Genome-Wide Association Study of Multiplex Schizophrenia Pedigrees

Levinson, Douglas F., Shi, Jianxin, Wang, Kai, Oh, Sang, Riley, Brien, Pulver, Ann E., Wildenauer, Dieter B., Laurent, Claudine, Mowry, Bryan J., Gejman, Pablo V., Owen, Michael J., Kendler, Kenneth S., Nestadt, Gerald, Schwab, Sibylle G., Mallet, Jacques, Nertney, Deborah, Sanders, Alan R., Williams, Nigel M., Wormley, Brandon, Lasseter, Virginia K., Albus, Margot, Godard-Bauche, Stephanie, Alexander, Madeline, Duan, Jubao, O'Donovan, Michael C., Walsh, Dermot, O'Neill, Anthony, Papadimitriou, George N., Dikeos, Dimitris, Maier, Wolfgang, Lerer, Bernard, Campion, Dominique, Cohen, David, Jay, Maurice, Fanous, Ayman, Eichhammer, Peter, Silverman, Jeremy M., Norton, Nadine, Zhang, Nancy, Hakonarson, Hakon, Gao, Cynthia, Citri, Ami, Hansen, Mark, Ripke, Stephan, The Schizophrenia Psychiatric GWAS Consortium, Dudbridge, Frank and Holmans, Peter A. (2012) Genome-Wide Association Study of Multiplex Schizophrenia Pedigrees. American Journal of Psychiatry, 169 9: 963-973. doi:10.1176/appi.ajp.2012.11091423


Author Levinson, Douglas F.
Shi, Jianxin
Wang, Kai
Oh, Sang
Riley, Brien
Pulver, Ann E.
Wildenauer, Dieter B.
Laurent, Claudine
Mowry, Bryan J.
Gejman, Pablo V.
Owen, Michael J.
Kendler, Kenneth S.
Nestadt, Gerald
Schwab, Sibylle G.
Mallet, Jacques
Nertney, Deborah
Sanders, Alan R.
Williams, Nigel M.
Wormley, Brandon
Lasseter, Virginia K.
Albus, Margot
Godard-Bauche, Stephanie
Alexander, Madeline
Duan, Jubao
O'Donovan, Michael C.
Walsh, Dermot
O'Neill, Anthony
Papadimitriou, George N.
Dikeos, Dimitris
Maier, Wolfgang
Lerer, Bernard
Campion, Dominique
Cohen, David
Jay, Maurice
Fanous, Ayman
Eichhammer, Peter
Silverman, Jeremy M.
Norton, Nadine
Zhang, Nancy
Hakonarson, Hakon
Gao, Cynthia
Citri, Ami
Hansen, Mark
Ripke, Stephan
The Schizophrenia Psychiatric GWAS Consortium
Dudbridge, Frank
Holmans, Peter A.
Title Genome-Wide Association Study of Multiplex Schizophrenia Pedigrees
Journal name American Journal of Psychiatry   Check publisher's open access policy
ISSN 0002-953X
Publication date 2012-09-01
Sub-type Article (original research)
DOI 10.1176/appi.ajp.2012.11091423
Open Access Status DOI
Volume 169
Issue 9
Start page 963
End page 973
Total pages 11
Place of publication Arlington, VA, United States
Publisher American Psychiatric Publishing
Language eng
Abstract Exposure to high levels of environmental lead, or biomarker evidence of high body lead content, is associated with anaemia, developmental and neurological deficits in children, and increased mortality in adults. Adverse effects of lead still occur despite substantial reduction in environmental exposure. There is genetic variation between individuals in blood lead concentration but the polymorphisms contributing to this have not been defined. We measured blood or erythrocyte lead content, and carried out genome-wide association analysis, on population-based cohorts of adult volunteers from Australia and UK (N = 5433). Samples from Australia were collected in two studies, in 1993-1996 and 2002-2005 and from UK in 1991-1992. One locus, at ALAD on chromosome 9, showed consistent association with blood lead across countries and evidence for multiple independent allelic effects. The most significant single nucleotide polymorphism (SNP), rs1805313 (P = 3.91 × 10(-14) for lead concentration in a meta-analysis of all data), is known to have effects on ALAD expression in blood cells but other SNPs affecting ALAD expression did not affect blood lead. Variants at 12 other loci, including ABO, showed suggestive associations (5 × 10(-6) > P > 5 × 10(-8)). Identification of genetic polymorphisms affecting blood lead reinforces the view that genetic factors, as well as environmental ones, are important in determining blood lead levels. The ways in which ALAD variation affects lead uptake or distribution are still to be determined.
Formatted 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. Withinfamily 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.
Keyword Susceptibility loci
Multicenter linkage
Common variants
Families
Q-Index Code C1
Q-Index Status Confirmed Code
Grant ID AA007535
AA013320
MC_UU_12013/3
AA013326
102215
DA012854
MC_PC_15018
MC_UU_12013/1
MC_UU_12013/4
AA014041
MC_UU_12013/5
WT088806
AA013321
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Queensland Brain Institute Publications
Official 2013 Collection
 
Versions
Version Filter Type
Citation counts: TR Web of Science Citation Count  Cited 33 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 38 times in Scopus Article | Citations
Google Scholar Search Google Scholar
Created: Fri, 16 Nov 2012, 00:42:52 EST by System User on behalf of Queensland Brain Institute