Elucidating the genetic architecture of familial schizophrenia using rare copy number variant and linkage scans

Departments of Psychiatry, Physiology and Cellular Biophysics, and Neuroscience, Columbia University Medical Center, New York, NY 10032.
Proceedings of the National Academy of Sciences (Impact Factor: 9.67). 09/2009; 106(39):16746-51. DOI: 10.1073/pnas.0908584106
Source: PubMed


To elucidate the genetic architecture of familial schizophrenia we combine linkage analysis with studies of fine-level chromosomal variation in families recruited from the Afrikaner population in South Africa. We demonstrate that individually rare inherited copy number variants (CNVs) are more frequent in cases with familial schizophrenia as compared to unaffected controls and affect almost exclusively genic regions. Interestingly, we find that while the prevalence of rare structural variants is similar in familial and sporadic cases, the type of variants is markedly different. In addition, using a high-density linkage scan with a panel of nearly 2,000 markers, we identify a region on chromosome 13q34 that shows genome-wide significant linkage to schizophrenia and show that in the families not linked to this locus, there is evidence for linkage to chromosome 1p36. No causative CNVs were identified in either locus. Overall, our results from approaches designed to detect risk variants with relatively low frequency and high penetrance in a well-defined and relatively homogeneous population, provide strong empirical evidence supporting the notion that multiple genetic variants, including individually rare ones, that affect many different genes contribute to the genetic risk of familial schizophrenia. They also highlight differences in the genetic architecture of the familial and sporadic forms of the disease.

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    • "Defects in SALMs and LAR-RPTPs have been implicated in diverse neuropsychiatric disorders, providing support for the clinical importance of these proteins. Specifically, SALM1/Lrfn2 and SALM5/Lrfn5 are associated with autism spectrum disorders and intellectual disability (de Bruijn et al., 2010; Mikhail et al., 2011; Voineagu and Yoo, 2013; Wang et al., 2009), as well as schizophrenia (Xu et al., 2009). In addition, PTPδ has been linked to autism spectrum disorders (Pinto et al., 2010), attention deficit/hyperactivity disorder (Elia et al., 2010), bipolar disorder (Malhotra et al., 2011), and restless leg syndrome (Schormair et al., 2008; Yang et al., 2011). "
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    ABSTRACT: Synaptic adhesion molecules regulate diverse aspects of synapse development and plasticity. SALM3 is a PSD-95-interacting synaptic adhesion molecule known to induce presynaptic differentiation in contacting axons, but little is known about its presynaptic receptors and in vivo functions. Here, we identify an interaction between SALM3 and LAR family receptor protein tyrosine phosphatases (LAR-RPTPs) that requires the mini-exon B splice insert in LAR-RPTPs. In addition, SALM3-dependent presynaptic differentiation requires all three types of LAR-RPTPs. SALM3 mutant (Salm3(-/-)) mice display markedly reduced excitatory synapse number but normal synaptic plasticity in the hippocampal CA1 region. Salm3(-/-) mice exhibit hypoactivity in both novel and familiar environments but perform normally in learning and memory tests administered. These results suggest that SALM3 regulates excitatory synapse development and locomotion behavior. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.
    Full-text · Article · Aug 2015 · Cell Reports
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    • "Schizophrenia-associated CNVs are found most only in sporadic cases, so their relationship with familial forms of schizophrenia is less studied. One previous study failed to detect the association of CNV with familial forms of schizophrenia (Xu et al., 2008), while another recent study reported that CNV also played an important role in familial forms of schizophrenia (Xu et al., 2009). To address this issue in our population, we conducted a CNV screening study in a sample of 60 index patients from multiplex schizophrenia families. "
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    ABSTRACT: Schizophrenia is a complex mental disorder with high degree of genetic influence in its etiology. Several recent studies revealed that copy number variations (CNVs) of genomic DNA contributed significantly to the genetic architecture of sporadic schizophrenia. This study aimed to investigate whether CNVs also contribute to the familial forms of schizophrenia. Using array-based comparative genomic hybridization technology, we searched for pathogenic CNV associated with schizophrenia in a sample of 60 index cases from multiplex schizophrenia families. We detected three inherited CNVs that were associated with schizophrenia in three families, including a microdeletion of ~4.4Mb at chromosome 6q12-q13, a microduplication of ~1Mb at chromosome 18q12.3, and an interstitial duplication of ~5Mb at chromosome 15q11.2-q13.1. Our data indicate that CNVs contribute to the genetic underpinnings of the familial forms of schizophrenia as well as of the sporadic form. As 15q11-13 duplication is a well-known recurrent CNV associated with autism in the literature, the detection of the 15q11.2-q13.1 duplication in our schizophrenia patients provides additional support to other studies reporting that schizophrenia is part of the clinical spectrum of 15q11-q13 duplication syndrome.
    Full-text · Article · Jun 2012 · Schizophrenia Research
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    • "The identification of structural variants (SVs) in mammalian genomes [1-4] has important implications for our understanding of genetic diversity, has elucidated the concept of genomic disorders [5,6] and has improved the analysis of genetic association in common and rare diseases [7-12], cancer development [13] and genomic evolution [14,15]. However, the accurate identification of SVs in mammalian genomes remains challenging. "
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    ABSTRACT: Accurate catalogs of structural variants (SVs) in mammalian genomes are necessary to elucidate the potential mechanisms that drive SV formation and to assess their functional impact. Next generation sequencing methods for SV detection are an advance on array-based methods, but are almost exclusively limited to four basic types: deletions, insertions, inversions and copy number gains. By visual inspection of 100 Mbp of genome to which next generation sequence data from 17 inbred mouse strains had been aligned, we identify and interpret 21 paired-end mapping patterns, which we validate by PCR. These paired-end mapping patterns reveal a greater diversity and complexity in SVs than previously recognized. In addition, Sanger-based sequence analysis of 4,176 breakpoints at 261 SV sites reveal additional complexity at approximately a quarter of structural variants analyzed. We find micro-deletions and micro-insertions at SV breakpoints, ranging from 1 to 107 bp, and SNPs that extend breakpoint micro-homology and may catalyze SV formation. An integrative approach using experimental analyses to train computational SV calling is essential for the accurate resolution of the architecture of SVs. We find considerable complexity in SV formation; about a quarter of SVs in the mouse are composed of a complex mixture of deletion, insertion, inversion and copy number gain. Computational methods can be adapted to identify most paired-end mapping patterns.
    Full-text · Article · Mar 2012 · Genome biology
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