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

Qian Zhao, 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*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

49 Citations (Scopus)


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.

Original languageEnglish
Pages (from-to)712-719
Number of pages8
JournalSchizophrenia Bulletin
Issue number3
Early online date8 Feb 2012
Publication statusPublished - 1 May 2013

Bibliographical note

National 863 program (2009AA022701); 973 program (2010CB529600); National Natural Science Fundation of China (81130022, 81121001, 31000553); the Foundation for the Author of National Excellent Doctoral Dissertation of China (201026); the Program for New Century Excellent Talents in University (NCET-09-0550); Shanghai Municipal Health Bureau program (2008095).

We sincerely thank all the participants for their participation in this study and all the medical staff involved in sample collection and diagnosis. We report no biomedical financial interests or potential conflicts of interest.


  • 15q11.2
  • copy number variation (CNV)
  • schizophrenia
  • tag SNP


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