Analysis of 1276 Haplotype-Resolved Genomes Allows Characterization of Cis- and Trans-Abundant Genes.

Many methods for haplotyping have materialized, but their application on a significant scale has been rare to date. Here we summarize analyses that were carried out in 1092 genomes from the 1000 Genomes Consortium and validated in an unprecedented number of 184 PGP genomes that have been experimentally haplotype-resolved by application of the Long-Fragment Read (LFR) technology. These analyses provided first insights into the diplotypic nature of human genomes and its potential functional implications. Thus, protein-changing variants were not randomly distributed between the two homologues of 18,121 autosomal protein-coding genes but occurred significantly more frequently in cis than in trans configurations in virtually each of the 1276 phased genomes. This resulted in global cis/trans ratios of ~60:40, establishing "cis abundance" as a universal characteristic of diploid human genomes. This phenomenon was based on two different classes of genes, a larger one exhibiting cis configurations of protein-changing variants in excess, so-called "cis-abundant" genes, and a smaller one of "trans-abundant" genes. These two gene classes, which together constitute a common diplotypic exome, were further functionally distinguished by means of gene ontology (GO) and pathway enrichment analysis. Moreover, they were distinguishable in terms of their effects on the human interactome, where they constitute distinct cis and trans modules, as shown with network propagation on a large integrated protein-protein interaction network. These analyses, recently performed with updated database and analysis tools, further consolidated the characterization of cis- and trans-abundant genes while expanding previous results. In this chapter, we present the key results along with the materials and methods to motivate readers to investigate these findings independently and gain further insights into the diplotypic nature of genes and genomes.

Cannabinoids: for better and for worse
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The use of cannabis as a drug has undergone a remarkable change of direction: considered as a symbol of countercultures in past decades, it is presently being hailed as a cure for any number of diseases and conditions. Thus, despite concerns about the safety of cannabis and cannabinoids, quite a few drugs that contain cannabinoids have recently been approved by several drug agencies, and the medicinal and recreational use of cannabis has been legalized in various countries and states. The promise of cannabinoids for therapeutic use, as well as potentially detrimental health risks and regulatory issues, will need to be carefully weighed.
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El consumo de cannabis como droga ha experimentado un notable cambio de dirección: considerado como un símbolo de las contraculturas en las últimas décadas, actualmente está siendo aclamado como cura para una serie de enfermedades y afecciones. Por lo tanto, a pesar de las preocupaciones sobre la seguridad del cannabis y de los cannabinoides, bastantes medicamentos que contienen cannabinoides han sido recientemente aprobados por varias agencias de edicamentos, y el uso medicinal y recreativo del cannabis se ha legalizado en varios países y estados. La promesa de los cannabinoides para uso terapéutico, así como los riesgos potencialmente perjudiciales para la salud y cuestiones reglamentarias, deberán ser cuidadosamente evaluados.

L'usage du cannabis en tant que drogue a subi un changement d'orientation remarquable: considéré comme un symbole des contre-cultures au cours des dernières décennies, il est actuellement salué comme remède pour un certain nombre de maladies et pathologies. Ainsi, malgré les inquiétudes concernant la sécurité du cannabis et des cannabinoïdes, de nombreux médicaments contenant des cannabinoïdes ont récemment été approuvés par plusieurs agences de médicaments, et l'usage médicinal et récréatif du cannabis a été légalisé dans divers pays et états. La promesse des cannabinoïdes à usage thérapeutique, ainsi que des risques sanitaires potentiellement néfastes et les questions réglementaires devront être soigneusement pesées.

Going digital: how technology use may influence human brains and behavior
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The digital revolution has changed, and continues to change, our world and our lives. Currently, major aspects of our lives have moved online due to the coronavirus pandemic, and social distancing has necessitated virtual togetherness. In a synopsis of 10 articles we present ample evidence that the use of digital technology may influence human brains and behavior in both negative and positive ways. For instance, brain imaging techniques show concrete morphological alterations in early childhood and during adolescence that are associated with intensive digital media use. Technology use apparently affects brain functions, for example visual perception, language, and cognition. Extensive studies could not confirm common concerns that excessive screen time is linked to mental health problems, or the deterioration of well-being. Nevertheless, it is important to use digital technology consciously, creatively, and sensibly to improve personal and professional relationships. Digital technology has great potential for mental health assessment and treatment, and the improvement of personal mental performance.
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La revolución digital ha cambiado y continúa cambiando nuestro mundo y nuestras vidas. Actualmente, los principales aspectos de nuestras vidas han migrado hacia el funcionamiento "online" debido a la pandemia del coronavirus, y el distanciamiento social ha requerido de cercanías virtuales. En una sinopsis de 10 artículos, se presenta una amplia evidencia de que el empleo de la tecnología digital puede influir en el cerebro y en el comportamiento humano de manera negativa y positiva. Por ejemplo, las técnicas de imágenes cerebrales muestran alteraciones morfológicas concretas en la primera infancia y durante la adolescencia, las cuales están asociadas con el empleo intenso de medios digitales. En apariencia, la utilización de la tecnología afecta las funciones cerebrales, como la percepción visual, el lenguaje y la cognición. Numerosos estudios no pudieron confirmar las preocupaciones comunes en cuanto a que el tiempo excesivo de pantalla esté relacionado con problemas de salud mental o el deterioro del bienestar. Sin embargo, es importante emplear la tecnología digital de manera consciente, creativa y sensata para mejorar las relaciones personales y profesionales. La tecnología digital tiene un gran potencial para la evaluación y el tratamiento de la salud mental, y el aumento del rendimiento mental personal.

La révolution numérique a modifié et continue à modifier notre monde et nos vies. La pandémie actuelle due au coronavirus a fait basculer en ligne de nombreux pans de notre existence et la distanciation sociale a imposé la virtualité des rassemblements. Les données des dix articles présentés ici attestent de l'influence de la technologie numérique sur les cerveaux et les comportements, de manière positive et négative. Par exemple,l'imagerie cérébrale montre des altérations morphologiques concrètes apparaissant tôt dans l'enfance et pendant l'adolescence lors d'une pratique intensive des media numériques. Cela concernerait certaines fonctions cérébrales comme la perception visuelle, le langage et la cognition. Des études approfondies n'ont pas confirmé les inquiétudes courantes quant aux répercussions d'un temps excessif passé devant un écran en termes de santé mentale ou de qualité de vie. Il est néanmoins important de privilégier une utilisation consciente, créative et raisonnable des technologies numériques afin d'améliorer les relations personnelles et professionnelles. Ces technologies ont un grand potentiel dans l'évaluation et le traitement de la santé mentale ainsi que dans l'amélioration des performances mentales personnelles.

Significant abundance of cis configurations of coding variants in diploid human genomes.

To fully understand human genetic variation and its functional consequences, the specific distribution of variants between the two chromosomal homologues of genes must be known. The 'phase' of variants can significantly impact gene function and phenotype. To assess patterns of phase at large scale, we have analyzed 18 121 autosomal genes in 1092 statistically phased genomes from the 1000 Genomes Project and 184 experimentally phased genomes from the Personal Genome Project. Here we show that genes with cis-configurations of coding variants are more frequent than genes with trans-configurations in a genome, with global cis/trans ratios of ∼60:40. Significant cis-abundance was observed in virtually all genomes in all populations. Moreover, we identified a large group of genes exhibiting cis-configurations of protein-changing variants in excess, so-called 'cis-abundant genes', and a smaller group of 'trans-abundant genes'. These two gene categories were functionally distinguishable, and exhibited strikingly different distributional patterns of protein-changing variants. Underlying these phenomena was a shared set of phase-sensitive genes of importance for adaptation and evolution. This work establishes common patterns of phase as key characteristics of diploid human exomes and provides evidence for their functional significance, highlighting the importance of phase for the interpretation of protein-coding genetic variation and gene function.

The role of genetics and genomics in clinical psychiatry.

The enormous successes in the genetics and genomics of many diseases have provided the basis for the advancement of precision medicine. Thus, the detection of genetic variants associated with neuropsychiatric disorders, as well as treatment outcome, has raised growing expectations that these findings could soon be translated into the clinic to improve diagnosis, the prediction of disease risk and individual response to drug therapy. In this article, we will provide an introduction to the search for genes involved in psychiatric illness and summarize the present findings in major psychiatric disorders. We will review the genetic variants in genes encoding drug metabolizing enzymes and specific drug targets which were found to be associated with variable drug response and severe side effects. We will evaluate the clinical translatability of these findings, whether there is currently any role for genetic testing and in this context, make valuable sources of information available to the clinician seeking guidance and advice in this rapidly developing field of psychiatric genetics.

Los enormes éxitos en la genética y la genómica de muchas enfermedades han proporcionado la base para el avance de la medicina de precisión. Por lo tanto, la detección de variantes genéticas asociadas con trastornos neuropsiquiátricos, así como el resultado del tratamiento, han aumentado las expectativas que estos hallazgos pronto podrían traducirse en la clínica para mejorar el diagnóstico, la predicción de riesgo de enfermar y la respuesta individual a la terapia farmacológica. En este artículo, se presentará una introducción sobre la búsqueda de genes implicados en enfermedades psiquiátricas y se resumirán los hallazgos actuales en los principales trastornos psiquiátricos. Se revisarán las variantes genéticas para genes que codifican enzimas metabolizadoras de fármacos y los blancos farmacológicos específicos que se encontraron asociados con una respuesta farmacológica variable y efectos secundarios graves. Se evaluará la traducción clínica de estos hallazgos, la posibilidad actual de algún papel para las pruebas genéticas y, en ese contexto, se pondrá a disposición del clínico que busca guía y consejo, valiosas fuentes de información para este campo de rápido desarrollo que es la psiquiatría genética.

Les énormes succès obtenus en génétique et génomique dans de nombreuses maladies ont fourni la base des avancées en médecine de précision. La détection de variants génétiques, associés à des troubles neuro-psychiatriques comme à des résultats thérapeutiques, a donc soulevé une attente grandissante de voir traduire ces résultats en pratique clinique pour améliorer le diagnostic, la prédiction du risque d'avoir la maladie et la réponse individuelle au traitement médicamenteux. Nous introduisons dans cet article la recherche de gènes impliqués en pathologie psychiatrique et nous résumons les résultats actuels pour les principaux troubles psychiatriques. Nous analysons les variants génétiques des gènes codant pour les enzymes métabolisant les médicaments et les cibles médicamenteuses spécifiques ayant montré une association avec une réponse variable au médicament et des effets indésirables sévères. Nous évaluons la traduction de ces résultats en pratique clinique, la possibilité actuelle d'un rôle du dépistage génétique et, dans ce contexte, la mise à disposition du médecin en recherche d'aide et de conseils, de sources valables d'information dans ce domaine en rapide développement qu'est la psychiatrie génétique.

A Fosmid Pool-Based Next Generation Sequencing Approach to Haplotype-Resolve Whole Genomes.

Haplotype resolution of human genomes is essential to describe and interpret genetic variation and its impact on biology and disease. Our approach to haplotyping relies on converting genomic DNA into a fosmid library, which represents the entire diploid genome as a collection of haploid DNA clones of ~40 kb in size. These can be partitioned into pools such that the probability that the same pool contains both parental haplotypes is reduced to ~1 %. This is the key principle of this method, allowing entire pools of fosmids to be massively parallel sequenced, yielding haploid sequence output. Here, we present a detailed protocol for fosmid pool-based next generation sequencing to haplotype-resolve whole genomes including the following steps: (1) generation of high molecular weight DNA fragments of ~40 kb in size from genomic DNA; (2) fosmid cloning and partitioning into 96-well plates; (3) barcoded sequencing library preparation from fosmid pools for next generation sequencing; and (4) computational analysis of fosmid sequences and assembly into contiguous haploid sequences.This method can be used in combination with, but also without, whole genome shotgun sequencing to extensively resolve heterozygous SNPs and structural variants within genomic regions, resulting in haploid contigs of several hundred kb up to several Mb. This method has a broad range of applications including population and ancestry genetics, the clinical interpretation of mutations in personal genomes, the analysis of cancer genomes and highly complex disease gene regions such as MHC. Moreover, haplotype-resolved genome sequencing allows description and interpretation of the diploid nature of genome biology, for example through the analysis of haploid gene forms and allele-specific phenomena. Application of this method has enabled the production of most of the molecular haplotype-resolved genomes reported to date.

Multiple haplotype-resolved genomes reveal population patterns of gene and protein diplotypes.

To fully understand human biology and link genotype to phenotype, the phase of DNA variants must be known. Here we present a comprehensive analysis of haplotype-resolved genomes to assess the nature and variation of haplotypes and their pairs, diplotypes, in European population samples. We use a set of 14 haplotype-resolved genomes generated by fosmid clone-based sequencing, complemented and expanded by up to 372 statistically resolved genomes from the 1000 Genomes Project. We find immense diversity of both haploid and diploid gene forms, up to 4.1 and 3.9 million corresponding to 249 and 235 per gene on average. Less than 15% of autosomal genes have a predominant form. We describe a 'common diplotypic proteome', a set of 4,269 genes encoding two different proteins in over 30% of genomes. We show moreover an abundance of cis configurations of mutations in the 386 genomes with an average cis/trans ratio of 60:40, and distinguishable classes of cis- versus trans-abundant genes. This work identifies key features characterizing the diplotypic nature of human genomes and provides a conceptual and analytical framework, rich resources and novel hypotheses on the functional importance of diploidy.

Fosmid-based whole genome haplotyping of a HapMap trio child: evaluation of Single Individual Haplotyping techniques.

Determining the underlying haplotypes of individual human genomes is an essential, but currently difficult, step toward a complete understanding of genome function. Fosmid pool-based next-generation sequencing allows genome-wide generation of 40-kb haploid DNA segments, which can be phased into contiguous molecular haplotypes computationally by Single Individual Haplotyping (SIH). Many SIH algorithms have been proposed, but the accuracy of such methods has been difficult to assess due to the lack of real benchmark data. To address this problem, we generated whole genome fosmid sequence data from a HapMap trio child, NA12878, for which reliable haplotypes have already been produced. We assembled haplotypes using eight algorithms for SIH and carried out direct comparisons of their accuracy, completeness and efficiency. Our comparisons indicate that fosmid-based haplotyping can deliver highly accurate results even at low coverage and that our SIH algorithm, ReFHap, is able to efficiently produce high-quality haplotypes. We expanded the haplotypes for NA12878 by combining the current haplotypes with our fosmid-based haplotypes, producing near-to-complete new gold-standard haplotypes containing almost 98% of heterozygous SNPs. This improvement includes notable fractions of disease-related and GWA SNPs. Integrated with other molecular biological data sets, this phase information will advance the emerging field of diploid genomics.

A comprehensively molecular haplotype-resolved genome of a European individual.

Independent determination of both haplotype sequences of an individual genome is essential to relate genetic variation to genome function, phenotype, and disease. To address the importance of phase, we have generated the most complete haplotype-resolved genome to date, "Max Planck One" (MP1), by fosmid pool-based next generation sequencing. Virtually all SNPs (>99%) and 80,000 indels were phased into haploid sequences of up to 6.3 Mb (N50 ~1 Mb). The completeness of phasing allowed determination of the concrete molecular haplotype pairs for the vast majority of genes (81%) including potential regulatory sequences, of which >90% were found to be constituted by two different molecular forms. A subset of 159 genes with potentially severe mutations in either cis or trans configurations exemplified in particular the role of phase for gene function, disease, and clinical interpretation of personal genomes (e.g., BRCA1). Extended genomic regions harboring manifold combinations of physically and/or functionally related genes and regulatory elements were resolved into their underlying "haploid landscapes," which may define the functional genome. Moreover, the majority of genes and functional sequences were found to contain individual or rare SNPs, which cannot be phased from population data alone, emphasizing the importance of molecular phasing for characterizing a genome in its molecular individuality. Our work provides the foundation to understand that the distinction of molecular haplotypes is essential to resolve the (inherently individual) biology of genes, genomes, and disease, establishing a reference point for "phase-sensitive" personal genomics. MP1's annotated haploid genomes are available as a public resource.

Haplotype misclassification resulting from statistical reconstruction and genotype error, and its impact on association estimates.

Haplotypes are an important concept for genetic association studies, but involve uncertainty due to statistical reconstruction from single nucleotide polymorphism (SNP) genotypes and genotype error. We developed a re-sampling approach to quantify haplotype misclassification probabilities and implemented the MC-SIMEX approach to tackle this as a 3 x 3 misclassification problem. Using a previously published approach as a benchmark for comparison, we evaluated the performance of our approach by simulations and exemplified it on real data from 15 SNPs of the APM1 gene. Misclassification due to reconstruction error was small for most, but notable for some, especially rarer haplotypes. Genotype error added misclassification to all haplotypes resulting in a non-negligible drop in sensitivity. In our real data example, the bias of association estimates due to reconstruction error alone reached -48.2% for a 1% genotype error, indicating that haplotype misclassification should not be ignored if high genotype error can be expected. Our 3 x 3 misclassification view of haplotype error adds a novel perspective to currently used methods based on genotype intensities and expected number of haplotype copies. Our findings give a sense of the impact of haplotype error under realistic scenarios and underscore the importance of high-quality genotyping, in which case the bias in haplotype association estimates is negligible.

Personal genomes in progress: from the human genome project to the personal genome project.

The cost of a diploid human genome sequence has dropped from about $70M to $2000 since 2007--even as the standards for redundancy have increased from 7x to 40x in order to improve call rates. Coupled with the low return on investment for common single-nucleotide polylmorphisms, this has caused a significant rise in interest in correlating genome sequences with comprehensive environmental and trait data (GET). The cost of electronic health records, imaging, and microbial, immunological, and behavioral data are also dropping quickly. Sharing such integrated GET datasets and their interpretations with a diversity of researchers and research subjects highlights the need for informed-consent models capable of addressing novel privacy and other issues, as well as for flexible data-sharing resources that make materials and data available with minimum restrictions on use. This article examines the Personal Genome Project's effort to develop a GET database as a public genomics resource broadly accessible to both researchers and research participants, while pursuing the highest standards in research ethics.

Meta-analysis of the INSIG2 association with obesity including 74,345 individuals: does heterogeneity of estimates relate to study design?

The INSIG2 rs7566605 polymorphism was identified for obesity (BMI> or =30 kg/m(2)) in one of the first genome-wide association studies, but replications were inconsistent. We collected statistics from 34 studies (n = 74,345), including general population (GP) studies, population-based studies with subjects selected for conditions related to a better health status ('healthy population', HP), and obesity studies (OB). We tested five hypotheses to explore potential sources of heterogeneity. The meta-analysis of 27 studies on Caucasian adults (n = 66,213) combining the different study designs did not support overall association of the CC-genotype with obesity, yielding an odds ratio (OR) of 1.05 (p-value = 0.27). The I(2) measure of 41% (p-value = 0.015) indicated between-study heterogeneity. Restricting to GP studies resulted in a declined I(2) measure of 11% (p-value = 0.33) and an OR of 1.10 (p-value = 0.015). Regarding the five hypotheses, our data showed (a) some difference between GP and HP studies (p-value = 0.012) and (b) an association in extreme comparisons (BMI> or =32.5, 35.0, 37.5, 40.0 kg/m(2) versus BMI<25 kg/m(2)) yielding ORs of 1.16, 1.18, 1.22, or 1.27 (p-values 0.001 to 0.003), which was also underscored by significantly increased CC-genotype frequencies across BMI categories (10.4% to 12.5%, p-value for trend = 0.0002). We did not find evidence for differential ORs (c) among studies with higher than average obesity prevalence compared to lower, (d) among studies with BMI assessment after the year 2000 compared to those before, or (e) among studies from older populations compared to younger. Analysis of non-Caucasian adults (n = 4889) or children (n = 3243) yielded ORs of 1.01 (p-value = 0.94) or 1.15 (p-value = 0.22), respectively. There was no evidence for overall association of the rs7566605 polymorphism with obesity. Our data suggested an association with extreme degrees of obesity, and consequently heterogeneous effects from different study designs may mask an underlying association when unaccounted for. The importance of study design might be under-recognized in gene discovery and association replication so far.

Outpatient Long-term Intensive Therapy for Alcoholics (OLITA): a successful biopsychosocial approach to the treatment of alcoholism.

Alcohol dependence is a frequent, chronic, relapsing, and incurable disease with enormous societal costs. Thus, alcoholism therapy and research into its outcome are of major importance for public health. The present article will: (i) give a brief overview of the epidemiology, pathogenesis, and treatment outcomes of alcohol dependence; (ii) introduce the basic principles of outpatient long-term therapy of alcohol-dependent patients; and (iii) discuss in detail process-outcome research on Outpatient Long-term Intensive Therapy for Alcoholics (OLITA). This successful biopsychosocial approach to the treatment of alcoholism shows a 9-year abstinence rate of over 50%, a re-employment rate of 60%, and a dramatic recovery from comorbid depression, anxiety disorders, and physical sequelae. The outcome data are empirically based on treatment processes that have proven high predictive validity and give concrete information about where to focus the therapeutic efforts. Thus, process-outcome research on OLITA can serve for the development of new therapeutic guidelines on adapting individual relapse prevention strategies.

Haplotype reconstruction for diploid populations.

The inference of haplotype pairs directly from unphased genotype data is a key step in the analysis of genetic variation in relation to disease and pharmacogenetically relevant traits. Most popular methods such as Phase and PL do require either the coalescence assumption or the assumption of linkage between the single-nucleotide polymorphisms (SNPs). We have now developed novel approaches that are independent of these assumptions. First, we introduce a new optimization criterion in combination with a block-wise evolutionary Monte Carlo algorithm. Based on this criterion, the 'haplotype likelihood', we develop two kinds of estimators, the maximum haplotype-likelihood (MHL) estimator and its empirical Bayesian (EB) version. Using both real and simulated data sets, we demonstrate that our proposed estimators allow substantial improvements over both the expectation-maximization (EM) algorithm and Clark's procedure in terms of capacity/scalability and error rate. Thus, hundreds and more ambiguous loci and potentially very large sample sizes can be processed. Moreover, applying our proposed EB estimator can result in significant reductions of error rate in the case of unlinked or only weakly linked SNPs.

Gene variants and binge eating as predictors of comorbidity and outcome of treatment in severe obesity.

Melanocortin-4 receptor gene (MC4R) variants are associated with obesity and binge eating disorder (BED), whereas the more prevalent proopiomelanocortin (POMC) and leptin receptor gene (LEPR) mutations are rarely associated with obesity or BED. The complete coding regions of MC4R, POMC, and leptin-binding domain of LEPR were comparatively sequenced in 300 patients (233 women and 67 men; mean +/- SEM age, 42 +/- 1 years; mean +/- SEM body mass index, 43.5 +/- 0.3 kg/m2) undergoing laparoscopic gastric banding. Eating behavior, esophagogastric pathology, metabolic syndrome prevalence, and postoperative weight loss and complications were retrospectively compared between carriers and noncarriers of gene variants with and without BED during 36 +/- 3-month follow-up. Nineteen patients (6.3%) carried 8 MC4R variants, 144 (48.0%) carried 13 POMC variants, and 247 (82.3%) carried 11 LEPR variants. All MC4R variant carriers had BED, compared with 18.1% of noncarriers (P < 0.001). BED rates were similar among POMC and LEPR variant carriers and noncarriers. Gastroscopy revealed more erosive esophagitis in bingers than in nonbingers before and after banding (P < 0.04), regardless of genotype. MC4R variant carriers lost less weight (P=0.003), showed less improvement in metabolic syndrome (P < 0.001), had dilated esophagi (P < 0.001) and more vomiting (P < 0.05), and had fivefold more gastric complications (P < 0.001) than noncarriers. Overall outcome was poorest in MC4R variant carriers, better in noncarriers with BED (P < 0.05), and best in noncarriers without BED (P < 0.001). MC4R variants influence comorbidities and treatment outcomes in severe obesity.

Relationship between serotonin transporter gene polymorphisms and platelet serotonin transporter sites among African-American cocaine-dependent individuals and healthy volunteers.

Alterations in the serotonin transporter (5-HTT) have been implicated in a variety of psychiatric disorders including cocaine dependence. A polymorphism in the promoter region of the serotonin transporter gene (5-HTTLPR) appears to influence the expression of 5-HTT in human cell lines. We investigated whether 5-HTTLPR variants were related to differences in measures of platelet 5-HTT sites in cocaine-dependent patients and healthy volunteers (controls). Polymerase chain reaction-based genotyping of a 44 base pair insertion/deletion polymorphism in 5-HTTLPR was performed in 138 cocaine-dependent African-American subjects and 60 African-American controls. This yielded a short (S) and a long (L) allele. Platelet 5-HTT sites were measured using the tritiated paroxetine binding assay. Relationships of 5-HTTLPR genotypes with Bmax (density of serotonin transporter) and Kd (affinity constant) were examined. Bmax values were significantly lower in cocaine-dependent patients (640 +/- 233) than controls (906 +/- 225) (P < 0.001); however, 5-HTTLPR genotype distributions or allele frequencies did not differ between the two groups. There were no significant differences in Bmax between the three genotypes among cocaine-dependent patients (LL = 690 +/- 246, LS = 620 +/- 235, SS = 587 +/- 183; P = 0.14) or controls (LL = 909 +/- 233, LS = 938 +/- 279, SS = 866 +/- 143; P = 0.65). All three genotypes in cocaine-dependent patients showed comparable reductions in Bmax from the corresponding genotypes in controls. Demographic variables, severity of substance use or depression were unrelated to Bmax or 5-HTTLPR genotypes. Although platelet 5-HTT densities are reduced in patients with cocaine dependence compared with healthy volunteers, these genotypic variations in the serotonin transporter do not seem to influence levels of platelet 5-HTT in cocaine-dependent patients or healthy volunteers.

Genetic variation and pharmacogenomics: concepts, facts, and challenges.

The analysis of genetic variation in candidate genes is an issue of central importance in pharmacogenomics. The specific approaches taken will have a critical impact on the successful identification of disease genes, the molecular correlates of drug response, and the establishment of meaningful relationships between genetic variants and phenotypes of biomedical and pharmaceutical importance in general. Against a historical background, this article distinguishes different approaches to candidate gene analysis, reflecting different stages in human genome research. Only recently has it become feasible to analyze genetic variation systematically at the ultimate level of resolution, ie, the DNA sequence. In this context, the importance of haplotype-based approaches to candidate gene analysis has at last been recognized; the determination of the specific combinations of variants for each of the two sequences of a gene defined as a haplotype is essential. An up-to-date summary of such maximum resolution data on the amount, nature, and structure of genetic variation in candidate genes will be given. These data demonstrate abundant gene sequence and haplotype diversity. Numerous individually different forms of a gene may exist. This presents major challenges to the analysis of relationships between genetic variation, gene function, and phenotype. First solutions seem within reach. The implications of naturally occurring variation for pharmacogenomics and "personalized" medicine are now evident. Future approaches to the identification, evaluation, and prioritization of drug targets, the optimization of clinical trials, and the development of efficient therapies must be based on in-depth knowledge of candidate gene variation as an essential prerequisite.

Human inter-individual DNA sequence variation in candidate genes, drug targets, the importance of haplotypes and pharmacogenomics.

The identification of genes predisposing to human diseases is of paramount importance for understanding the molecular basis of the disease and individually different drug response, and will establish new routes to diagnosis and therapeutic advances of immense medical benefit. A key step common to all strategies for disease gene identification is the systematic analysis of candidate gene sequences to identify specific sequence variations associated with disease or any other phenotype of pharmaceutical relevance. In this article, current concepts and approaches to haplotype-based candidate gene analysis are reviewed. Moreover, a comprehensive summary of recent studies and data on the amount, nature, pattern and structure of genetic variation in candidate genes is given. These data demonstrate altogether remarkable gene sequence and haplotype diversity. Numerous individually different forms of a gene may exist. This presents challenges to the traditional views of the concept of "a" gene with far-reaching implications on the functional analysis of candidate gene variation, on the establishment of "sequence"-"structure"-"function" and complex haplotype/genotype-phenotype relationships, on the identification, evaluation and prioritization of drug targets and the concept of a "personalized medicine" in general. Moreover, present and future approaches to the identification of candidate and disease genes will be addressed. These include whole genome-based approaches such as integrative genomics as well as functional genomics-based approaches to analyze and model complex biological and medical processes. The analysis of whole complex systems in particular will provide the basis to make "maximally informed" guesses on candidate genes and address complex variability patterns in genes as well as complex genotype-phenotype relationships comprehensively at an advanced level.

Haplotypes and the systematic analysis of genetic variation in genes and genomes.

Haplotypes have been used in various fields of genetics for a long time, in a variety of contexts, and for different purposes. Now, haplotype-based approaches to the analysis of candidate genes and genome-wide linkage disequilibrium (LD) mapping have gained center stage. It is time to explicitly distinguish the different concepts implied in the present haplotype approaches: haplotypes are not haplotypes, after all. The distinction of three different categories, ancestral, common haplotypes or haplotype blocks, gene-based haplotypes as complex genetic markers and gene-based functional haplotypes, is proposed. These categories serve as framework to review and analyze in particular the recent work suggesting evidence for a haplotype block structure of the human genome and the body of comparative sequencing studies addressing haplotype and LD structures at the gene level. Haplotype approaches will be evaluated along the dimensions preselection of variants versus complete DNA sequence information, role of LD and stages in the process of disease gene identification. Overall, the content of haplotypes is conceived as a function of available technologies to evaluate genetic variation and general advances in human genome research.

Identification and characterization of KAT, a novel gene preferentially expressed in several human cancer cell lines.

We describe the molecular characterization of a novel human gene on chromosome 1q23.3, termed KAT, which is highly conserved among mammals. The KAT gene spans a genomic region of approximately 1.6 kilobases and consists of 4 exons encoding a 115 amino acid protein with a molecular mass of about 12.5 kDa. The gene is expressed in several human tissues, including kidney, liver, skeletal muscle, heart, colon, thymus, spleen, placenta and lung. We identified an alternatively spliced form, lacking exon 2, in human and mouse tissues. In silico analysis of expressed sequence tags, derived from different types of human tumors, revealed another splice variant. This transcript is characterized by retention of the third intron, leading to a truncated translation product. The KAT protein is localized around the nuclear membranes. It was found to be expressed in several breast, colon and lung carcinoma cell lines, but not in normal breast epithelial cell lines. In addition, KAT protein was detected in invasive ductal carcinoma, but not in adjacent tissues. This suggests a role of this gene in tumorigenesis.