- Email: [email protected]
Targeted re-sequencing of sorl1 in early-onset Alzheimer’s dementia: The european early onset dementia consortium
Podium Presentations: Tuesday, July 21, 2015 Background: To identify rare mutations by targeted sequencing
in eight genes initially detected in genome-wide association studies (GWASs) of late onset Alzheimer’s disease (LOAD). Methods: We conducted targeted sequencing of ABCA7, BIN1, CD2AP, CLU, CR1, EPHA1, MS4A4A/MS4A6A and PICALMin three independent LOAD cohorts: 176 patients from 124 Caribbean Hispanics families, 120 patients and 33 unaffected individuals from the 129 NIA-LOAD Family Study; and 263 unrelated Canadian individuals of European ancestry (210 sporadic patients and 53 controls). The variants were called using the BWA-GATK pipeline. Rare coding mutations found in at least two datasets were genotyped in independent controls similar in age and sex distributions and ancestry to the cases in all datasets to estimate population-based frequencies. Results: We detected a statistically significant 3.71-fold enrichment of the non-synonymous mutations in both cohorts of Caucasian LOAD cases compared with controls (p¼0.001) but the mutation rate of non-coding mutations was same in cases and controls. In total, we detected 88 rare damaging mutations, 12 of which were found in at least two datasets: four mutations in ABCA7, two each in CD2AP and PICALM, and one each in BIN1, EPHA1, CLU and MS4A6A. Three of these mutations were observed in all datasets: rs138047593 (BIN1 p.K358R), rs202178565 (EPHA1 p.P460L), and rs138650483 (MS4A6A p.V218M).. The variant in EPHA1 segregated completely in an extended Caribbean Hispanic family and was observed in only one of 300 controls of similar ancestry. Additionally, p.K358R in BIN1segregated in two of the six families where the mutations were discovered. Conclusions: Targeted sequencing of well-confirmed GWAS loci revealed an excess burden of deleterious coding mutations in LOAD with the greatest burden observed in ABCA7 and BIN1. The rarity of these mutations does not fully explain all the associations observed in GWAS, but do represent independent contributions to LOAD pathogenesis. Identifying coding sequence variants in LOAD will facilitate the creation of tractable models for investigation of disease related mechanisms and potential therapies.
O3-13-06
TARGETED RE-SEQUENCING OF SORL1 IN EARLY-ONSET ALZHEIMER’S DEMENTIA: THE EUROPEAN EARLY ONSET DEMENTIA CONSORTIUM
Kristel Sleegers1,2, Jan Verheijen1,2, Julie van der Zee1,2, Karolien Bettens1,2, Sebastiaan Engelborghs3,4, Mathieu Vandenbulcke5, Raquel Sanchez-Valle6, Luisa Benussi7, Alexandre de Mendonc¸a8, Pau Pastor9,10,11, Caroline Graff12,13, Barbara Borroni14, Rik Vandenberghe5, Peter P. De Deyn4,15, Christine Van Broeckhoven1,2 BELNEU Consortium, EU EOD Consortium, 1Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp,
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Belgium; 2Neurodegenerative Brain Diseases Group, Department of Molecular Genetics, VIB, Antwerp, Belgium; 3Institute Born-Bunge, University of Antwerp, Antwerp, Belgium; 4Hospital Network Antwerp (ZNA), Antwerp, Belgium; 5KU Leuven, Leuven, Belgium; 6Alzheimer’s Disease and Other Cognitive Disorders Unit, Neurology Department, Hospital Clınic, IDIBAPS, Barcelona, Spain; 7Molecular Markers Laboratory - IRCCS Istituto Centro San Giovanni di Dio-Fatebenefratelli, Brescia, Italy; 8University of Lisbon, Lisbon, Portugal; 9Neurogenetics Laboratory, Division of Neurosciences, Center for Applied Medical Research, Universidad de Navarra, Pamplona, Spain; 10Department of Neurology, Hospital Universitari Mutua de Terrassa, Terrassa, Barcelona, Spain; 11Centro de Investigacion Biomedica en Red de Enfermedades Neurodegenerativas, CIBERNED, Instituto de Salud Carlos III, Madrid, Spain; 12Karolinska Institutet, Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Neurogeriatrics, Huddinge, Sweden; 13Department of Geriatric Medicine, Genetics Unit, Karolinska University Hospital, Stockholm, Sweden; 14Neurology Unit, University of Brescia, Brescia, Italy; 15University of Antwerp, Antwerp, Belgium. Contact e-mail: [email protected] Background: The sortilin-related receptor 1 (SORL1) gene has been implicated in increased susceptibility to Alzheimer’s disease (AD), but also in autosomal dominant early-onset AD (EOAD). At least one missense mutation has been reported to segregate with EOAD. Here we report a large-scale investigation of the contribution of genetic variability in SORL1 to EOAD in a European EOAD cohort. Methods: We performed massive parallel amplicon-based re-sequencing of the full coding region of SORL1 on an Illumina MiSeq sequencer in 1004 EOAD patients and 1649 age- and origin-matched control individuals through the European Early-Onset Dementia (EU EOD) consortium, originating from Belgium, Spain, Portugal, Italy, Sweden, Germany, and Czech Republic. Alignment and mapping of reads was performed with Burrows-Wheeler Aligner. Variant calling and annotation was performed using GATKv2.2 in combination with GenomeComb software. Results: We identified 4 novel frameshift mutations (p.Y350fs, p.P656fs, p.P751fs and p.D1102fs) and 2 novel nonsense mutations (p.R416stop and p.R1442stop) in patients only, three of whom had a positive family history of disease. The gene further harbored many missense variants, of which 36 were identified in patients only, including the mutation p.G511R, which was previously found to segregate with disease in an autosomal dominant French EOAD pedigree. We found the mutation in an Italian patient (onset age 55 years) with no evidence of a positive family history. Gene burden association analysis indicated an increased frequency of rare variants in patients (OR 1.19 (95%CI 1.04-1.37), p-value 0.01). Conclusions: In this European study on EOAD we found evidence of association of rare variants in SORL1 with AD. The presence of predicted null mutations is in line with evidence from in vitro studies suggesting a loss of function of SORL1 in APP trafficking.
in eight genes initially detected in genome-wide association studies (GWASs) of late onset Alzheimer’s disease (LOAD). Methods: We conducted targeted sequencing of ABCA7, BIN1, CD2AP, CLU, CR1, EPHA1, MS4A4A/MS4A6A and PICALMin three independent LOAD cohorts: 176 patients from 124 Caribbean Hispanics families, 120 patients and 33 unaffected individuals from the 129 NIA-LOAD Family Study; and 263 unrelated Canadian individuals of European ancestry (210 sporadic patients and 53 controls). The variants were called using the BWA-GATK pipeline. Rare coding mutations found in at least two datasets were genotyped in independent controls similar in age and sex distributions and ancestry to the cases in all datasets to estimate population-based frequencies. Results: We detected a statistically significant 3.71-fold enrichment of the non-synonymous mutations in both cohorts of Caucasian LOAD cases compared with controls (p¼0.001) but the mutation rate of non-coding mutations was same in cases and controls. In total, we detected 88 rare damaging mutations, 12 of which were found in at least two datasets: four mutations in ABCA7, two each in CD2AP and PICALM, and one each in BIN1, EPHA1, CLU and MS4A6A. Three of these mutations were observed in all datasets: rs138047593 (BIN1 p.K358R), rs202178565 (EPHA1 p.P460L), and rs138650483 (MS4A6A p.V218M).. The variant in EPHA1 segregated completely in an extended Caribbean Hispanic family and was observed in only one of 300 controls of similar ancestry. Additionally, p.K358R in BIN1segregated in two of the six families where the mutations were discovered. Conclusions: Targeted sequencing of well-confirmed GWAS loci revealed an excess burden of deleterious coding mutations in LOAD with the greatest burden observed in ABCA7 and BIN1. The rarity of these mutations does not fully explain all the associations observed in GWAS, but do represent independent contributions to LOAD pathogenesis. Identifying coding sequence variants in LOAD will facilitate the creation of tractable models for investigation of disease related mechanisms and potential therapies.
O3-13-06
TARGETED RE-SEQUENCING OF SORL1 IN EARLY-ONSET ALZHEIMER’S DEMENTIA: THE EUROPEAN EARLY ONSET DEMENTIA CONSORTIUM
Kristel Sleegers1,2, Jan Verheijen1,2, Julie van der Zee1,2, Karolien Bettens1,2, Sebastiaan Engelborghs3,4, Mathieu Vandenbulcke5, Raquel Sanchez-Valle6, Luisa Benussi7, Alexandre de Mendonc¸a8, Pau Pastor9,10,11, Caroline Graff12,13, Barbara Borroni14, Rik Vandenberghe5, Peter P. De Deyn4,15, Christine Van Broeckhoven1,2 BELNEU Consortium, EU EOD Consortium, 1Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp,
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Belgium; 2Neurodegenerative Brain Diseases Group, Department of Molecular Genetics, VIB, Antwerp, Belgium; 3Institute Born-Bunge, University of Antwerp, Antwerp, Belgium; 4Hospital Network Antwerp (ZNA), Antwerp, Belgium; 5KU Leuven, Leuven, Belgium; 6Alzheimer’s Disease and Other Cognitive Disorders Unit, Neurology Department, Hospital Clınic, IDIBAPS, Barcelona, Spain; 7Molecular Markers Laboratory - IRCCS Istituto Centro San Giovanni di Dio-Fatebenefratelli, Brescia, Italy; 8University of Lisbon, Lisbon, Portugal; 9Neurogenetics Laboratory, Division of Neurosciences, Center for Applied Medical Research, Universidad de Navarra, Pamplona, Spain; 10Department of Neurology, Hospital Universitari Mutua de Terrassa, Terrassa, Barcelona, Spain; 11Centro de Investigacion Biomedica en Red de Enfermedades Neurodegenerativas, CIBERNED, Instituto de Salud Carlos III, Madrid, Spain; 12Karolinska Institutet, Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Neurogeriatrics, Huddinge, Sweden; 13Department of Geriatric Medicine, Genetics Unit, Karolinska University Hospital, Stockholm, Sweden; 14Neurology Unit, University of Brescia, Brescia, Italy; 15University of Antwerp, Antwerp, Belgium. Contact e-mail: [email protected] Background: The sortilin-related receptor 1 (SORL1) gene has been implicated in increased susceptibility to Alzheimer’s disease (AD), but also in autosomal dominant early-onset AD (EOAD). At least one missense mutation has been reported to segregate with EOAD. Here we report a large-scale investigation of the contribution of genetic variability in SORL1 to EOAD in a European EOAD cohort. Methods: We performed massive parallel amplicon-based re-sequencing of the full coding region of SORL1 on an Illumina MiSeq sequencer in 1004 EOAD patients and 1649 age- and origin-matched control individuals through the European Early-Onset Dementia (EU EOD) consortium, originating from Belgium, Spain, Portugal, Italy, Sweden, Germany, and Czech Republic. Alignment and mapping of reads was performed with Burrows-Wheeler Aligner. Variant calling and annotation was performed using GATKv2.2 in combination with GenomeComb software. Results: We identified 4 novel frameshift mutations (p.Y350fs, p.P656fs, p.P751fs and p.D1102fs) and 2 novel nonsense mutations (p.R416stop and p.R1442stop) in patients only, three of whom had a positive family history of disease. The gene further harbored many missense variants, of which 36 were identified in patients only, including the mutation p.G511R, which was previously found to segregate with disease in an autosomal dominant French EOAD pedigree. We found the mutation in an Italian patient (onset age 55 years) with no evidence of a positive family history. Gene burden association analysis indicated an increased frequency of rare variants in patients (OR 1.19 (95%CI 1.04-1.37), p-value 0.01). Conclusions: In this European study on EOAD we found evidence of association of rare variants in SORL1 with AD. The presence of predicted null mutations is in line with evidence from in vitro studies suggesting a loss of function of SORL1 in APP trafficking.