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. 2013 May;39(3):712-9.
doi: 10.1093/schbul/sbr197. Epub 2012 Feb 8.

Rare CNVs and tag SNPs at 15q11.2 are associated with schizophrenia in the Han Chinese population

Qian Zhao  1 , Tao Li, XinZhi Zhao, Ke Huang, Ti Wang, ZhiQiang Li, Jue Ji, Zhen Zeng, Zhao Zhang, Kan Li, GuoYin Feng, David St Clair, Lin He, YongYong Shi
Affiliations

Rare CNVs and tag SNPs at 15q11.2 are associated with schizophrenia in the Han Chinese population

Qian Zhao et al. Schizophr Bull. 2013 May.

Abstract

Background: Rare copy number variations (CNVs) were involved in the etiology of neuropsychiatric disorders, and some of them appeared to be shared risk factors for several different diseases. One of those promising loci is the CNV at 15q11.2, including 4 genes, TUBGCP5, CYFIP1, NIPA2, and NIPA1. Several studies showed that microdeletions at this locus were significant associated with schizophrenia. In the current study, we investigated the role of both rare CNVs and common single nucleotide polymorphisms (SNPs) at 15q11.2 in schizophrenia in the Chinese Han population.

Methods: We screened deletions at 15q11.2 in 2058 schizophrenia patients and 3275 normal controls in Chinese Han population by Affymetrix 500K/6.0 SNP arrays and SYBR green real-time polymerase chain reaction and then validated deletions by multiplex ligation-dependent probe amplification and Taqman real-time assays. We successfully genotyped 27 tag SNPs in total and tested associations in 1144 schizophrenia cases and 1144 normal controls.

Results: We found a triple increase of deletions in cases over controls, with OR=4.45 (95% CI=1.36-14.60) and P=.014. In the analysis of common SNPs, we found that the most significant SNP in schizophrenia was rs4778334 (OR=.72, 95% CI=0.60-0.87, allelic P=.0056 after permutation, genotypic P=.015 after permutation). We also found SNP rs1009153 in CYFIP1 was associated with schizophrenia (OR=0.82, 95% CI=0.73-0.93, allelic P=.044 after permutation).

Conclusion: We found that both rare deletions and common variants at 15q11.2 were associated with schizophrenia in the Chinese Han population.

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Figures

Fig. 2.
Fig. 2.
Deletions at 15q11.2 identified by Affymetrix 500K (in blue) and Affymetrix SNP6.0 (in red) in the University of California, Santa Cruz Genome Browser (Human March 2006 assembly, hg18).
Fig. 1.
Fig. 1.
Locations of all 33 tag SNPs in the human genome browser. Top: the coordinate in the human genome (March 2006 [NCBI36/hg18] assembly); middle: tag SNPs chosen in our study; and bottom: reference genes (TUBGCP5, CYFIP1, NIPA2, and NIPA1). Two SNPs in dark gray failed in the test experiments; 4 SNPs in green deviated from Hardy-Weinberg equilibrium in controls; and 2 SNPs in red remained positive in schizophrenia after permutation.
See this image and copyright information in PMC

References

    1. Sullivan PF, Kendler KS, Neale MC. Schizophrenia as a complex trait: evidence from a meta-analysis of twin studies. Arch Gen Psychiatry. 2003;60:1187–1192. - PubMed
    1. Iafrate AJ, Feuk L, Rivera MN, et al. Detection of large-scale variation in the human genome. Nat Genet. 2004;36:949–951. - PubMed
    1. Sebat J, Lakshmi B, Troge J, et al. Large-scale copy number polymorphism in the human genome. Science. 2004;305:525–528. - PubMed
    1. Lupski JR. Structural variation in the human genome. N Engl J Med. 2007;356:1169–1171. - PubMed
    1. Feuk L, Carson AR, Scherer SW. Structural variation in the human genome. Nat Rev Genet. 2006;7:85–97. - PubMed

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