Please use this identifier to cite or link to this item: http://hdl.handle.net/20.500.11861/7399
Title: Genome-Wide Search for SNP Interactions in GWAS Data: Algorithm, Feasibility, Replication Using Schizophrenia Datasets
Authors: Lee, Kwan-Yeung 
Prof. LEUNG Kwong Sak 
Ma, Suk Ling 
So, Hon Cheong 
Huang, Dan 
Tang, Nelson, Leung-Sang 
Wong, Man-Hon 
Issue Date: 2020
Source: Frontiers in Genetics, 2020, vol. 11
Journal: Frontiers in Genetics 
Abstract: In this study, we looked for potential gene-gene interaction in susceptibility to schizophrenia by an exhaustive searching for SNP–SNP interactions in 3 GWAS datasets (phs000021:phg000013, phs000021:phg000014, phs000167) using our recently published algorithm. The search space for SNP–SNP interaction was confined to 8 biologically plausible ways of interaction under dominant-dominant or recessive-recessive modes. First, we performed our search of all pair-wise combination of 729,454 SNPs after filtering by SNP genotype quality. All possible pairwise interactions of any 2 SNPs (5 × 1011) were exhausted to search for significant interaction which was defined by p-value of chi-square tests. Nine out the top 10 interactions, protein coding genes were partnered with non-coding RNA (ncRNA) which suggested a new alternative insight into interaction biology other than the frequently sought-after protein–protein interaction. Therefore, we extended to look for replication among the top 10,000 interaction SNP pairs and high proportion of concurrent genes forming the interaction pairs were found. The results indicated that an enrichment of signals over noise was present in the top 10,000 interactions. Then, replications of SNP–SNP interaction were confirmed for 14 SNPs-pairs in both replication datasets. Biological insight was highlighted by a potential binding between FHIT (protein coding gene) and LINC00969 (lncRNA) which showed a replicable interaction between their SNPs. Both of them were reported to have expression in brain. Our study represented an early attempt of exhaustive interaction analysis of GWAS data which also yield replicated interaction and new insight into understanding of genetic interaction in schizophrenia.
Type: Peer Reviewed Journal Article
URI: http://hdl.handle.net/20.500.11861/7399
DOI: 10.3389/fgene.2020.01003
Appears in Collections:Applied Data Science - Publication

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