IntroductionLate-onset Alzheimer's disease (LOAD, onset age > 60 years) is the most prevalent dementia in the elderly 1 , and risk is partially driven by genetics 2 . Many of the loci responsible for this genetic risk were identified by genome-wide association studies (GWAS) [3][4][5][6][7][8] . To identify additional LOAD risk loci, the we performed the largest GWAS to date (89,769 individuals), analyzing both common and rare variants. We confirm 20 previous LOAD risk loci and identify four new genome-wide loci (IQCK, ACE, ADAM10, and ADAMTS1). Pathway analysis of these data implicates the immune system and lipid metabolism, and for the first time tau binding proteins and APP metabolism. These findings show that genetic variants affecting APP and Aβ processing are not only associated with early-onset autosomal dominant AD but also with LOAD. Analysis of AD risk genes and pathways show enrichment for rare variants (P = 1.32 x 10 -7 ) indicating that additional rare variants remain to be identified. Main TextOur previous work identified 19 genome-wide significant common variant signals in addition to APOE 9 , that influence risk for LOAD. These signals, combined with 'subthreshold' common variant associations, account for ~31% of the genetic variance of LOAD 2 , leaving the majority of genetic risk uncharacterized 10 . To search for additional signals, we conducted a GWAS metaanalysis of non-Hispanic Whites (NHW) using a larger sample (17 new, 46 total datasets) from our group, the International Genomics of Alzheimer's Project (IGAP) (composed of four AD consortia: ADGC, CHARGE, EADI, and GERAD). This sample increases our previous discovery sample (Stage 1) by 29% for cases and 13% for controls (N=21,982 cases; 41,944 controls) ( Supplementary Table 1 and 2, and Supplementary Note). To sample both common and rare variants (minor allele frequency MAF ≥ 0.01, and MAF < 0.01, respectively), we imputed the discovery datasets using a 1000 Genomes reference panel consisting of . CC-BY-NC-ND 4.0 International license peer-reviewed) is the author/funder. It is made available under a 11 36,648,992 single-nucleotide variants, 1,380,736 insertions/deletions, and 13,805 structural variants. After quality control, 9,456,058 common variants and 2,024,574 rare variants were selected for analysis (a 63% increase from our previous common variant analysis in 2013).Genotype dosages were analyzed within each dataset, and then combined with meta-analysis ( Supplementary Figures 1 and 2 and Supplementary Table 3). The Stage 1 discovery metaanalysis was first followed by Stage 2 using the I-select chip we previously developed in Lambert et al (including 11,632 variants, N=18,845) and finally stage 3A (N=6,998). The final sample was 33,692 clinical AD cases and 56,077 controls.Meta-analysis of Stages 1 and 2 produced 21 associations with P ≤ 5x10 -8 (Table 1 and Figure 1). Of these, 18 were previously reported as genome-wide significant and three of them are signals not initially described in Lambert et al: the rare R47H TREM2 coding va...

Reticuloendotheliosis virus strain T (Rev-T) is a highly oncogenic replication-defective retrovirus which contains the oncogene v-rel. It is thought that Rev-T arose when a virus similar to Rev-A, the helper virus of Rev-T, infected a turkey and recombined with c-rel from that turkey. There is one large c-rel locus in the turkey genome which contains all of the sequences homologous to v-rel (K. C. Wilhelmsen and H. M. Temin, J. Virol. 49:521-529, 1984). We have sequenced v-rel and its flanking sequences, each of the regions of the c-rel locus from turkey that are homologous to v-rel and their flanking sequences, and the coding sequence for env and part of pol of Rev-A. The v-rel coding sequences can be translated into a 503-amino acid env-v-rel-out-offrame-env fusion polypeptide. We have not detected any sequences in the Los Alamos or University of California-San Diego data bases that are more significantly related to the amino acid or nucleic acid sequence of v-rel than to the randomized sequence of v-rel. Comparison of Rev-A, Rev-T, and c-rel indicates that the v-rel sequences may have been transduced from the c-rel (turkey) locus by a novel mechanism. There are sequences in Rev-A and c-rel that are similar to splicing signals, indicating that the 5' virus-rel junction of Rev-T may have been formed by cellular RNA splicing machinery. Eight presumed introns have presumably been spliced out of c-rel to generate v-rel. There are also short imperfect regions of homology between sequences at the boundaries of v-rel and sequences in Rev-A and c-rel (turkey), indicating that c-rel may have been transduced by homologous recombination. There are many differences between the amino acid sequences of the predicted translational products of v-rel and c-rel which may account for their difference in transformation potential. These sequence differences between v-rel and c-rel include 10 missense transitions, four missense transversions, and three places where Rev-T has a small in-frame deletion of sequences relative to c-rel. Most of the coding sequence differences between c-rel and v-rel are nonconservative amino acid changes. * Corresponding author. 172 gene appears to be the result of a quantitative difference in the level of their expression (13, 30). We have been studying the highly oncogenic retrovirus reticuloendotheliosis virus strain T (Rev-T), which contains the oncogene v-rel. Rev-T was first isolated from a turkey (28). It is thought that Rev-T arose when a virus similar to Rev-A infected a turkey and recombined with c-rel from that turkey. Analysis of molecular clones of proviruses of Rev-T and Rev-A (Rev-A is the nondefective helper virus of Rev-T) shows that in Rev-T, v-rel is substituted for most of env in Rev-A (see Fig. 1) (3, 8, 18). Rev-T also has a large deletion of sequences which encode much of gag and pol in Rev-A. This deletion is necessary for transformation of cells by v-rel (4). In Rev-T-infected cells, there are two viral RNA transcripts that contain v-rel sequences: a full-length genomic size tran...

The cellular homolog of the onc sequences in the avian retrovirus reticuloendotheliosis virus strain T (v-ret) was studied by molecular cloning and nucleic acid hybridization. In contrast to v-rel sequences, which are 1.4 kilobase pairs long, the cellular homolog, c-rel, from line 15B chickens is at least 25 kilobase pairs long, with multiple apparent introns. A 4.0-kilobase polyadenylic acid-containing RNA transcript is the primary species of c-rel RNA present in uninfected chicken cells. Sequences at the 3' end of this c-rel RNA are not present in v-rel.

Genetic variation, both single-nucleotide variations and copy number variations (CNV), contribute to changes in gene expression. In some cases these variations are meaningfully correlated with disease states. We hypothesized that in a genetically heterogeneous disorder such as sporadic Alzheimer's disease (AD), utilizing gene expression as a quantitative trait and CNVs as a genetic marker map within the same individuals in the context of case–control status may increase the power to detect relevant loci. Using this approach an 8-kb deletion was identified that contains a PAX6-binding site on chr2q33.3 upstream of CREB1 encoding the cAMP responsive element-binding protein1 transcription factor. The association of the CNV to AD was confirmed by a case–control association study consisting of the Texas Alzheimer Research and Care Consortium and NIA-LOAD Family Study data sets.

A locus has been identified in turkey DNA that contains nucleotide sequences homologous to the oncogene (v-rel) in the avian retrovirus, reticuloendotheliosis virus strain T. This locus, c-rel, has been molecularly cloned from an apparently heterozygous turkey. c-rel is approximately 23 kilobase pairs in length, with at least seven apparent introns, and contains sequences sufficient to account for all of v-rel. Nucleic acid sequence differences exist between v-rel and homologous regions of c-rel. We examined a population of turkeys to determine whether these sequence differences are the result of polymorphism in the population. Within the turkey population, c-rel is dimorphic in apparent introns and 3' flanking sequences, but polymorphism has not been detected within the regions of the c-rel locus that are homologous to v-rel. Additionally, no nucleic acid sequence differences have been detected between the regions of c-rel in turkeys that are homologous to v-rel and the sequences related to v-rel of a homologous locus in chickens (Chen et al., J. Virol. 245:104-113, 1983). The general organization of introns and flanking sequences is conserved for both c-rel in turkeys and this locus in chickens, indicating that c-rel, like other protooncogenes, may have an important developmental or metabolic function.