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      A rare loss-of-function variant of ADAM17 is associated with late-onset familial Alzheimer disease

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          Abstract

          Common variants of about 20 genes contributing to AD risk have so far been identified through genome-wide association studies (GWAS). However, there is still a large proportion of heritability that might be explained by rare but functionally important variants. One of the so far identified genes with rare AD causing variants is ADAM10. Using whole-genome sequencing we now identified a single rare nonsynonymous variant (SNV) rs142946965 [p.R215I] in ADAM17 co-segregating with an autosomal-dominant pattern of late-onset AD in one family. Subsequent genotyping and analysis of available whole-exome sequencing data of additional case/control samples from Germany, UK, and USA identified five variant carriers among AD patients only. The mutation inhibits pro-protein cleavage and the formation of the active enzyme, thus leading to loss-of-function of ADAM17 alpha-secretase. Further, we identified a strong negative correlation between ADAM17 and APP gene expression in human brain and present in vitro evidence that ADAM17 negatively controls the expression of APP. As a consequence, p.R215I mutation of ADAM17 leads to elevated Aß formation in vitro. Together our data supports a causative association of the identified ADAM17 variant in the pathogenesis of AD.

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          Most cited references25

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          Systematic meta-analyses of Alzheimer disease genetic association studies: the AlzGene database.

          The past decade has witnessed hundreds of reports declaring or refuting genetic association with putative Alzheimer disease susceptibility genes. This wealth of information has become increasingly difficult to follow, much less interpret. We have created a publicly available, continuously updated database that comprehensively catalogs all genetic association studies in the field of Alzheimer disease (http://www.alzgene.org). We performed systematic meta-analyses for each polymorphism with available genotype data in at least three case-control samples. In addition to identifying the epsilon4 allele of APOE and related effects, we pinpointed over a dozen potential Alzheimer disease susceptibility genes (ACE, CHRNB2, CST3, ESR1, GAPDHS, IDE, MTHFR, NCSTN, PRNP, PSEN1, TF, TFAM and TNF) with statistically significant allelic summary odds ratios (ranging from 1.11-1.38 for risk alleles and 0.92-0.67 for protective alleles). Our database provides a powerful tool for deciphering the genetics of Alzheimer disease, and it serves as a potential model for tracking the most viable gene candidates in other genetically complex diseases.
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            dbNSFP v3.0: A One-Stop Database of Functional Predictions and Annotations for Human Nonsynonymous and Splice-Site SNVs.

            The purpose of the dbNSFP is to provide a one-stop resource for functional predictions and annotations for human nonsynonymous single-nucleotide variants (nsSNVs) and splice-site variants (ssSNVs), and to facilitate the steps of filtering and prioritizing SNVs from a large list of SNVs discovered in an exome-sequencing study. A list of all potential nsSNVs and ssSNVs based on the human reference sequence were created and functional predictions and annotations were curated and compiled for each SNV. Here, we report a recent major update of the database to version 3.0. The SNV list has been rebuilt based on GENCODE 22 and currently the database includes 82,832,027 nsSNVs and ssSNVs. An attached database dbscSNV, which compiled all potential human SNVs within splicing consensus regions and their deleteriousness predictions, add another 15,030,459 potentially functional SNVs. Eleven prediction scores (MetaSVM, MetaLR, CADD, VEST3, PROVEAN, 4× fitCons, fathmm-MKL, and DANN) and allele frequencies from the UK10K cohorts and the Exome Aggregation Consortium (ExAC), among others, have been added. The original seven prediction scores in v2.0 (SIFT, 2× Polyphen2, LRT, MutationTaster, MutationAssessor, and FATHMM) as well as many SNV and gene functional annotations have been updated. dbNSFP v3.0 is freely available at http://sites.google.com/site/jpopgen/dbNSFP.
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              Analysis of genetic inheritance in a family quartet by whole-genome sequencing.

              We analyzed the whole-genome sequences of a family of four, consisting of two siblings and their parents. Family-based sequencing allowed us to delineate recombination sites precisely, identify 70% of the sequencing errors (resulting in > 99.999% accuracy), and identify very rare single-nucleotide polymorphisms. We also directly estimated a human intergeneration mutation rate of approximately 1.1 x 10(-8) per position per haploid genome. Both offspring in this family have two recessive disorders: Miller syndrome, for which the gene was concurrently identified, and primary ciliary dyskinesia, for which causative genes have been previously identified. Family-based genome analysis enabled us to narrow the candidate genes for both of these Mendelian disorders to only four. Our results demonstrate the value of complete genome sequencing in families.
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                Author and article information

                Contributors
                +49 (0)6841 1626355 , daniela.hartl@uks.eu
                Journal
                Mol Psychiatry
                Mol. Psychiatry
                Molecular Psychiatry
                Nature Publishing Group UK (London )
                1359-4184
                1476-5578
                9 July 2018
                9 July 2018
                2020
                : 25
                : 3
                : 629-639
                Affiliations
                [1 ]ISNI 0000 0001 2167 7588, GRID grid.11749.3a, Department of Psychiatry and Psychotherapy, Saarland University Hospital, , Saarland University, ; Homburg, Germany
                [2 ]ISNI 0000 0001 2295 9843, GRID grid.16008.3f, Luxembourg Centre for Systems Biomedicine (LCSB), , University of Luxembourg, ; Esch-sur-Alzette, Luxembourg
                [3 ]ISNI 0000 0004 0463 2320, GRID grid.64212.33, Institute for Systems Biology, ; Seattle, WA USA
                [4 ]ISNI 0000 0004 0477 2438, GRID grid.15474.33, Department of Psychiatry and Psychotherapy, , Klinikum Rechts der Isar, TU-Muenchen, ; Munich, Germany
                [5 ]ISNI 0000 0004 1936 8868, GRID grid.4563.4, School of Life Sciences, Queens Medical Centre, , University of Nottingham, ; Nottingham, UK
                [6 ]ISNI 0000000419368729, GRID grid.21729.3f, Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, College of Physicians and Surgeons, , Columbia University, ; New York City, NY USA
                [7 ]ISNI 0000000419368729, GRID grid.21729.3f, Department of Neurology, College of Physicians and Surgeons, , Columbia University, ; New York City, NY USA
                [8 ]ISNI 0000000419368729, GRID grid.21729.3f, Gertrude H. Sergievsky Center, College of Physicians and Surgeons, , Columbia University, ; New York City, NY USA
                [9 ]ISNI 0000000419368729, GRID grid.21729.3f, Department of Epidemiology, Mailman School of Public Health, , Columbia University, ; New York City, NY USA
                [10 ]ISNI 0000000121901201, GRID grid.83440.3b, Department of Molecular Neuroscience, Institute of Neurology, , University College London, ; London, UK
                [11 ]UK Dementia Research Institute at UCL (UK DRI), London, UK
                [12 ]ISNI 0000000123236065, GRID grid.7311.4, Department of Medical Sciences, Institute of Biomedicine-iBiMED, , University of Aveiro, ; Aveiro, Portugal
                [13 ]ISNI 0000 0001 2248 7639, GRID grid.7468.d, Department of Experimental Neurology, Center for Stroke Research Berlin (CSB), Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, , Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, ; Berlin, Germany
                [14 ]ISNI 0000 0001 2297 5165, GRID grid.94365.3d, Laboratory of Neurogenetics, National Institute on Aging, , National Institutes of Health, ; Bethesda, MD USA
                [15 ]ISNI 0000 0004 1936 8868, GRID grid.4563.4, Translation Cell Sciences-Human Genetics, School of Life Sciences, Queens Medical Centre, , University of Nottingham, ; Nottingham, UK
                [16 ]ISNI 0000 0001 2322 6764, GRID grid.13097.3c, Brains for Dementia Research Resource, Wolfson Centre for Age Related Diseases, , King’s College London, ; London, UK
                [17 ]ISNI 0000 0001 2294 1395, GRID grid.1049.c, QIMR Berghofer Medical Research Institute, ; Brisbane, Queensland, Australia
                [18 ]King’s College London, Institute of Psychiatry, Psychology and Neuroscience, London, UK
                Author information
                http://orcid.org/0000-0001-8698-3770
                http://orcid.org/0000-0002-8217-2396
                Article
                91
                10.1038/s41380-018-0091-8
                7042727
                29988083
                aeef2fca-883a-4383-82b3-22586620427a
                © The Author(s) 2018

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 16 February 2018
                : 5 April 2018
                : 11 April 2018
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                © Springer Nature Limited 2020

                Molecular medicine
                neuroscience,molecular biology,genetics
                Molecular medicine
                neuroscience, molecular biology, genetics

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