Lack of support for association between the copy number variants in the FCGR locus and schizophrenia: A case control study

The missing heritability of polygenic schizophrenia after genome-wide association studies (GWAS) can be potentially accounted for by the fact that most dynamic multiallelic copy number variants (CNVs) overlap segmental duplications (SDs). The FCGR locus covers this category of complex CNVs and it has long been postulated to harbor variants conferring the risk of schizophrenia. However, such association remains unproven. We used a case-control design to investigate CNV-based association with the disease. Data were obtained from 598 unrelated schizophrenia patients and 959 normal controls of Han ancestry from Shanghai. A total of four copy number (CN) probes in the FCGR locus were detected using TaqMan® Copy Number Assay. SPSS version 16.0 was used for the statistical analyses. And the frequency distributions of target CN in FCGR locus were very similar between controls and cases, whereas the CNV frequency differed markedly among different target CN analyzed in the two cohorts. When compared with the predominant two copies per diploid genome, a distinct non-protein-coding CN deletion region containing regulatory sequences was detected by probe Hs04194069_cn. Taken together, we found no evidence of association of target CNVs in the FCGR locus with schizophrenia. However, our negative findings suggest that more detailed next generation sequencing-based association studies are needed to fully evaluate the contribution of this category of complex CNVs to the disease.

► The target copy number frequency in FCGR locus is similar between controls and cases. ► We found no clear association of target CNVs in the FCGR locus with schizophrenia. ► The frequency differed markedly among different target copy number in the two cohorts. ► A non-protein-coding CNV deletion region containing regulatory sequences was detected. ► We confirmed the complexity of the FCGR locus.