Gene-Based Analysis in HRC Imputed Genome Wide Association Data Identifies Three Novel Genes For Alzheimer’s Disease

Baker, E.; Sims, R.; Leonenko, G.; Frizzati, A.; Harwood, J.; Grozeva, D.; Genetic and Environmental Risk in Alzheimer's Disease (GERAD) Consortium,; PERADES consortium,; IGAP consortia,; Morgan, K.; Passmore, P.; Holmes, C.; Powell, J.; Brayne, C.; Gill, M.; Mead, S.; Heun, R.; Bossu, P.; Spalletta, G.; Goate, A.; Cruchaga, C.; van Duijn, C.; Maier, W.; Ramirez, A.; Jones, L.; Hardy, J.; Ivanov, D.; Hill, M.; Holmans, P.; Allen, N.; Morgan, P.; Williams, J.; Escott-Price, V.

doi:10.1101/374876

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bioRxiv · 10.1101/374876

Gene-Based Analysis in HRC Imputed Genome Wide Association Data Identifies Three Novel Genes For Alzheimer’s Disease

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Abstract

A novel POLARIS gene-based analysis approach was employed to compute gene-based polygenic risk score (PRS) for all individuals in the latest HRC imputed GERAD (N cases=3,332 and N controls=9,832) data using the International Genomics of Alzheimers Project summary statistics (N cases=13,676 and N controls=27,322, excluding GERAD subjects) to identify the SNPs and weight their risk alleles for the PRS score. SNPs were assigned to known, protein coding genes using GENCODE (v19). SNPs are assigned using both 1) no window around the gene and 2) a window of 35kb upstream and 10kb downstream to include transcriptional regulatory elements. The overall association of a gene is determined using a logistic regression model, adjusting for population covariates.\n\nThree novel gene-wide significant genes were determined from the POLARIS gene-based analysis using a gene window; PPARGC1A, RORA and ZNF423. The ZNF423 gene resides in an Alzheimers disease (AD)-specific protein network which also includes other AD-related genes. The PPARGC1A gene has been linked to energy metabolism and the generation of amyloid beta plaques and the RORA has strong links with genes which are differentially expressed in the hippocampus. We also demonstrate no enrichment for genes in either loss of function intolerant or conserved noncoding sequence regions.

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Baker, E., Sims, R., Leonenko, G., Frizzati, A., Harwood, J., Grozeva, D., Genetic and Environmental Risk in Alzheimer's Disease (GERAD) Consortium,, PERADES consortium,, IGAP consortia,, Morgan, K., Passmore, P., Holmes, C., Powell, J., Brayne, C., Gill, M., Mead, S., Heun, R., Bossu, P., Spalletta, G., Goate, A., Cruchaga, C., van Duijn, C., Maier, W., Ramirez, A., Jones, L., Hardy, J., Ivanov, D., Hill, M., Holmans, P., Allen, N., Morgan, P., Williams, J., Escott-Price, V.. 2018-07-23. Gene-Based Analysis in HRC Imputed Genome Wide Association Data Identifies Three Novel Genes For Alzheimer’s Disease. https://doi.org/10.1101/374876

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