- Email: [email protected]
Protective variant for rate of hippocampal volume loss identified by whole exome sequencing in APOE-ε3ε3 males with MCI
Oral Sessions: O3-01: Basic Science: Genetics I—Role of Rare Variation in Risk for Alzheimer’s Disease
States; 2Boston University, Boston, Massachusetts, United States; 3 Columbia University, Boston, Massachusetts, United States; 4Boston University School of Public Health, Boston, Massachusetts, United States; 5 Johns Hopkins University, Baltimore, Maryland, United States. Contact e-mail: [email protected] Background: Much less is known about the genetic basis of Alzheimer’s disease (AD) in African-Americans (AAs) than in white non-Hispanics (WNH). Methods: To identify potentially functional AD-related genetic variants in AAs, we sequenced and analyzed the exomes of seven AA participants with AD from the Multi-Institutional Research on Alzheimer Genetic Epidemiology (MIRAGE) Study. The 88,867 identified single nucleotide polymorphisms (SNPs) were filtered based on novelty, sequencing quality, potential for functionality, gene-network analysis findings, and previous association with AD. The 63 SNPs passing these filters were genotyped in 435 AA cases and 422 AA controls from the MIRAGE and Genetic and Environmental Risk Factors for Alzheimer’s Disease Among African-Americans (GenerAAtions) Studies. Results: Among the 44 successfully genotyped SNPs, nominally significant association was observed with one variant each in TACR2, PMCA4, and with two AKAP9 SNPs (rs144662445 and rs149979685; See table). The AKAP9 SNPs are missense mutations which have not been observed in WNHs and are < 1% frequent in AAs. The frequency of APOE-ε4 was significantly lower in the 11 AKAP9 variant-harboring cases (18%) than in the 425 cases without either variant (41%; p¼0.0080) suggesting that at least one of these variants may be sufficient to cause disease. These SNPs usually co-occur on the same infrequent (5%) haplotype (as defined by common GWAS-generated SNPS). This haplotype, which we dub HAP0, is significantly associated with risk of AD (p¼0.038, OR¼1.6). An examination of HAP0 in the 1000 Genomes database indicates that there are 69 uncommon (< 10%) SNPs which differentiate HAP0 with both rs144662445 and rs149979685 variants from HAP0 with neither AD-associated variant. Of these, rs144662445 and rs149979685 are the only non-synonymous SNPs. Rs144662445 is located 5 amino acids away from the RII binding site of the long AKAP9 isoform (AKAP450). Bioinformatic analysis indicated that rs149979685 is likely damaging and located in a highly conserved domain which anchors AKAP450 to the centrosome. Conclusions: This study indicates a potential new mechanism for AD and demonstrates that whole exome sequencing a small number of individuals from populations with unique ancestry can lead to discovery of rare variants that influence risk of a common disease.
Gene a
AKAP9 TACR2b AKAP9a ATP2B4
Position
SNP ID
Freq Cases
Freq Controls
OR
Pc
7:91709085 10:71167027 7:91732110 1:203672867
rs144662445 rs142415572 rs149979685 rs145963279
0.012 0.076 0.008 0.024
0.002 0.045 0.001 0.012
5.4 1.8 6.8 2.1
0.013 0.025 0.038 0.042
States; 4University of Washington, Seattle, Washington, United States; Genentech, Inc., South San Francisco, California, United States; 6 Columbia University, New York, New York, United States; 7Vanderbilt University, Nashville, Tennessee, United States; 8Boston University, Boston, Massachusetts, United States; 9University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States. Contact e-mail: [email protected] 5
Background: Alzheimer’s disease (AD) is a neurodegenerative disease with a common late-onset (LOAD) subtype and a less frequent early-onset (EOAD) subtype, defined by onset before age 65 and accounting for only 5-10% of AD cases. While approximately half of EOAD cases are familial forms of AD driven by highly-penetrant monogenic mutations, the rest of EOAD cases are phenotypically similar to LOAD cases, though few genetic contributors are known. We performed exome-wide association analyses in 16,525 subjects in the Alzheimer’s Disease Genetics Consortium in order to identify coding variants associated with EOAD risk. Methods: We examined genotype data from the Illumina HumanExome Array on 220,724 exonic SNPs from 1,349 EOAD cases with no known monogenic mutations and no documented family history and 5,748 cognitive controls age 65 years and older, as well as 6,872 LOAD cases used for additional comparisons, after thorough sample and genotyping quality control. We performed gene-based association testing using SKAT-O (Lee et al. 2012) with covariate adjustment for population substructure. Among genes with statistically significant associations with two or more variants tested by SKAT-O, we also examined the associations of individual variants to determine whether gene associations observed were driven by one or multiple variants within the gene. Results: Gene-based analyses identified a strong aggregate association of multiple APOE variants (minor allele frequencies (MAFs)¼0.0002-0.21) with LOAD risk (P ¼1.02310 -30), likely due to strong correlation of individual variants with APOE-ε2 and APOE-ε4 alleles. Among 17,818 genes examined, only one other gene-based association exceeded the Bonferroni-adjusted statistical significance threshold (a ¼ 2.81310 -6), ZNRF4 (P¼2.74310 -6) at 5.45 megabases (Mb) on chromosome 19. Two variants, rs145022317 (MAF¼0.001) and rs200586901 (MAF¼0.0002), were both individually nominally associated (P ¼1.1310 -4 and P ¼0.024, respectively). Two other genes demonstrated marginally significant associations of P<10 -5, LATS2 (chromosome 13, 21.5Mb; P ¼5.24310 -6) and ST8SIA2 (chromosome 15, 92.9Mb P ¼6.46310 -6). Conclusions: Preliminary gene-based analyses among non-familial EOAD cases identified aggregated effects of rare variants in the APOE region, as well as aggregated effects in three other genes (ZNRF4, LATS2, and ST8SIA2) with borderline or marginally statistically significant associations. Replication analyses in other datasets are necessary to confirm the association of rare variants in these genes with non-familial EOAD.
O3-01-03 a
Genotypes for AKAP9 SNPs confirmed via Sanger sequencing. b The nominally significant association with TACR2 was obtained with a control sample which excluded controls related to AD probands from the MIRAGE study. c One-sided Fisher’s exact test of association.
O3-01-02
EXOME ARRAY ANALYSIS IDENTIFIES NOVEL RISK VARIANTS FOR NON-FAMILIAL EARLY-ONSET ALZHEIMER’S DISEASE
Adam Naj1, Carlos Cruchaga2, Brian Kunkle3, Shubhabrata Mukherjee4, Robert Graham5, Timothy Behrens5, Richard Mayeux6, Jonathan Haines7, Lindsay Farrer8, Margaret Pericak-Vance3, Gerard Schellenberg1, LiSan Wang1, The Alzheimer’s Disease Genetics Consortium9, 1University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States; 2Washington University School of Medicine, Saint Louis, Missouri, United States; 3University of Miami, Miami, Florida, United
P517
PROTECTIVE VARIANT FOR RATE OF HIPPOCAMPAL VOLUME LOSS IDENTIFIED BY WHOLE EXOME SEQUENCING IN APOE-ε3ε3 MALES WITH MCI
Kwangsik Nho1, Jason Corneveaux2, Sungeun Kim1, Hai Lin1, Shannon Risacher1, Li Shen1, Shanker Swaminathan1, Vijay Ramanan1, Yunlong Liu1, Tatiana Foroud1, Mark Inlow3, Rebecca Reiman2, Paul Aisen4, Ronald Petersen5, Robert Green6, Clifford Jack5, Michael Weiner6, Clinton Baldwin7, Lindsay Farrer8, Simon Lovestone9, Andrew Simmons9, Patrizia Mecocci10, Bruno Vellas11, Magda Tsolaki12, Iwona Kloszewska13, Hilkka Soininen14, Brenna McDonald1, Martin Farlow1, Matthew Huentelman2, Andrew Saykin1, 1Indiana University School of Medicine, Indianapolis, Indiana, United States; 2 TGen, Phoenix, Arizona, United States; 3Rose-Hulman Institute of Technology, Indianapolis, Indiana, United States; 4University of California, San Diego, La Jolla, California, United States; 5Mayo Clinic Rochester, Rochester, Minnesota, United States; 6Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States; 6Center for
P518
Oral Sessions: O3-01: Basic Science: Genetics I—Role of Rare Variation in Risk for Alzheimer’s Disease
Imaging of Neurodegenerative Diseases; VA Medical Center and UCSF, San Francisco, California, United States; 7Boston University School of Medicine, Boston, Massachusetts, United States; 8Boston University, Boston, Massachusetts, United States; 9King’s College London, London,, United Kingdom; 10University of Perugia, Italy, Perugia, Italy; 11Clinic of Internal Medicine and Gerontology, Toulouse, France; 12Aristotle University of Thessaloniki, Thessaloniki, Greece; 13Medical University of Lodz, Lodz, Poland; 14Kuopio University and University Hospital, Kuopio, Finland. Contact e-mail: [email protected] Background: Identifying genetic variants other than APOE ε4 associated with rate of hippocampal volume loss, a key AD endophenotype, has been an important goal. Combining whole exome sequencing (WES) and imaging genetics we recently identified two functional single nucleotide variants (SNVs) in participants with APOE-ε3/ε3 genotypes (Nho 2013). Minor alleles were associated with more rapid hippocampal volume loss. In further analyses of the same WES data, we identified protective functional SNVs. Methods: WES with an extreme trait design was used to compare matched unrelated APOE-ε3 homozygous male Caucasian participants with mild cognitive impairment (MCI) from ADNI selected on the basis of extremes of the 2-year longitudinal change distribution of hippocampal volume (8 subjects with rapid rates of atrophy and 8 with slow/stable rates of atrophy). To validate and extend the exome findings in a larger sample, we conducted quantitative trait analysis including whole-brain search and meta-analysis across 5 independent cohorts (ADNI-1/2, AddNeuroMed, MIRAGE, and Indiana Memory and Aging Study). Results: We identified 56 non-synonymous SNVs that were found exclusively in at least 4 of 8 subjects in the slow atrophy group, but not in any of the 8 subjects in the rapid atrophy group. Among these SNVs, the variant that accounted for the greatest group difference and was predicted in silico as a "functional" missense variant was rs3796529 (REST; RE1-Silencing Transcription factor, Chr.
Table 1 Association results (p values) of quantitative trait analysis using a dominant model in the remaining ADNI-1. (APC: Annual percentage of change)
Right Hippocampus Volume APC Slope Left Hippocampus Volume APC Slope Mean Hippocampus Volume APC Slope
Figure 2. Plots of meta-analysis results for rs3796529 using 5 independent cohorts: The initial phase of ADNI (ADNI-1), its subsequent phases (ADNIGO and ADNI-2), the AddNeuroMed Consortium, Multi-Institutional Research on Alzheimer Genetic Epidemiology (MIRAGE) Study, Indiana Memory and Aging Study (IMAS).
APOE ε3/ε3 MCI (N ¼ 135)
0.0182 0.8964 0.6568
0.0451 0.8268 0.7524
0.0850 0.7013 0.1010
0.0751 0.5046 0.4515
0.0307 0.8725 0.2838
0.0470 0.6047 0.9110
4q12). Quantitative trait analysis including whole-brain search in the remaining ADNI APOE-ε3/ε3 group (N¼315) showed that genetic variation within REST was significantly associated with hippocampal volume at baseline (Table 1, and Fig. 1,). Meta-analysis across 5 independent cross-sectional cohorts indicated that rs3796529 is significantly associated with hippocampal volume in APOE-ε3/ε3 individuals (N¼923) (Fig. 2). The minor allele of rs3796529 confers a protective effect on hippocampal volume loss. Conclusions: REST, also known as neuron-restrictive silencer factor, is a master negative transcriptional regulator of adult hippocampal neurogenesis (Gao 2011) that recruits chromatin-modifying enzymes indicating a potential epigenetic role. These findings warrant further investigation and illustrate the potential of next generation sequencing combined with quantitative imaging phenotypes for discovery of disease mechanisms and novel therapeutic targets. O3-01-04
Figure 1. Association of WES-identified variant (rs3796529) with brain structure using surface- based analysis. rs3796529 demonstrated a positive effect on cortical thickness at baseline. Statistical maps computed using SurfStat were thresholded using random field theory (RFT) at P-corrected < 0.05. Left figure is left hemisphere.
All APOE ε3/ε3 (N ¼ 315)
THE IDENTIFICATION OF RARE VARIANTS IN LATE-ONSET ALZHEIMER’S DISEASE USING EXTENDED FAMILIES
Martin Kohli1, Brian Kunkle1, Adam Naj2, Regina M. Carney1, Kara Hamilton-Nelson1, Sophie Rolati1, Patrice L. Whitehead1, John Gilbert3, Eden Martin3, Gary Beecham1, Li-San Wang2, Richard Mayeux4, Jonathan Haines5, Lindsay Farrer6, Gerard Schellenberg7, Stephan Zuchner3, Margaret Pericak-Vance5 the Alzheimer’s Disease Genetics Consortium2, 1Hussman Institute for Human Genomics, University of Miami, Miami, Florida, United States; 2University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States; 3University of Miami, Miami, Florida, United States; 4 Columbia University, New York, New York, United States; 5Vanderbilt University, Nashville, Tennessee, United States; 6Boston University, Boston, Massachusetts, United States; 7University of Pennsylvania, Philadelphia, Pennsylvania, Massachusetts, United States. Contact e-mail: mkohli@med. miami.edu Background: Alzheimer’s disease (AD) is genetically complex and highly heritable (h 2 estimates up to 79%). Mutations in APP, PSEN1 and 2, and MAPT lead to rare, autosomal-dominant, early-onset forms of AD. The ε4 allele of APOE is a common genetic variant that confers considerable risk to late-onset AD (LOAD). Genome-wide association studies have identified numerous other loci of modest effect. Recently, a rare variant in TREM2 presented with an effect size similar to APOE-ε4. Thus, rare variants, each with stronger individual effects than common variants, likely account for some of the remaining unexplained heritability of LOAD. Methods: We analyzed a subset of 6 pedigrees characterized by an autosomal-dominant pattern of inheritance from our collection of >60 extended multi-generational LOAD families. Whole-exome sequencing (WES) was performed on 4-9 affected individuals per pedigree comprising 2-6 cousin or avuncular pairs. We selected potentially deleterious variants with population minor allele frequencies (MAF) <1% that segregated with LOAD.
States; 2Boston University, Boston, Massachusetts, United States; 3 Columbia University, Boston, Massachusetts, United States; 4Boston University School of Public Health, Boston, Massachusetts, United States; 5 Johns Hopkins University, Baltimore, Maryland, United States. Contact e-mail: [email protected] Background: Much less is known about the genetic basis of Alzheimer’s disease (AD) in African-Americans (AAs) than in white non-Hispanics (WNH). Methods: To identify potentially functional AD-related genetic variants in AAs, we sequenced and analyzed the exomes of seven AA participants with AD from the Multi-Institutional Research on Alzheimer Genetic Epidemiology (MIRAGE) Study. The 88,867 identified single nucleotide polymorphisms (SNPs) were filtered based on novelty, sequencing quality, potential for functionality, gene-network analysis findings, and previous association with AD. The 63 SNPs passing these filters were genotyped in 435 AA cases and 422 AA controls from the MIRAGE and Genetic and Environmental Risk Factors for Alzheimer’s Disease Among African-Americans (GenerAAtions) Studies. Results: Among the 44 successfully genotyped SNPs, nominally significant association was observed with one variant each in TACR2, PMCA4, and with two AKAP9 SNPs (rs144662445 and rs149979685; See table). The AKAP9 SNPs are missense mutations which have not been observed in WNHs and are < 1% frequent in AAs. The frequency of APOE-ε4 was significantly lower in the 11 AKAP9 variant-harboring cases (18%) than in the 425 cases without either variant (41%; p¼0.0080) suggesting that at least one of these variants may be sufficient to cause disease. These SNPs usually co-occur on the same infrequent (5%) haplotype (as defined by common GWAS-generated SNPS). This haplotype, which we dub HAP0, is significantly associated with risk of AD (p¼0.038, OR¼1.6). An examination of HAP0 in the 1000 Genomes database indicates that there are 69 uncommon (< 10%) SNPs which differentiate HAP0 with both rs144662445 and rs149979685 variants from HAP0 with neither AD-associated variant. Of these, rs144662445 and rs149979685 are the only non-synonymous SNPs. Rs144662445 is located 5 amino acids away from the RII binding site of the long AKAP9 isoform (AKAP450). Bioinformatic analysis indicated that rs149979685 is likely damaging and located in a highly conserved domain which anchors AKAP450 to the centrosome. Conclusions: This study indicates a potential new mechanism for AD and demonstrates that whole exome sequencing a small number of individuals from populations with unique ancestry can lead to discovery of rare variants that influence risk of a common disease.
Gene a
AKAP9 TACR2b AKAP9a ATP2B4
Position
SNP ID
Freq Cases
Freq Controls
OR
Pc
7:91709085 10:71167027 7:91732110 1:203672867
rs144662445 rs142415572 rs149979685 rs145963279
0.012 0.076 0.008 0.024
0.002 0.045 0.001 0.012
5.4 1.8 6.8 2.1
0.013 0.025 0.038 0.042
States; 4University of Washington, Seattle, Washington, United States; Genentech, Inc., South San Francisco, California, United States; 6 Columbia University, New York, New York, United States; 7Vanderbilt University, Nashville, Tennessee, United States; 8Boston University, Boston, Massachusetts, United States; 9University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States. Contact e-mail: [email protected] 5
Background: Alzheimer’s disease (AD) is a neurodegenerative disease with a common late-onset (LOAD) subtype and a less frequent early-onset (EOAD) subtype, defined by onset before age 65 and accounting for only 5-10% of AD cases. While approximately half of EOAD cases are familial forms of AD driven by highly-penetrant monogenic mutations, the rest of EOAD cases are phenotypically similar to LOAD cases, though few genetic contributors are known. We performed exome-wide association analyses in 16,525 subjects in the Alzheimer’s Disease Genetics Consortium in order to identify coding variants associated with EOAD risk. Methods: We examined genotype data from the Illumina HumanExome Array on 220,724 exonic SNPs from 1,349 EOAD cases with no known monogenic mutations and no documented family history and 5,748 cognitive controls age 65 years and older, as well as 6,872 LOAD cases used for additional comparisons, after thorough sample and genotyping quality control. We performed gene-based association testing using SKAT-O (Lee et al. 2012) with covariate adjustment for population substructure. Among genes with statistically significant associations with two or more variants tested by SKAT-O, we also examined the associations of individual variants to determine whether gene associations observed were driven by one or multiple variants within the gene. Results: Gene-based analyses identified a strong aggregate association of multiple APOE variants (minor allele frequencies (MAFs)¼0.0002-0.21) with LOAD risk (P ¼1.02310 -30), likely due to strong correlation of individual variants with APOE-ε2 and APOE-ε4 alleles. Among 17,818 genes examined, only one other gene-based association exceeded the Bonferroni-adjusted statistical significance threshold (a ¼ 2.81310 -6), ZNRF4 (P¼2.74310 -6) at 5.45 megabases (Mb) on chromosome 19. Two variants, rs145022317 (MAF¼0.001) and rs200586901 (MAF¼0.0002), were both individually nominally associated (P ¼1.1310 -4 and P ¼0.024, respectively). Two other genes demonstrated marginally significant associations of P<10 -5, LATS2 (chromosome 13, 21.5Mb; P ¼5.24310 -6) and ST8SIA2 (chromosome 15, 92.9Mb P ¼6.46310 -6). Conclusions: Preliminary gene-based analyses among non-familial EOAD cases identified aggregated effects of rare variants in the APOE region, as well as aggregated effects in three other genes (ZNRF4, LATS2, and ST8SIA2) with borderline or marginally statistically significant associations. Replication analyses in other datasets are necessary to confirm the association of rare variants in these genes with non-familial EOAD.
O3-01-03 a
Genotypes for AKAP9 SNPs confirmed via Sanger sequencing. b The nominally significant association with TACR2 was obtained with a control sample which excluded controls related to AD probands from the MIRAGE study. c One-sided Fisher’s exact test of association.
O3-01-02
EXOME ARRAY ANALYSIS IDENTIFIES NOVEL RISK VARIANTS FOR NON-FAMILIAL EARLY-ONSET ALZHEIMER’S DISEASE
Adam Naj1, Carlos Cruchaga2, Brian Kunkle3, Shubhabrata Mukherjee4, Robert Graham5, Timothy Behrens5, Richard Mayeux6, Jonathan Haines7, Lindsay Farrer8, Margaret Pericak-Vance3, Gerard Schellenberg1, LiSan Wang1, The Alzheimer’s Disease Genetics Consortium9, 1University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States; 2Washington University School of Medicine, Saint Louis, Missouri, United States; 3University of Miami, Miami, Florida, United
P517
PROTECTIVE VARIANT FOR RATE OF HIPPOCAMPAL VOLUME LOSS IDENTIFIED BY WHOLE EXOME SEQUENCING IN APOE-ε3ε3 MALES WITH MCI
Kwangsik Nho1, Jason Corneveaux2, Sungeun Kim1, Hai Lin1, Shannon Risacher1, Li Shen1, Shanker Swaminathan1, Vijay Ramanan1, Yunlong Liu1, Tatiana Foroud1, Mark Inlow3, Rebecca Reiman2, Paul Aisen4, Ronald Petersen5, Robert Green6, Clifford Jack5, Michael Weiner6, Clinton Baldwin7, Lindsay Farrer8, Simon Lovestone9, Andrew Simmons9, Patrizia Mecocci10, Bruno Vellas11, Magda Tsolaki12, Iwona Kloszewska13, Hilkka Soininen14, Brenna McDonald1, Martin Farlow1, Matthew Huentelman2, Andrew Saykin1, 1Indiana University School of Medicine, Indianapolis, Indiana, United States; 2 TGen, Phoenix, Arizona, United States; 3Rose-Hulman Institute of Technology, Indianapolis, Indiana, United States; 4University of California, San Diego, La Jolla, California, United States; 5Mayo Clinic Rochester, Rochester, Minnesota, United States; 6Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States; 6Center for
P518
Oral Sessions: O3-01: Basic Science: Genetics I—Role of Rare Variation in Risk for Alzheimer’s Disease
Imaging of Neurodegenerative Diseases; VA Medical Center and UCSF, San Francisco, California, United States; 7Boston University School of Medicine, Boston, Massachusetts, United States; 8Boston University, Boston, Massachusetts, United States; 9King’s College London, London,, United Kingdom; 10University of Perugia, Italy, Perugia, Italy; 11Clinic of Internal Medicine and Gerontology, Toulouse, France; 12Aristotle University of Thessaloniki, Thessaloniki, Greece; 13Medical University of Lodz, Lodz, Poland; 14Kuopio University and University Hospital, Kuopio, Finland. Contact e-mail: [email protected] Background: Identifying genetic variants other than APOE ε4 associated with rate of hippocampal volume loss, a key AD endophenotype, has been an important goal. Combining whole exome sequencing (WES) and imaging genetics we recently identified two functional single nucleotide variants (SNVs) in participants with APOE-ε3/ε3 genotypes (Nho 2013). Minor alleles were associated with more rapid hippocampal volume loss. In further analyses of the same WES data, we identified protective functional SNVs. Methods: WES with an extreme trait design was used to compare matched unrelated APOE-ε3 homozygous male Caucasian participants with mild cognitive impairment (MCI) from ADNI selected on the basis of extremes of the 2-year longitudinal change distribution of hippocampal volume (8 subjects with rapid rates of atrophy and 8 with slow/stable rates of atrophy). To validate and extend the exome findings in a larger sample, we conducted quantitative trait analysis including whole-brain search and meta-analysis across 5 independent cohorts (ADNI-1/2, AddNeuroMed, MIRAGE, and Indiana Memory and Aging Study). Results: We identified 56 non-synonymous SNVs that were found exclusively in at least 4 of 8 subjects in the slow atrophy group, but not in any of the 8 subjects in the rapid atrophy group. Among these SNVs, the variant that accounted for the greatest group difference and was predicted in silico as a "functional" missense variant was rs3796529 (REST; RE1-Silencing Transcription factor, Chr.
Table 1 Association results (p values) of quantitative trait analysis using a dominant model in the remaining ADNI-1. (APC: Annual percentage of change)
Right Hippocampus Volume APC Slope Left Hippocampus Volume APC Slope Mean Hippocampus Volume APC Slope
Figure 2. Plots of meta-analysis results for rs3796529 using 5 independent cohorts: The initial phase of ADNI (ADNI-1), its subsequent phases (ADNIGO and ADNI-2), the AddNeuroMed Consortium, Multi-Institutional Research on Alzheimer Genetic Epidemiology (MIRAGE) Study, Indiana Memory and Aging Study (IMAS).
APOE ε3/ε3 MCI (N ¼ 135)
0.0182 0.8964 0.6568
0.0451 0.8268 0.7524
0.0850 0.7013 0.1010
0.0751 0.5046 0.4515
0.0307 0.8725 0.2838
0.0470 0.6047 0.9110
4q12). Quantitative trait analysis including whole-brain search in the remaining ADNI APOE-ε3/ε3 group (N¼315) showed that genetic variation within REST was significantly associated with hippocampal volume at baseline (Table 1, and Fig. 1,). Meta-analysis across 5 independent cross-sectional cohorts indicated that rs3796529 is significantly associated with hippocampal volume in APOE-ε3/ε3 individuals (N¼923) (Fig. 2). The minor allele of rs3796529 confers a protective effect on hippocampal volume loss. Conclusions: REST, also known as neuron-restrictive silencer factor, is a master negative transcriptional regulator of adult hippocampal neurogenesis (Gao 2011) that recruits chromatin-modifying enzymes indicating a potential epigenetic role. These findings warrant further investigation and illustrate the potential of next generation sequencing combined with quantitative imaging phenotypes for discovery of disease mechanisms and novel therapeutic targets. O3-01-04
Figure 1. Association of WES-identified variant (rs3796529) with brain structure using surface- based analysis. rs3796529 demonstrated a positive effect on cortical thickness at baseline. Statistical maps computed using SurfStat were thresholded using random field theory (RFT) at P-corrected < 0.05. Left figure is left hemisphere.
All APOE ε3/ε3 (N ¼ 315)
THE IDENTIFICATION OF RARE VARIANTS IN LATE-ONSET ALZHEIMER’S DISEASE USING EXTENDED FAMILIES
Martin Kohli1, Brian Kunkle1, Adam Naj2, Regina M. Carney1, Kara Hamilton-Nelson1, Sophie Rolati1, Patrice L. Whitehead1, John Gilbert3, Eden Martin3, Gary Beecham1, Li-San Wang2, Richard Mayeux4, Jonathan Haines5, Lindsay Farrer6, Gerard Schellenberg7, Stephan Zuchner3, Margaret Pericak-Vance5 the Alzheimer’s Disease Genetics Consortium2, 1Hussman Institute for Human Genomics, University of Miami, Miami, Florida, United States; 2University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States; 3University of Miami, Miami, Florida, United States; 4 Columbia University, New York, New York, United States; 5Vanderbilt University, Nashville, Tennessee, United States; 6Boston University, Boston, Massachusetts, United States; 7University of Pennsylvania, Philadelphia, Pennsylvania, Massachusetts, United States. Contact e-mail: mkohli@med. miami.edu Background: Alzheimer’s disease (AD) is genetically complex and highly heritable (h 2 estimates up to 79%). Mutations in APP, PSEN1 and 2, and MAPT lead to rare, autosomal-dominant, early-onset forms of AD. The ε4 allele of APOE is a common genetic variant that confers considerable risk to late-onset AD (LOAD). Genome-wide association studies have identified numerous other loci of modest effect. Recently, a rare variant in TREM2 presented with an effect size similar to APOE-ε4. Thus, rare variants, each with stronger individual effects than common variants, likely account for some of the remaining unexplained heritability of LOAD. Methods: We analyzed a subset of 6 pedigrees characterized by an autosomal-dominant pattern of inheritance from our collection of >60 extended multi-generational LOAD families. Whole-exome sequencing (WES) was performed on 4-9 affected individuals per pedigree comprising 2-6 cousin or avuncular pairs. We selected potentially deleterious variants with population minor allele frequencies (MAF) <1% that segregated with LOAD.