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Am J Med Genet B Neuropsychiatr Genet. 2018 Jun;177(4):454-467. doi: 10.1002/ajmg.b.32634. Epub 2018 Apr 28.

A molecule-based genetic association approach implicates a range of voltage-gated calcium channels associated with schizophrenia.

Author information

1
NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
2
Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway.
3
Department of Neurosciences, University of California, San Diego, La Jolla, California.
4
Multimodal Imaging Laboratory, University of California, San Diego, La Jolla, California.
5
Department of Psychiatry, University of California, San Diego, La Jolla, California.
6
Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Mental Health Services, Copenhagen, Denmark.
7
The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Copenhagen, Denmark.
8
Department of Cognitive Sciences, University of California, San Diego, La Jolla, California.
9
Department of Medical Genetics, Oslo University Hospital, Oslo, Norway.
10
NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway.
11
Department of Radiology, University of California, San Diego, La Jolla, California.

Abstract

Traditional genome-wide association studies (GWAS) have successfully detected genetic variants associated with schizophrenia. However, only a small fraction of heritability can be explained. Gene-set/pathway-based methods can overcome limitations arising from single nucleotide polymorphism (SNP)-based analysis, but most of them place constraints on size which may exclude highly specific and functional sets, like macromolecules. Voltage-gated calcium (Cav ) channels, belonging to macromolecules, are composed of several subunits whose encoding genes are located far away or even on different chromosomes. We combined information about such molecules with GWAS data to investigate how functional channels associated with schizophrenia. We defined a biologically meaningful SNP-set based on channel structure and performed an association study by using a validated method: SNP-set (sequence) kernel association test. We identified eight subtypes of Cav channels significantly associated with schizophrenia from a subsample of published data (N = 56,605), including the L-type channels (Cav 1.1, Cav 1.2, Cav 1.3), P-/Q-type Cav 2.1, N-type Cav 2.2, R-type Cav 2.3, T-type Cav 3.1, and Cav 3.3. Only genes from Cav 1.2 and Cav 3.3 have been implicated by the largest GWAS (N = 82,315). Each subtype of Cav channels showed relatively high chip heritability, proportional to the size of its constituent gene regions. The results suggest that abnormalities of Cav channels may play an important role in the pathophysiology of schizophrenia and these channels may represent appropriate drug targets for therapeutics. Analyzing subunit-encoding genes of a macromolecule in aggregate is a complementary way to identify more genetic variants of polygenic diseases. This study offers the potential of power for discovery the biological mechanisms of schizophrenia.

KEYWORDS:

SKAT; SNP-sets; channels; molecule-based GWAS; schizophrenia

PMID:
29704319
DOI:
10.1002/ajmg.b.32634
[Indexed for MEDLINE]

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