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Genetic similarity matrices are commonly used to assess population substructure (PS) in genetic studies. Through simulation studies and by the application to whole-genome sequencing (WGS) data, we evaluate the performance of three genetic similarity matrices: the unweighted and weighted Jaccard similarity matrices and the genetic relationship matrix. We describe different scenarios that can create numerical pitfalls and lead to incorrect conclusions in some instances. We consider scenarios in which PS is assessed based on loci that are located across the genome (‘globally’) and based on loci from a specific genomic region (‘locally’). We also compare scenarios in which PS is evaluated based on loci from different minor allele frequency bins: common (>5%), low-frequency (5–0.5%) and rare (

INTRODUCTIONGenome-wide association studies have led to numerous genetic loci associated with Alzheimer’s disease (AD). Whole-genome sequencing (WGS) now permit genome-wide analyses to identify rare variants contributing to AD risk.METHODSWe performed single-variant and spatial clustering-based testing on rare variants (minor allele frequency ≤1%) in a family-based WGS-based association study of 2,247 subjects from 605 multiplex AD families, followed by replication in 1,669 unrelated individuals.RESULTSWe identified 13 new AD candidate loci that yielded consistent rare-variant signals in discovery and replication cohorts (4 from single-variant, 9 from spatial-clustering), implicating these genes: FNBP1L, SEL1L, LINC00298, PRKCH, C15ORF41, C2CD3, KIF2A, APC, LHX9, NALCN, CTNNA2, SYTL3, CLSTN2.DISCUSSIONDownstream analyses of these novel loci highlight synaptic function, in contrast to common AD-associated variants, which implicate innate immunity. These loci have not been previously associated with AD, emphasizing the ability of WGS to identify AD-associated rare variants, particularly outside of coding regions.

With the advent of whole genome-sequencing (WGS) studies, family-based designs enable sex-specific analysis approaches that can be applied to only affected individuals; tests using family-based designs are attractive because they are completely robust against the effects of population substructure. These advantages make family-based association tests (FBATs) that use siblings as well as parents especially suited for the analysis of late-onset diseases such as Alzheimer’s Disease (AD). However, the application of FBATs to assess sex-specific effects can require additional filtering steps, as sensitivity to sequencing errors is amplified in this type of analysis. Here, we illustrate the implementation of robust analysis approaches and additional filtering steps that can minimize the chances of false positive-findings due to sex-specific sequencing errors. We apply this approach to two family-based AD datasets and identify four novel loci (GRID1, RIOK3, MCPH1, ZBTB7C) showing sex-specific association with AD risk. Following stringent quality control filtering, the strongest candidate is ZBTB7C (Pinter = 1.83 × 10−7), in which the minor allele of rs1944572 confers increased risk for AD in females and protection in males. ZBTB7C encodes the Zinc Finger and BTB Domain Containing 7C, a transcriptional repressor of membrane metalloproteases (MMP). Members of this MMP family were implicated in AD neuropathology.

Alzheimer's disease (AD) is a genetically complex disease for which nearly 40 loci have now been identified via genome-wide association studies (GWAS). We attempted to identify groups of rare variants (alternate allele frequency0.01) associated with AD in a region-based, whole-genome sequencing (WGS) association study (rvGWAS) of two independent AD family datasets (NIMH/NIA; 2247 individuals; 605 families). Employing a sliding window approach across the genome, we identified several regions that achieved association p values10

Alzheimer’s disease (AD) is a genetically complex disease for which roughly 30 genes have been identified via genome-wide association studies. We attempted to identify rare variants (minor allele frequency −6, using the burden test or the SKAT statistic. The genomic region around the dystobrevin beta (DTNB) gene was identified with the burden test and replicated in case/control samples from the ADSP study (pmeta = 4.74×10−8). SKAT analysis revealed region-based association around the discs large homolog 2 (DLG2) gene and replicated in case/control samples from the ADSP study (pmeta =1×10−6). Here, in a region-based GSAS of AD we identified two novel AD genes, DLG2 and DTNB, based on association with rare variants.

Polygenic risk scores are a popular means to predict the disease risk or disease susceptibility of an individual based on its genotype information. When adding other important epidemiological covariates such as age or sex, we speak of an integrated risk model. Methodological advances for fitting more accurate integrated risk models are of immediate importance to improve the precision of risk prediction, thereby potentially identifying patients at high risk early on when they are still able to benefit from preventive steps/interventions targeted at increasing their odds of survival, or at reducing their chance of getting a disease in the first place. This article proposes a smoothed version of the “Lassosum” penalty used to fit polygenic risk scores and integrated risk models. The smoothing allows one to obtain explicit gradients everywhere for efficient minimization of the Lassosum objective function while guaranteeing bounds on the accuracy of the fit. An experimental section on both Alzheimer’s disease and COPD (chronic obstructive pulmonary disease) demonstrates the increased accuracy of the proposed smoothed Lassosum penalty compared to the original Lassosum algorithm, allowing it to draw equal with state-of-the-art methodology such as LDpred2 when evaluated via the AUC (area under the ROC curve) metric.

Polygenic risk scores are a popular means to predict the disease risk or disease susceptibility of an individual based on its genotype information. When adding other important epidemiological covariates such as age or sex, we speak of an integrated risk model. Methodological advances for fitting more accurate integrated risk models are of immediate importance to improve the precision of risk prediction, thereby potentially identifying patients at high risk early on when they are still able to benefit from preventive steps/interventions targeted at increasing their odds of survival, or at reducing their chance of getting a disease in the first place. This article proposes a smoothed version of the “Lassosum” penalty used to fit polygenic risk scores and integrated risk models using either summary statistics or raw data. The smoothing allows one to obtain explicit gradients everywhere for efficient minimization of the Lassosum objective function while guaranteeing bounds on the accuracy of the fit. An experimental section on both Alzheimer’s disease and COPD (chronic obstructive pulmonary disease) demonstrates the increased accuracy of the proposed smoothed Lassosum penalty compared to the original Lassosum algorithm (for the datasets under consideration), allowing it to draw equal with state-of-the-art methodology such as LDpred2 when evaluated via the AUC (area under the ROC curve) metric.

Alzheimer's disease (AD) causes unrelenting, progressive cognitive impairments, but its course is heterogeneous, with a broad range of rates of cognitive decline1. The spread of tau aggregates (neurofibrillary tangles) across the cerebral cortex parallels symptom severity2,3. We hypothesized that the kinetics of tau spread may vary if the properties of the propagating tau proteins vary across individuals. We carried out biochemical, biophysical, MS and both cell- and animal-based-bioactivity assays to characterize tau in 32 patients with AD. We found striking patient-to-patient heterogeneity in the hyperphosphorylated species of soluble, oligomeric, seed-competent tau. Tau seeding activity correlates with the aggressiveness of the clinical disease, and some post-translational modification (PTM) sites appear to be associated with both enhanced seeding activity and worse clinical outcomes, whereas others are not. These data suggest that different individuals with 'typical' AD may have distinct biochemical features of tau. These data are consistent with the possibility that individuals with AD, much like people with cancer, may have multiple molecular drivers of an otherwise common phenotype, and emphasize the potential for personalized therapeutic approaches for slowing clinical progression of AD.

Expansion of CAG trinucleotide repeats in the Ataxin-1 gene (ATXN1) causes spinocerebellar ataxia type 1 (SCA1), a neurodegenerative disease that impairs coordinated movement and cognitive functions. ATXN1 is associated with genetic risk for Alzheimer's disease (AD). Here, we show loss of Ataxin-1 potentiates AD pathogenesis. Specifically, knockout of Atxn1 in mice led to increased expression of β-secretase (BACE1) and elevated BACE1-mediated cleavage of the amyloid precursor protein (APP), selectively in AD-vulnerable brain regions. Ataxin-1 depletion exacerbated Aβ plaque deposition and gliosis in AD mice, and impaired hippocampal neurogenesis and axonal targeting. The SCA1-linked CAG repeat number was normal in AD patients. However, in SCA1 mice, aggregation of mutant Ataxin-1 led to BACE1 up-regulation and axon guidance defects in the hippocampal CA2 region. Together, these findings indicate that loss of Ataxin-1 potentiates Aβ pathology, and BACE1 elevation may represent a shared pathogenic mechanism underlying cognitive deficits in SCA1 and AD.

Summary Expansion of CAG trinucleotide repeats in ATXN1 causes spinocerebellar ataxia type 1 (SCA1), a neurodegenerative disease that impairs coordination and cognition. While ATXN1 is associated with increased Alzheimer’s disease (AD) risk, CAG repeat number in AD patients is not changed. Here, we investigated the consequences of ataxin-1 loss of function and discovered that knockout of Atxn1 reduced CIC-ETV4/5-mediated inhibition of Bace1 transcription, leading to increased BACE1 levels and enhanced amyloidogenic cleavage of APP, selectively in AD-vulnerable brain regions. Elevated BACE1 expression exacerbated Aβ deposition and gliosis in AD mouse models and impaired hippocampal neurogenesis and olfactory axonal targeting. In SCA1 mice, polyglutamine-expanded mutant ataxin-1 led to the increase of BACE1 post-transcriptionally, both in cerebrum and cerebellum, and caused axonal-targeting deficit and neurodegeneration in the hippocampal CA2 region. These findings suggest that loss of ataxin-1 elevates BACE1 expression and Aβ pathology, rendering it a potential contributor to AD risk and pathogenesis.

Objectives: Recently, 2 independent studies reported that a rare missense variant, rs75932628 (R47H), in exon 2 of the gene encoding the “triggering receptor expressed on myeloid cells 2” ( TREM2 ) significantly increases the risk of Alzheimer disease (AD) with an effect size comparable to that of the APOE e4 allele. Methods: In this study, we attempted to replicate the association between rs75932628 and AD risk by directly genotyping rs75932628 in 2 independent Caucasian family cohorts consisting of 927 families (with 1,777 affected and 1,235 unaffected) and in 2 Caucasian case-control cohorts composed of 1,314 cases and 1,609 controls. In addition, we imputed genotypes in 3 independent Caucasian case-control cohorts containing 1,906 cases and 1,503 controls. Results: Meta-analysis of the 2 family-based and the 5 case-control cohorts yielded a p value of 0.0029, while the overall summary estimate (using case-control data only) resulted in an odds ratio of 1.67 (95% confidence interval 0.95–2.92) for the association between the TREM2 R47H and increased AD risk. Conclusions: While our results serve to confirm the association between R47H and risk of AD, the observed effect on risk was substantially smaller than that previously reported.

Golgi-localized gamma-ear-containing ADP-ribosylation factor-binding protein (GGA3) is a central regulator of trafficking and degradation of BACE1 (beta-site A beta PP-cleaving enzyme), the rate-limiting enzyme in the production of amyloid-beta (A beta) in Alzheimer's disease (AD). Here, we assessed the potential role of GGA3 in AD pathogenesis using independent neuropathological, case-control, and family-based human sample cohorts. Increased BACE1 levels coincided with decreased GGA3 levels and with elevated phosphorylation status of eIF2 alpha-Ser51 in the temporal cortex of AD patients as compared to age-matched controls. Severity of the disease did not alter mRNA or protein levels of GGA3 in the inferior temporal cortex of AD patients, while a positive correlation between GGA3 and the levels of total, but not phosphorylated, tau was observed. Genetically, we did not observe consistent evidence for association between AD risk and common GGA3 polymorphisms across a number of independent sample cohorts. However, a nominally significant association was observed with rs2242230 (p < 0.05) among the Finnish case-control cohort. Accordingly, mRNA and protein levels of GGA3 in the inferior temporal cortex of AD patients did not significantly correlate with rs2242230 genotype status. While the present study indicates that GGA3 is involved in the cellular processes relevant for AD pathogenesis, the genetic data do not support the idea that common GGA3 polymorphisms would contribute to AD risk.

SummaryThe transmembrane protein CD33 is a sialic acid-binding immunoglobulin-like lectin that regulates innate immunity but has no known functions in the brain. We have previously shown that the CD33 gene is a risk factor for Alzheimer’s disease (AD). Here, we observed increased expression of CD33 in microglial cells in AD brain. The minor allele of the CD33 SNP rs3865444, which confers protection against AD, was associated with reductions in both CD33 expression and insoluble amyloid beta 42 (Aβ42) levels in AD brain. Furthermore, the numbers of CD33-immunoreactive microglia were positively correlated with insoluble Aβ42 levels and plaque burden in AD brain. CD33 inhibited uptake and clearance of Aβ42 in microglial cell cultures. Finally, brain levels of insoluble Aβ42 as well as amyloid plaque burden were markedly reduced in APPSwe/PS1ΔE9/CD33−/− mice. Therefore, CD33 inactivation mitigates Aβ pathology and CD33 inhibition could represent a novel therapy for AD.Video Abstract

Introduction TREM2 is a lipid-sensing activating receptor on microglia known to be important for Alzheimer's disease (AD), but whether it plays a beneficial or detrimental role in disease pathogenesis is controversial. Methods We analyzed AD risk of TREM2 variants in the NIMH AD Genetics Initiative Study and AD Sequencing Project. We compared each variant's risk and functional impact by a reporter assay. Finally, we analyzed expression of TREM2 on human monocytes. Results We provide more evidence for increased AD risk associated with several TREM2 variants, and show that these variants decreased or markedly increased binding to TREM2 ligands. We identify HDL and LDL as novel TREM2 ligands. We also show that TREM2 expression in human monocytes is minimal compared to monocyte-derived dendritic cells. Discussion Our results suggest that TREM2 signaling helps protect against AD but can cause harm in excess, supporting the idea that proper TREM2 function is important to counteract disease progression.

Alzheimer’s disease (AD) is a progressive dementia disorder characterized by synaptic degeneration and amyloid-β (Aβ) accumulation in the brain. Through whole-genome sequencing of 1345 individuals from 410 families with late-onset AD (LOAD), we identified three highly penetrant variants in PRKCA , the gene that encodes protein kinase Cα (PKCα), in five of the families. All three variants linked with LOAD displayed increased catalytic activity relative to wild-type PKCα as assessed in live-cell imaging experiments using a genetically encoded PKC activity reporter. Deleting PRKCA in mice or adding PKC antagonists to mouse hippocampal slices infected with a virus expressing the Aβ precursor CT100 revealed that PKCα was required for the reduced synaptic activity caused by Aβ. In PRKCA −/− neurons expressing CT100, introduction of PKCα, but not PKCα lacking a PDZ interaction moiety, rescued synaptic depression, suggesting that a scaffolding interaction bringing PKCα to the synapse is required for its mediation of the effects of Aβ. Thus, enhanced PKCα activity may contribute to AD, possibly by mediating the actions of Aβ on synapses. In contrast, reduced PKCα activity is implicated in cancer. Hence, these findings reinforce the importance of maintaining a careful balance in the activity of this enzyme.

The genetic basis of Alzheimer's disease (AD) is complex and heterogeneous. Over 200 highly penetrant pathogenic variants in the genes APP, PSEN1, and PSEN2 cause a subset of early-onset familial AD. On the other hand, susceptibility to late-onset forms of AD (LOAD) is indisputably associated to the ɛ4 allele in the gene APOE, and more recently to variants in more than two-dozen additional genes identified in the large-scale genome-wide association studies (GWAS) and meta-analyses reports. Taken together however, although the heritability in AD is estimated to be as high as 80%, a large proportion of the underlying genetic factors still remain to be elucidated. In this study, we performed a systematic family-based genome-wide association and meta-analysis on close to 15 million imputed variants from three large collections of AD families (~3500 subjects from 1070 families). Using a multivariate phenotype combining affection status and onset age, meta-analysis of the association results revealed three single nucleotide polymorphisms (SNPs) that achieved genome-wide significance for association with AD risk: rs7609954 in the gene PTPRG (P-value=3.98 × 10(-8)), rs1347297 in the gene OSBPL6 (P-value=4.53 × 10(-8)), and rs1513625 near PDCL3 (P-value=4.28 × 10(-8)). In addition, rs72953347 in OSBPL6 (P-value=6.36 × 10(-7)) and two SNPs in the gene CDKAL1 showed marginally significant association with LOAD (rs10456232, P-value=4.76 × 10(-7); rs62400067, P-value=3.54 × 10(-7)). In summary, family-based GWAS meta-analysis of imputed SNPs revealed novel genomic variants in (or near) PTPRG, OSBPL6, and PDCL3 that influence risk for AD with genome-wide significance.Molecular Psychiatry advance online publication, 2 February 2016; doi:10.1038/mp.2015.218.

background Recent analyses suggest that the known Alzheimer’s disease genes account for less than half the genetic variance in this disease. The gene encoding ubiquilin 1 ( UBQLN1 ) is one of several candidate genes for Alzheimer’s disease located near a well-established linkage peak on chromosome 9q22. methods We evaluated 19 single-nucleotide polymorphisms in three genes within the chromosome 9q linkage region in 437 multiplex families with Alzheimer’s disease from the National Institute of Mental Health (NIMH) sample (1439 subjects). We then tested the single-nucleotide polymorphisms showing a positive result in an independently identified set of 217 sibships discordant for Alzheimer’s disease (Consortium on Alzheimer’s Genetics [CAG] sample; 489 subjects) and assessed the functional effect of an implicated single-nucleotide polymorphism in brain tissue from 25 patients with Alzheimer’s disease and 17 controls. results In the NIMH sample, we observed a significant association between Alzheimer’s disease and various single-nucleotide polymorphisms in UBQLN1 . We confirmed these associations in the CAG sample. The risk-conferring haplotype in both samples was defined by a single intronic single-nucleotide polymorphism located downstream of exon 8. The risk allele was associated with a dose-dependent increase in an alternatively spliced UBQLN1 (lacking exon 8) transcript in RNA extracted from brain samples of patients with Alzheimer’s disease. conclusions Our findings suggest that genetic variants in UBQLN1 on chromosome 9q22 substantially increase the risk of Alzheimer’s disease, possibly by influencing alternative splicing of this gene in the brain.

Alzheimer’s disease (AD) is a genetically complex and heterogeneous disorder. To date, a large number of candidate genes have been associated with the disease, however none of these findings has been consistently replicated in independent datasets. In this study we report the results of family-based analyses for polymorphisms of five such candidates on chromosomes 2 (interleukin-1b, IL-1B), 3 (butyrylcholinesterase, BCHE), 11 (cathepsin D, CTSD; Fe65, APBB1) and 12 (lipoprotein receptorrelated protein-1, LRP1) that were all suggested to be associated with AD in recent case-control studies. To minimize the possibility of spurious findings due to population admixture, we used a family-based design applying the sibship disequilibrium test (SDT) as well as two-point parametric linkage analyses on families from the National Institute of Mental Health (NIMH) Genetics Initiative. Contrary to the initial reports, none of the polymorphisms that were analyzed showed evidence for association or linkage with AD in our families. Our results suggest that the previously reported associations from case-control studies are either (a) false positive results, e.g. due to type I error or population admixture, (b) smaller than initially proposed, or (c) due to linkage disequilibrium with an as yet unidentified polymorphism nearby. q 2000 Elsevier Science Inc. All rights reserved.

Over 200 rare and fully penetrant pathogenic mutations in amyloid precursor protein (APP), presenilin 1 and 2 (PSEN1 and PSEN2) cause a subset of early-onset familial Alzheimer's disease (EO-FAD). Of these, 21 cases of EO-FAD families carrying unique APP locus duplications remain the only pathogenic copy number variations (CNVs) identified to date in Alzheimer's disease (AD). Using high-density DNA microarrays, we performed a comprehensive genome-wide analysis for the presence of rare CNVs in 261 EO-FAD and early/mixed-onset pedigrees. Our analysis revealed 10 novel private CNVs in 10 EO-FAD families overlapping a set of genes that includes: A2BP1, ABAT, CDH2, CRMP1, DMRT1, EPHA5, EPHA6, ERMP1, EVC, EVC2, FLJ35024 and VLDLR. In addition, CNVs encompassing two known frontotemporal dementia genes, CHMP2B and MAPT were found. To our knowledge, this is the first study reporting rare gene-rich CNVs in EO-FAD and early/mixed-onset AD that are likely to underlie pathogenicity in familial AD and perhaps related dementias.Molecular Psychiatry advance online publication, 11 June 2013; doi:10.1038/mp.2013.77.

P2-154 SIGNIFICANTASSOCIATION OF CODING (MISSENSE) SNPS WITH FAMILIAL LOAD BASED ON A FUNCTIONAL GENOME-WIDE ASSOCIATION SCREEN Tony Parrado, Basavaraj Hooli, Kristina Mullin, Lucille Gotta, Lars Bertram, Christoph Lange, Rudolph Tanzi, Mass. General Hopsital/ Harvard University, Charlestown, Massachusetts, United States; Massachusetts General Hospital, Charlestown, Massachusetts, United States; Max-Planck Institute, Berlin, Germany; Harvard School of Public Health, Boston, Massachusetts, United States.

Two recent case-control studies have suggested a strong association of a missense polymorphism in exon 2 of the cathepsin D gene (CTSD) and Alzheimer disease (AD). However, these findings were not confirmed in another independent study. We analyzed this polymorphism in two large and independent AD study populations and did not detect an association between CTSD and AD. The first sample was family-based and included 436 subjects from 134 sibships discordant for AD that were analyzed using the sibship disequilibrium test (SDT, p = 0.68) and the sib transmission/disequilibrium test (Sib-TDT, p = 0.81). The second sample of 200 AD cases and 182 cognitively normal controls also failed to show significant differences in the allele or genotype distribution in cases versus controls (X2, p = 0.91 and p = 0.88, respectively). In addition, two-point linkage analyses in an enlarged family sample (n = 670) did not show evidence for linkage of the chromosomal region around CTSD. Thus, our analyses on more than 800 subjects suggest that if an association between the CTSD exon 2 polymorphism and AD exists, it is likely to be smaller than previously reported. Ann Neurol 2001;49:114–116

ADAM10, a member of a disintegrin and metalloprotease family, is an alpha-secretase capable of anti-amyloidogenic proteolysis of the amyloid precursor protein. Here, we present evidence for genetic association of ADAM10 with Alzheimer's disease (AD) as well as two rare potentially disease-associated non-synonymous mutations, Q170H and R181G, in the ADAM10 prodomain. These mutations were found in 11 of 16 affected individuals (average onset age 69.5 years) from seven late-onset AD families. Each mutation was also found in one unaffected subject implying incomplete penetrance. Functionally, both mutations significantly attenuated alpha-secretase activity of ADAM10 (70% decrease), and elevated Abeta levels (1.5-3.5-fold) in cell-based studies. In summary, we provide the first evidence of ADAM10 as a candidate AD susceptibility gene, and report two potentially pathogenic mutations with incomplete penetrance for late-onset familial AD.

Alzheimer's disease (AD) is a genetically complex and heterogeneous disorder. To date four genes have been established to either cause early-onset autosomal-dominant AD (APP, PSEN1, and PSEN2(1-4)) or to increase susceptibility for late-onset AD (APOE5). However, the heritability of late-onset AD is as high as 80%, (6) and much of the phenotypic variance remains unexplained to date. We performed a genome-wide association (GWA) analysis using 484,522 single-nucleotide polymorphisms (SNPs) on a large (1,376 samples from 410 families) sample of AD families of self-reported European descent. We identified five SNPs showing either significant or marginally significant genome-wide association with a multivariate phenotype combining affection status and onset age. One of these signals (p = 5.7 x 10(-14)) was elicited by SNP rs4420638 and probably reflects APOE-epsilon4, which maps 11 kb proximal (r2 = 0.78). The other four signals were tested in three additional independent AD family samples composed of nearly 2700 individuals from almost 900 families. Two of these SNPs showed significant association in the replication samples (combined p values 0.007 and 0.00002). The SNP (rs11159647, on chromosome 14q31) with the strongest association signal also showed evidence of association with the same allele in GWA data generated in an independent sample of approximately 1,400 AD cases and controls (p = 0.04). Although the precise identity of the underlying locus(i) remains elusive, our study provides compelling evidence for the existence of at least one previously undescribed AD gene that, like APOE-epsilon4, primarily acts as a modifier of onset age.

The genetics of Alzheimer's disease (AD) is heterogeneous and remains only ill-defined. We have recently created a freely available and continuously updated online database (AlzGene; http://www.alzgene.org ) for which we collect all published genetic association studies in AD and perform systematic meta-analyses on all polymorphisms with sufficient genotype data. In this study, we tested 27 genes (ACE, BDNF, CH25H, CHRNB2, CST3, CTSD, DAPK1, GALP, hCG2039140, IL1B, LMNA, LOC439999, LOC651924, MAPT, MTHFR, MYH13, PCK1, PGBD1, PRNP, PSEN1, SORCS1, SORL1, TF, TFAM, TNK1, GWA_14q32.13, and GWA_7p15.2), all showing significant association with AD risk in the AlzGene meta-analyses, in a large collection of family-based samples comprised of 4,180 subjects from over 1,300 pedigrees. Overall, we observe significant association with risk for AD and polymorphisms in ACE, CHRNB2, TF, and an as yet uncharacterized locus on chromosome 7p15.2 [rs1859849]. For all four loci, the association was observed with the same alleles as in the AlzGene meta-analyses. The convergence of case-control and family-based findings suggests that these loci currently represent the most promising AD gene candidates. Further fine-mapping and functional analyses are warranted to elucidate the potential biochemical mechanisms and epidemiological relevance of these genes.

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.

Objectives: Several studies suggested chromosome 12 harbours an Alzheimer’s disease (AD) risk factor gene. Significant association of a single nucleotide polymorphism (SNP) in the 3′ UTR of transcription factor CP2 ( LBP-1c/CP2/LSF or TFCP2 ) at 12q13 was reported in three independent case-control studies, but no family based analyses have been performed to date. Methods: Genotypes for three SNPs were generated in two independent AD family samples. A meta-analysis on all published case-control studies was also performed. Results: The A allele of the 3′ UTR SNP was associated with increased risk for AD in one sample (odds ratio (OR) 2.1, 95% confidence interval (95% CI) 1.1 to 4.3), but not in the other, possibly due to low power. Haplotype analyses showed that this allele is part of a putative risk-haplotype overtransmitted to affected individuals in one sample and in both samples combined. Meta-analysis of the previously associated 3′ UTR SNP showed a trend towards a protective effect of the A allele in AD (OR 0.73, 95% CI 0.5 to 1.1). Conclusions: This is the first study to examine LBP-1c/CP2/LSF in AD families, and the fifth to independently show significant association. While our results support a role of this gene in AD pathogenesis, the direction of the effect remains uncertain, possibly indicating linkage disequilibrium with another variant nearby.

Objective: To use fMRI to investigate whether hippocampal and entorhinal activation during learning is altered in the earliest phase of mild cognitive impairment (MCI). Methods: Three groups of older individuals were studied: 10 cognitively intact controls, 9 individuals at the mild end of the spectrum of MCI, and 10 patients with probable Alzheimer disease (AD). Subjects performed a face-name associative encoding task during fMRI scanning, and were tested for recognition of stimuli afterward. Data were analyzed using a functional-anatomic method in which medial temporal lobe (MTL) regions of interest were identified from each individual9s structural MRI, and fMRI activation was quantified within each region. Results: Significantly greater hippocampal activation was present in the MCI group compared to controls; there were no differences between these two groups in hippocampal or entorhinal volumes. In contrast, the AD group showed hippocampal and entorhinal hypoactivation and atrophy in comparison to controls. The subjects with MCI performed similarly to controls on the fMRI recognition memory task; patients with AD exhibited poorer performance. Across all 29 subjects, greater mean entorhinal activation was found in the subgroup of 13 carriers of the APOE e4 allele than in the 16 noncarriers. Conclusions: The authors hypothesize that there is a phase of increased medial temporal lobe activation early in the course of prodromal Alzheimer disease followed by a subsequent decrease as the disease progresses.

Recently, two studies1,2 reported independent evidence of genetic association between a 3′ UTR single nucleotide polymorphism (SNP; rs1050283 , also known as “+1073”) in the oxidised LDL receptor 1 gene ( OLR1 ) on chromosome 12p13.2 and risk for Alzheimer’s disease (AD). The implied chromosomal area is a highly promising AD candidate region because both genetic linkage and association studies have reported significant signals to two different locations separated by about 40 Mb (about 44 cM): the more proximal region is located near 10 Mb, on 12p13, and contains OLR1 as well as the gene encoding α2-macroglobulin ( A2M ), while the more distal region near 50 Mb, on 12q13, maps close to the genes encoding LRP1 (low density lipoprotein-related protein 1) and TFCP2 (transcription factor CP2). All four of these genes have shown independent associations with AD risk, although the results for A2M and LRP1 have been controversial (for recent reviews see Bertram and Tanzi3 and Saunders et al 4). For OLR1 , Luedecking-Zimmer and colleagues first reported evidence of association with the 3′ UTR SNP ( rs1050283 ) in a white North American case-control sample of more than 1500 subjects.1 This association showed a strong interaction with APOE (apolipoprotein E) e4-genotype, and led to opposite effects in subgroups stratified by APOE e4. Specifically, APOE e4-positive carriers of the TT-genotype had a 1.7-fold increased AD risk, whereas APOE e4-negative carriers of the same genotype showed a significantly reduced (OR = 0.7) risk for AD. Performing electrophoretic mobility shift assays (EMSAs) indicated reduced binding of nuclear proteins related to the T-allele of this variant. The more recently published results by Lambert et al were obtained on a large French case-control sample and a considerably smaller North American family-based sample, and also showed significant effects with this polymorphism.2 However, no APOE e4-dependence was …

Calls of blue whales (Balaenoptera musculus), fin whales (Balaenoptera physalus), and humpback whales (Megaptera novaeangliae) were identified in the data from U.S. Navy Sound Surveillance System (SOSUS) and other hydrophone arrays. These data on calling whales from November 1995 through July 1999 have been listed here for four offshore, deep-water Regions along continental margins of the North and Northeast Pacific. The occurrence of calling whales was monitored during two-day periods each week. Call data recorded from each array identified species, call occurrence, variation, received beam, and relative numbers of calling whales. This allowed assessment of seasonal distribution of calls for the different species, and provided locations for sources received at multiple arrays. Blue whale tonal sounds were distributed widely, received most in the NW Region, with a peak in occurrence in the fall. Fin whale "20-Hz" repetitive pulse sequences were received from whales grouped in local areas in all Regions, with a peak in occurrence in midwinter. Humpback songs were received from December through May particularly in the SE Region. The offshore listening systems allowed basin-wide monitoring of the seasonal distribution of these calling whales.

In a recent paper in Cell, Dreses-Werringloer et al. (2008) reported the identification and functional characterization of a new Alzheimer’s disease (AD) gene, CALHM1, encoding calcium homeostasis modulator 1. CALHM1 (formerly annotated as FAM26C) represents a compelling candidate gene for late-onset AD as it is located on chromosome 10q24, a consistently replicated AD linkage region (Bertram et al., 2007), is highly expressed in the hippocampus, which is severely affected by AD-related pathology, and is involved in calcium ion homeostasis, which may be disrupted in AD. In view of these converging leads, Dreses-Werringloer et al. (2008) sequenced the open reading frame of CALHM1 in a small sample of AD patients and healthy controls and identified a nonsynonymous polymorphism (Pro86Leu, rs2986017) whose minor leucine allele showed a higher frequency in the AD patients. Followup analyses in four additional independent samples of ~3400 DNAs revealed a consistent overrepresentation of the same allele in AD cases compared to controls in each dataset. From the combined analyses the authors estimated that inheritance of the leucine allele modestly, but significantly, elevated the risk for AD by ~40% (p value = 2 × 10−10). Their genetics findings were supported by data generated in a large number of functional genomics and biochemical experiments showing evidence that the risk-associated leucine allele leads to a loss of protein function, including attenuated permeability to calcium ions and reduced cytosolic calcium ion levels, which, in turn, were associated with an increase in the pathogenic peptide, amyloid-β (Aβ). Here, we present an independent assessment of the potential association between AD and the Pro-86Leu single-nucleotide polymorphism (SNP) in CALHM1 in more than 8100 subjects from several independent datasets comprised of AD families—including those in which the original chromosome 10q24 linkage signal was identified (Bertram et al., 2000)—as well as unrelated cases and controls, and we find no evidence of a genetic association in these samples. The family-based datasets (CAG, NIA, NIMH, NCRAD) tested in this project are of self-reported European (Caucasian) ancestry collected in the US for the study of genetic factors in AD (see Table S1, available online, for a summary of sample characteristics). All samples were primarily sibships and lacked parental genotypes. With the exception of the CAG sample, the majority of pedigrees analyzed here were nuclear families ascertained on the basis of multiple affected individuals. In addition to containing at least one affected relative pair, many pedigrees also had DNA available from additional affected or unaffected individuals (mostly siblings). The diagnosis of definite, probable, or possible AD was made according to NINCDS/ADRDA criteria for affected individuals in all four samples (McKhann et al., 1984). In addition to the family samples, we genotyped ~1300 unrelated AD cases and controls, which were collected at two sites in Northern Europe, Sweden, and Finland (Table S1). All subjects were Caucasian, and AD patients fulfilled NINCDS/ADRDA criteria for probable AD. The Swedish AD patients were ascertained at the Memory Disorder Unit at Uppsala University Hospital. Healthy control subjects were recruited from the same geographic region following advertisements in local newspapers and displayed no signs of dementia upon neuropsychological testing. The Finnish subjects were gathered from Eastern Finland and were examined in the Department of Neurology of Kuopio University Hospital. Control subjects had no signs of dementia following neuropsychological testing. Finally, we assessed the CALHM1 locus in two previously published high-density genome-wide association studies (GWAS) (Li et al., 2008; Reiman et al., 2007) for which genotype data are publicly available. Together, these studies investigated 2900 unrelated AD cases and controls. Given that the rs2986017 (Pro86Leu) variant was not tested directly in either of the GWAS, we tested two SNPs showing strong and significant linkage disequilibrium with the rs2986017 (Pro86Leu) variant (rs2986030 [D′ = 0.89, r2 = 0.71] and rs1555823 [D′ = 0.89, r2 = 0.64]). Note that the power to detect the effect sizes described in the original report (Dreses-Werringloer et al., 2008) was still very high (>90%) due to the strong linkage disequilibrium between these variants (Table S2). Genotyping of the rs2986017 (Pro86Leu) variant in the US family samples and the Northern European case-control datasets was based on an individually optimized single-base extension reaction detected by high-efficiency fluorescent polarization (HEFP; described in Bertram et al., 2005; protocols available on request). Overall, genotyping efficiency was 97.6%, and the average error rate was below 0.2%. Resequencing of the Pro86Leu variant in 20 individuals revealed 100% concordance with the HEFP genotype results. None of the markers deviated significantly from Hardy-Weinberg equilibrium. To test for association with AD risk in the family-based samples we used PBAT (http://www.biostat.harvard.edu/~clange/default.htm) applying an additive model. Odds ratios (ORs) for the family samples were calculated by fitting a conditional logistic regression model to each dataset, where family defines the stratum. To test for association in the case-control samples (including the markers extracted from the GWAS) we calculated allele-based study-specific crude ORs, 95% confidence intervals, and p values for each marker (Bertram et al., 2007). To combine the effect size estimates obtained in this study with those estimated in the original publication, summary ORs across all samples were calculated using the DerSimonian and Laird random effects model, in line with the analyses routinely performed for the AlzGene database (Bertram et al., 2007). Power calculations (performed in PBAT) suggested that we had sufficient (i.e., 70% or greater) power to detect the genetic effect size estimated in the original study in each of the samples, with the exception of the CAG dataset (Table S2). As shown in Figure S1 and Table S2, none of the eight samples we investigated showed evidence for significant association between the rs2986017 (Pro86Leu) variant in CALHM1 and AD risk (p values ranging from 0.15 to 0.84). Stratification by age of AD onset (using 65 years as cutoff) or APOE e4-genotype did not appreciably change these results (data not shown; stratified analyses were not possible in the GWAS samples as no onset age or APOE e4 data were supplied). Effect size estimates indicated insignificant ORs that were opposite in direction to those reported by Dreses-Werringloer et al. (2008) in six of the eight samples (see Figure S1). Accordingly, summary ORs calculated across the newly genotyped samples in our study (labeled “This study” in Figure S1) were insignificant (OR = 0.94 [95% CI: 0.83–1.07], p = 0.4) and tended toward null when combined with the published GWAS genotype data (“All follow-up”; OR = 0.99 [95% CI: 0.91–1.09], p = 0.9). Upon combining these data with the results of the original study (“All studies”), that is, generating a meta-analysis on all ~11,700 currently available subjects, the overall summary OR became insignificant as well (OR = 1.13 [95% CI: 0.99–1.27], p = 0.06). Using rs1555823 (instead of rs2986030) as proxy for the rs2986017 (Pro86Leu) variant in the GWAS samples revealed even less pronounced and less significant overall effects (data not shown). Thus, we have independently assessed the potential association between AD risk and the rs2986017 (Pro86Leu) variant in the CALHM1 gene in a large number of independent datasets, including AD families in which the original chromosome 10q24 linkage signal was identified (Bertram et al., 2000). Despite good to excellent power to detect genetic effect sizes on the order described by Dreses-Werringloer et al. (2008), no association between CALHM1 and AD was observed, either in the individual samples or in the combined analyses of more than 8100 subjects. Based on these negative data, it is doubtful that CALHM1 represents more than a minor genetic determinant of AD risk.

Recent studies suggest that insulin-degrading enzyme (IDE) in neurons and microglia degrades Aβ, the principal component of β-amyloid and one of the neuropathological hallmarks of Alzheimer's disease (AD). We performed parametric and nonparametric linkage analyses of seven genetic markers on chromosome 10q, six of which map near the IDE gene, in 435 multiplex AD families. These analyses revealed significant evidence of linkage for adjacent markers (D10S1671, D10S583, D10S1710, and D10S566), which was most pronounced in late-onset families. Furthermore, we found evidence for allele-specific association between the putative disease locus and marker D10S583, which has recently been located within 195 kilobases of the IDE gene.

Genetic linkage studies suggest the presence of an Alzheimer's disease (AD) risk gene on chromosome 19, acting independently of apolipoprotein E (apoE), a known AD risk factor on 19q13. The low density lipoprotein receptor (LDLR) is an interesting candidate because it maps within the linked interval, and is intimately involved in cholesterol homeostasis and the function of apoE. We tested three previously reported single nucleotide polymorphisms (SNPs) within LDLR in a large sample of discordant sibships from multiplex AD families, and failed to find evidence for genetic association with disease risk. In addition, we performed meta-analyses for SNP rs5925 on published data from five independent case control samples, but did not detect any significant summary odds ratios. Based on our data, it seems unlikely that these genetic variants in LDLR make a significant contribution to AD risk in the general population.

Background: Recently, conflicting reports have been published on the potential role of genetic variants in the α-T catenin gene ( VR22 ; CTNNA3 ) on the risk for Alzheimer’s disease. In these papers, evidence for association is mostly observed in multiplex families with Alzheimer’s disease, whereas case–control samples of sporadic Alzheimer’s disease are predominantly negative. Methods: After sequencing VR22 in multiplex families with Alzheimer’s disease linked to chromosome 10q21, we identified a novel non-synonymous (Ser596Asn; rs4548513) single nucleotide polymorphism (SNP). This and four non-coding SNPs were assessed in two independent samples of families with Alzheimer’s disease, one with 1439 subjects from 437 multiplex families with Alzheimer’s disease and the other with 489 subjects from 217 discordant sibships. Results: A weak association with the Ser596Asn SNP in the multiplex sample, predominantly in families with late-onset Alzheimer’s disease (p = 0.02), was observed. However, this association does not seem to contribute substantially to the chromosome 10 Alzheimer’s disease linkage signal that we and others have reported previously. No evidence was found of association with any of the four additional SNPs tested in the multiplex families with Alzheimer’s disease. Finally, the Ser596Asn change was not associated with the risk for Alzheimer’s disease in the independent discordant sibship sample. Conclusions: This is the first study to report evidence of an association between a potentially functional, non-synonymous SNP in VR22 and the risk for Alzheimer’s disease. As the underlying effects are probably small, and are only seen in families with multiple affected members, the population-wide significance of this finding remains to be determined.

Background In family-based association analysis, each family is typically ascertained from a single proband, which renders the effects of ascertainment bias heterogeneous among family members. This is contrary to case–control studies, and may introduce sample or ascertainment bias. Statistical efficiency is affected by ascertainment bias, and careful adjustment can lead to substantial improvements in statistical power. However, genetic association analysis has often been conducted using family-based designs, without addressing the fact that each proband in a family has had a great influence on the probability for each family member to be affected. Method We propose a powerful and efficient statistic for genetic association analysis that considered the heterogeneity of ascertainment bias among family members, under the assumption that both prevalence and heritability of disease are available. With extensive simulation studies, we showed that the proposed method performed better than the existing methods, particularly for diseases with large heritability. Results We applied the proposed method to the genome-wide association analysis of Alzheimer’s disease. Four significant associations with the proposed method were found. Conclusion Our significant findings illustrated the practical importance of this new analysis method. Electronic supplementary material The online version of this article (doi:10.1186/s12881-015-0198-6) contains supplementary material, which is available to authorized users.