although restless legs syndrome (RLS) commonly accompanies Parkinson disease (PD), the mechanism of RLS development in PD is still unclear. We investigated the prevalence of RLS in Korean patients with PD, and the possible contributing factors to the development of RLS in those patients. Four hundred forty-seven consecutive patients with PD were interviewed and examined. Among them, 73 patients (16.3%) were diagnosed with RLS. PD patients with RLS had a longer duration of PD symptoms, more severe PD disability, a greater degree of cognitive decline, and a longer duration of antiparkinson therapy than those without RLS. Multivariate logistic regression analysis revealed that the duration of antiparkinson therapy was the most significant factor contributing to the development of RLS in patients with PD. The present results support a higher prevalence of RLS in patients with PD and suggest that long-term antiparkinson therapy, rather than PD itself, may contribute to the development of RLS.

Genome-wide association study of alcohol dependence

CONTEXT

Alcohol dependence is a serious and common public health problem. It is well established that genetic factors play a major role in the development of this disorder. Identification of genes that contribute to alcohol dependence will improve our understanding of the mechanisms that underlie this disorder.

OBJECTIVE

To identify susceptibility genes for alcohol dependence through a genome-wide association study (GWAS) and a follow-up study in a population of German male inpatients with an early age at onset.

DESIGN

The GWAS tested 524,396 single-nucleotide polymorphisms (SNPs). All SNPs with P < 10(-4) were subjected to the follow-up study. In addition, nominally significant SNPs from genes that had also shown expression changes in rat brains after long-term alcohol consumption were selected for the follow-up step.

SETTING

Five university hospitals in southern and central Germany.

PARTICIPANTS

The GWAS included 487 male inpatients with alcohol dependence as defined by the DSM-IV and an age at onset younger than 28 years and 1358 population-based control individuals. The follow-up study included 1024 male inpatients and 996 age-matched male controls. All the participants were of German descent.

MAIN OUTCOME MEASURES

Significant association findings in the GWAS and follow-up study with the same alleles.

RESULTS

The GWAS produced 121 SNPs with nominal P < 10(-4). These, together with 19 additional SNPs from homologues of rat genes showing differential expression, were genotyped in the follow-up sample. Fifteen SNPs showed significant association with the same allele as in the GWAS. In the combined analysis, 2 closely linked intergenic SNPs met genome-wide significance (rs7590720, P = 9.72 x 10(-9); rs1344694, P = 1.69 x 10(-8)). They are located on chromosome region 2q35, which has been implicated in linkage studies for alcohol phenotypes. Nine SNPs were located in genes, including the CDH13 and ADH1C genes, that have been reported to be associated with alcohol dependence.

CONCLUSIONS

This is the first GWAS and follow-up study to identify a genome-wide significant association in alcohol dependence. Further independent studies are required to confirm these findings.

Transcriptional activation by MEIS1A in response to protein kinase A signaling requires the transducers of regulated CREB family of CREB co-activators

The transcription factor encoded by the murine ecotropic integration site 1 gene (MEIS1) is a partner of HOX and PBX proteins. It has been implicated in embryonic patterning and leukemia, and causally linked to restless legs syndrome. The MEIS1A C terminus harbors a transcriptional activation domain that is stimulated by protein kinase A (PKA) in a manner dependent on the co-activator of cAMP response element-binding protein (CREB), CREB-binding protein (CBP). We explored the involvement of another mediator of PKA-inducible transcription, namely the CREB co-activators transducers of regulated CREB activity (TORCs). Overexpression of TORC1 or TORC2 bypassed PKA for activation by MEIS1A. Co-immunoprecipitation experiments demonstrated a physical interaction between MEIS1 and TORC2 that is dependent on the MEIS1A C terminus, whereas chromatin immunoprecipitation revealed PKA-inducible recruitment of MEIS1, PBX1, and TORC2 on the MEIS1 target genes Hoxb2 and Meis1. The MEIS1 interaction domain on TORC1 was mapped to the N-terminal coiled-coil region, and TORC1 mutants lacking this domain attenuated the response to PKA on a natural MEIS1A target enhancer. Thus, TORCs physically cooperate with MEIS1 to achieve PKA-inducible transactivation through the MEIS1A C terminus, suggesting a concerted action in developmental and oncogenic processes.

Exploring the genetic link between RLS and ADHD

Attention deficit/hyperactivity disorder (ADHD) is a highly heritable neurodevelopmental disorder of childhood onset. Clinical and biological evidence points to shared common central nervous system (CNS) pathology of ADHD and restless legs syndrome (RLS). It was hypothesized that variants previously found to be associated with RLS in two large genome-wide association studies (GWA), will also be associated with ADHD. SNPs located in MEIS1 (rs2300478), BTBD9 (rs9296249, rs3923809, rs6923737), and MAP2K5 (rs12593813, rs4489954) as well as three SNPs tagging the identified haplotype in MEIS1 (rs6710341, rs12469063, rs4544423) were genotyped in a well characterized German sample of 224 families comprising one or more affected sibs (386 children) and both parents. We found no evidence for preferential transmission of the hypothesized variants to ADHD. Subsequent analyses elicited nominal significant association with haplotypes consisting of the three SNPs in BTBD9 (chi2 = 14.8, df = 7, nominal p = 0.039). According to exploratory post hoc analyses, the major contribution to this finding came from the A-A-A-haplotype with a haplotype-wise nominal p-value of 0.009. However, this result did not withstand correction for multiple testing. In view of our results, RLS risk alleles may have a lower effect on ADHD than on RLS or may not be involved in ADHD. The negative findings may additionally result from genetic heterogeneity of ADHD, i.e. risk alleles for RLS may only be relevant for certain subtypes of ADHD. Genes relevant to RLS remain interesting candidates for ADHD; particularly BTBD9 needs further study, as it has been related to iron storage, a potential pathophysiological link between RLS and certain subtypes of ADHD.