Genome-wide association study of multiplex schizophrenia pedigrees

Abstract

Objective: The authors used a genome-wide association study (GWAS) of multiply affected families to investigate the association of schizophrenia to common single-nucleotide polymorphisms (SNPs) and rare copy number variants (CNVs).

Method: The family sample included 2,461 individuals from 631 pedigrees (581 in the primary European-ancestry analyses). Association was tested for single SNPs and genetic pathways. Polygenic scores based on family study results were used to predict case-control status in the Schizophrenia Psychiatric GWAS Consortium (PGC) data set, and consistency of direction of effect with the family study was determined for top SNPs in the PGC GWAS analysis. Within-family segregation was examined for schizophrenia-associated rare CNVs.

Results: No genome-wide significant associations were observed for single SNPs or for pathways. PGC case and control subjects had significantly different genome-wide polygenic scores (computed by weighting their genotypes by log-odds ratios from the family study) (best p=10(-17), explaining 0.4% of the variance). Family study and PGC analyses had consistent directions for 37 of the 58 independent best PGC SNPs (p=0.024). The overall frequency of CNVs in regions with reported associations with schizophrenia (chromosomes 1q21.1, 15q13.3, 16p11.2, and 22q11.2 and the neurexin-1 gene [NRXN1]) was similar to previous case-control studies. NRXN1 deletions and 16p11.2 duplications (both of which were transmitted from parents) and 22q11.2 deletions (de novo in four cases) did not segregate with schizophrenia in families.

Conclusions: Many common SNPs are likely to contribute to schizophrenia risk, with substantial overlap in genetic risk factors between multiply affected families and cases in large case-control studies. Our findings are consistent with a role for specific CNVs in disease pathogenesis, but the partial segregation of some CNVs with schizophrenia suggests that researchers should exercise caution in using them for predictive genetic testing until their effects in diverse populations have been fully studied.

FIGURE 1.. GWAS Results for 583 European-Ancestry Families^a

^a Each dot represents the −log(p value) for one of the 544,131 autosomal and X chromosome SNPs included in the European-ancestry analysis. Chromosome numbers are shown on the x-axis.

FIGURE 2.. Prediction of Psychiatric GWAS Consortium Case-Control Status^a

^a Each bar shows the proportion of variance explained (R²) in analyses using polygenic scores (1), computed based on association test results from this family-based study, to predict the case-control status of 9,394 schizophrenia case subjects and 12,462 control subjects from the Psychiatric GWAS Consortium (PGC) GWAS (6). A subset of 112,869 family study SNPs was selected for which PGC had data (genotyped or imputed from HapMap 3 information with information content >0.9), with minor allele frequency >2% in both data sets, and correlation (r²) between SNPs <0.25. Shown below each bar is the proportion of the SNPs (rank-ordered by family study p value) used in that analysis. For each PGC subject, a polygenic score was computed by multiplying (for each SNP) the family study association test result (log[odds ratio]) by the subject’s genotype (how many of the designated test alleles the subject carried) and then summing these products across SNPs. The p value shown within each bar is from a logistic regression of PGC case-control status predicted by polygenic scores plus seven ancestry-based covariates. The R² is the difference between Nagelkerke’s R² for prediction using scores and covariates minus the R² for covariates alone. (See Table S3 in the online data supplement for additional details.) The best prediction was observed when SNPs with the best 20% of p values were included. The prediction is highly significant, although with a very small proportion of total variance explained.

FIGURE 3.. Families With CNVs in Regions Previously Shown to Be Associated With Schizophrenia^a

^a Shown are the eight pedigrees with carriers of CNVs in five chromosomal regions with well-documented association of CNVs to schizophrenia, including 1q21.1 (typical HG18 boundaries 144.6–146.3 Mb), NRXN1 (interrupting exons of the gene, which lies on chromosome 2, 50–51.1 Mb), 15q13.3 (28.7–30.3 Mb), 16p11.2 (29.5–30.1 Mb), and 22q11.2 (17.1–20.2 Mb, or less commonly, a proximal 1.5 Mb deletion, as observed in individual NW33–4). Only genotyped offspring and their parents are shown, but all families were multiply affected. An illustrative example of each CNV is shown: the top plot shows the log(R) intensity (also known as log[R] ratio) for each probe location, with point-by-point estimates (in red) of changes in copy number (up for duplications, down for deletions) using a second algorithm (33). The bottom plot shows the B-allele frequency, i.e., where copy number=2, the designated “B” allele has 0%, 50%, or 100% of the total fluorescent intensity, but when copy number=1, only values of 0% or 100% are seen, while with copy number=3, some alleles have 33% or 67% of the total intensity, producing a distinctive pattern as shown. (Family IDs are masked.)