Abstract
Schizophrenia (SZ) is a common and severe psychiatric disorder with both environmental and genetic risk factors, and a high heritability. After over 20 years of molecular genetics research, new molecular strategies, primarily genome-wide association studies (GWAS), have generated major tangible progress. This new data provides evidence for: 1) A number of chromosomal regions with common polymorphisms showing genome-wide association with SZ (the major histocompatibility complex, MHC, region at 6p22-p21; 18q21.2; and 2q32.1). The associated alleles present small odds ratios (the odds of a risk variant being present in cases versus controls) and suggest causative involvement of gene regulatory mechanisms in SZ. 2) Polygenic inheritance. 3) Involvement of rare (<1%) and large (>100kb) copy number variants (CNVs). 4) A genetic overlap of SZ with autism and with bipolar disorder (BP) challenging the classical clinical classifications. Most new SZ findings (chromosomal regions and genes) have generated new biological leads. These new findings, however, still need to be translated into a better understanding of the underlying biology and into causal mechanisms. Furthermore, a considerable amount of heritability still remains unexplained (missing heritability). Deep resequencing for rare variants and system biology approaches (e.g., integrating DNA sequence and functional data) are expected to further improve our understanding of the genetic architecture of SZ and its underlying biology.
Keywords: genome-wide association, schizophrenia, polygenic, CNV, rare variant, gene expression, systems biology
1. Overview
The GWAS approach is based on linkage disequilibrium (LD), which is the non-random association of alleles (alternative forms of a polymorphism) at different loci, and is implemented with single nucleotide polymorphism (SNP) arrays that interrogate common variation across the genome. GWAS experiments have been remarkable successful. Over 900 genes have been reported to be associated at genome-wide significant levels (p<5×10−8) [1] to one or more of ~200 complex phenotypes (www.genome.gov/gwastudies as of 02/12/2010 [2, 3]). Current array platforms capture ~80% of the common variation in the genome for European ancestry (EA) samples [4]. Imputation, the computational prediction of genotypes of untyped SNPs, extends GWAS map coverage [5, 6], and enables the combined analysis of samples genotyped with different platforms. The same arrays used for testing SNP associations carry probes designed for the detection of CNVs, but lower accuracy, particularly for duplications.
2. Main GWAS findings in SZ
Table 1 summarizes the published GWAS for SZ [7–13]. No single study detected genome-wide significant association with individual SNPs. Only a meta-analysis of 8,008 EA cases and 19,077 EA controls, in regions with individual study p-values <0.001, detected a genome-wide significant association at the MHC locus on chromosome 6p [11–13]. The most significant SNP (rs13194053) reached p=9.54×10−9 (Table 1). The odds ratios, a measure of effect size, are small (e.g., the strongest associations at the MHC had ORs ranging 1.14–1.16; other associations with common SNPs also show low ORs). The MHC region is very gene-dense, containing over 200 genes. The low recombination rate at the MHC causes long LD blocks within the region [14]. Because of this long range LD and high gene density, it has not yet been determined whether one or more genes or intergenic regions are implicated. The MHC region contains many genes with roles in immunity and self-recognition, and has been implicated by GWAS in multiple common immune diseases, including type 1 diabetes (T1D), multiple sclerosis, Crohn's disease (CD), and rheumatoid arthritis (RA) (see review [2]). Furthermore, one of the three studies also found a suggestive association for SZ with the FAM69A-EVI-RPL5 gene cluster (1p22) [13], which was previously reported as associated with multiple sclerosis [15]. Consistent with an immune hypothesis of SZ [16], a recent Danish registry study indicated that autoimmune disorders increase the risk for SZ [17]. However, final proof of immune abnormalities in SZ is still missing.
Table 1.
Top genes or genomic regions identified in recent SZ GWAS.
First author and year | Sample | Gene or region | Lowest p-values | OR | Reference |
---|---|---|---|---|---|
Lencz 2007 | 178/144 (EA) | CSF2RA, SHOX | 3.7 × 10−7 | 3.23 | [7] |
Sullivan 2008 | 738/733 (EA) | AGBL1 | 1.71 × 10−6 | 6.01 | [8] |
O'Donovan 2008 | Discovery: 479/2,937 (EA) | ZNF804A | 1.61 × 10−7 | 1.12 | [22] |
Follow up: 6,829/9,897 (EA) | |||||
Need 2009 | Discovery: 871/863 (EA) | ADAMTSL3 | 1.35 × 10−7 | 0.68 | [10] |
Follow up: 1,460/12,995 (EA) | |||||
Purcell 2009 (ISC) | 3,322/3,587 (EA) | MHC regiona | 9.5 × 10−9 | 0.82 | [11] |
MYO18B | 3.4 × 10−7 | ||||
Stefansson 2009 (SGENE) | Discovery: 2,663/13,498 (EA) | MHC regionb | 1.4 × 10−12 | 1.16c | [12] |
Follow up: 4,999/15,555 (EA) | NRGN b | 2.4 × 10−9 | 1.15 | ||
TCF4 b | 4.1 × 10−9 | 1.23 | |||
Shi 2009 (MGS) | 2,681/2,653 (EA) | MHC regiona | 9.5 × 10−9 | 0.88 | [13] |
1,286/973 (AA) | CENTG2 (in EA only) | 4.59 × 10−7 | 1.23 | ||
ERBB4 (in AA only) | 2.14 × 10−6 | 0.73 |
Combined analysis of ISC, SGENE, and MGS GWAS.
Combined analysis of ISC, SGENE (including SGENE follow up samples) and MGS.
OR is for common allele of the associated SNP, which is different from that in ISC and MGS.
TCF4 (transcription factor 4), located in chromosome 18q21, has also been identified as another novel SZ susceptibility locus [12]. TCF4 is a neuronal transcription factor essential for neurogenesis [18]. Mutations in TCF4 cause Pitt–Hopkins syndrome, a disorder characterized by severe motor and mental retardation [19–21].
Another GWAS reported an association of SZ with zinc finger protein 804A (ZNF804A) in 2q32.1 [22]. Although not genome-wide significant for SZ (p=1.61×10−7 with rs1344706), the association reached genome-wide significance in the combined analysis of SZ and BP (p =9.96 × 10−9) [22]. In a subsequent meta-analysis of a much larger data set with 18,945 SZ cases, 2,329 BP cases, and 38,675 controls, support strengthened: p=2.5×10−11 for SZ and p=4.1×10−13 for SZ and BP [23]. ZNF804A was reported associated with altered neuronal connectivity in the dorsolateral prefrontal cortex in a functional magnetic resonance imaging study of healthy controls [9].
Thus, several SZ susceptibility loci have emerged from GWAS and meta-analyses thereof. None of the genome-wide significant loci implicated by GWAS span leading pathophysiological SZ candidate genes (e.g., those examined in [24]), and thus may represent new biological leads.
3. Evidence for a polygenic model
Purcell et al. [11] tested the polygenic hypothesis of SZ [25] by evaluating whether many common variants with small effects could explain a large proportion of the variation in disease risk. Based on different thresholds of association p-values in the International SZ Consortium (ISC) dataset, sets of common variants with small effects (“score” alleles”) were first defined. For each set, an aggregate risk score was then generated for each subject from the Molecular Genetics of SZ (MGS) EA and African American (AA) datasets, and a SZ UK sample [13, 22]. Aggregate risk scores in SZ cases were found to be higher than in controls in SZ samples (and also for BP cases from two BP samples [26, 27]. Performing the same basic analysis for T1D, T2D, hypertension, CD, RA, and coronary artery disease [11, 27] subsequently showed that the result was not an artifact of population stratification, genotyping quality, or other potential systematic biases. Although the variance explained by the observed score alleles derived from ISC study was only ~3%, with simulated datasets, the variance explained by a set of score alleles reached ~1/3. A set of causal alleles with minor allele frequency (MAF) <5% did not fit the model well [11], but a role for rare susceptibility variants could not be excluded. Like for other complex disorders, a large proportion of SZ heritability still remains unexplained by GWAS. Further increasing GWAS sample sizes, including meta-analyses (e.g., the ongoing Psychiatric GWAS Consortium, PGC, for SZ [28]), is expected to provide incremental evidence for the known and as yet undiscovered common loci.
4. Rare CNVs implicated in SZ
About one-quarter of the human genome harbors CNVs, stretches of DNA deletions or duplications ranging from 1kb to several Mb [29]. Multiple CNVs have been suggested associated with SZ (Table 2). So far, only rare (<1%) and large (>100kb) CNVs have been implicated in SZ [10, 30–35] as reflected by overall CNV burden (aggregate) and individual CNV loci. Initial genome-wide CNV scans using 200~400 subjects observed 3- to 8-fold over-representation in SZ cases [31, 32], but subsequent studies with larger sample sizes (>2,000) revealed smaller effects of CNVs in aggregate (Table 2) [33, 34]. A 3Mb 22q11.21 deletion, known as 22q11 deletion syndrome (22qDS), was increasingly linked to SZ in the 1990s [36–38]. 22qDS still is the only CNV that has reached genome-wide significance in a single GWAS of SZ [34]. 22qDS causes DiGeorge or velocardiofacial syndrome (DGS/VCFS), one of the most common anomaly syndromes with 180 variable clinical features, both physical and behavioral, such as congenital heart disease, cleft palate, learning disabilities, facial abnormalities, thymic aplasia, and recurrent infections [39]. Over than 30% of 22qDS carriers develop psychosis, of which 80% manifests as SZ [40] (see also [37, 40]). Other SZ susceptibility CNVs, however, seem less penetrant (i.e., some, albeit very few, controls also carried such CNVs), and many candidate CNVs are singletons and their penetrance remains unknown.
Table 2.
Summary of recent genome-wide CNV studies of SZ.
CNVs in case/control (interval in Mb and longest interval indicated; NA=data not available) | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|
Study | Sample | Assay platform |
Major findings | 1q21.1 | 2p16.3 (NRXN1) |
15q11.2 | 15q13.2 | 16p11.2 | 22q11.21 | Reference |
Kirov 2008 | 93 SZ trios | Array CGH | Two CNVs likely to be pathogenic | NA | 1 del (51.14–51.32) | NA | 1 dup (26.94–28.01) | NA | NA | [30] |
Walsh 2008 | 150 cases/268 controls; 92 childhood onset SZ cases | Array CGH | Rare CNVs in 15% cases vs. 5% controls | 1/0 del (144.94–146.29) | 1/0 del (50.02–50.14) | NA | NA | 2/0 dup (29.65–30.23) | NA | [31] |
Xu 2008 | 359 SZ trios as screening sample; 152 cases/159 controls | Affy 5.0 | In sporadic cases, frequency of rare de novo CNVs was 10% vs. 1.3% in controls | 1/0 del (144.32–144.44) | NA | NA | NA | NA | 3/0 del (17.05–19.99) | [32] |
Stefansson 2008 | 1433 cases / 33,250 controls; 3 CNVs (1q21.1, 15q11.2 and 15q13.3) were followed up in 3,285 cases / 7,951 controls | Varies | Three rare CNVs (1q21.1, 15q11.2, and 15q13.3) showed nominal association | 11/8 del (144.94–146.29) | 0/2 del (50.95–51.16) | 26/79 del (20.3–20.8) | 7/8 del (28.72–30.30) | 2/11 del (29.56–30.09) | 8/0 del | [33] |
ISC 2008 | 3,391 cases / 3,181 controls | Affy 5.0/6.0 | Rare (<1%) and large CNVs (>100kb) are enriched in cases (1.15-fold); 3 regions (1q21.1, 15q13.2, and 22q11.21) showed significant association | 10/1 del (143.72–146.95) | 5/6 del (50.8–51.50) | 26/11 del (20.3–20.8) | 9/0 del (28.0–31.0) | NA | 13/0 del (17.11–19.92) | [34] |
Kirov 2009 | 471 cases / 2,792 controls | Affy 500K | Large CNVs (>1Mb) were 2.26 times over-represented in cases | 0/2 del (144.9–146.3) | 1/3 del | 4/14 del (20.3–20.8) | 0/0 del | NA | 2/0 del (17.3–19.8) | [35] |
Need 2009 | 1,013 cases / 1,084 controls | HumanHa p300, 550, or 610 | Large CNVs (>2Mb) are enriched in cases | 1/0 del (144.1–146.3) | 3/1 del | NA | NA | NA | 4/0 del (16.4–19.8) | [10] |
Summary frequency of implicated CNV (case vs. control) | 0.23% vs. 0.02% (del) | 0.17% vs. 0.03% (del) | 0.65% vs. 0.22% (del) | 0.18% vs. 0.02% (del) | 0.19% vs. 0.003% (dup) | 0.44% vs. 0% (del) |
Of the individual CNVs, the 2p16.3 deletion has the clearest connection to a single causal gene (i.e., exon disruptions of just one gene: NRXN1) [41]. For other CNV regions spanning multiple genes, it is unclear which genes are causative. For example, the 16p11.2 duplication [42] spans 29 genes, of which 22 are brain-expressed and at least 9 (MAZ, CDIPT, DOC2A, TBX6, MAPK3, TAOK2, QPRT, MVP, SEZ6L2) have functions of potential relevance to SZ pathogenesis, such as neuronal differentiation, glutamate neurotransmission, synaptic plasticity, and cognition [43–51]. Similarly, 22qDS spans 51 genes, of which 36 are brain-expressed, and some have been previously studied as SZ candidate genes, including COMT (see review [52], PRODH (see review [53], ARVCF [54], and GNB1L [55]; several (ZDHHC8, PRODH, TBX1, COMT, DGCR8, and GNB1L) have also been suggested to be linked with a range of cognitive and psychiatric phenotypes as demonstrated by mouse models [56–60].
A CNV may manifest phenotypic effects through a variety of structural and regulatory mechanisms [61]: (1) alteration of gene expression due to a gene dosage effect, gene loss-of-function or gene fusion when a CNV disrupts a gene (thought to be the most common mechanisms underlying disease associations); (2) deletion-related hemizygous expression of a recessive mutation or exacerbation of the effect from a functional variant on the non-deleted chromosomal segment [62]; 3) abnormal gene expression of a gene outside the CNV, a positional effect [63] or alteration of gene trans-regulation (e.g., deletion of the trans-acting regulatory sequence element), a transvection effect [64]. In addition, interactions between CNVs (i.e., a hit in a second CNV that would act as a genetic modifier) should also be considered. About ¼ of the subjects with developmental delay with a large 16p12.1 deletion also carried a 2nd large CNV elsewhere [65]. Furthermore, the 2nd hit accompanying a CNV could also be a common risk variant.
Because the dosage change caused by a duplication (1.5-fold via 2N→3N duplication) is less pronounced than by deletion (2-fold via 2N→1N deletion), duplications are expected to have on average smaller phenotypic effects than deletions. The study of knockout mice (null for single or multiple genes within the CNV) is used to model the effect of deletions. A 22q11.2 deletion mouse exhibits impaired sensorimotor gating (a neurophysiological trait associated with SZ), deficits in working memory, spontaneous sensitization of hyperactivity, and a lack of habituation [58, 59], which have been hypothesized as models of clinical SZ characteristics. It is noteworthy that regular knockout or duplication of a syntenic CNV region in the mouse may not always be fully informative of the actual causal mechanisms because a CNV can affect expression of genes as far as ~500kb away from the CNV [66]. Modifying large chromosomal segments [67] will probably be required to unravel the phenotypes associated with most CNVs.
A role for more common, smaller CNVs in SZ pathogenesis remains unknown, largely due to a number of limitations of hybridization-based array platforms for CNV detection and current CNV calling algorithms, including poor probe coverage, low detection sensitivity, and poor reproducibility [68, 69]. These technical limitations especially affect duplication-rich regions (because of the cross-hybridization of probes), leading to low sensitivity (18–55%) and specificity (39–77%) there [70]. Other technical artifacts (e.g., plate effects and cell line artifacts) may also confound the estimation of the prevalence of a CNV [71, 72]. Next-generation sequencing has been shown to outperform microarrays in sensitivity and specificity of CNV detection [73–75], and thus may provide a more comprehensive and accurate estimation of the contribution of both common and rare CNVs to the genetic basis of common disease.
5. Overlap with BP and autism
SZ and BP
As discussed above, polygenic SZ score alleles were found enriched in BP datasets [11, 26, 27]. ZNF804A [22, 23] and CACNA1C (calcium channel, voltage-dependent, L type, alpha 1C subunit) are possibly shared by both disorders [9, 76]. Family studies have also suggested genetic overlap between SZ and BP [77–83]. A recent large family study, with 35,985 SZ and over 40,487 BP Swedish probands, concluded that ~63% of familial coaggregation between SZ and BP was due to additive genetic effects common to both disorders [83].
SZ and autism
All the individual CNVs implicated in SZ in Table 2 were also reported to be associated with autism (and mental retardation, and some also with seizures) [42, 84–94]. Some data from common variation also suggests shared susceptibilities. For example, the MGS EA GWAS had its strongest SNP association (p=4.6×10−7) in centaurin gamma 2 (CENTG2, also known as AGAP1), a gene that has been implicated by linkage evidence in autism [95]. The molecular data is consistent with reports of increased rates of SZ in the parents of autism cases [96], and an increased rate of autism in the presence of parental history of SZ-like psychosis [97].
The associations of a SNP or a CNV to both SZ and BP, or to SZ and autism, can be explained by pleiotropy, which refers to situations where more than one major independent phenotype is associated with a single gene. Pleiotropy is common [98], and in humans, the evidence includes the associations of the same gene with functionally related traits such as body weight and height [99], as well as seemingly unrelated disorders such as T2D [100] and prostate cancer [101] (both associated with JAZF1), and colon/lung cancer and familial Parkinson's disease (both associated with PARK2) [102]. Alternatively, a common association of two disorders to a single gene can be explained by shared phenotypic characteristics (for example, psychosis in BP and in SZ). The integrated analysis of GWAS and other genome-wide approaches (e.g., expression) [103] may disentangle the different alternatives. For example, a pleiotropic effect would be supported if the associated gene was shown to preferentially regulate different gene expression modules in each disorder. It is possible that the association of SZ-implicated CNVs with mental retardation, seizures, and autism, although still challenging the clinical classification, reflects a phenomenon mainly occurring on a subset of subjects with SZ at the clinical boundaries of the core disorder (i.e., CNVs appear to be less common in the more mainstream SZ presentation with less cognitive impairment and absence of seizures).
6. What to do next?
Study of rare variants
The genetic architecture of SZ is still elusive, likely involving a combination of both common and rare risk variants, but with non-linear phenotype-genotype correlations. It has been suggested that endophenotypes, such as neurophysiological, neuroimaging, and cognitive traits [104], are more informative to index the underlying genetic effects than dichotomous diagnostic assessments of SZ [105], but none of the proposed endophenotypes shows stronger heritability than the typical heritability estimates for SZ [106, 107], and association studies of endophenotypes have not produced any stronger associations with SZ than using categorical SZ diagnosis [108]. The common and rare variations identified up-to-now show substantial clinical phenotype overlap across the different types of identified genetic loci, but also substantial differences (such as an enrichment of cognitive impairment and seizures in SZ cases with CNVs). Rare variants have been hypothesized to constitute the bulk of mutations for SZ [109]. Negative selection predicts removal of most risk alleles with major deleterious effects, which is consistent with the small effect of common susceptibility loci and the rarity of mutations of larger penetrance (such as CNVs). As SZ is associated with decreased fertility [110], SZ risk alleles are likely under negative selection. Rare risk variants are either of recent origin if highly penetrant, or older mutations with smaller effect that have not yet been eliminated by selection. Rare risk variants not present in parental genomes are known as de novo mutations, and if only identified in a single individual, they are referred as “private” mutations. It has been proposed that many rare risk variants from a large genetic interval may explain associations first detected with common variants (“synthetic associations”) [111].
The common disease/rare variant (CDRV) hypothesis for SZ has not been robustly tested yet since rare mutations are not reliably captured by current GWAS SNP panels or imputed with high accuracy, and awaits for deep genomic resequencing studies (i.e., sequencing of a large number of individuals). Rapid advances in next generation sequencing technology [112] have made the study of rare variants feasible in principle, at least in the exome (the exons in the aggregate). The 1,000 genomes project will deliver a comprehensive reference catalog with LD maps of sequence and structural DNA variants (MAF>1%) in the general population [113, 114], which will be instrumental for the testing of the CDRV hypothesis.
Conventional single-marker based association testing with rare variants has little statistical power (because few subjects have each mutation), but the analysis in the aggregate is more robust [115, 116]. It is important to distinguish functional from nonfunctional DNA variation since collapsing nonfunctional and functional variants also diminishes statistical power (e.g., cases may be enriched for functional variants, but including in the analysis nonfunctional variants will dilute that signal) [115, 116]. Non-synonymous mutations (altering amino acids) are relatively straightforward to interpret by using programs such as PolyPhen and SIFT [117, 118] to predict the functional effect of non-synonymous SNPs. However, many other non-coding DNA changes are more difficult to interpret, largely due to the lack of extensive functional annotation of sequence elements within noncoding regions [2].
Systems biology approaches
Whether biological interpretations relying only on single genes will be likely to capture the fundamental genetic architecture of most complex human traits is a matter of active controversy. Instead, it merits a systems biology approach (integration of genomic, transcriptomic, and proteomic data, metabolomics, gene networks, epigenetics, and environmental factors), where gene expression profiling is an important component of the gene networks [119]. The genetic regulation of gene expression is central to most biological processes. A gene variant may modify the transcript abundances of other genes from the same network or modify protein-protein interactions. Often associated variants are located in intronic (45%) and intergenic (43%) regions [2], and if functional, these variants are thought to regulate gene expression [120]. Even coding polymorphisms may alter transcript levels through affecting mRNA stability [121–126] or mRNA splicing [127]. A genetic variant within a microRNA (miRNA, 19~22 nt small noncoding RNA mostly transcribed from intronic or intergenic sequences) or in an miRNA targeting site may impair the inhibitory effect of miRNA on expression of ~30% of human genes [128]. Interestingly, miRNAs are known to play a pivotal role in regulating synaptic development and function [129], providing relevancy to SZ pathogenesis.
Interestingly, in SZ GWAS, TCF4 and ZNF804A [12, 22] are transcription factors that may regulate expression of many genes. Many of the best GWAS hits in the MHC and other regions are intergenic, and may also affect gene transcription through either cis-regulatory sequence (e.g., enhancers) or through noncoding RNAs transcribed from intergenic regions (e.g., enhancer RNAs) [130, 131]. This raises the interesting possibility that common variation may confer susceptibility to SZ, at least in part, by affecting gene expression regulation. It has been shown that regulatory variants are over-represented in GWAS findings [132], for instance, in celiac disease >50% of the associated risk variants influence immune gene expression [133]. This might be particularly relevant to psychiatric disorders, as genetic regulation of gene expression has been shown to be more important than protein functional changes, such as amino acid substitutions, in shaping human-specific brain function [134, 135]. Indeed, a recent follow up study of ZNF804A suggested that the SNP (rs1344706) associated with SZ is also associated with gene expression changes in lymphocytes [23], suggesting a regulatory mechanism underlying the GWAS association.
GWAS data provide a static and linear correlation between individual risk variants and disease status [136]. Integrating GWAS and gene expression variation (expression quantitative trait loci, eQTL mapping) data has been successfully used to locate causal genes. For example, in a 206kb region with 19 genes and strong LD, eQTL mapping showed that the asthma-associated SNPs were strongly associated with transcript abundance of ORMDL3, suggesting ORMDL3 as the gene explaining this association [137, 138]. It is encouraging that, for some central nervous system disorders, there are consistent gene expression patterns in both lymphocytes and the brain for some loci with strong genetic evidence, e.g., the Parkinson disease susceptibility gene α-synuclein [139–141] and the Alzheimer's disease susceptibility gene APOE [142–144]. High throughput sequencing-based transcriptome profiling (RNA-seq), compared to traditional hybridization-based microarray platforms, gives absolute quantification of RNA transcripts with higher sensitivity and larger dynamic range [145], enabling the detection of more eQTL [146, 147], novel transcripts [131, 148], widespread alternative splicing [149, 150], and even proteome profiling through quantifying ribosome-associated RNA transcripts [151]. Pathway analyses of GWAS data and gene expression profiles are important for understanding the causal mechanisms underlying GWAS associations, because complex disorders likely result from dynamic and higher order perturbations of pathways at a systems level [136]. Pathway analysis translates the effects of individual SNPs or genes to a set of genes known a priori to have related functions. Furthermore, integrating gene co-expression and protein-protein interaction data into pathway analysis adds directional information within and between pathways [98, 136], thus leading to a more comprehensive view of the disease causal mechanism (e.g., interconnected pathways may imply a pleiotropy effect). Animal models (e.g., knockout of a gene or introduction of a putative causal variant) will still remain important for interpreting the phenotypic effect of a genetic variant, although all animal models of SZ suffer from the absence of any unequivocally demonstrated neurobiological features of SZ and a clear definition of a SZ-like behavioral phenotypes [152]. Animal models may also be used to test genetic interactions through crossing animals bearing different mutations, or to examine the interactions with developmental stage or environmental factors through temporal and spatial control of gene expression (see review [153]). In addition, the recent development of induced pluripotent stem cells (iPS) derived from somatic cells, followed by neuronal re-differentiation, may offer a cellular model suitable for studying psychiatric phenotypes (see review [154]).
Footnotes
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References
- [1].Dudbridge F, Gusnanto A. Estimation of significance thresholds for genomewide association scans. Genet Epidemiol. 2008;32:227–234. doi: 10.1002/gepi.20297. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [2].Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS, Manolio TA. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci U S A. 2009;106:9362–9367. doi: 10.1073/pnas.0903103106. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [3].Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, Hunter DJ, McCarthy MI, Ramos EM, Cardon LR, Chakravarti A, Cho JH, Guttmacher AE, Kong A, Kruglyak L, Mardis E, Rotimi CN, Slatkin M, Valle D, Whittemore AS, Boehnke M, Clark AG, Eichler EE, Gibson G, Haines JL, Mackay TF, McCarroll SA, Visscher PM. Finding the missing heritability of complex diseases. Nature. 2009;461:747–753. doi: 10.1038/nature08494. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [4].Li M, Li C, Guan W. Evaluation of coverage variation of SNP chips for genome-wide association studies. Eur J Hum Genet. 2008;16:635–643. doi: 10.1038/sj.ejhg.5202007. [DOI] [PubMed] [Google Scholar]
- [5].Halperin E, Stephan DA. SNP imputation in association studies. Nat Biotechnol. 2009;27:349–351. doi: 10.1038/nbt0409-349. [DOI] [PubMed] [Google Scholar]
- [6].Nothnagel M, Ellinghaus D, Schreiber S, Krawczak M, Franke A. A comprehensive evaluation of SNP genotype imputation. Hum Genet. 2009;125:163–171. doi: 10.1007/s00439-008-0606-5. [DOI] [PubMed] [Google Scholar]
- [7].Lencz T, Morgan TV, Athanasiou M, Dain B, Reed CR, Kane JM, Kucherlapati R, Malhotra AK. Converging evidence for a pseudoautosomal cytokine receptor gene locus in schizophrenia. Mol Psychiatry. 2007;12:572–580. doi: 10.1038/sj.mp.4001983. [DOI] [PubMed] [Google Scholar]
- [8].Sullivan PF, Lin D, Tzeng JY, van den Oord E, Perkins D, Stroup TS, Wagner M, Lee S, Wright FA, Zou F, Liu W, Downing AM, Lieberman J, Close SL. Genomewide association for schizophrenia in the CATIE study: results of stage 1. Mol Psychiatry. 2008;13:570–584. doi: 10.1038/mp.2008.25. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [9].Esslinger C, Walter H, Kirsch P, Erk S, Schnell K, Arnold C, Haddad L, Mier D, Opitz von Boberfeld C, Raab K, Witt SH, Rietschel M, Cichon S, Meyer-Lindenberg A. Neural mechanisms of a genome-wide supported psychosis variant. Science. 2009;324:605. doi: 10.1126/science.1167768. [DOI] [PubMed] [Google Scholar]
- [10].Need AC, Ge D, Weale ME, Maia J, Feng S, Heinzen EL, Shianna KV, Yoon W, Kasperaviciute D, Gennarelli M, Strittmatter WJ, Bonvicini C, Rossi G, Jayathilake K, Cola PA, McEvoy JP, Keefe RS, Fisher EM, St Jean PL, Giegling I, Hartmann AM, Moller HJ, Ruppert A, Fraser G, Crombie C, Middleton LT, St Clair D, Roses AD, Muglia P, Francks C, Rujescu D, Meltzer HY, Goldstein DB. A genome-wide investigation of SNPs and CNVs in schizophrenia. PLoS Genet. 2009;5:e1000373. doi: 10.1371/journal.pgen.1000373. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [11].Purcell SM, Wray NR, Stone JL, Visscher PM, O'Donovan MC, Sullivan PF, Sklar P. Common polygenic variation contributes to risk of schizophrenia and bipolar disorder. Nature. 2009;460:748–752. doi: 10.1038/nature08185. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [12].Stefansson H, Ophoff RA, Steinberg S, Andreassen OA, Cichon S, Rujescu D, Werge T, Pietilainen OP, Mors O, Mortensen PB, Sigurdsson E, Gustafsson O, Nyegaard M, Tuulio-Henriksson A, Ingason A, Hansen T, Suvisaari J, Lonnqvist J, Paunio T, Borglum AD, Hartmann A, Fink-Jensen A, Nordentoft M, Hougaard D, Norgaard-Pedersen B, Bottcher Y, Olesen J, Breuer R, Moller HJ, Giegling I, Rasmussen HB, Timm S, Mattheisen M, Bitter I, Rethelyi JM, Magnusdottir BB, Sigmundsson T, Olason P, Masson G, Gulcher JR, Haraldsson M, Fossdal R, Thorgeirsson TE, Thorsteinsdottir U, Ruggeri M, Tosato S, Franke B, Strengman E, Kiemeney LA, Melle I, Djurovic S, Abramova L, Kaleda V, Sanjuan J, de Frutos R, Bramon E, Vassos E, Fraser G, Ettinger U, Picchioni M, Walker N, Toulopoulou T, Need AC, Ge D, Yoon JL, Shianna KV, Freimer NB, Cantor RM, Murray R, Kong A, Golimbet V, Carracedo A, Arango C, Costas J, Jonsson EG, Terenius L, Agartz I, Petursson H, Nothen MM, Rietschel M, Matthews PM, Muglia P, Peltonen L, St Clair D, Goldstein DB, Stefansson K, Collier DA. Common variants conferring risk of schizophrenia. Nature. 2009;460:744–747. doi: 10.1038/nature08186. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [13].Shi J, Levinson DF, Duan J, Sanders AR, Zheng Y, Pe'er I, Dudbridge F, Holmans PA, Whittemore AS, Mowry BJ, Olincy A, Amin F, Cloninger CR, Silverman JM, Buccola NG, Byerley WF, Black DW, Crowe RR, Oksenberg JR, Mirel DB, Kendler KS, Freedman R, Gejman PV. Common variants on chromosome 6p22.1 are associated with schizophrenia. Nature. 2009;460:753–757. doi: 10.1038/nature08192. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [14].Traherne JA. Human MHC architecture and evolution: implications for disease association studies. Int J Immunogenet. 2008;35:179–192. doi: 10.1111/j.1744-313X.2008.00765.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [15].Oksenberg JR, Baranzini SE, Sawcer S, Hauser SL. The genetics of multiple sclerosis: SNPs to pathways to pathogenesis. Nat Rev Genet. 2008;9:516–526. doi: 10.1038/nrg2395. [DOI] [PubMed] [Google Scholar]
- [16].Heath RG, Krupp IM. Schizophrenia as an immunologic disorder. I. Demonstration of antibrain globulins by fluorescent antibody techniques. Arch Gen Psychiatry. 1967;16:1–9. doi: 10.1001/archpsyc.1967.01730190003001. [DOI] [PubMed] [Google Scholar]
- [17].Eaton WW, Byrne M, Ewald H, Mors O, Chen CY, Agerbo E, Mortensen PB. Association of schizophrenia and autoimmune diseases: linkage of Danish national registers. Am J Psychiatry. 2006;163:521–528. doi: 10.1176/appi.ajp.163.3.521. [DOI] [PubMed] [Google Scholar]
- [18].Gulacsi AA, Anderson SA. Beta-catenin-mediated Wnt signaling regulates neurogenesis in the ventral telencephalon. Nat Neurosci. 2008;11:1383–1391. doi: 10.1038/nn.2226. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [19].Flora A, Garcia JJ, Thaller C, Zoghbi HY. The E-protein Tcf4 interacts with Math1 to regulate differentiation of a specific subset of neuronal progenitors. Proc Natl Acad Sci U S A. 2007;104:15382–15387. doi: 10.1073/pnas.0707456104. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [20].Kalscheuer VM, Feenstra I, Van Ravenswaaij-Arts CM, Smeets DF, Menzel C, Ullmann R, Musante L, Ropers HH. Disruption of the TCF4 gene in a girl with mental retardation but without the classical Pitt-Hopkins syndrome. Am J Med Genet A. 2008;146A:2053–2059. doi: 10.1002/ajmg.a.32419. [DOI] [PubMed] [Google Scholar]
- [21].Brockschmidt A, Todt U, Ryu S, Hoischen A, Landwehr C, Birnbaum S, Frenck W, Radlwimmer B, Lichter P, Engels H, Driever W, Kubisch C, Weber RG. Severe mental retardation with breathing abnormalities (Pitt-Hopkins syndrome) is caused by haploinsufficiency of the neuronal bHLH transcription factor TCF4. Hum Mol Genet. 2007;16:1488–1494. doi: 10.1093/hmg/ddm099. [DOI] [PubMed] [Google Scholar]
- [22].O'Donovan MC, Craddock N, Norton N, Williams H, Peirce T, Moskvina V, Nikolov I, Hamshere M, Carroll L, Georgieva L, Dwyer S, Holmans P, Marchini JL, Spencer CC, Howie B, Leung HT, Hartmann AM, Moller HJ, Morris DW, Shi Y, Feng G, Hoffmann P, Propping P, Vasilescu C, Maier W, Rietschel M, Zammit S, Schumacher J, Quinn EM, Schulze TG, Williams NM, Giegling I, Iwata N, Ikeda M, Darvasi A, Shifman S, He L, Duan J, Sanders AR, Levinson DF, Gejman PV, Cichon S, Nothen MM, Gill M, Corvin A, Rujescu D, Kirov G, Owen MJ, Buccola NG, Mowry BJ, Freedman R, Amin F, Black DW, Silverman JM, Byerley WF, Cloninger CR. Identification of loci associated with schizophrenia by genome-wide association and follow-up. Nat Genet. 2008;40:1053–1055. doi: 10.1038/ng.201. [DOI] [PubMed] [Google Scholar]
- [23].Williams HJ, Norton N, Dwyer S, Moskvina V, Nikolov I, Carroll L, Georgieva L, Williams NM, Morris DW, Quinn EM, Giegling I, Ikeda M, Wood J, Lencz T, Hultman C, Lichtenstein P, Thiselton D, Maher BS, Malhotra AK, Riley B, Kendler KS, Gill M, Sullivan P, Sklar P, Purcell S, Nimgaonkar VL, Kirov G, Holmans P, Corvin A, Rujescu D, Craddock N, Owen MJ, O'Donovan MC. Fine mapping of ZNF804A and genome-wide significant evidence for its involvement in schizophrenia and bipolar disorder. Mol Psychiatry. doi: 10.1038/mp.2010.36. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [24].Sanders AR, Duan J, Levinson DF, Shi J, He D, Hou C, Burrell GJ, Rice JP, Nertney DA, Olincy A, Rozic P, Vinogradov S, Buccola NG, Mowry BJ, Freedman R, Amin F, Black DW, Silverman JM, Byerley WF, Crowe RR, Cloninger CR, Martinez M, Gejman PV. No Significant Association of 14 Candidate Genes With Schizophrenia in a Large European Ancestry Sample: Implications for Psychiatric Genetics. Am J Psychiatry. 2008 doi: 10.1176/appi.ajp.2007.07101573. [DOI] [PubMed] [Google Scholar]
- [25].Gottesman, Shields J. A polygenic theory of schizophrenia. Proc Natl Acad Sci U S A. 1967;58:199–205. doi: 10.1073/pnas.58.1.199. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [26].Sklar P, Smoller JW, Fan J, Ferreira MA, Perlis RH, Chambert K, Nimgaonkar VL, McQueen MB, Faraone SV, Kirby A, de Bakker PI, Ogdie MN, Thase ME, Sachs GS, Todd-Brown K, Gabriel SB, Sougnez C, Gates C, Blumenstiel B, Defelice M, Ardlie KG, Franklin J, Muir WJ, McGhee KA, MacIntyre DJ, McLean A, VanBeck M, McQuillin A, Bass NJ, Robinson M, Lawrence J, Anjorin A, Curtis D, Scolnick EM, Daly MJ, Blackwood DH, Gurling HM, Purcell SM. Whole-genome association study of bipolar disorder. Mol Psychiatry. 2008;13:558–569. doi: 10.1038/sj.mp.4002151. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [27].WTCCC Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature. 2007;447:661–678. doi: 10.1038/nature05911. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [28].Cichon S, Craddock N, Daly M, Faraone SV, Gejman PV, Kelsoe J, Lehner T, Levinson DF, Moran A, Sklar P, Sullivan PF. Genomewide association studies: history, rationale, and prospects for psychiatric disorders. Am J Psychiatry. 2009;166:540–556. doi: 10.1176/appi.ajp.2008.08091354. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [29].Iafrate AJ, Feuk L, Rivera MN, Listewnik ML, Donahoe PK, Qi Y, Scherer SW, Lee C. Detection of large-scale variation in the human genome. Nat Genet. 2004;36:949–951. doi: 10.1038/ng1416. [DOI] [PubMed] [Google Scholar]
- [30].Kirov G, Gumus D, Chen W, Norton N, Georgieva L, Sari M, O'Donovan MC, Erdogan F, Owen MJ, Ropers HH, Ullmann R. Comparative genome hybridization suggests a role for NRXN1 and APBA2 in schizophrenia. Hum Mol Genet. 2008;17:458–465. doi: 10.1093/hmg/ddm323. [DOI] [PubMed] [Google Scholar]
- [31].Walsh T, McClellan JM, McCarthy SE, Addington AM, Pierce SB, Cooper GM, Nord AS, Kusenda M, Malhotra D, Bhandari A, Stray SM, Rippey CF, Roccanova P, Makarov V, Lakshmi B, Findling RL, Sikich L, Stromberg T, Merriman B, Gogtay N, Butler P, Eckstrand K, Noory L, Gochman P, Long R, Chen Z, Davis S, Baker C, Eichler EE, Meltzer PS, Nelson SF, Singleton AB, Lee MK, Rapoport JL, King MC, Sebat J. Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia. Science. 2008;320:539–543. doi: 10.1126/science.1155174. [DOI] [PubMed] [Google Scholar]
- [32].Xu B, Roos JL, Levy S, van Rensburg EJ, Gogos JA, Karayiorgou M. Strong association of de novo copy number mutations with sporadic schizophrenia. Nat Genet. 2008;40:880–885. doi: 10.1038/ng.162. [DOI] [PubMed] [Google Scholar]
- [33].Stefansson H, Rujescu D, Cichon S, Pietilainen OP, Ingason A, Steinberg S, Fossdal R, Sigurdsson E, Sigmundsson T, Buizer-Voskamp JE, Hansen T, Jakobsen KD, Muglia P, Francks C, Matthews PM, Gylfason A, Halldorsson BV, Gudbjartsson D, Thorgeirsson TE, Sigurdsson A, Jonasdottir A, Bjornsson A, Mattiasdottir S, Blondal T, Haraldsson M, Magnusdottir BB, Giegling I, Moller HJ, Hartmann A, Shianna KV, Ge D, Need AC, Crombie C, Fraser G, Walker N, Lonnqvist J, Suvisaari J, Tuulio-Henriksson A, Paunio T, Toulopoulou T, Bramon E, Di Forti M, Murray R, Ruggeri M, Vassos E, Tosato S, Walshe M, Li T, Vasilescu C, Muhleisen TW, Wang AG, Ullum H, Djurovic S, Melle I, Olesen J, Kiemeney LA, Franke B, Sabatti C, Freimer NB, Gulcher JR, Thorsteinsdottir U, Kong A, Andreassen OA, Ophoff RA, Georgi A, Rietschel M, Werge T, Petursson H, Goldstein DB, Nothen MM, Peltonen L, Collier DA, St Clair D, Stefansson K. Large recurrent microdeletions associated with schizophrenia. Nature. 2008;455:232–236. doi: 10.1038/nature07229. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [34].ISC Rare chromosomal deletions and duplications increase risk of schizophrenia. Nature. 2008;455:237–241. doi: 10.1038/nature07239. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [35].Kirov G, Grozeva D, Norton N, Ivanov D, Mantripragada KK, Holmans P, Craddock N, Owen MJ, O'Donovan MC. Support for the involvement of large copy number variants in the pathogenesis of schizophrenia. Hum Mol Genet. 2009;18:1497–1503. doi: 10.1093/hmg/ddp043. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [36].Karayiorgou M, Morris MA, Morrow B, Shprintzen RJ, Goldberg R, Borrow J, Gos A, Nestadt G, Wolyniec PS, Lasseter VK, et al. Schizophrenia susceptibility associated with interstitial deletions of chromosome 22q11. Proc Natl Acad Sci U S A. 1995;92:7612–7616. doi: 10.1073/pnas.92.17.7612. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [37].Shprintzen RJ, Goldberg R, Golding-Kushner KJ, Marion RW. Late-onset psychosis in the velo-cardio-facial syndrome. Am J Med Genet. 1992;42:141–142. doi: 10.1002/ajmg.1320420131. [DOI] [PubMed] [Google Scholar]
- [38].Bassett AS, Hodgkinson K, Chow EW, Correia S, Scutt LE, Weksberg R. 22q11 deletion syndrome in adults with schizophrenia. Am J Med Genet. 1998;81:328–337. [PMC free article] [PubMed] [Google Scholar]
- [39].Shprintzen RJ. Velo-cardio-facial syndrome: 30 Years of study. Dev Disabil Res Rev. 2008;14:3–10. doi: 10.1002/ddrr.2. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [40].Murphy KC, Jones LA, Owen MJ. High rates of schizophrenia in adults with velo-cardio-facial syndrome. Arch. Gen. Psychiatry. 1999;56:940–945. doi: 10.1001/archpsyc.56.10.940. [DOI] [PubMed] [Google Scholar]
- [41].Rujescu D, Ingason A, Cichon S, Pietilainen OP, Barnes MR, Toulopoulou T, Picchioni M, Vassos E, Ettinger U, Bramon E, Murray R, Ruggeri M, Tosato S, Bonetto C, Steinberg S, Sigurdsson E, Sigmundsson T, Petursson H, Gylfason A, Olason PI, Hardarsson G, Jonsdottir GA, Gustafsson O, Fossdal R, Giegling I, Moller HJ, Hartmann AM, Hoffmann P, Crombie C, Fraser G, Walker N, Lonnqvist J, Suvisaari J, Tuulio-Henriksson A, Djurovic S, Melle I, Andreassen OA, Hansen T, Werge T, Kiemeney LA, Franke B, Veltman J, Buizer-Voskamp JE, Sabatti C, Ophoff RA, Rietschel M, Nothen MM, Stefansson K, Peltonen L, St Clair D, Stefansson H, Collier DA. Disruption of the neurexin 1 gene is associated with schizophrenia. Hum Mol Genet. 2009;18:988–996. doi: 10.1093/hmg/ddn351. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [42].McCarthy SE, Makarov V, Kirov G, Addington AM, McClellan J, Yoon S, Perkins DO, Dickel DE, Kusenda M, Krastoshevsky O, Krause V, Kumar RA, Grozeva D, Malhotra D, Walsh T, Zackai EH, Kaplan P, Ganesh J, Krantz ID, Spinner NB, Roccanova P, Bhandari A, Pavon K, Lakshmi B, Leotta A, Kendall J, Lee YH, Vacic V, Gary S, Iakoucheva LM, Crow TJ, Christian SL, Lieberman JA, Stroup TS, Lehtimaki T, Puura K, Haldeman-Englert C, Pearl J, Goodell M, Willour VL, Derosse P, Steele J, Kassem L, Wolff J, Chitkara N, McMahon FJ, Malhotra AK, Potash JB, Schulze TG, Nothen MM, Cichon S, Rietschel M, Leibenluft E, Kustanovich V, Lajonchere CM, Sutcliffe JS, Skuse D, Gill M, Gallagher L, Mendell NR, Craddock N, Owen MJ, O'Donovan MC, Shaikh TH, Susser E, Delisi LE, Sullivan PF, Deutsch CK, Rapoport J, Levy DL, King MC, Sebat J. Microduplications of 16p11.2 are associated with schizophrenia. Nat Genet. 2009;41:1223–1227. doi: 10.1038/ng.474. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [43].Foster AC, Whetsell WO, Jr., Bird ED, Schwarcz R. Quinolinic acid phosphoribosyltransferase in human and rat brain: activity in Huntington's disease and in quinolinate-lesioned rat striatum. Brain Res. 1985;336:207–214. doi: 10.1016/0006-8993(85)90647-x. [DOI] [PubMed] [Google Scholar]
- [44].Okamoto S, Sherman K, Bai G, Lipton SA. Effect of the ubiquitous transcription factors, SP1 and MAZ, on NMDA receptor subunit type 1 (NR1) expression during neuronal differentiation. Brain Res Mol Brain Res. 2002;107:89–96. doi: 10.1016/s0169-328x(02)00440-0. [DOI] [PubMed] [Google Scholar]
- [45].Gunnersen JM, Kim MH, Fuller SJ, De Silva M, Britto JM, Hammond VE, Davies PJ, Petrou S, Faber ES, Sah P, Tan SS. Sez-6 proteins affect dendritic arborization patterns and excitability of cortical pyramidal neurons. Neuron. 2007;56:621–639. doi: 10.1016/j.neuron.2007.09.018. [DOI] [PubMed] [Google Scholar]
- [46].Mazzucchelli C, Vantaggiato C, Ciamei A, Fasano S, Pakhotin P, Krezel W, Welzl H, Wolfer DP, Pages G, Valverde O, Marowsky A, Porrazzo A, Orban PC, Maldonado R, Ehrengruber MU, Cestari V, Lipp HP, Chapman PF, Pouyssegur J, Brambilla R. Knockout of ERK1 MAP kinase enhances synaptic plasticity in the striatum and facilitates striatal-mediated learning and memory. Neuron. 2002;34:807–820. doi: 10.1016/s0896-6273(02)00716-x. [DOI] [PubMed] [Google Scholar]
- [47].Mochida S, Orita S, Sakaguchi G, Sasaki T, Takai Y. Role of the Doc2 alpha-Munc13-1 interaction in the neurotransmitter release process. Proc Natl Acad Sci U S A. 1998;95:11418–11422. doi: 10.1073/pnas.95.19.11418. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [48].Hori T, Takai Y, Takahashi T. Presynaptic mechanism for phorbol ester-induced synaptic potentiation. J Neurosci. 1999;19:7262–7267. doi: 10.1523/JNEUROSCI.19-17-07262.1999. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [49].Groffen AJ, Friedrich R, Brian EC, Ashery U, Verhage M. DOC2A and DOC2B are sensors for neuronal activity with unique calcium-dependent and kinetic properties. J Neurochem. 2006;97:818–833. doi: 10.1111/j.1471-4159.2006.03755.x. [DOI] [PubMed] [Google Scholar]
- [50].Yasuda S, Tanaka H, Sugiura H, Okamura K, Sakaguchi T, Tran U, Takemiya T, Mizoguchi A, Yagita Y, Sakurai T, De Robertis EM, Yamagata K. Activity-induced protocadherin arcadlin regulates dendritic spine number by triggering N-cadherin endocytosis via TAO2beta and p38 MAP kinases. Neuron. 2007;56:456–471. doi: 10.1016/j.neuron.2007.08.020. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [51].Paspalas CD, Perley CC, Venkitaramani DV, Goebel-Goody SM, Zhang Y, Kurup P, Mattis JH, Lombroso PJ. Major vault protein is expressed along the nucleus-neurite axis and associates with mRNAs in cortical neurons. Cereb Cortex. 2009;19:1666–1677. doi: 10.1093/cercor/bhn203. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [52].Williams HJ, Owen MJ, O'Donovan MC. Is COMT a susceptibility gene for schizophrenia? Schizophr Bull. 2007;33:635–641. doi: 10.1093/schbul/sbm019. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [53].Willis A, Bender HU, Steel G, Valle D. PRODH variants and risk for schizophrenia. Amino Acids. 2008;35:673–679. doi: 10.1007/s00726-008-0111-0. [DOI] [PubMed] [Google Scholar]
- [54].Sanders AR, Rusu I, Duan J, Vander Molen JE, Hou C, Schwab SG, Wildenauer DB, Martinez M, Gejman PV. Haplotypic association spanning the 22q11.21 genes COMT and ARVCF with schizophrenia. Mol Psychiatry. 2005;10:353–365. doi: 10.1038/sj.mp.4001586. [DOI] [PubMed] [Google Scholar]
- [55].Williams NM, Glaser B, Norton N, Williams H, Pierce T, Moskvina V, Monks S, Del Favero J, Goossens D, Rujescu D, Giegling I, Kirov G, Craddock N, Murphy KC, O'Donovan MC, Owen MJ. Strong evidence that GNB1L is associated with schizophrenia. Hum Mol Genet. 2008;17:555–566. doi: 10.1093/hmg/ddm330. [DOI] [PubMed] [Google Scholar]
- [56].Paterlini M, Zakharenko SS, Lai WS, Qin J, Zhang H, Mukai J, Westphal KG, Olivier B, Sulzer D, Pavlidis P, Siegelbaum SA, Karayiorgou M, Gogos JA. Transcriptional and behavioral interaction between 22q11.2 orthologs modulates schizophrenia-related phenotypes in mice. Nat Neurosci. 2005;8:1586–1594. doi: 10.1038/nn1562. [DOI] [PubMed] [Google Scholar]
- [57].Paylor R, Glaser B, Mupo A, Ataliotis P, Spencer C, Sobotka A, Sparks C, Choi CH, Oghalai J, Curran S, Murphy KC, Monks S, Williams N, O'Donovan MC, Owen MJ, Scambler PJ, Lindsay E. Tbx1 haploinsufficiency is linked to behavioral disorders in mice and humans: implications for 22q11 deletion syndrome. Proc Natl Acad Sci U S A. 2006;103:7729–7734. doi: 10.1073/pnas.0600206103. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [58].Stark KL, Xu B, Bagchi A, Lai WS, Liu H, Hsu R, Wan X, Pavlidis P, Mills AA, Karayiorgou M, Gogos JA. Altered brain microRNA biogenesis contributes to phenotypic deficits in a 22q11-deletion mouse model. Nat Genet. 2008;40:751–760. doi: 10.1038/ng.138. [DOI] [PubMed] [Google Scholar]
- [59].Mukai J, Dhilla A, Drew LJ, Stark KL, Cao L, MacDermott AB, Karayiorgou M, Gogos JA. Palmitoylation-dependent neurodevelopmental deficits in a mouse model of 22q11 microdeletion. Nat Neurosci. 2008;11:1302–1310. doi: 10.1038/nn.2204. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [60].Hiroi N, Zhu H, Lee M, Funke B, Arai M, Itokawa M, Kucherlapati R, Morrow B, Sawamura T, Agatsuma S. A 200-kb region of human chromosome 22q11.2 confers antipsychotic-responsive behavioral abnormalities in mice. Proc Natl Acad Sci U S A. 2005;102:19132–19137. doi: 10.1073/pnas.0509635102. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [61].Zhang F, Gu W, Hurles ME, Lupski JR. Copy number variation in human health, disease, and evolution. Annu Rev Genomics Hum Genet. 2009;10:451–481. doi: 10.1146/annurev.genom.9.081307.164217. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [62].Lupski JR, Stankiewicz P. Genomic disorders: molecular mechanisms for rearrangements and conveyed phenotypes. PLoS Genet. 2005;1:e49. doi: 10.1371/journal.pgen.0010049. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [63].Kleinjan DA, van Heyningen V. Long-range control of gene expression: emerging mechanisms and disruption in disease. Am J Hum Genet. 2005;76:8–32. doi: 10.1086/426833. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [64].Duncan IW. Transvection effects in Drosophila. Annu Rev Genet. 2002;36:521–556. doi: 10.1146/annurev.genet.36.060402.100441. [DOI] [PubMed] [Google Scholar]
- [65].Girirajan S, Rosenfeld JA, Cooper GM, Antonacci F, Siswara P, Itsara A, Vives L, Walsh T, McCarthy SE, Baker C, Mefford HC, Kidd JM, Browning SR, Browning BL, Dickel DE, Levy DL, Ballif BC, Platky K, Farber DM, Gowans GC, Wetherbee JJ, Asamoah A, Weaver DD, Mark PR, Dickerson J, Garg BP, Ellingwood SA, Smith R, Banks VC, Smith W, McDonald MT, Hoo JJ, French BN, Hudson C, Johnson JP, Ozmore JR, Moeschler JB, Surti U, Escobar LF, El-Khechen D, Gorski JL, Kussmann J, Salbert B, Lacassie Y, Biser A, McDonald-McGinn DM, Zackai EH, Deardorff MA, Shaikh TH, Haan E, Friend KL, Fichera M, Romano C, Gecz J, DeLisi LE, Sebat J, King MC, Shaffer LG, Eichler EE. A recurrent 16p12.1 microdeletion supports a two-hit model for severe developmental delay. Nat Genet. 42:203–209. doi: 10.1038/ng.534. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [66].Henrichsen CN, Vinckenbosch N, Zollner S, Chaignat E, Pradervand S, Schutz F, Ruedi M, Kaessmann H, Reymond A. Segmental copy number variation shapes tissue transcriptomes. Nat Genet. 2009;41:424–429. doi: 10.1038/ng.345. [DOI] [PubMed] [Google Scholar]
- [67].van der Weyden L, Shaw-Smith C, Bradley A. Chromosome engineering in ES cells. Methods Mol Biol. 2009;530:49–77. doi: 10.1007/978-1-59745-471-1_4. [DOI] [PubMed] [Google Scholar]
- [68].Cooper GM, Zerr T, Kidd JM, Eichler EE, Nickerson DA. Systematic assessment of copy number variant detection via genome-wide SNP genotyping. Nat Genet. 2008;40:1199–1203. doi: 10.1038/ng.236. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [69].McCarroll SA, Kuruvilla FG, Korn JM, Cawley S, Nemesh J, Wysoker A, Shapero MH, de Bakker PI, Maller JB, Kirby A, Elliott AL, Parkin M, Hubbell E, Webster T, Mei R, Veitch J, Collins PJ, Handsaker R, Lincoln S, Nizzari M, Blume J, Jones KW, Rava R, Daly MJ, Gabriel SB, Altshuler D. Integrated detection and population-genetic analysis of SNPs and copy number variation. Nat Genet. 2008;40:1166–1174. doi: 10.1038/ng.238. [DOI] [PubMed] [Google Scholar]
- [70].Oldridge DA, Banerjee S, Setlur SR, Sboner A, Demichelis F. Optimizing copy number variation analysis using genome-wide short sequence oligonucleotide arrays. Nucleic Acids Res. doi: 10.1093/nar/gkq073. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [71].Korn JM, Kuruvilla FG, McCarroll SA, Wysoker A, Nemesh J, Cawley S, Hubbell E, Veitch J, Collins PJ, Darvishi K, Lee C, Nizzari MM, Gabriel SB, Purcell S, Daly MJ, Altshuler D. Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs. Nat Genet. 2008;40:1253–1260. doi: 10.1038/ng.237. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [72].WTCCC-b Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls. Nature. 464:713–720. doi: 10.1038/nature08979. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [73].Yoon S, Xuan Z, Makarov V, Ye K, Sebat J. Sensitive and accurate detection of copy number variants using read depth of coverage. Genome Res. 2009;19:1586–1592. doi: 10.1101/gr.092981.109. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [74].Alkan C, Kidd JM, Marques-Bonet T, Aksay G, Antonacci F, Hormozdiari F, Kitzman JO, Baker C, Malig M, Mutlu O, Sahinalp SC, Gibbs RA, Eichler EE. Personalized copy number and segmental duplication maps using next-generation sequencing. Nat Genet. 2009;41:1061–1067. doi: 10.1038/ng.437. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [75].Park H, Kim JI, Ju YS, Gokcumen O, Mills RE, Kim S, Lee S, Suh D, Hong D, Kang HP, Yoo YJ, Shin JY, Kim HJ, Yavartanoo M, Chang YW, Ha JS, Chong W, Hwang GR, Darvishi K, Kim H, Yang SJ, Yang KS, Hurles ME, Scherer SW, Carter NP, Tyler-Smith C, Lee C, Seo JS. Discovery of common Asian copy number variants using integrated high-resolution array CGH and massively parallel DNA sequencing. Nat Genet. doi: 10.1038/ng.555. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [76].Green EK, Grozeva D, Jones I, Jones L, Kirov G, Caesar S, Gordon-Smith K, Fraser C, Forty L, Russell E, Hamshere ML, Moskvina V, Nikolov I, Farmer A, McGuffin P, Holmans PA, Owen MJ, O'Donovan MC, Craddock N. The bipolar disorder risk allele at CACNA1C also confers risk of recurrent major depression and of schizophrenia. Mol Psychiatry. 2009 doi: 10.1038/mp.2009.49. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [77].Maier W, Lichtermann D, Minges J, Hallmayer J, Heun R, Benkert O, Levinson DF. Continuity and discontinuity of affective disorders and schizophrenia. Results of a controlled family study. Arch Gen Psychiatry. 1993;50:871–883. doi: 10.1001/archpsyc.1993.01820230041004. [DOI] [PubMed] [Google Scholar]
- [78].Maier W, Lichtermann D, Franke P, Heun R, Falkai P, Rietschel M. The dichotomy of schizophrenia and affective disorders in extended pedigrees. Schizophr Res. 2002;57:259–266. doi: 10.1016/s0920-9964(01)00288-2. [DOI] [PubMed] [Google Scholar]
- [79].Gershon ES, DeLisi LE, Hamovit J, Nurnberger JI, Jr., Maxwell ME, Schreiber J, Dauphinais D, Dingman CW, 2nd, Guroff JJ. A controlled family study of chronic psychoses. Schizophrenia and schizoaffective disorder. Arch Gen Psychiatry. 1988;45:328–336. doi: 10.1001/archpsyc.1988.01800280038006. [DOI] [PubMed] [Google Scholar]
- [80].Kendler KS, McGuire M, Gruenberg AM, O'Hare A, Spellman M, Walsh D. The Roscommon Family Study. I. Methods, diagnosis of probands, and risk of schizophrenia in relatives. Arch. Gen. Psychiatry. 1993;50:527–540. doi: 10.1001/archpsyc.1993.01820190029004. [DOI] [PubMed] [Google Scholar]
- [81].Valles V, Van Os J, Guillamat R, Gutierrez B, Campillo M, Gento P, Fananas L. Increased morbid risk for schizophrenia in families of in-patients with bipolar illness. Schizophr Res. 2000;42:83–90. doi: 10.1016/s0920-9964(99)00117-6. [DOI] [PubMed] [Google Scholar]
- [82].Van Snellenberg JX, de Candia T. Meta-analytic evidence for familial coaggregation of schizophrenia and bipolar disorder. Arch Gen Psychiatry. 2009;66:748–755. doi: 10.1001/archgenpsychiatry.2009.64. [DOI] [PubMed] [Google Scholar]
- [83].Lichtenstein P, Yip BH, Bjork C, Pawitan Y, Cannon TD, Sullivan PF, Hultman CM. Common genetic determinants of schizophrenia and bipolar disorder in Swedish families: a population-based study. Lancet. 2009;373:234–239. doi: 10.1016/S0140-6736(09)60072-6. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [84].Christian SL, Brune CW, Sudi J, Kumar RA, Liu S, Karamohamed S, Badner JA, Matsui S, Conroy J, McQuaid D, Gergel J, Hatchwell E, Gilliam TC, Gershon ES, Nowak NJ, Dobyns WB, Cook EH., Jr. Novel submicroscopic chromosomal abnormalities detected in autism spectrum disorder. Biol Psychiatry. 2008;63:1111–1117. doi: 10.1016/j.biopsych.2008.01.009. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [85].Sebat J, Lakshmi B, Malhotra D, Troge J, Lese-Martin C, Walsh T, Yamrom B, Yoon S, Krasnitz A, Kendall J, Leotta A, Pai D, Zhang R, Lee YH, Hicks J, Spence SJ, Lee AT, Puura K, Lehtimaki T, Ledbetter D, Gregersen PK, Bregman J, Sutcliffe JS, Jobanputra V, Chung W, Warburton D, King MC, Skuse D, Geschwind DH, Gilliam TC, Ye K, Wigler M. Strong association of de novo copy number mutations with autism. Science. 2007;316:445–449. doi: 10.1126/science.1138659. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [86].Marshall CR, Noor A, Vincent JB, Lionel AC, Feuk L, Skaug J, Shago M, Moessner R, Pinto D, Ren Y, Thiruvahindrapduram B, Fiebig A, Schreiber S, Friedman J, Ketelaars CE, Vos YJ, Ficicioglu C, Kirkpatrick S, Nicolson R, Sloman L, Summers A, Gibbons CA, Teebi A, Chitayat D, Weksberg R, Thompson A, Vardy C, Crosbie V, Luscombe S, Baatjes R, Zwaigenbaum L, Roberts W, Fernandez B, Szatmari P, Scherer SW. Structural variation of chromosomes in autism spectrum disorder. Am J Hum Genet. 2008;82:477–488. doi: 10.1016/j.ajhg.2007.12.009. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [87].Brunetti-Pierri N, Berg JS, Scaglia F, Belmont J, Bacino CA, Sahoo T, Lalani SR, Graham B, Lee B, Shinawi M, Shen J, Kang SH, Pursley A, Lotze T, Kennedy G, Lansky-Shafer S, Weaver C, Roeder ER, Grebe TA, Arnold GL, Hutchison T, Reimschisel T, Amato S, Geragthy MT, Innis JW, Obersztyn E, Nowakowska B, Rosengren SS, Bader PI, Grange DK, Naqvi S, Garnica AD, Bernes SM, Fong CT, Summers A, Walters WD, Lupski JR, Stankiewicz P, Cheung SW, Patel A. Recurrent reciprocal 1q21.1 deletions and duplications associated with microcephaly or macrocephaly and developmental and behavioral abnormalities. Nat Genet. 2008;40:1466–1471. doi: 10.1038/ng.279. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [88].Kumar RA, KaraMohamed S, Sudi J, Conrad DF, Brune C, Badner JA, Gilliam TC, Nowak NJ, Cook EH, Jr., Dobyns WB, Christian SL. Recurrent 16p11.2 microdeletions in autism. Hum Mol Genet. 2008;17:628–638. doi: 10.1093/hmg/ddm376. [DOI] [PubMed] [Google Scholar]
- [89].de Kovel CG, Trucks H, Helbig I, Mefford HC, Baker C, Leu C, Kluck C, Muhle H, von Spiczak S, Ostertag P, Obermeier T, Kleefuss-Lie AA, Hallmann K, Steffens M, Gaus V, Klein KM, Hamer HM, Rosenow F, Brilstra EH, Trenite DK, Swinkels ME, Weber YG, Unterberger I, Zimprich F, Urak L, Feucht M, Fuchs K, Moller RS, Hjalgrim H, De Jonghe P, Suls A, Ruckert IM, Wichmann HE, Franke A, Schreiber S, Nurnberg P, Elger CE, Lerche H, Stephani U, Koeleman BP, Lindhout D, Eichler EE, Sander T. Recurrent microdeletions at 15q11.2 and 16p13.11 predispose to idiopathic generalized epilepsies. Brain. 133:23–32. doi: 10.1093/brain/awp262. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [90].Dibbens LM, Mullen S, Helbig I, Mefford HC, Bayly MA, Bellows S, Leu C, Trucks H, Obermeier T, Wittig M, Franke A, Caglayan H, Yapici Z, Sander T, Eichler EE, Scheffer IE, Mulley JC, Berkovic SF. Familial and sporadic 15q13.3 microdeletions in idiopathic generalized epilepsy: precedent for disorders with complex inheritance. Hum Mol Genet. 2009;18:3626–3631. doi: 10.1093/hmg/ddp311. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [91].Helbig I, Mefford HC, Sharp AJ, Guipponi M, Fichera M, Franke A, Muhle H, de Kovel C, Baker C, von Spiczak S, Kron KL, Steinich I, Kleefuss-Lie AA, Leu C, Gaus V, Schmitz B, Klein KM, Reif PS, Rosenow F, Weber Y, Lerche H, Zimprich F, Urak L, Fuchs K, Feucht M, Genton P, Thomas P, Visscher F, de Haan GJ, Moller RS, Hjalgrim H, Luciano D, Wittig M, Nothnagel M, Elger CE, Nurnberg P, Romano C, Malafosse A, Koeleman BP, Lindhout D, Stephani U, Schreiber S, Eichler EE, Sander T. 15q13.3 microdeletions increase risk of idiopathic generalized epilepsy. Nat Genet. 2009;41:160–162. doi: 10.1038/ng.292. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [92].Mefford HC, Sharp AJ, Baker C, Itsara A, Jiang Z, Buysse K, Huang S, Maloney VK, Crolla JA, Baralle D, Collins A, Mercer C, Norga K, de Ravel T, Devriendt K, Bongers EM, de Leeuw N, Reardon W, Gimelli S, Bena F, Hennekam RC, Male A, Gaunt L, Clayton-Smith J, Simonic I, Park SM, Mehta SG, Nik-Zainal S, Woods CG, Firth HV, Parkin G, Fichera M, Reitano S, Lo Giudice M, Li KE, Casuga I, Broomer A, Conrad B, Schwerzmann M, Raber L, Gallati S, Striano P, Coppola A, Tolmie JL, Tobias ES, Lilley C, Armengol L, Spysschaert Y, Verloo P, De Coene A, Goossens L, Mortier G, Speleman F, van Binsbergen E, Nelen MR, Hochstenbach R, Poot M, Gallagher L, Gill M, McClellan J, King MC, Regan R, Skinner C, Stevenson RE, Antonarakis SE, Chen C, Estivill X, Menten B, Gimelli G, Gribble S, Schwartz S, Sutcliffe JS, Walsh T, Knight SJ, Sebat J, Romano C, Schwartz CE, Veltman JA, de Vries BB, Vermeesch JR, Barber JC, Willatt L, Tassabehji M, Eichler EE. Recurrent rearrangements of chromosome 1q21.1 and variable pediatric phenotypes. N Engl J Med. 2008;359:1685–1699. doi: 10.1056/NEJMoa0805384. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [93].Sharp AJ, Mefford HC, Li K, Baker C, Skinner C, Stevenson RE, Schroer RJ, Novara F, De Gregori M, Ciccone R, Broomer A, Casuga I, Wang Y, Xiao C, Barbacioru C, Gimelli G, Bernardina BD, Torniero C, Giorda R, Regan R, Murday V, Mansour S, Fichera M, Castiglia L, Failla P, Ventura M, Jiang Z, Cooper GM, Knight SJ, Romano C, Zuffardi O, Chen C, Schwartz CE, Eichler EE. A recurrent 15q13.3 microdeletion syndrome associated with mental retardation and seizures. Nat Genet. 2008;40:322–328. doi: 10.1038/ng.93. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [94].Fernandez BA, Roberts W, Chung B, Weksberg R, Meyn S, Szatmari P, Joseph-George AM, Mackay S, Whitten K, Noble B, Vardy C, Crosbie V, Luscombe S, Tucker E, Turner L, Marshall CR, Scherer SW. Phenotypic spectrum associated with de novo and inherited deletions and duplications at 16p11.2 in individuals ascertained for diagnosis of autism spectrum disorder. J Med Genet. 47:195–203. doi: 10.1136/jmg.2009.069369. [DOI] [PubMed] [Google Scholar]
- [95].Wassink TH, Piven J, Vieland VJ, Jenkins L, Frantz R, Bartlett CW, Goedken R, Childress D, Spence MA, Smith M, Sheffield VC. Evaluation of the chromosome 2q37.3 gene CENTG2 as an autism susceptibility gene. Am J Med Genet B Neuropsychiatr Genet. 2005;136B:36–44. doi: 10.1002/ajmg.b.30180. [DOI] [PubMed] [Google Scholar]
- [96].Daniels JL, Forssen U, Hultman CM, Cnattingius S, Savitz DA, Feychting M, Sparen P. Parental psychiatric disorders associated with autism spectrum disorders in the offspring. Pediatrics. 2008;121:e1357–1362. doi: 10.1542/peds.2007-2296. [DOI] [PubMed] [Google Scholar]
- [97].Larsson HJ, Eaton WW, Madsen KM, Vestergaard M, Olesen AV, Agerbo E, Schendel D, Thorsen P, Mortensen PB. Risk factors for autism: perinatal factors, parental psychiatric history, and socioeconomic status. Am J Epidemiol. 2005;161:916–925. doi: 10.1093/aje/kwi123. discussion 926–918. [DOI] [PubMed] [Google Scholar]
- [98].Mackay TF, Stone EA, Ayroles JF. The genetics of quantitative traits: challenges and prospects. Nat Rev Genet. 2009;10:565–577. doi: 10.1038/nrg2612. [DOI] [PubMed] [Google Scholar]
- [99].Weedon MN, Lango H, Lindgren CM, Wallace C, Evans DM, Mangino M, Freathy RM, Perry JR, Stevens S, Hall AS, Samani NJ, Shields B, Prokopenko I, Farrall M, Dominiczak A, Johnson T, Bergmann S, Beckmann JS, Vollenweider P, Waterworth DM, Mooser V, Palmer CN, Morris AD, Ouwehand WH, Zhao JH, Li S, Loos RJ, Barroso I, Deloukas P, Sandhu MS, Wheeler E, Soranzo N, Inouye M, Wareham NJ, Caulfield M, Munroe PB, Hattersley AT, McCarthy MI, Frayling TM. Genome-wide association analysis identifies 20 loci that influence adult height. Nat Genet. 2008;40:575–583. doi: 10.1038/ng.121. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [100].Zeggini E, Scott LJ, Saxena R, Voight BF, Marchini JL, Hu T, de Bakker PI, Abecasis GR, Almgren P, Andersen G, Ardlie K, Bostrom KB, Bergman RN, Bonnycastle LL, Borch-Johnsen K, Burtt NP, Chen H, Chines PS, Daly MJ, Deodhar P, Ding CJ, Doney AS, Duren WL, Elliott KS, Erdos MR, Frayling TM, Freathy RM, Gianniny L, Grallert H, Grarup N, Groves CJ, Guiducci C, Hansen T, Herder C, Hitman GA, Hughes TE, Isomaa B, Jackson AU, Jorgensen T, Kong A, Kubalanza K, Kuruvilla FG, Kuusisto J, Langenberg C, Lango H, Lauritzen T, Li Y, Lindgren CM, Lyssenko V, Marvelle AF, Meisinger C, Midthjell K, Mohlke KL, Morken MA, Morris AD, Narisu N, Nilsson P, Owen KR, Palmer CN, Payne F, Perry JR, Pettersen E, Platou C, Prokopenko I, Qi L, Qin L, Rayner NW, Rees M, Roix JJ, Sandbaek A, Shields B, Sjogren M, Steinthorsdottir V, Stringham HM, Swift AJ, Thorleifsson G, Thorsteinsdottir U, Timpson NJ, Tuomi T, Tuomilehto J, Walker M, Watanabe RM, Weedon MN, Willer CJ, Illig T, Hveem K, Hu FB, Laakso M, Stefansson K, Pedersen O, Wareham NJ, Barroso I, Hattersley AT, Collins FS, Groop L, McCarthy MI, Boehnke M, Altshuler D. Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes. Nat Genet. 2008;40:638–645. doi: 10.1038/ng.120. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [101].Thomas G, Jacobs KB, Yeager M, Kraft P, Wacholder S, Orr N, Yu K, Chatterjee N, Welch R, Hutchinson A, Crenshaw A, Cancel-Tassin G, Staats BJ, Wang Z, Gonzalez-Bosquet J, Fang J, Deng X, Berndt SI, Calle EE, Feigelson HS, Thun MJ, Rodriguez C, Albanes D, Virtamo J, Weinstein S, Schumacher FR, Giovannucci E, Willett WC, Cussenot O, Valeri A, Andriole GL, Crawford ED, Tucker M, Gerhard DS, Fraumeni JF, Jr., Hoover R, Hayes RB, Hunter DJ, Chanock SJ. Multiple loci identified in a genome-wide association study of prostate cancer. Nat Genet. 2008;40:310–315. doi: 10.1038/ng.91. [DOI] [PubMed] [Google Scholar]
- [102].Veeriah S, Taylor BS, Meng S, Fang F, Yilmaz E, Vivanco I, Janakiraman M, Schultz N, Hanrahan AJ, Pao W, Ladanyi M, Sander C, Heguy A, Holland EC, Paty PB, Mischel PS, Liau L, Cloughesy TF, Mellinghoff IK, Solit DB, Chan TA. Somatic mutations of the Parkinson's disease-associated gene PARK2 in glioblastoma and other human malignancies. Nat Genet. 42:77–82. doi: 10.1038/ng.491. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [103].Mehan MR, Nunez-Iglesias J, Dai C, Waterman MS, Zhou XJ. An integrative modular approach to systematically predict gene-phenotype associations. BMC Bioinformatics. 11(Suppl 1):S62. doi: 10.1186/1471-2105-11-S1-S62. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [104].Jablensky A. Subtyping schizophrenia: implications for genetic research. Mol Psychiatry. 2006;11:815–836. doi: 10.1038/sj.mp.4001857. [DOI] [PubMed] [Google Scholar]
- [105].Gottesman, Gould TD. The endophenotype concept in psychiatry: etymology and strategic intentions. Am J Psychiatry. 2003;160:636–645. doi: 10.1176/appi.ajp.160.4.636. [DOI] [PubMed] [Google Scholar]
- [106].Horan WP, Braff DL, Nuechterlein KH, Sugar CA, Cadenhead KS, Calkins ME, Dobie DJ, Freedman R, Greenwood TA, Gur RE, Gur RC, Light GA, Mintz J, Olincy A, Radant AD, Schork NJ, Seidman LJ, Siever LJ, Silverman JM, Stone WS, Swerdlow NR, Tsuang DW, Tsuang MT, Turetsky BI, Green MF. Verbal working memory impairments in individuals with schizophrenia and their first-degree relatives: findings from the Consortium on the Genetics of Schizophrenia. Schizophr Res. 2008;103:218–228. doi: 10.1016/j.schres.2008.02.014. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [107].Tuulio-Henriksson A, Haukka J, Partonen T, Varilo T, Paunio T, Ekelund J, Cannon TD, Meyer JM, Lonnqvist J. Heritability and number of quantitative trait loci of neurocognitive functions in families with schizophrenia. Am J Med Genet. 2002;114:483–490. doi: 10.1002/ajmg.10480. [DOI] [PubMed] [Google Scholar]
- [108].Shaikh M, Hall MH, Schulze K, Dutt A, Walshe M, Williams I, Constante M, Picchioni M, Toulopoulou T, Collier D, Rijsdijk F, Powell J, Arranz M, Murray RM, Bramon E. Do COMT, BDNF and NRG1 polymorphisms influence P50 sensory gating in psychosis? Psychol Med. :1–14. doi: 10.1017/S003329170999239X. [DOI] [PubMed] [Google Scholar]
- [109].Akil H, Brenner S, Kandel E, Kendler KS, King MC, Scolnick E, Watson JD, Zoghbi HY. Medicine. The future of psychiatric research: genomes and neural circuits. Science. 327:1580–1581. doi: 10.1126/science.1188654. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [110].McGrath J, Saha S, Chant D, Welham J. Schizophrenia: a concise overview of incidence, prevalence, and mortality. Epidemiol Rev. 2008;30:67–76. doi: 10.1093/epirev/mxn001. [DOI] [PubMed] [Google Scholar]
- [111].Dickson SP, Wang K, Krantz I, Hakonarson H, Goldstein DB. Rare variants create synthetic genome-wide associations. PLoS Biol. 8:e1000294. doi: 10.1371/journal.pbio.1000294. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [112].Mardis ER. New strategies and emerging technologies for massively parallel sequencing: applications in medical research. Genome Med. 2009;1:40. doi: 10.1186/gm40. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [113].von Bubnoff A. Next-generation sequencing: the race is on. Cell. 2008;132:721–723. doi: 10.1016/j.cell.2008.02.028. [DOI] [PubMed] [Google Scholar]
- [114].Biesecker LG, Mullikin JC, Facio FM, Turner C, Cherukuri PF, Blakesley RW, Bouffard GG, Chines PS, Cruz P, Hansen NF, Teer JK, Maskeri B, Young AC, Manolio TA, Wilson AF, Finkel T, Hwang P, Arai A, Remaley AT, Sachdev V, Shamburek R, Cannon RO, Green ED. The ClinSeq Project: piloting large-scale genome sequencing for research in genomic medicine. Genome Res. 2009;19:1665–1674. doi: 10.1101/gr.092841.109. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [115].Li B, Leal SM. Methods for detecting associations with rare variants for common diseases: application to analysis of sequence data. Am J Hum Genet. 2008;83:311–321. doi: 10.1016/j.ajhg.2008.06.024. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [116].Morris AP, Zeggini E. An evaluation of statistical approaches to rare variant analysis in genetic association studies. Genet Epidemiol. 2009 doi: 10.1002/gepi.20450. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [117].Sunyaev S, Ramensky V, Koch I, Lathe W, 3rd, Kondrashov AS, Bork P. Prediction of deleterious human alleles. Hum Mol Genet. 2001;10:591–597. doi: 10.1093/hmg/10.6.591. [DOI] [PubMed] [Google Scholar]
- [118].Ng PC, Henikoff S. SIFT: Predicting amino acid changes that affect protein function. Nucleic Acids Res. 2003;31:3812–3814. doi: 10.1093/nar/gkg509. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [119].Gehlenborg N, O'Donoghue SI, Baliga NS, Goesmann A, Hibbs MA, Kitano H, Kohlbacher O, Neuweger H, Schneider R, Tenenbaum D, Gavin AC. Visualization of omics data for systems biology. Nat Methods. 7:S56–68. doi: 10.1038/nmeth.1436. [DOI] [PubMed] [Google Scholar]
- [120].Visel A, Zhu Y, May D, Afzal V, Gong E, Attanasio C, Blow MJ, Cohen JC, Rubin EM, Pennacchio LA. Targeted deletion of the 9p21 non-coding coronary artery disease risk interval in mice. Nature. 464:409–412. doi: 10.1038/nature08801. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [121].Duan J, Wainwright MS, Comeron JM, Saitou N, Sanders AR, Gelernter J, Gejman PV. Synonymous mutations in the human dopamine receptor D2 (DRD2) affect mRNA stability and synthesis of the receptor. Hum Mol Genet. 2003;12:205–216. doi: 10.1093/hmg/ddg055. [DOI] [PubMed] [Google Scholar]
- [122].Capon F, Allen MH, Ameen M, Burden AD, Tillman D, Barker JN, Trembath RC. A synonymous SNP of the corneodesmosin gene leads to increased mRNA stability and demonstrates association with psoriasis across diverse ethnic groups. Hum Mol Genet. 2004;13:2361–2368. doi: 10.1093/hmg/ddh273. [DOI] [PubMed] [Google Scholar]
- [123].Wang D, Johnson AD, Papp AC, Kroetz DL, Sadee W. Multidrug resistance polypeptide 1 (MDR1, ABCB1) variant 3435C>T affects mRNA stability. Pharmacogenet Genomics. 2005;15:693–704. [PubMed] [Google Scholar]
- [124].Nackley AG, Shabalina SA, Tchivileva IE, Satterfield K, Korchynskyi O, Makarov SS, Maixner W, Diatchenko L. Human catechol-O-methyltransferase haplotypes modulate protein expression by altering mRNA secondary structure. Science. 2006;314:1930–1933. doi: 10.1126/science.1131262. [DOI] [PubMed] [Google Scholar]
- [125].Thorleifsson G, Magnusson KP, Sulem P, Walters GB, Gudbjartsson DF, Stefansson H, Jonsson T, Jonasdottir A, Stefansdottir G, Masson G, Hardarson GA, Petursson H, Arnarsson A, Motallebipour M, Wallerman O, Wadelius C, Gulcher JR, Thorsteinsdottir U, Kong A, Jonasson F, Stefansson K. Common sequence variants in the LOXL1 gene confer susceptibility to exfoliation glaucoma. Science. 2007;317:1397–1400. doi: 10.1126/science.1146554. [DOI] [PubMed] [Google Scholar]
- [126].Chen GL, Miller GM. Rhesus monkey tryptophan hydroxylase-2 coding region haplotypes affect mRNA stability. Neuroscience. 2008;155:485–491. doi: 10.1016/j.neuroscience.2008.05.050. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [127].Chamary JV, Parmley JL, Hurst LD. Hearing silence: non-neutral evolution at synonymous sites in mammals. Nat Rev Genet. 2006;7:98–108. doi: 10.1038/nrg1770. [DOI] [PubMed] [Google Scholar]
- [128].Lewis BP, Burge CB, Bartel DP. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell. 2005;120:15–20. doi: 10.1016/j.cell.2004.12.035. [DOI] [PubMed] [Google Scholar]
- [129].Schratt G. microRNAs at the synapse. Nat Rev Neurosci. 2009;10:842–849. doi: 10.1038/nrn2763. [DOI] [PubMed] [Google Scholar]
- [130].Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermuller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaoz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Loytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Xu M, Haidar JN, Yu Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrimsdottir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007;447:799–816. doi: 10.1038/nature05874. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [131].Kim TK, Hemberg M, Gray JM, Costa AM, Bear DM, Wu J, Harmin DA, Laptewicz M, Barbara-Haley K, Kuersten S, Markenscoff-Papadimitriou E, Kuhl D, Bito H, Worley PF, Kreiman G, Greenberg ME. Widespread transcription at neuronal activity-regulated enhancers. Nature. doi: 10.1038/nature09033. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [132].Nicolae DL, Gamazon E, Zhang W, Duan S, Dolan ME, Cox NJ. Trait-associated SNPs are more likely to be eQTLs: annotation to enhance discovery from GWAS. PLoS Genet. 6:e1000888. doi: 10.1371/journal.pgen.1000888. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [133].Dubois PC, Trynka G, Franke L, Hunt KA, Romanos J, Curtotti A, Zhernakova A, Heap GA, Adany R, Aromaa A, Bardella MT, van den Berg LH, Bockett NA, de la Concha EG, Dema B, Fehrmann RS, Fernandez-Arquero M, Fiatal S, Grandone E, Green PM, Groen HJ, Gwilliam R, Houwen RH, Hunt SE, Kaukinen K, Kelleher D, Korponay-Szabo I, Kurppa K, MacMathuna P, Maki M, Mazzilli MC, McCann OT, Mearin ML, Mein CA, Mirza MM, Mistry V, Mora B, Morley KI, Mulder CJ, Murray JA, Nunez C, Oosterom E, Ophoff RA, Polanco I, Peltonen L, Platteel M, Rybak A, Salomaa V, Schweizer JJ, Sperandeo MP, Tack GJ, Turner G, Veldink JH, Verbeek WH, Weersma RK, Wolters VM, Urcelay E, Cukrowska B, Greco L, Neuhausen SL, McManus R, Barisani D, Deloukas P, Barrett JC, Saavalainen P, Wijmenga C, van Heel DA. Multiple common variants for celiac disease influencing immune gene expression. Nat Genet. 42:295–302. doi: 10.1038/ng.543. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [134].Gu J, Gu X. Induced gene expression in human brain after the split from chimpanzee. Trends Genet. 2003;19:63–65. doi: 10.1016/s0168-9525(02)00040-9. [DOI] [PubMed] [Google Scholar]
- [135].King MC, Wilson AC. Evolution at two levels in humans and chimpanzees. Science. 1975;188:107–116. doi: 10.1126/science.1090005. [DOI] [PubMed] [Google Scholar]
- [136].Schadt EE. Molecular networks as sensors and drivers of common human diseases. Nature. 2009;461:218–223. doi: 10.1038/nature08454. [DOI] [PubMed] [Google Scholar]
- [137].Moffatt MF, Kabesch M, Liang L, Dixon AL, Strachan D, Heath S, Depner M, von Berg A, Bufe A, Rietschel E, Heinzmann A, Simma B, Frischer T, Willis-Owen SA, Wong KC, Illig T, Vogelberg C, Weiland SK, von Mutius E, Abecasis GR, Farrall M, Gut IG, Lathrop GM, Cookson WO. Genetic variants regulating ORMDL3 expression contribute to the risk of childhood asthma. Nature. 2007;448:470–473. doi: 10.1038/nature06014. [DOI] [PubMed] [Google Scholar]
- [138].Cookson W, Liang L, Abecasis G, Moffatt M, Lathrop M. Mapping complex disease traits with global gene expression. Nat Rev Genet. 2009;10:184–194. doi: 10.1038/nrg2537. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [139].Satake W, Nakabayashi Y, Mizuta I, Hirota Y, Ito C, Kubo M, Kawaguchi T, Tsunoda T, Watanabe M, Takeda A, Tomiyama H, Nakashima K, Hasegawa K, Obata F, Yoshikawa T, Kawakami H, Sakoda S, Yamamoto M, Hattori N, Murata M, Nakamura Y, Toda T. Genome-wide association study identifies common variants at four loci as genetic risk factors for Parkinson's disease. Nat Genet. 2009;41:1303–1307. doi: 10.1038/ng.485. [DOI] [PubMed] [Google Scholar]
- [140].Kim S, Jeon BS, Heo C, Im PS, Ahn TB, Seo JH, Kim HS, Park CH, Choi SH, Cho SH, Lee WJ, Suh YH. Alpha-synuclein induces apoptosis by altered expression in human peripheral lymphocyte in Parkinson's disease. FASEB J. 2004;18:1615–1617. doi: 10.1096/fj.04-1917fje. [DOI] [PubMed] [Google Scholar]
- [141].Fuchs J, Tichopad A, Golub Y, Munz M, Schweitzer KJ, Wolf B, Berg D, Mueller JC, Gasser T. Genetic variability in the SNCA gene influences alpha-synuclein levels in the blood and brain. FASEB J. 2008;22:1327–1334. doi: 10.1096/fj.07-9348com. [DOI] [PubMed] [Google Scholar]
- [142].van Es MA, van den Berg LH. Alzheimer's disease beyond APOE. Nat Genet. 2009;41:1047–1048. doi: 10.1038/ng1009-1047. [DOI] [PubMed] [Google Scholar]
- [143].Lambert JC, Mann D, Richard F, Tian J, Shi J, Thaker U, Merrot S, Harris J, Frigard B, Iwatsubo T, Lendon C, Amouyel P. Is there a relation between APOE expression and brain amyloid load in Alzheimer's disease? J Neurol Neurosurg Psychiatry. 2005;76:928–933. doi: 10.1136/jnnp.2004.048983. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [144].Corbo RM, Gambina G, Ruggeri M, Scacchi R. Association of estrogen receptor alpha (ESR1) PvuII and XbaI polymorphisms with sporadic Alzheimer's disease and their effect on apolipoprotein E concentrations. Dement Geriatr Cogn Disord. 2006;22:67–72. doi: 10.1159/000093315. [DOI] [PubMed] [Google Scholar]
- [145].Rajasethupathy P, Fiumara F, Sheridan R, Betel D, Puthanveettil SV, Russo JJ, Sander C, Tuschl T, Kandel E. Characterization of small RNAs in aplysia reveals a role for miR-124 in constraining synaptic plasticity through CREB. Neuron. 2009;63:803–817. doi: 10.1016/j.neuron.2009.05.029. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [146].Pickrell JK, Marioni JC, Pai AA, Degner JF, Engelhardt BE, Nkadori E, Veyrieras JB, Stephens M, Gilad Y, Pritchard JK. Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature. 464:768–772. doi: 10.1038/nature08872. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [147].Montgomery SB, Sammeth M, Gutierrez-Arcelus M, Lach RP, Ingle C, Nisbett J, Guigo R, Dermitzakis ET. Transcriptome genetics using second generation sequencing in a Caucasian population. Nature. 464:773–777. doi: 10.1038/nature08903. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [148].Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 2009;10:57–63. doi: 10.1038/nrg2484. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [149].Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet. 2008;40:1413–1415. doi: 10.1038/ng.259. [DOI] [PubMed] [Google Scholar]
- [150].Sultan M, Schulz MH, Richard H, Magen A, Klingenhoff A, Scherf M, Seifert M, Borodina T, Soldatov A, Parkhomchuk D, Schmidt D, O'Keeffe S, Haas S, Vingron M, Lehrach H, Yaspo ML. A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science. 2008;321:956–960. doi: 10.1126/science.1160342. [DOI] [PubMed] [Google Scholar]
- [151].Ingolia NT, Ghaemmaghami S, Newman JR, Weissman JS. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science. 2009;324:218–223. doi: 10.1126/science.1168978. [DOI] [PMC free article] [PubMed] [Google Scholar]
- [152].Inta D, Monyer H, Sprengel R, Meyer-Lindenberg A, Gass P. Mice with genetically altered glutamate receptors as models of schizophrenia: a comprehensive review. Neurosci Biobehav Rev. 34:285–294. doi: 10.1016/j.neubiorev.2009.07.010. [DOI] [PubMed] [Google Scholar]
- [153].Gondo Y. Trends in large-scale mouse mutagenesis: from genetics to functional genomics. Nat Rev Genet. 2008;9:803–810. doi: 10.1038/nrg2431. [DOI] [PubMed] [Google Scholar]
- [154].Kim KS. Induced pluripotent stem (iPS) cells and their future in psychiatry. Neuropsychopharmacology. 35:346–348. doi: 10.1038/npp.2009.108. [DOI] [PMC free article] [PubMed] [Google Scholar]