Structural variation of the genome involves kilobase- to megabase-sized deletions, duplications, insertions, inversions, and complex combinations of rearrangements. We introduce high-throughput and massive paired-end mapping (PEM), a large-scale genome-sequencing method to identify structural variants (SVs) approximately 3 kilobases (kb) or larger that combines the rescue and capture of paired ends of 3-kb fragments, massive 454 sequencing, and a computational approach to map DNA reads onto a reference genome. PEM was used to map SVs in an African and in a putatively European individual and identified shared and divergent SVs relative to the reference genome. Overall, we fine-mapped more than 1000 SVs and documented that the number of SVs among humans is much larger than initially hypothesized; many of the SVs potentially affect gene function. The breakpoint junction sequences of more than 200 SVs were determined with a novel pooling strategy and computational analysis. Our analysis provided insights into the mechanisms of SV formation in humans.

SUMMARY Autism spectrum disorder (ASD) is a disorder of brain development. Most cases lack a clear etiology or genetic basis, and the difficulty of reenacting human brain development has precluded understanding of ASD pathophysiology. Here we use three-dimensional neural cultures (organoids) derived from induced pluripotent stem cells (iPSCs) to investigate neurodevelopmental alterations in individuals with severe idiopathic ASD. While no known underlying genomic mutation could be identified, transcriptome and gene network analyses revealed upregulation of genes involved in cell proliferation, neuronal differentiation, and synaptic assembly. ASD-derived organoids exhibit an accelerated cell cycle and overproduction of GABAergic inhibitory neurons. Using RNA interference, we show that overexpression of the transcription factor FOXG1 is responsible for the overproduction of GABAergic neurons. Altered expression of gene network modules and FOXG1 are positively correlated with symptom severity. Our data suggest that a shift towards GABAergic neuron fate caused by FOXG1 is a developmental precursor of ASD.

Human induced pluripotent stem cells (hiPSCs) are emerging as a tool for understanding human brain development at cellular, molecular, and genomic levels. Here we show that hiPSCs grown in suspension in the presence of rostral neuralizing factors can generate 3D structures containing polarized radial glia, intermediate progenitors, and a spectrum of layer-specific cortical neurons reminiscent of their organization in vivo. The hiPSC-derived multilayered structures express a gene expression profile typical of the embryonic telencephalon but not that of other CNS regions. Their transcriptome is highly enriched in transcription factors controlling the specification, growth, and patterning of the dorsal telencephalon and displays highest correlation with that of the early human cerebral cortical wall at 8-10 wk after conception. Thus, hiPSC are capable of enacting a transcriptional program specifying human telencephalic (pallial) development. This model will allow the study of human brain development as well as disorders of the human cerebral cortex.human embryonic stem cell | embryo | differentiation | cortical layer E merging data highlight the complexity and dynamic nature of gene expression in the central nervous system (CNS) and the divergence between human and other mammalian species, which is especially pronounced in the developing brain (1-4). Exploring such differences may reveal the genetic underpinnings of the larger size and complex architecture of the human brain and elucidate the molecular and cellular substrates of higher cognitive functions, as well as of our vulnerability to neurodevelopmental and neurodegenerative disorders. To understand the genetic programs that drive cell specification and differentiation in the human brain, it is important to develop model systems that recapitulate dynamic aspects of neural development, in addition to making inferences from commonly used models of lower mammalian species.Recapitulating human neural development in vitro using human induced pluripotent stem cells (hiPSCs) can provide our first understanding of how genetic variation and disease-causing mutations influence neural development. Human iPSCs generated from reprogrammed cells can be differentiated into any tissue, including the CNS, while maintaining the genetic background of the individual of origin. These critical features have been exploited to model monogenic forms of neurodevelopmental disorders, such as Rett and Timothy syndromes, and even psychiatric disorders with complex inheritance, such as schizophrenia (5-7). The brain and spinal cord develop according to distinct differentiation programs from the earliest stages of CNS development (i.e., at the progenitor stage during gastrulation) (8, 9). Regional differences in gene expression within stem and progenitor cells appear at the onset of the formation of both mouse (10, 11) and human CNS, as shown by recent studies of the human transcriptome using postmortem tissue (4).Neural cells are thought to differentiate by "default" into an anterior, for...

Reprogramming human somatic cells into induced pluripotent stem cells (iPSCs) has been suspected of causing de novo copy number variations (CNVs)1-4. To explore this issue, we performed a whole-genome and transcriptome analysis of 20 human iPSC lines derived from primary skin fibroblasts of 7 individuals using next-generation sequencing. We find that, on average, an iPSC line manifests two CNVs not apparent in the fibroblasts from which the iPSC was derived. Using qPCR, PCR, and digital droplet PCR (ddPCR), we show that at least 50% of those CNVs are present as low frequency somatic genomic variants in parental fibroblasts (i.e. the fibroblasts from which each corresponding hiPSC line is derived) and are manifested in iPSC colonies due to the colonies’ clonal origin. Hence, reprogramming does not necessarily lead to de novo CNVs in iPSC, since most of line-manifested CNVs reflect somatic mosaicism in the human skin. Moreover, our findings demonstrate that clonal expansion, and iPSC lines in particular, can be used as a discovery tool to reliably detect low frequency CNVs in the tissue of origin. Overall, we estimate that approximately 30% of the fibroblast cells have somatic CNVs in their genomes, suggesting widespread somatic mosaicism in the human body. Our study paves the way to understanding the fundamental question of the extent to which cells of the human body normally acquire structural alterations in their DNA post-zygotically.

Background: Genome wide association studies have not revealed any risk-conferring common genetic variants in Tourette syndrome (TS), requiring the adoption of alternative approaches to investigate the pathophysiology of this disorder. Methods: We obtained the basal ganglia transcriptome by RNA sequencing in the caudate and putamen of 9 TS and 9 matched normal controls. Results: We found 309 down-regulated and 822 up-regulated genes in the caudate and putamen (striatum) of TS individuals. Using data-driven gene network analysis, we identified seventeen gene co-expression modules associated with TS. The top-scoring down-regulated module in TS was enriched in striatal interneuron transcripts, which was confirmed by decreased numbers of cholinergic and GABAergic interneurons by immunohistochemistry in the same regions. The top-scoring up-regulated module was enriched in immune-related genes, consistent with activation of microglia in patients’ striatum. Genes implicated by copy number variants (CNV) in TS were enriched in the interneuron module as well as in a protocadherin module. Module clustering revealed that the interneuron module was correlated with a neuronal metabolism module. Conclusions: Convergence of differential expression, network analyses and module clustering, together with CNVs implicated in TS, strongly implicates disrupted interneuron signaling in the pathophysiology of severe TS, and suggests that metabolic alterations may be linked to their death or dysfunction.

Highly specific amplification of complex DNA pools without bias or template-independent products (TIPs) remains a challenge. We have developed a method using phi29 DNA polymerase and trehalose and optimized control of amplification to create micrograms of specific amplicons without TIPs from down to subfemtograms of DNA. With an input of as little as 0.5-2.5 ng of human gDNA or a few cells, the product could be close to native DNA in locus representation. The amplicons from 5 and 0.5 ng of DNA faithfully demonstrated all previously known heterozygous segmental duplications and deletions (3 Mb to 18 kb) located on chromosome 22 and even a homozygous deletion smaller than 1 kb with high-resolution chromosome-wide comparative genomic hybridization. With 550k Infinium BeadChip SNP typing, the >99.7% accuracy was compared favorably with results on unamplified DNA. Importantly, underrepresentation of chromosome termini that occurred with GenomiPhi v2 was greatly rescued with the present procedure, and the call rate and accuracy of SNP typing were also improved for the amplicons with a 0.5-ng, partially degraded DNA input. In addition, the amplification proceeded logarithmically in terms of total yield before saturation; the intact cells was amplified >50 times more efficiently than an equivalent amount of extracted DNA; and the locus imbalance for amplicons with 0.1 ng or lower input of DNA was variable, whereas for higher input it was largely reproducible. This procedure facilitates genomic analysis with single cells or other traces of DNA, and generates products suitable for analysis by massively parallel sequencing as well as microarray hybridization. copy number variation ͉ single nucleotide polymorphism ͉ comparative genomic hybridization ͉ multiple displacement amplification

Epstein-Barr virus (EBV) is

This article describes the results of an epidemiological study of developmental language disorder (DLD) in an isolated rural Russian population. We report an atypically high prevalence of DLD across all age groups when contrasted with a comparison population. The results are corroborated by a set of comparisons of school-aged children from the target population with their age peers and mean length of utterance matches from the comparison population. We also investigate the relationship between nonverbal cognition, verbal working memory, and expressive language performance in the population, and find statistically significant but small effect sizes. Finally, we describe the complex and heterogeneous structure of the phenotype in the population along with patterns of its vertical transmission on the basis of the exemplar pedigrees, and discuss the implications of our findings for genetic and clinical studies of DLD.