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    ABCA7 frameshift deletion associated with Alzheimer disease in African Americans.

    Neurol Genet 2016 Jun 17;2(3):e79. Epub 2016 May 17.
    John P. Hussman Institute for Human Genomics (H.N.C., B.W.K., S.R., K.L.H.-N., M.A.K., P.L.W., D.V.B., D.M.D., M.L.C., J.M.V., J.R.G., G.W.B., E.R.M., R.M.C., M.A.P.-V.), Department of Neurology (H.N.C., J.M.V., M.A.P.-V.), Dr. John T. Macdonald Foundation Department of Human Genetics (D.M.D., M.L.C., J.M.V., J.R.G., G.W.B., E.R.M., R.M.C.), Miller School of Medicine, University of Miami, FL; The Taub Institute for Research on Alzheimer's Disease and the Aging Brain (B.N.V., R.M.), Gertrude H. Sergievsky Center, Departments of Neurology, Psychiatry, and Epidemiology, College of Physicians and Surgeons, Columbia University, New York, NY; Department of Pathology and Laboratory Medicine (B.A.D., G.D.S.), University of Pennsylvania Perelman School of Medicine, Philadelphia, PA; Department of Biology (R.L., G.S.B., M.A.P.-V.), North Carolina A&T State University, Greensboro, NC; Departments of Medicine, Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics (L.A.F.), Boston University, MA; and Department of Epidemiology and Biostatistics (J.L.H.), Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH.
    Objective: To identify a causative variant(s) that may contribute to Alzheimer disease (AD) in African Americans (AA) in the ATP-binding cassette, subfamily A (ABC1), member 7 (ABCA7) gene, a known risk factor for late-onset AD.

    Methods: Custom capture sequencing was performed on ∼150 kb encompassing ABCA7 in 40 AA cases and 37 AA controls carrying the AA risk allele (rs115550680). Association testing was performed for an ABCA7 deletion identified in large AA data sets (discovery n = 1,068; replication n = 1,749) and whole exome sequencing of Caribbean Hispanic (CH) AD families.

    Results: A 44-base pair deletion (rs142076058) was identified in all 77 risk genotype carriers, which shows that the deletion is in high linkage disequilibrium with the risk allele. The deletion was assessed in a large data set (531 cases and 527 controls) and, after adjustments for age, sex, and APOE status, was significantly associated with disease (p = 0.0002, odds ratio [OR] = 2.13 [95% confidence interval (CI): 1.42-3.20]). An independent data set replicated the association (447 cases and 880 controls, p = 0.0117, OR = 1.65 [95% CI: 1.12-2.44]), and joint analysis increased the significance (p = 1.414 × 10(-5), OR = 1.81 [95% CI: 1.38-2.37]). The deletion is common in AA cases (15.2%) and AA controls (9.74%), but in only 0.12% of our non-Hispanic white cohort. Whole exome sequencing of multiplex, CH families identified the deletion cosegregating with disease in a large sibship. The deleted allele produces a stable, detectable RNA strand and is predicted to result in a frameshift mutation (p.Arg578Alafs) that could interfere with protein function.

    Conclusions: This common ABCA7 deletion could represent an ethnic-specific pathogenic alteration in AD.
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