Journal article
Independent component analysis of SNPs reflects polygenic risk scores for schizophrenia
Schizophrenia research, Vol.181, pp.83-85
03/2017
DOI: 10.1016/j.schres.2016.09.011
PMCID: PMC5348276
PMID: 27637363
Abstract
Schizophrenia is a psychiatric disorder with high heritability. Recent genome-wide association studies have provided a list of risk loci reliably derived from unprecedentedly large samples. However, further delineation of the diagnosis-associated susceptibility variants is needed to better characterize the genetic architecture given the disease's complex nature. In this sense, a data-driven approach might hold promise for identifying functionally related clusters of genetic variants that might not be captured by hypothesis-based models. In the current study, independent component analysis (ICA) was applied to the Psychiatric Genomics Consortium's schizophrenia-related single nucleotide polymorphisms (SNPs) in 104 schizophrenia patients and 142 healthy controls of European Ancestry. We found that, for 13 out of 16 extracted independent components, the associated loadings correlated highly (r>0.5) with the polygenic risk scores for SZ of the corresponding SNPs. These correlations were likely not inflated by the linkage disequilibrium structure (permutation p<0.001). In brief, we demonstrate an example of ICA analysis on SNP data yielding functionally meaningful clusters, which motivates further application of data-driven approaches as a complimentary tool for hypothesis-based methods to enrich our knowledge on the genetic basis of complex disorders.
Details
- Title: Subtitle
- Independent component analysis of SNPs reflects polygenic risk scores for schizophrenia
- Creators
- Jiayu Chen - The Mind Research Network, Albuquerque, NM, USAVince D Calhoun - The Mind Research Network, Albuquerque, NM, USAGodfrey D Pearlson - Olin Neuropsychiatry Research Center, Institute of Living, Hartford, CT, USANora I Perrone-Bizzozero - Departments of Neurosciences and Psychiatry, University of New Mexico School of Medicine, Albuquerque, NM, USAJessica A Turner - The Mind Research Network, Albuquerque, NM, USAStefan Ehrlich - Division of Psychological and Social Medicine and Developmental Neurosciences, Faculty of Medicine, TU Dresden, GermanyBeng-Choon Ho - Department of Psychiatry, University of Iowa, Iowa City, IA, USAJingyu Liu - The Mind Research Network, Albuquerque, NM, USA
- Resource Type
- Journal article
- Publication Details
- Schizophrenia research, Vol.181, pp.83-85
- DOI
- 10.1016/j.schres.2016.09.011
- PMID
- 27637363
- PMCID
- PMC5348276
- NLM abbreviation
- Schizophr Res
- ISSN
- 0920-9964
- eISSN
- 1573-2509
- Publisher
- Elsevier B.V
- Grant note
- DOI: 10.13039/100000002, name: National Institutes of Health, award: P20GM103472, R01EB005846, 1R01EB006841, 1R01MH094524-01A1; DOI: 10.13039/100015388, name: NSF EPSCoR, award: 1539067
- Language
- English
- Date published
- 03/2017
- Academic Unit
- Psychiatry
- Record Identifier
- 9984004088102771
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