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Whole‐exome sequencing of the BDR cohort: evidence to support the role of the PILRA gene in Alzheimer's disease
Author(s) -
Patel T.,
Brookes K. J.,
Turton J.,
Chaudhury S.,
GuettaBaranes T.,
Guerreiro R.,
Bras J.,
Hernandez D.,
Singleton A.,
Francis P. T.,
Hardy J.,
Morgan K.
Publication year - 2018
Publication title -
neuropathology and applied neurobiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.538
H-Index - 95
eISSN - 1365-2990
pISSN - 0305-1846
DOI - 10.1111/nan.12452
Subject(s) - exome sequencing , genome wide association study , dementia , genetics , exome , alzheimer's disease , genetic association , pleiotropy , biology , disease , candidate gene , gene , medicine , single nucleotide polymorphism , mutation , phenotype , genotype
Aim Late‐onset Alzheimer's disease ( LOAD ) accounts for 95% of all Alzheimer's cases and is genetically complex in nature. Overlapping clinical and neuropathological features between AD , FTD and Parkinson's disease highlight the potential role of genetic pleiotropy across diseases. Recent genome‐wide association studies ( GWAS s) have uncovered 20 new loci for AD risk; however, these exhibit small effect sizes. Using NGS , here we perform association analyses using exome‐wide and candidate‐gene‐driven approaches. Methods Whole‐exome sequencing was performed on 132 AD cases and 53 control samples. Exome‐wide single‐variant association and gene burden tests were performed for 76 640 nonsingleton variants. Samples were also screened for known causative mutations in familial genes in AD and other dementias. Single‐variant association and burden analysis was also carried out on variants in known AD and other neurological dementia genes. Results Tentative single‐variant and burden associations were seen in several genes with kinase and protease activity. Exome‐wide burden analysis also revealed significant burden of variants in PILRA ( P = 3.4 × 10 −5 ), which has previously been linked to AD via GWAS , hit ZCWPW 1 . Screening for causative mutations in familial AD and other dementia genes revealed no pathogenic variants. Variants identified in ABCA 7 , SLC 24A4 , CD 33 and LRRK 2 were nominally associated with disease ( P < 0.05) but did not withstand correction for multiple testing. APOE ( P = 0.02) and CLU ( P = 0.04) variants showed significant burden on AD . Conclusions In addition, polygenic risk scores ( PRS ) were able to distinguish between cases and controls with 83.8% accuracy using 3268 variants, sex, age at death and APOE ε4 and ε2 status as predictors.