Ontogenetic de novo copy number variations (CNVs) as a source of genetic individuality: studies on two families with MZD twins for schizophrenia

High-resolution genomic profiling and locus-specific FISH in subcutaneous and visceral adipose tissue of obese patients

Obesity is known as a heterogeneous and multifactorial disease. The distribution of body fat is crucial for the development of metabolic complications. Comprehensive genetic analyses on different fat tissues are rare but necessary to provide more detailed information. Therefore, we performed genetic analyses of three patients with obesity using high resolution genome wide SNP array (blood, visceral fat tissue) and fluorescence in situ hybridization (FISH) analyses (visceral and subcutaneous fat tissue). Altogether, we identified 31 small Copy Number Variations (losses: 1p31.1, 1p22.2, 1q21.3, 2q34, 2q37.1, 3q28, 6p25.3, 7q31.33, 7q33, 8p23.3, 10q22.3, 11p15.4, 11p15.1, 11p14.2, 11p12, 13q12.3, 15q11.2-q13.1, 15q13.3, 20q13.2, 22q11.21; gains: 2q22.1-q22.2, 3p14.3, 4p16.3, 4q32.2, 6q27, 7p14.3, 7q34, 11p12, 12p11.21, 16p11.2-p11.1, 17q21.31) and 289 small copy-neutral Loss of Heterozygosity (cn-LOH). For the chromosomal region 15q11.2-q13.1, we detected a microdeletion (Prader-Willi-Syndrome) in one patient. Interestingly, we identified chromosomal SNP differences between EDTA-blood and visceral fat tissue (deletion and gain). Small losses of 7q31.33, 7q33, 11p14.2, 11p12, 13q12.3 as well as small gain of 7q34 were detected only in fat tissue and not in blood. Furthermore, FISH analyses on 7q31.33, 7q33 and 11p12 revealed differences between subcutaneous and visceral fat tissue. Generally, the deletions were detected more frequent in visceral fat tissue. Predominantly detected cn-LOH vs. CNV suggests a meaning of these cn-LOH for the pathogenesis of obesity. We conclude that the SNP array and FISH analyses used is applicable to generate more information for basic research on difficult cell subpopulations (e.g., visceral adipose tissue) and could opens up new diagnostic aspects in the field of obesity. Altogether, the significance of these mostly not yet described genetic aberrations in different fat tissues needs to confirmed in a larger series.

Somatic copy number variants in neuropsychiatric disorders

Copy number variants (CNVs) have been implicated in neuropsychiatric disorders, with rare-inherited and de novo CNVs (dnCNVs) having large effects on disease liability. Recent studies started exploring a class of dnCNVs that occur post-zygotically, and are therefore present in some but not all cells of the body. Analogous to conditional mutations in animal models, the presence of risk mutations in a fraction of cells has the potential to enlighten how damaging mutations affect cell-type/cell-circuit specific pathologies leading to neuropsychiatric manifestations. Although mosaic CNVs appear to contribute to a modest fraction of risk (0.3-0.5%), expanding our insights about them with more sensitive experimental and statistical methods, has the potential to help clarify mechanisms of neuropsychiatric disease.

Genetic and environmental factors of schizophrenia and autism spectrum disorder: insights from twin studies

Twin studies of psychiatric disorders such as schizophrenia and autism spectrum disorder have employed epidemiological approaches that determine heritability by comparing the concordance rate between monozygotic twins (MZs) and dizygotic twins. The basis for these studies is that MZs share 100% of their genetic information. Recently, biological studies based on molecular methods are now being increasingly applied to examine the differences between MZs discordance for psychiatric disorders to unravel their possible causes. Although recent advances in next-generation sequencing have increased the accuracy of this line of research, there has been greater emphasis placed on epigenetic changes versus DNA sequence changes as the probable cause of discordant psychiatric disorders in MZs. Since the epigenetic status differs in each tissue type, in addition to the DNA from the peripheral blood, studies using DNA from nerve cells induced from postmortem brains or induced pluripotent stem cells are being carried out. Although it was originally thought that epigenetic changes occurred as a result of environmental factors, and thus were not transmittable, it is now known that such changes might possibly be transmitted between generations. Therefore, the potential possible effects of intestinal flora inside the body are currently being investigated as a cause of discordance in MZs. As a result, twin studies of psychiatric disorders are greatly contributing to the elucidation of genetic and environmental factors in the etiology of psychiatric conditions.

Postzygotic Somatic Mutations in the Human Brain Expand the Threshold-Liability Model of Schizophrenia

The search for what causes schizophrenia has been onerous. This research has included extensive assessment of a variety of genetic and environmental factors using ever emerging high-resolution technologies and traditional understanding of the biology of the brain. These efforts have identified a large number of schizophrenia-associated genes, some of which are altered by mutational and epi-mutational mechanisms in a threshold liability model of schizophrenia development. The results, however, have limited predictability and the actual cause of the disease remains unknown. This current state asks for conceptualizing the problem differently in light of novel insights into the nature of mutations, the biology of the brain and the fine precision and resolution of emerging technologies. There is mounting evidence that mutations acquired during postzygotic development are more common than germline mutations. Also, the postzygotic somatic mutations including epimutations (PZMs), which often lead to somatic mosaicism, are relatively common in the mammalian brain in comparison to most other tissues and PZMs are more common in patients with neurodevelopmental mental disorders, including schizophrenia. Further, previously inaccessible, detection of PZMs is becoming feasible with the advent of novel technologies that include single-cell genomics and epigenomics and the use of exquisite experimental designs including use of monozygotic twins discordant for the disease. These developments allow us to propose a working hypothesis and expand the threshold liability model of schizophrenia that already encompasses familial genetic, epigenetic and environmental factors to include somatic de novo PZMs. Further, we offer a test for this expanded model using currently available genome sequences and methylome data on monozygotic twins discordant for schizophrenia (MZD) and their parents. The results of this analysis argue that PZMs play a significant role in the development of schizophrenia and explain extensive heterogeneity seen across patients. It also offers the potential to convincingly link PZMs to both nervous system health and disease, an area that has remained challenging to study and relatively under explored.

Exploration of genetic factors determining cleft side in a pair of monozygotic twins with mirror-image cleft lip and palate using whole-genome sequencing and comparison of craniofacial morphology

OBJECTIVE

The aim of the present study is to explore genetic factors determining difference of cleft side using whole-genome sequencing and evaluation of craniofacial morphology using cephalometric analysis between Japanese monozygotic (MZ) twins with mirror-image cleft lip and palate (CLP).

DESIGN

We selected a Japanese MZ twin pair (MZ-A and MZ-B) affected with unilateral CLP who are discordant for cleft side (left/right) and conducted whole-genome sequencing to identify genetic factors determining cleft side. Moreover, we compared their craniofacial morphologies using cephalograms.

RESULTS

Whole-genome sequencing results suggested that no discordant DNA variants were found between MZ-A and MZ-B. The comparison of craniofacial morphology between the MZ twins revealed that MZ-B had maxillary deficiency and slightly more mandibular protrusion than MZ-A.

CONCLUSIONS

It is indicated that environmental factors might be a critical factor that influences the determination of difference of cleft side in orofacial clefts. In addition, we found some differences in craniofacial morphology between MZ-A and MZ-B. Our findings suggest that various environmental factors, such as epigenetics, might be a critical factor that influences the determination of difference of cleft side in CLP rather than inherited genetic factors.

NRDE-2, the human homolog of fission yeast Nrl1, prevents DNA damage accumulation in human cells

The RNA helicase Mtr4 is a versatile protein that is a crucial component of several distinct RNA surveillance complexes. Here we describe a novel complex that contains Mtr4, but has a role distinct from any of those previously described. We found that Mtr4 association with the human homolog of fission yeast Nrl1, NRDE-2, defines a novel function for Mtr4 in the DNA damage response pathway. We provide biochemical evidence that Mtr4 and NRDE-2 are part of the same complex and show that both proteins play a role in the DNA damage response by maintaining low DNA double-strand break levels. Importantly, the DNA damage response function of the Mtr4/NRDE-2 complex does not depend on the formation of R loops. We show however that NRDE-2 and Mtr4 can affect R-loop signals at a subset of distinct genes, possibly regulating their expression. Our work not only expands the wide range of Mtr4 functions, but also elucidates an important role of the less characterized human NRDE-2 protein.

Whole‑genome sequencing of a monozygotic twin discordant for systemic lupus erythematosus

Systemic lupus erythematosus (SLE) is an autoimmune disease, and its genetic causes remain to be fully elucidated. Previous studies have identified several susceptibility genes for SLE, such as deoxyribonuclease 1‑like 3. In the present study, whole‑genome sequencing (30X coverage) was performed on the leukocytes of a monozygotic twin discordant for SLE to assess the potential association of de novo variants and copy number variations (CNVs) with the susceptibility to SLE. After analyzing the genomic data, 8 putative discordant exonic variants between the twins were selected. However, the 8 variants that were chosen for validation with Sanger sequencing exhibited no discrepancy in the leukocytes from the twins. Of note, CNV alterations in genes of SLE‑associated pathways were identified between the twins, which may be linked with the phenotype of the monozygotic twin discordant for SLE. The above results suggest that genomic sequences of leukocytes in the monozygotic twins may exhibit a rare difference, and that CNV changes may be associated with phenotype differences in the twin discordant for SLE.

Role of DNA copy number variation in dyslipidemias

PURPOSE OF REVIEW

DNA copy number variations (CNVs) are quantitative structural rearrangements that include deletions, duplications, and higher order amplifications. Because of technical limitations, the contribution of this common form of genetic variation to regulation of lipid metabolism and dyslipidemia has been underestimated.

RECENT FINDINGS

Recent literature involving CNVs and dyslipidemias has focused mainly on rare CNVs causing familial hypercholesterolemia, and a common CNV polymorphism as the major determinant of lipoprotein(a) plasma concentrations. Additionally, there is tantalizing evidence of largely uninvestigated but plausible presence of CNVs underlying other dyslipidemias. We also discuss the future role of improved technologies in facilitating more economic, routine CNV assessment in dyslipidemias.

SUMMARY

CNVs account for large proportion of human genetic variation and are already known to contribute to susceptibility of dyslipidemias, particularly in about 10% of familial hypercholesterolemia patients. Increasing availability of clinical next-generation sequencing and bioinformatics presents a cost-effective opportunity for novel CNV discoveries in dyslipidemias.

Post-zygotic genomic changes in glutamate and dopamine pathway genes may explain discordance of monozygotic twins for schizophrenia

Background

Monozygotic twins are valuable in assessing the genetic vs environmental contribution to diseases. In the era of complete genome sequences, they allow identification of mutational mechanisms and specific genes and pathways that offer predisposition to the development of complex diseases including schizophrenia.

Methods

We sequenced the complete genomes of two pairs of monozygotic twins discordant for schizophrenia (MZD), including one representing a family tetrad. The family specific complete sequences have allowed identification of post zygotic mutations between MZD genomes. It allows identification of affected genes including relevant network and pathways that may account for the diseased state in pair specific patient.

Results

We found multiple twin specific sequence differences between co-twins that included small nucleotides [single nucleotide variants (SNV), small indels and block substitutions], copy number variations (CNVs) and structural variations. The genes affected by these changes belonged to a number of canonical pathways, the most prominent ones are implicated in schizophrenia and related disorders. Although these changes were found in both twins, they were more frequent in the affected twin in both pairs. Two specific pathway defects, glutamate receptor signaling and dopamine feedback in cAMP signaling pathways, were uniquely affected in the two patients representing two unrelated families.

Conclusions

We have identified genome-wide post zygotic mutations in two MZD pairs affected with schizophrenia. It has allowed us to use the threshold model and propose the most likely cause of this disease in the two patients studied. The results support the proposition that each schizophrenia patient may be unique and heterogeneous somatic de novo events may contribute to schizophrenia threshold and discordance of the disease in monozygotic twins.

Electronic supplementary material

The online version of this article (10.1186/s40169-017-0174-1) contains supplementary material, which is available to authorized users.

Subjectivity: A Case of Biological Individuation and an Adaptive Response to Informational Overflow

The article presents a perspective on the scientific explanation of the subjectivity of conscious experience. It proposes plausible answers for two empirically valid questions: the 'how' question concerning the developmental mechanisms of subjectivity, and the 'why' question concerning its function. Biological individuation, which is acquired in several different stages, serves as a provisional description of how subjective perspectives may have evolved. To the extent that an individuated informational space seems the most efficient way for a given organism to select biologically valuable information, subjectivity is deemed to constitute an adaptive response to informational overflow. One of the possible consequences of this view is that subjectivity might be (at least functionally) dissociated from consciousness, insofar as the former primarily facilitates selection, the latter action.

Failure to Identify Somatic Mutations in Monozygotic Twins Discordant for Schizophrenia by Whole Exome Sequencing

Background:

Schizophrenia (SCZ) is a severe, debilitating, and complex psychiatric disorder with multiple causative factors. An increasing number of studies have determined that rare variations play an important role in its etiology. A somatic mutation is a rare form of genetic variation that occurs at an early stage of embryonic development and is thought to contribute substantially to the development of SCZ. The aim of the study was to explore the novel pathogenic somatic single nucleotide variations (SNVs) and somatic insertions and deletions (indels) of SCZ.

Methods:

One Chinese family with a monozygotic (MZ) twin pair discordant for SCZ was included. Whole exome sequencing was performed in the co-twin and their parents. Rigorous filtering processes were conducted to prioritize pathogenic somatic variations, and all identified SNVs and indels were further confirmed by Sanger sequencing.

Results:

One somatic SNV and two somatic indels were identified after rigorous selection processes. However, none was validated by Sanger sequencing.

Conclusions:

This study is not alone in the failure to identify pathogenic somatic variations in MZ twins, suggesting that exonic somatic variations are extremely rare. Further efforts are warranted to explore the potential genetic mechanism of SCZ.

Stochastic developmental variation, an epigenetic source of phenotypic diversity with far-reaching biological consequences

This article reviews the production of different phenotypes from the same genotype in the same environment by stochastic cellular events, nonlinear mechanisms during patterning and morphogenesis, and probabilistic self-reinforcing circuitries in the adult life. These aspects of phenotypic variation are summarized under the term 'stochastic developmental variation' (SDV) in the following. In the past, SDV has been viewed primarily as a nuisance, impairing laboratory experiments, pharmaceutical testing, and true-to-type breeding. This article also emphasizes the positive biological effects of SDV and discusses implications for genotype-to-phenotype mapping, biological individuation, ecology, evolution, and applied biology. There is strong evidence from experiments with genetically identical organisms performed in narrowly standardized laboratory set-ups that SDV is a source of phenotypic variation in its own right aside from genetic variation and environmental variation. It is obviously mediated by molecular and higher-order epigenetic mechanisms. Comparison of SDV in animals, plants, fungi, protists, bacteria, archaeans, and viruses suggests that it is a ubiquitous and phylogenetically old phenomenon. In animals, it is usually smallest for morphometric traits and highest for life history traits and behaviour. SDV is thought to contribute to phenotypic diversity in all populations but is particularly relevant for asexually reproducing and genetically impoverished populations, where it generates individuality despite genetic uniformity. In each generation, SDV produces a range of phenotypes around a well-adapted target phenotype, which is interpreted as a bet-hedging strategy to cope with the unpredictability of dynamic environments. At least some manifestations of SDV are heritable, adaptable, selectable, and evolvable, and therefore, SDV may be seen as a hitherto overlooked evolution factor. SDV is also relevant for husbandry, agriculture, and medicine because most pathogens are asexuals that exploit this third source of phenotypic variation to modify infectivity and resistance to antibiotics. Since SDV affects all types of organisms and almost all aspects of life, it urgently requires more intense research and a better integration into biological thinking.

Genetic and environmental impacts on DNA methylation levels in twins

Epigenetics describes the study of cellular modifications that can modify the expression of genes without changing the DNA sequence. DNA methylation is one of the most stable and prevalent epigenetic mechanisms. Twin studies have been a valuable model for unraveling the genetic and epigenetic epidemiology of complex traits, and now offer a potential to dissect the factors that impact DNA methylation variability and its biomedical significance. The twin design specifically allows for the study of genetic, environmental and lifestyle factors, and their potential interactions, on epigenetic profiles. Furthermore, genetically identical twins offer a unique opportunity to assess nongenetic impacts on epigenetic profiles. Here, we summarize recent findings from twin studies of DNA methylation profiles across tissues, to define current knowledge regarding the genetic and nongenetic factors that influence epigenetic variation.

It is time to take timing seriously in clinical genetics

Observations made by molecular techniques on the genome along the individuals' lifetime indicate that the genome in somatic cells displays changes at molecular, cellular, and organismal levels. Timing of genetic events leading to somatic mosaicism and gene expression dynamism results in a highly important variable for comprehending the role of genetics in health and disease. Consideration of time in clinical genetics should be enthusiastically invested into research strategy, interpretation of the results, diagnostic routine, and particularly in ethical discussions.

DNA methylation in psychosis: insights into etiology and treatment

Evidence for involvement of DNA methylation in psychosis forms the focus of this perspective. Of interest are results from two independent sets of experiments including rats treated with antipsychotic drugs and monozygotic twins discordant for schizophrenia. The results show that DNA methylation is increased in rats treated with antipsychotic drugs, reflecting the global effect of the drugs. Some of these changes are also seen in affected schizophrenic twins that were treated with antipsychotics. The genes and pathways identified in the unrelated experiments are relevant to neurodevelopment and psychiatric disorders. The common cause is hypothesized to be aberrations resulting from medication use. However, this needs to be established by future studies that address the origin of methylation changes in psychosis.

Consciousness: individuated information in action

Within theoretical and empirical enquiries, many different meanings associated with consciousness have appeared, leaving the term itself quite vague. This makes formulating an abstract and unifying version of the concept of consciousness - the main aim of this article -into an urgent theoretical imperative. It is argued that consciousness, characterized as dually accessible (cognized from the inside and the outside), hierarchically referential (semantically ordered), bodily determined (embedded in the working structures of an organism or conscious system), and useful in action (pragmatically functional), is a graded rather than an all-or-none phenomenon. A gradational approach, however, despite its explanatory advantages, can lead to some counterintuitive consequences and theoretical problems. In most such conceptions consciousness is extended globally (attached to primitive organisms or artificial systems), but also locally (connected to certain lower-level neuronal and bodily processes). For example, according to information integration theory (as introduced recently by Tononi and Koch, 2014), even such simple artificial systems as photodiodes possess miniscule amounts of consciousness. The major challenge for this article, then, is to establish reasonable, empirically justified constraints on how extended the range of a graded consciousness could be. It is argued that conscious systems are limited globally by the ability to individuate information (where individuated information is understood as evolutionarily embedded, socially altered, and private), whereas local limitations should be determined on the basis of a hypothesis about the action-oriented nature of the processes that select states of consciousness. Using these constraints, an abstract concept of consciousness is arrived at, hopefully contributing to a more unified state of play within consciousness studies itself.

DNA methylation differences in monozygotic twin pairs discordant for schizophrenia identifies psychosis related genes and networks

Background

Despite their singular origin, monozygotic twin pairs often display discordance for complex disorders including schizophrenia. It is a common (1%) and often familial disease with a discordance rate of ~50% in monozygotic twins. This high discordance is often explained by the role of yet unknown environmental, random, and epigenetic factors. The involvement of DNA methylation in this disease appears logical, but remains to be established.

Methods

We have used blood DNA from two pairs of monozygotic twins discordant for schizophrenia and their parents in order to assess genome-wide methylation using a NimbleGen Methylation Promoter Microarray.

Results

The genome-wide results show that differentially methylated regions (DMRs) exist between members representing discordant monozygotic twins. Some DMRs are shared with parent(s) and others appear to be de novo. We found twenty-seven genes affected by DMR changes that were shared in the affected member of two discordant monozygotic pairs from unrelated families. Interestingly, the genes affected by pair specific DMRs share specific networks. Specifically, this study has identified two networks; “cell death and survival” and a “cellular movement and immune cell trafficking”. These two networks and the genes affected have been previously implicated in the aetiology of schizophrenia.

Conclusions

The results are compatible with the suggestion that DNA methylation may contribute to the discordance of monozygotic twins for schizophrenia. Also, this may be accomplished by the direct effect of gene specific methylation changes on specific biological networks rather than individual genes. It supports the extensive genetic, epigenetic and phenotypic heterogeneity implicated in schizophrenia.

Electronic supplementary material

The online version of this article (doi:10.1186/s12920-015-0093-1) contains supplementary material, which is available to authorized users.

Genetics of aging, health, and survival: dynamic regulation of human longevity related traits

Background: The roles of genetic factors in human longevity would be better understood if one can use more efficient methods in genetic analyses and investigate pleiotropic effects of genetic variants on aging and health related traits.

Data and methods: We used EMMAX software with modified correction for population stratification to perform genome wide association studies (GWAS) of female lifespan from the original FHS cohort. The male data from the original FHS cohort and male and female data combined from the offspring FHS cohort were used to confirm findings. We evaluated pleiotropic effects of selected genetic variants as well as gene-smoking interactions on health and aging related traits. Then we reviewed current knowledge on functional properties of genes related to detected variants.

Results: The eight SNPs with genome-wide significant variants were negatively associated with lifespan in both males and females. After additional QC, two of these variants were selected for further analyses of their associations with major diseases (cancer and CHD) and physiological aging changes. Gene-smoking interactions contributed to these effects. Genes closest to detected variants appear to be involved in similar biological processes and health disorders, as those found in other studies of aging and longevity e.g., in cancer and neurodegeneration.

Conclusions: The impact of genes on longevity may involve trade-off-like effects on different health traits. Genes that influence lifespan represent various molecular functions but may be involved in similar biological processes and health disorders, which could contribute to genetic heterogeneity of longevity and the lack of replication in genetic association studies.

Hardy-Weinberg equilibrium revisited for inferences on genotypes featuring allele and copy-number variations

Copy number variations represent a substantial source of genetic variation and are associated with a plethora of physiological and pathophysiological conditions. Joint copy number and allelic variations (CNAVs) are difficult to analyze and require new strategies to unravel the properties of genotype distributions. We developed a Bayesian hidden Markov model (HMM) approach that allows dissecting intrinsic properties and metastructures of the distribution of CNAVs within populations, in particular haplotype phases of genes with varying copy numbers. As a key feature, this approach incorporates an extension of the Hardy-Weinberg equilibrium, allowing both a comprehensive and parsimonious model design. We demonstrate the quality of performance and applicability of the HMM approach with a real data set describing the Fcγ receptor (FcγR) gene region. Our concept, using a dynamic process to analyze a static distribution, establishes the basis for a novel understanding of complex genomic data sets.

CNV Concordance in 1,097 MZ Twin Pairs

Monozygotic (MZ) twins are genetically identical at conception, making them informative subjects for studies on somatic mutations. Copy number variants (CNVs) are responsible for a substantial part of genetic variation, have relatively high mutation rates, and are likely to be involved in phenotypic variation. We conducted a genome-wide survey for post-twinning de novo CNVs in 1,097 MZ twin pairs. Comparisons between MZ twins were made by CNVs measured in DNA from blood or buccal epithelium with the Affymetrix 6.0 microarray and two calling algorithms. In addition, CNV concordance rates were compared between the different sources of DNA, and gene-enrichment association analyses were conducted for thought problems (TP) and attention problems (AP) using CNVs concordant within MZ pairs. We found a total of 153 putative post-twinning de novo CNVs >100 kb, of which the majority resided in 15q11.2. Based on the discordance of raw intensity signals a selection was made of 20 de novo CNVs for a qPCR validation experiments. Two out of 20 post-twinning de novo CNVs were validated with qPCR in the same twin pair. The 13-year-old MZ twin pair that showed two discordances in CN in 15q11.2 in their buccal DNA did not show large phenotypic differences. From the remaining 18 putative de novo CNVs, 17 were deletions or duplications that were concordant within MZ twin pairs. Concordance rates within twin pairs of CNV calls with CN ≠ 2 were ~80%. Buccal epithelium-derived DNA showed a slightly but significantly higher concordance rate, and blood-derived DNA showed significantly more concordant CNVs per twin pair. The gene-enrichment analyses on concordant CNVs showed no significant associations between CNVs overlapping with genes involved in neuronal processes and TP or AP after accounting for the source of DNA.

A Bayesian framework for de novo mutation calling in parents-offspring trios

MOTIVATION

Spontaneous (de novo) mutations play an important role in the disease etiology of a range of complex diseases. Identifying de novo mutations (DNMs) in sporadic cases provides an effective strategy to find genes or genomic regions implicated in the genetics of disease. High-throughput next-generation sequencing enables genome- or exome-wide detection of DNMs by sequencing parents-proband trios. It is challenging to sift true mutations through massive amount of noise due to sequencing error and alignment artifacts. One of the critical limitations of existing methods is that for all genomic regions the same pre-specified mutation rate is assumed, which has a significant impact on the DNM calling accuracy.

RESULTS

In this study, we developed and implemented a novel Bayesian framework for DNM calling in trios (TrioDeNovo), which overcomes these limitations by disentangling prior mutation rates from evaluation of the likelihood of the data so that flexible priors can be adjusted post-hoc at different genomic sites. Through extensively simulations and application to real data we showed that this new method has improved sensitivity and specificity over existing methods, and provides a flexible framework to further improve the efficiency by incorporating proper priors. The accuracy is further improved using effective filtering based on sequence alignment characteristics.

AVAILABILITY AND IMPLEMENTATION

The C++ source code implementing TrioDeNovo is freely available at https://medschool.vanderbilt.edu/cgg.

CONTACT

bingshan.li@vanderbilt.edu

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

BiDil in the Clinic: An Interdisciplinary Investigation of Physicians' Prescription Patterns of a Race-Based Therapy

BACKGROUND

The African American Heart Failure Trial (A-HeFT) and the FDA approval of BiDil for race-specific prescription have stirred the debate about the scientific and medical status of race. Yet there is no assessment of the potential fallouts of this dispute on physicians' willingness to prescribe the drug. We present here an analysis of the factors influencing physicians' prescription of BiDil and investigate whether exposure to the controversy has an impact on their therapeutic judgments about the drug.

METHODS

We conducted an electronic survey with physicians in the department of internal medicine at the University of Cincinnati. Participants were randomly assigned to two groups, with one group receiving information about the controversy over BiDil. We used various statistical tests, including a linear mixed effects model, to analyze the results.

RESULTS

27% of the participants reported using patients' race as a major factor in making treatment decisions. 33% reported the inefficacy of standard therapies, 25% the severity of the disease, and 15% other unspecified factors as primary determining criteria in prescribing BiDil. With respect to the controversy, 68% of physicians reported that they were not aware of any controversy surrounding BiDil. Physicians' willingness to prescribe BiDil as a therapy was associated with their awareness of the controversy surrounding A-HeFT (p < 0.003). But their willingness to prescribe the therapy along racial lines did not vary significantly with exposure to the controversy.

CONCLUSIONS

Overall, physicians prescribe and are willing to prescribe BiDil more to black patients than to white patients. However, physicians' lack of awareness about the controversial scientific status of A-HeFT suggests the need for more efficient ways to convey scientific information about BiDil to clinicians. Furthermore, the uncertainties about the determination of clinical utility of BiDil for the individual patient raise questions about whether this specific race-based therapy is in patients' best interest.

Whole genome and exome sequencing of monozygotic twins with trisomy 21, discordant for a congenital heart defect and epilepsy

Congenital heart defects (CHD) occur in 40% of patients with trisomy 21, while the other 60% have a structurally normal heart. This suggests that the increased dosage of genes on chromosome 21 is a risk factor for abnormal heart development. Interaction of genes on chromosome 21 or their gene products with certain alleles of genes on other chromosomes could contribute to CHD. Here, we identified a pair of monozygotic twins with trisomy 21 but discordant for a ventricular septal defect and epilepsy. Twin-zygosity was confirmed by microsatellite genotyping. We hypothesized that some genetic differences from post-twinning mutations caused the discordant phenotypes. Thus, next generation sequencing (NGS) technologies were applied to sequence both whole genome and exome of their leukocytes. The post-analyses of the sequencing data revealed 21 putative discordant exonic variants between the twins from either genome or exome data. However, of the 15 variants chosen for validation with conventional Sanger sequencing, these candidate variants showed no differences in both twins. The fact that no discordant DNA variants were found suggests that sequence differences of DNA from leukocytes of monozygotic twins might be extremely rare. It also emphasizes the limitation of the current NGS technology in identifying causative genes for discordant phenotypes in monozygotic twins.

Rare autosomal copy number variations in early-onset familial Alzheimer's disease

Over 200 rare and fully penetrant pathogenic mutations in amyloid precursor protein (APP), presenilin 1 and 2 (PSEN1 and PSEN2) cause a subset of early-onset familial Alzheimer's disease (EO-FAD). Of these, 21 cases of EO-FAD families carrying unique APP locus duplications remain the only pathogenic copy number variations (CNVs) identified to date in Alzheimer's disease (AD). Using high-density DNA microarrays, we performed a comprehensive genome-wide analysis for the presence of rare CNVs in 261 EO-FAD and early/mixed-onset pedigrees. Our analysis revealed 10 novel private CNVs in 10 EO-FAD families overlapping a set of genes that includes: A2BP1, ABAT, CDH2, CRMP1, DMRT1, EPHA5, EPHA6, ERMP1, EVC, EVC2, FLJ35024 and VLDLR. In addition, CNVs encompassing two known frontotemporal dementia genes, CHMP2B and MAPT were found. To our knowledge, this is the first study reporting rare gene-rich CNVs in EO-FAD and early/mixed-onset AD that are likely to underlie pathogenicity in familial AD and perhaps related dementias.

Personalized medicine, availability, and group disparity: an inquiry into how physicians perceive and rate the elements and barriers of personalized medicine

BACKGROUND

The success of personalized medicine depends on factors influencing the availability and implementation of its new tools to individualize clinical care. However, little is known about physicians' views of the availability of personalized medicine across racial/ethnic groups and the relationship between perceived availability and clinical implementation. This study examines physicians' perceptions of key elements/tools and potential barriers to personalized medicine in connection with their perceptions of the availability of the latter across subpopulations.

METHODS

Study subjects consisted of physicians recruited from Cincinnati Children's Hospital Medical Center and UC Health. An electronic survey conducted from September 2012 to November 2012 recruited 104 physicians. Wilcoxon rank sum analysis compared groups.

RESULTS

Physicians were divided about whether personalized medicine contributes to health equality, as 37.4% of them believe that personalized medicine is currently available only for some subpopulations. They also rated the importance of racial/ethnic background almost as high as the importance of genetic information in the delivery of personalized medicine. Actual elements of personalized medicine rated highest include family history, drug-drug interaction alerts in medical records, and biomarker measurements to guide therapy. Costs of gene-based therapies and genetic testing were rated the most significant barriers. The ratings of several elements and barriers were associated with perceived availability of personalized medicine across subpopulations.

CONCLUSION

While physicians hold differing views about the availability and implementation of personalized medicine, they likewise establish complex relationships between race/ethnicity and personalized medicine that may carry serious implications for its clinical success.

Biological relevance of CNV calling methods using familial relatedness including monozygotic twins

BACKGROUND

Studies involving the analysis of structural variation including Copy Number Variation (CNV) have recently exploded in the literature. Furthermore, CNVs have been associated with a number of complex diseases and neurodevelopmental disorders. Common methods for CNV detection use SNP, CNV, or CGH arrays, where the signal intensities of consecutive probes are used to define the number of copies associated with a given genomic region. These practices pose a number of challenges that interfere with the ability of available methods to accurately call CNVs. It has, therefore, become necessary to develop experimental protocols to test the reliability of CNV calling methods from microarray data so that researchers can properly discriminate biologically relevant data from noise.

RESULTS

We have developed a workflow for the integration of data from multiple CNV calling algorithms using the same array results. It uses four CNV calling programs: PennCNV (PC), Affymetrix® Genotyping Console™ (AGC), Partek® Genomics Suite™ (PGS) and Golden Helix SVS™ (GH) to analyze CEL files from the Affymetrix® Human SNP 6.0 Array™. To assess the relative suitability of each program, we used individuals of known genetic relationships. We found significant differences in CNV calls obtained by different CNV calling programs.

CONCLUSIONS

Although the programs showed variable patterns of CNVs in the same individuals, their distribution in individuals of different degrees of genetic relatedness has allowed us to offer two suggestions. The first involves the use of multiple algorithms for the detection of the largest possible number of CNVs, and the second suggests the use of PennCNV over all other methods when the use of only one software program is desirable.

Transposable elements and psychiatric disorders

Transposable Elements (TEs) or transposons are low-complexity elements (e.g., LINEs, SINEs, SVAs, and HERVs) that make up to two-thirds of the human genome. There is mounting evidence that TEs play an essential role in genomic architecture and regulation related to both normal function and disease states. Recently, the identification of active TEs in several different human brain regions suggests that TEs play a role in normal brain development and adult physiology and quite possibly in psychiatric disorders. TEs have been implicated in hemophilia, neurofibromatosis, and cancer. With the advent of next-generation whole-genome sequencing approaches, our understanding of the relationship between TEs and psychiatric disorders will greatly improve. We will review the biology of TEs and early evidence for TE involvement in psychiatric disorders.

Copy number variation distribution in six monozygotic twin pairs discordant for schizophrenia

We have evaluated copy number variants (CNVs) in six monozygotic twin pairs discordant for schizophrenia. The data from Affymetrix® Human SNP 6.0 arrays™ were analyzed using Affymetrix® Genotyping Console™, Partek® Genomics Suite™, PennCNV, and Golden Helix SVS™. This yielded both program-specific and overlapping results. Only CNVs called by Affymetrix Genotyping Console, Partek Genomics Suite, and PennCNV were used in further analysis. This analysis included an assessment of calls in each of the six twin pairs towards identification of unique CNVs in affected and unaffected co-twins. Real time polymerase chain reaction (PCR) experiments confirmed one CNV loss at 7q11.21 that was found in the affected patient but not in the unaffected twin. The results identified CNVs and genes that were previously implicated in mental abnormalities in four of the six twin pairs. It included PYY (twin pairs 1 and 5), EPHA3 (twin pair 3), KIAA1211L (twin pair 4), and GPR139 (twin pair 5). They represent likely candidate genes and CNVs for the discordance of four of the six monozygotic twin pairs for this heterogeneous neurodevelopmental disorder. An explanation for these differences is ontogenetic de novo events that differentiate in the monozygotic twins during development.

New findings in the genetics of schizophrenia

New findings in schizophrenia genetics are based on genome-wide association studies (GWAS), research into DNA copy number variations (CNVs), and endophenotypes. More than 70 genes have recently been suspected to be involved in the genetic background of schizophrenia based on the GWAS´s results. They are typically related to neurodevelopment/neuroplasticity, immunology and neuroendocrinology. Nevertheless, for many detected genes their possible relationship to schizophrenia etiopathogenesis is still unknown. The CNVs at genome loci 1q21.1 (candidate gene e.g., PRKAB2), 2p16.3 (candidate gene e.g., NRXN1), 3q29 (candidate genes e.g., BDH1, DLG1, PAK2 or TFRC), 15q11.2 (candidate gene e.g., CYFIP1), 15q13.3 (candidate gene e.g., CHRNA7), 16p13.1 (candidate genes e.g.,NTAN1 or NDE1) and 22q11.2 (candidate genes e.g., COMT, GSTT2 or PRODH) were associated with schizophrenia most frequently. Genetic research of schizophrenia endophenotypes, usually neurophysiological, neuromotoric, neurocognitive, neuroanatomical, neurological or personality-related, will help us to discover the role of relevant genes in the pathogenesis of schizophrenia. It is also necessary to integrate knowledge from other research platforms in schizophrenia, like epigenetics, studies of gene-environment interactions, transcriptomics, proteomics, metabolomics, neuroimaging and psychopathology. A better knowledge of the genetic background of schizophrenia can lead to changes in the treatment, prevention and genetic counselling. It may also reduce stigma in this severe mental disorder.

Theoretical framework of population genetics with somatic mutations taken into account: application to copy number variations in humans

Traditionally, population genetics focuses on the dynamics of frequencies of alleles acquired by mutations on germ-lines, because only such mutations are heritable. Typical genotyping experiments, however, use DNA from some somatic tissues such as blood, which harbors somatic mutations at the current generation in addition to germ-line mutations accumulated since the most recent common ancestor of the sample. This common practice may sometimes cause erroneous interpretations of polymorphism data, unless we properly understand the role of somatic mutations in population genetics. We here introduce a very basic theoretical framework of population genetics with somatic mutations taken into account. It is easy to imagine that somatic mutations at the current generation simply add individual-specific variations, as errors in mutation detection do. Our theory quantifies this increment under various conditions. We find that the major contribution of somatic mutations plus errors is to very rare variants, particularly to singletons. The relative contribution is markedly large when mutations are deleterious. Because negative selection also increases rare variants, it is important to distinguish the roles of these mutually confounding factors when we interpret the data, even after correcting for demography. We apply this theory to human copy number variations (CNVs), for which the composite effect of somatic mutations and errors may not be negligible. Using genome-wide CNV data, we demonstrate how the joint action of the two factors, selection and somatic mutations plus errors, shapes the observed pattern of polymorphism.

Search for missing schizophrenia genes will require a new developmental neurogenomic perspective

Even the most powerful experimental designs in search of genetic causes of schizophrenia have not met the desired goal. It is imperative to review the reasons for such an outcome and to formulate novel strategies for the future direction of this research in the new era of individual genomes. Here, we will review aspects of neurodevelopmental hypothesis of schizophrenia in the light of novel genomic and epigenomic insights. Specifically, we will argue for the involvement of de novo mutations and epigenetic modifications during neurodevelopment that may result in schizophrenia. Our conclusion is that the successful elucidation of hereditary mechanisms in neuropsychiatric disorders must begin with attention to discrete endophenotypes; consideration of ontogeny, forethought of genome structure including temporal and spatial patterns of (epi) mutations and the use of judicious techniques that go beyond association studies.

A novel deletion cluster at 13q14.2-q21.33 in an 80-year man with late onset leukemia: Clinical and molecular findings

Chromosomal deletions are among the most common genetic events observed in hematologic malignancies; loss of genetic material is regarded as a hallmark of putative tumor suppressor gene localization. We have identified an unusual cluster of deletions at 13q14.2-13q21.33 in an 80-year-old father of a monozygotic twin pair discordant for schizophrenia, who developed chronic leukemia (CLL) at age 69.

MATERIALS AND METHODS:

The breakpoints for individual deletions in this cluster was identified by Affymetrix Human Array 6.0 screening.

RESULTS:

The deleted segments harbours a number of genes, most associated with cancer as well as a high concentration of LINEs, SINEs and related repeats. The derived chromosome represents an intra-chromosomal re-arrangement that quickly overtook blood progenitor cells probably before age 69 as a cause of CLL.

CONCLUSIONS:

The study highlights the role of ongoing de novo changes at susceptible sites, such as repeat rich regions, in the human genome. Also, it argues for the involvement of genes/deletions in the 13q(14.2-21.33) region in the development of CCL.

Twin Mitochondrial Sequence Analysis

When applying genome-wide sequencing technologies to disease investigation, it is increasingly important to resolve sequence variation in regions of the genome that may have homologous sequences. The human mitochondrial genome challenges interpretation given the potential for heteroplasmy, somatic variation, and homologous nuclear mitochondrial sequences (numts). Identical twins share the same mitochondrial DNA (mtDNA) from early life, but whether the mitochondrial sequence remains similar is unclear. We compared an adult monozygotic twin pair using high-throughput sequencing and evaluated variants with primer extension and mitochondrial preenrichment. Thirty-seven variants were shared between the twin individuals, and the variants were verified on the original genomic DNA. These studies support highly identical genetic sequence in this case. Certain low-level variant calls were of high quality and homology to the mtDNA, and they were further evaluated. When we assessed calls in preenriched mtDNA templates, we found that these may represent numts, which can be differentiated from mtDNA variation. We conclude that twin identity extends to mtDNA, and it is critical to differentiate between numts and mtDNA in genome sequencing, particularly as significant heteroplasmy could influence genome interpretation. Further studies on mtDNA and numts will aid in understanding how variation occurs and persists.

Monozygotic twins with early-onset schizophrenia and late-onset bipolar disorder: a case report

INTRODUCTION

Schizophrenia and bipolar disorder are generally considered to be distinct illnesses. One piece of evidence supporting their distinctness is the rarity of schizophrenia and bipolar disorder occurring in monozygotic co‒twins.

CASE PRESENTATION

We describe a well-characterized pair of African American, female, monozygotic twins assessed at 53 years of age.Case 1: Twin A developed psychotic symptoms at age 23. She was hospitalized and diagnosed with schizophrenia. Twin A was subsequently hospitalized several more times and was consistently diagnosed as suffering from schizophrenia. At the time of assessment, Twin A was single, lived with her parents and attended a day program. Case 2: In contrast, Twin B worked in a professional career, married and raised a family. She remained well until age 48 when she developed a depressive disorder requiring medication treatment. Four years later, Twin B abruptly developed grandiose delusions and mood-congruent auditory hallucinations. She was hospitalized and diagnosed with a manic episode. Since then Twin B has remained symptom-free on the mood stabilizer sodium valproate.

CONCLUSION

Schizophrenia and bipolar disorder can occur in identical co-twins. We speculate on what it tells us about the meaning of discordance and the putative role of de novo mutations.

Comprehensive analysis of copy number variation in monozygotic twins discordant for bipolar disorder or schizophrenia

Copy number variation plays a clear role in the etiology of many psychiatric disorders, particularly schizophrenia. We performed array-CGH to look for copy number variants between five pairs of monozygotic twins discordant for bipolar disorder or schizophrenia. Our study found no differences in copy number variants between the sets of twins. Although alluring, realistic accounting for heterogeneity and chimerism highlights the technological limitations in studying monozygotic twins discordant for psychiatric disorders.

Role of perfumes in pathogenesis of autism

Autism spectrum disorders (ASDs) are developmental conditions characterized by deficits in social interaction, verbal and nonverbal communication, and obsessive/stereotyped patterns of behavior. Although there is no reliable neurophysiological marker associated with ASDs, dysfunction of the parieto-frontal mirror neuron system and underdeveloped olfactory bulb (OB) has been associated with the disorder. It has been reported that the number of children who have ASD has increased considerably since the early 1990 s. In developed countries, it is now reported that 1-1.5% of children have ASD, and in the US it is estimated that one in 88 children suffer from ASD. Currently, there is no known cause for ASD. During the last three decades, the most commonly accepted paradigm about autism is that it is a genetically inherited disease. The recent trio analyses, in which both biological parents and the autistic child's exomes are sequenced, do not support this paradigm. On the other hand, the environmental factors that may induce genetic mutations in vitro have not been clearly identified, and there is little irrefutable evidence that pesticides, water born chemicals, or food preservatives play critical roles in inducing the genetic mutations associated with known intellectual deficiencies that have been linked to autism spectrum disorder (ASD). Here, we hypothesize and provide scientific evidence that ASD is the result of exposure to perfumes and cosmetics. The highly mutagenic, neurotoxic, and neuromodulatory chemicals found in perfumes are often overlooked and ignored as a result of a giant loophole in the Federal Fair Packaging and Labeling Act of 1973, which explicitly exempts fragrance producers from having to disclose perfume ingredients on product labels. We hypothesize that perfumes and cosmetics may be important factors in the pathogenesis of ASD. Synthetic perfumes have gained global utility not only as perfumes but also as essential chemicals in detergents, cosmetics, soap, and a wide variety of commonly used items, even in food flavoring to enhance product taste. Here we provide evidence that a majority of perfumes are highly mutagenic at femtomolar concentrations, and cause significant neuromodulations in human neuroblastoma cells at extremely low levels of concentration, levels that are expected to reach a developing fetal brain if the pregnant mothers are exposed to these chemicals.

Monozygotic twins discordant for submicroscopic chromosomal anomalies in 2p25.3 region detected by array CGH

Although discordant phenotypes in monozygotic twins with developmental disorder are not an exception, underlying genetic discordance is rarely reported. Here, we report on the clinical and cytogenetic details of 4-year-old female monozygotic twins with discordant phenotypes. Twin 1 exhibited global developmental delay, overweight and hyperactivity. Twin 2 had an autistic spectrum disorder. Molecular karyotyping in twin 1 identified a 2p25.3 deletion, further confirmed by Fluorescence in situ hybridization (FISH) analysis on leukocytes. Interestingly, array comparative genomic hybridization was normal in twin 2 but FISH analysis using the same probe as twin 1 showed mosaicism with one-third of cells with a 2p25.3 deletion, one-third of cells with a 2p25.3 duplication, and one-third of normal cells. Genotyping with microsatellite markers confirmed the monozygosity of the twins. We propose that the chromosome imbalance may be due to a mitotic non-allelic recombination occurring during blastomeric divisions of a normal zygote. Such event will result in three distinct cell populations, whose proportion in each embryo formed after separation from the zygote may differ, leading to discordant chromosomal anomalies between twins. We also discuss that the MYTL1L and the SNTG2 genes within the reported region could probably relate to the phenotypic discordance of the monozygotic twins.

Analysis of copy number variations in brain DNA from patients with schizophrenia and other psychiatric disorders

BACKGROUND

Clinical studies have identified several regions of the genome with copy number variations (CNVs) associated with diverse neurodevelopmental behavioral disorders.

METHODS

We analyzed 1 million (M) single nucleotide polymorphism genotype arrays for evidence of previously reported recurrent CNVs and enriched genome-wide CNV burden in DNA from 600 brains, including 441 individuals with various psychiatric diagnoses. We explored gene expression in the dorsolateral prefrontal cortex in selected cases with CNVs and in other subjects with Illumina BeadArrays (568 subjects in total) and additionally in 66-92 subjects with quantitative real-time polymerase chain reaction.

RESULTS

The CNVs in previously reported genomic regions were identified in 4 of 193 patients with the diagnosis of schizophrenia (1q21.1, 11q25, 15q11.2, 22q11), 4 of 238 patients with mood disorders (11q25, 15q11.2, 22q11), and 1 of 10 patients with autism (2p16.3). No evidence of increased genome-wide CNV burden was observed in cases with schizophrenia or mood disorders, although the study is underpowered to observe rare events. Messenger RNA expression patterns suggested incomplete molecular penetrance of observed CNVs.

CONCLUSIONS

Our data confirm in brain DNA the presence of certain recurrent CNVs in a small percentage of patients with psychiatric diagnoses.

Animal models and conserved processes

BACKGROUND

The concept of conserved processes presents unique opportunities for using nonhuman animal models in biomedical research. However, the concept must be examined in the context that humans and nonhuman animals are evolved, complex, adaptive systems. Given that nonhuman animals are examples of living systems that are differently complex from humans, what does the existence of a conserved gene or process imply for inter-species extrapolation?

METHODS

We surveyed the literature including philosophy of science, biological complexity, conserved processes, evolutionary biology, comparative medicine, anti-neoplastic agents, inhalational anesthetics, and drug development journals in order to determine the value of nonhuman animal models when studying conserved processes.

RESULTS

Evolution through natural selection has employed components and processes both to produce the same outcomes among species but also to generate different functions and traits. Many genes and processes are conserved, but new combinations of these processes or different regulation of the genes involved in these processes have resulted in unique organisms. Further, there is a hierarchy of organization in complex living systems. At some levels, the components are simple systems that can be analyzed by mathematics or the physical sciences, while at other levels the system cannot be fully analyzed by reducing it to a physical system. The study of complex living systems must alternate between focusing on the parts and examining the intact whole organism while taking into account the connections between the two. Systems biology aims for this holism. We examined the actions of inhalational anesthetic agents and anti-neoplastic agents in order to address what the characteristics of complex living systems imply for inter-species extrapolation of traits and responses related to conserved processes.

CONCLUSION

We conclude that even the presence of conserved processes is insufficient for inter-species extrapolation when the trait or response being studied is located at higher levels of organization, is in a different module, or is influenced by other modules. However, when the examination of the conserved process occurs at the same level of organization or in the same module, and hence is subject to study solely by reductionism, then extrapolation is possible.

Chromosome 22q11.2 microdeletion in monozygotic twins with discordant phenotype and deletion size

We report on a pair of male monozygotic twins with 22q11.2 microdeletion, discordant phenotype and discordant deletion size. The second twin had findings suggestive of DiGeorge syndrome, while the first twin had milder anomalies without any cardiac malformation. The second twin had presented with intractable convulsion, cyanosis and cardiovascular failure in the fourth week of life and expired on the sixth week of life, whereas the first twin had some characteristic facial appearance with developmental delay but no other signs of the 22q11.2 microdeletion syndrome including cardiovascular malformation. The fluorescence in situ hybridization (FISH) analysis had shown a microdeletion on the chromosome 22q11.2 in both twins. The interphase FISH did not find any evidence for the mosaicism. The genomic DNA microarray analysis, using HumanCytoSNP-12 BeadChip (Illumina), was identical between the twins except different size of deletion of 22q11.2. The zygosity using HumanCytoSNP-12 BeadChip (Illumina) microarray analysis suggested monozygosity. This observation indicates that altered size of the deletion may be the underlying etiology for the discordance in phenotype in monozygotic twins. We think early post zygotic events (mitotic non-allelic homologous recombination) could have been played a role in the alteration of 22q11.2 deletion size and, thus phenotypic variability in the monozygotic twins.

Clinical applications of schizophrenia genetics: genetic diagnosis, risk, and counseling in the molecular era

Schizophrenia is a complex neuropsychiatric disease with documented clinical and genetic heterogeneity, and evidence for neurodevelopmental origins. Driven by new genetic technologies and advances in molecular medicine, there has recently been concrete progress in understanding some of the specific genetic causes of this serious psychiatric illness. In particular, several large rare structural variants have been convincingly associated with schizophrenia, in targeted studies over two decades with respect to 22q11.2 microdeletions, and more recently in large-scale, genome-wide case-control studies. These advances promise to help many families afflicted with this disease. In this review, we critically appraise recent developments in the field of schizophrenia genetics through the lens of immediate clinical applicability. Much work remains in translating the recent surge of genetic research discoveries into the clinic. The epidemiology and basic genetic parameters (such as penetrance and expression) of most genomic disorders associated with schizophrenia are not yet well characterized. To date, 22q11.2 deletion syndrome is the only established genetic subtype of schizophrenia of proven clinical relevance. We use this well-established association as a model to chart the pathway for translating emerging genetic discoveries into clinical practice. We also propose new directions for research involving general genetic risk prediction and counseling in schizophrenia.

Copy number variants in a sample of patients with psychotic disorders: is standard screening relevant for actual clinical practice?

With the introduction of new genetic techniques such as genome-wide array comparative genomic hybridization, studies on the putative genetic etiology of schizophrenia have focused on the detection of copy number variants (CNVs), ie, microdeletions and/or microduplications, that are estimated to be present in up to 3% of patients with schizophrenia. In this study, out of a sample of 100 patients with psychotic disorders, 80 were investigated by array for the presence of CNVs. The assessment of the severity of psychiatric symptoms was performed using standardized instruments and ICD-10 was applied for diagnostic classification. In three patients, a submicroscopic CNV was demonstrated, one with a loss in 1q21.1 and two with a gain in 1p13.3 and 7q11.2, respectively. The association between these or other CNVs and schizophrenia or schizophrenia-like psychoses and their clinical implications still remain equivocal. While the CNV affected genes may enhance the vulnerability for psychiatric disorders via effects on neuronal architecture, these insights have not resulted in major changes in clinical practice as yet. Therefore, genome-wide array analysis should presently be restricted to those patients in whom psychotic symptoms are paired with other signs, particularly dysmorphisms and intellectual impairment.

The landscape of inherited and de novo copy number variants in a Plasmodium falciparum genetic cross

BACKGROUND

Copy number is a major source of genome variation with important evolutionary implications. Consequently, it is essential to determine copy number variant (CNV) behavior, distributions and frequencies across genomes to understand their origins in both evolutionary and generational time frames. We use comparative genomic hybridization (CGH) microarray and the resolution provided by a segregating population of cloned progeny lines of the malaria parasite, Plasmodium falciparum, to identify and analyze the inheritance of 170 genome-wide CNVs.

RESULTS

We describe CNVs in progeny clones derived from both Mendelian (i.e. inherited) and non-Mendelian mechanisms. Forty-five CNVs were present in the parent lines and segregated in the progeny population. Furthermore, extensive variation that did not conform to strict Mendelian inheritance patterns was observed. 124 CNVs were called in one or more progeny but in neither parent: we observed CNVs in more than one progeny clone that were not identified in either parent, located more frequently in the telomeric-subtelomeric regions of chromosomes and singleton de novo CNVs distributed evenly throughout the genome. Linkage analysis of CNVs revealed dynamic copy number fluctuations and suggested mechanisms that could have generated them. Five of 12 previously identified expression quantitative trait loci (eQTL) hotspots coincide with CNVs, demonstrating the potential for broad influence of CNV on the transcriptional program and phenotypic variation.

CONCLUSIONS

CNVs are a significant source of segregating and de novo genome variation involving hundreds of genes. Examination of progeny genome segments provides a framework to assess the extent and possible origins of CNVs. This segregating genetic system reveals the breadth, distribution and dynamics of CNVs in a surprisingly plastic parasite genome, providing a new perspective on the sources of diversity in parasite populations.