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Results of a high-resolution genome screen of 437 Alzheimer's Disease families

Results of a high-resolution genome screen of 437 Alzheimer's Disease families Abstract Alzheimer's disease (AD) is a devastating neurodegenerative disorder of late life with complex inheritance. Mutations in three known genes lead to the rare early-onset autosomal dominant form of AD, while a common polymorphism (ε4) in the gene encoding apolipoprotein E (APOE ) is a risk factor for more typical late-onset (>60 years) AD. A recent study concluded that there are up to four additional genes with an equal or greater contribution to the disease. We performed a 9 cM genome screen of 437 families with AD, the full National Institute of Mental Health (NIMH) sample, which has been carefully ascertained, evaluated and followed by our group over the last decade. Performing standard parametric and non-parametric linkage analyses, we observed a ‘highly significant’ linkage peak by Lander and Kruglyak criteria on chromosome 19q13, which probably represents APOE. Twelve additional locations—on 1q23, 3p26, 4q32, 5p14, 6p21, 6q27, 9q22, 10q24, 11q25, 14q22, 15q26 and 21q22—met criteria for ‘suggestive’ linkage [i.e. two-point lod score (TLS) ≥1.9 and/or multipoint lod score (MLS) ≥2.2] in at least one of our analyses. Although some of these will surely prove to be false positives, these linkage signals should provide a valuable framework for future studies aimed at identifying additional susceptibility genes for late-onset AD. INTRODUCTION Alzheimer's disease (AD) is a devastating neurodegenerative disorder of late life with complex inheritance. A rare Mendelian subform with early onset exhibits autosomal dominant inheritance and both locus and allelic heterogeneity. This form can be caused by any of over 120 mutations in three known genes (reviewed in 1): the amyloid precursor protein (APP), presenilin 1 (PSEN1) and presenilin 2 (PSEN2). For the much more common late-onset form of AD, which shows complex inheritance, only one gene has been consistently associated with the disease. A common polymorphism (ε4) in the gene encoding apolipoprotein E (APOE) confers increased risk for late-onset AD (2, 3), and lowers the age of onset in a dose-dependent fashion (4–6). Although APOE plays a major role in the risk for late-onset AD, a variety of genetic and epidemiological studies have shown that genes beyond APOE are involved in disease etiology (7,8). A recent study (9) in which age of onset was examined as a quantitative trait estimated that up to four additional major genes as well as several minor AD genes remain to be identified. Although in theory age of onset is distinct from risk, for a late-onset disease like AD there is considerable overlap in practice, as has been observed in studies of APOE. In any case, efforts to find genes affecting risk and/or age of onset of AD have made limited progress. Genome screens for AD reported to date (10–12) have selected their samples in a variety of ways, have used both disease risk and age of onset as outcomes, and have employed a wide variety of analytic methods. Many studies use overlapping portions of the NIMH sample used here (10–13), which only adds to the difficulty in understanding the relationship among the various results. Beyond APOE, for which nearby markers have shown detectable (but not necessarily statistically significant) linkage on chromosome 19q13, the major linkage findings reported to date have been on chromosomes 12 (11,13–15), 10 (16–18), and 9 (10,13). In addition, there have been over three dozen reports of genetic association, mostly with genes thought to influence pathobiological pathways in AD (1). Here we report our parametric and non-parametric linkage analyses of a 9 cM genome screen of the 437 multiplex families in the full NIMH Genetics Initiative sample. RESULTS The results of our affecteds-only parametric two-point analyses in FASTLINK (19,20) and non-parametric multipoint analyses in GENEHUNTER-PLUS (21,22) on the full NIMH sample are summarized in Table 1. Our analyses were performed for the total sample (which includes the 437 families in which no sampled affected subject experienced disease onset before age 50; see Methods), and in strata based on age of onset—a ‘late-onset’ stratum (families in which all sampled affected subjects onset ≥65), and an ‘early/mixed-onset’ stratum (all others, i.e. at least one sampled affected subject onsets <65). Table 1 shows multipoint lod score (MLS; also shown in Figure 1 across the genome) and multipoint likelihood ratio Z-score (Zlr), as well as two-point lod score (TLS) and estimated recombination fraction (𝛉) for all loci with MLS>1.0 or ‘suggestive linkage’ in the two-point analyses alone. There is one region—on 19q13—that meets Lander and Kruglyak criteria for ‘highly significant’ linkage (23); this is presumed to represent APOE, as the best linked marker (D19S178) maps within ∼1 Mb upstream of this locus (24). There are 10 additional regions—1q23, 3p26, 4q32, 6p21, 6q27, 9q22, 10q24, 14q22, 15q26 and 21q22—that meet criteria for ‘suggestive’ linkage in the total sample and/or at least one onset-age stratum in at least one of the analyses (23). We chose to analyze the data rounding up all rare marker allele frequencies to at least 0.01 (and adjusting the frequencies of the most common alleles to compensate) in order to decrease the likelihood of false-positive linkage due to the effect of rare alleles (25). We also analyzed the data using ‘unrounded’ allele frequencies estimated from the data, and the results did not change appreciably, although several regions had slightly weaker linkage signals (data not shown). In addition, because of concerns about population heterogeneity, we also analyzed the data excluding the 26 non-Caucasian families; there were no appreciable differences in the results (data not shown). Last, we also analyzed the data allowing for heterogeneity using the two-point HLOD option in GENEHUNTER. Overall, the results were consistent with the regular two-point analyses. However, after accounting for heterogeneity, two new regions, on 5p14 [at 37 cM, HLOD (late-onset)=2.6, α=0.25] and 11q25 [at 148 cM, HLOD (total sample)=2.4, α=0.23], both of which gave modest signals previously, crossed the Lander and Kruglyak threshold, making a total of 12 ‘suggestive’ regions in at least one of our analyses. In addition, one new minor peak appeared on 3p12 [at 114 cM, HLOD (total sample)=1.6, α=0.16] where in the regular two-point analyses no linkage was observed, and one existing peak on 9q22 [at 101 cM, HLOD (late-onset)=2.6, α=0.29] had a notably stronger signal. Because of the overlap among our sample and these reported by other groups, we obtained a list of the NIMH subjects used in the report of Kehoe and colleagues from the NIMH Center for Genetic Studies (http://zork.wustl.edu/∼nimh), and repeated all analyses including only those individuals not used in the Kehoe report (13) or the follow-up Stage II screen of Myers and colleagues (11), which uses approximately the same sample. The remaining sample has markedly less power: it includes only 238 analyzable families with 808 individuals. Nonetheless, most of the observed peaks were still present, and were sometimes larger (1p36, 1p31, 3p26, 3p14, 6q27, 10p14, 13q32, 14q22, 19q13, and 21q22) in the smaller ‘non-Kehoe’ sample in at least one of the analyses (Table 2). DISCUSSION As expected, there is a ‘highly significant’ peak (TLS=3.9, MLS=7.7) in the early/mixed stratum on chromosome 19q13 at marker D19S178, which maps within ∼1 Mb of APOE (24). Interestingly, linkage evidence for late-onset families was less pronounced, and peaked 17 cM (∼14 Mb) proximal at marker D19S433 (TLS=2.3 at 𝛉=0.2, MLS=1.6), which is in agreement with previous reports in this and other samples, suggesting that APOE-ε4 acts in part through a decrease of onset age (6,26). Our findings are consistent with prior findings on chromosome 9, although, as is common in the analysis of complex diseases (27,28), the location information is indistinct within each study, and can vary considerably across studies. Our chromosome 9q22 linkage at ∼101 cM is ∼10 cM distal to a ‘suggestive’ peak (at ∼91 cM) reported in the Kehoe genome screen in a subset of the NIMH sample (13), and again in the Myers (11) screen (stage II of the Kehoe screen), which used the same subset of the NIMH sample plus additional families from the USA and UK. These ‘Kehoe’ families appear to be driving the linkage, since there is no peak observed in this region in the ‘non-Kehoe’ families. In addition, our 9q22 peak and a smaller 9p21 peak at ∼55 cM are flanked by two peaks reported by Pericak-Vance and colleagues (10): a ‘significant’ proximal peak (at ∼43 cM) in the autopsy-confirmed subset of an overlapping sample, and a less pronounced distal peak (at ∼151 cM). The Pericak-Vance genome screen pooled portions of the NIMH sample with other samples, and had access to approximately the same families as the Kehoe group. While both chromosome 9 peaks are absent in the non-Kehoe families, Pericak-Vance and colleagues specifically noted that their peaks were observed consistently across the various subsamples (10). The picture on chromosome 10 is also largely consistent with prior findings, and equally indistinct. The chromosome 10q24 finding at 134 cM was only marginally suggestive in the present analyses (Table 1), but we recently reported significant linkage nearby using a different set of markers in the same sample (18). Our findings were published in tandem with reports from two other groups demonstrating significant linkage ∼30–50 cM proximal (16,17). Very recently, Li and colleagues have reanalyzed their data using age of onset as a quantitative trait (12), and report a peak around 125 cM, i.e. closer to the linkage region that we had identified earlier (between 115 and 127 cM) (18). Interestingly, the multi-point peak in the present analyses (∼92 cM) lies between the peak observed by the latter two studies (16,17) (∼80 cM) and our earlier linkage region, while the two-point peak here (134 cM) lies beyond our earlier peak and close to the region identified in the age at onset analyses of Li and colleagues (12). Similar to the findings on chromosome 9, almost no linkage evidence was observed in the subset of ‘non-Kehoe’ families alone (Table 2). In order to gain a better understanding of the broad signal on chromosome 10, additional analyses of the chromosome 10 data were performed in GENEFINDER (29), which estimates the location and a 95% confidence interval for an unobserved trait locus using multipoint marker information to approximate identity by descent (IBD) sharing in affected sib pairs, yielded strong signals with overlapping confidence intervals across a very broad region from 62 to 131 cM in the late-onset stratum [with Z-scores ranging from 2.5 (P=0.006) to 3.1 (P=0.001)], while the early/mixed stratum had a weaker but somewhat narrower signal from 13 to 37 cM [Z-score 1.6 (P=0.054)]. Thus, it is still unclear whether there are one or two underlying genes located on the long arm of chromosome 10. Many of the remaining linkage peaks lie near interesting candidate genes for AD. Our ‘suggestive’ linkage peak in late-onset families on chromosome 1q23 [which falls in a region where Kehoe and colleagues reported an MLS of 2.7 (13), but we see virtually no signal in the non-Kehoe sample (see Table 2)] is immediately adjacent to the gene encoding nicastrin (NCSTN ), which binds presenilin and is required for γ-secretase activity and Aβ generation (30). The peak on 4q32 maps to a general region that also gave weak evidence for linkage in both genome scans by Pericak-Vance and colleagues (10,14). The gene encoding α-synuclein (SNCA, at 4q21), which has been suggested as an AD candidate gene (31), is more than 70 Mb proximal, and thus is unlikely to account for this signal. The suggestive two-point signal on 6p21, a region that has also only been weakly linked or associated in previous studies (12–14,32) lies within 15 Mb of the gene encoding the tumor necrosis factor-α (TNFA), for which a significant haplotype association has been reported in the NIMH dataset (33). The suggestive multipoint signal on 6q27 (see Table 1) maps within ∼8 Mb of the plasminogen gene (PLG), which is a protease implicated in cleavage of Aβ (34). This region also shows a fairly strong signal in the ‘non-Kehoe’ sample (Table 2). Moreover, a similar region has been implicated in a recent re-analysis of the Kehoe-subset of the NIMH dataset (35). The linked interval on chromosome 14q22 in the early/mixed onset stratum could reflect linkage to the early-onset AD gene PSEN1, which maps ∼20 Mb distal of the best linked marker (D14S587; TLS=2.1 at 𝛉=0.15) and only ∼3 Mb distal of the next best linked marker (D14S588; TLS=1.9 at 𝛉=0.15). This finding is consistent with recent reports that many early-onset AD patients carry mutations in this gene (36) and that a promoter polymorphism 48 bp upstream of PSEN1 increases risk for early onset AD (37). To our knowledge, there are no prior reports of linkage or association near chromosome 15q26, and it should be noted that this ‘suggestive’ peak is driven almost entirely by a single marker (D15S642) at the q-terminal and thus is less likely to be confirmed. Finally, it is of note that the suggestive two-point peak on chromosome 21q22 lies ∼12 Mb from the early-onset AD gene APP, but only 5 Mb from BACE2 [which has been reported to cleave APP near the α-secretase site within the Aβ-domain and is the homolog of the β-secretase (BACE)] (38). Interestingly, there is a linkage signal on chromosome 11q25 (HLOD=2.4, just over the Lander and Kruglyak threshold for suggestive linkage when accounting for heterogeneity, and MLS=2.1 in the regular multipoint analyses) that maps within ∼20 Mb of BACE itself. Of note, no evidence of linkage was observed in the analyses here on chromosome 12 (maximum MLS=0.2 at 57 cM for the early/mixed stratum; maximum TLS=0.8 for marker C12S916 at 57 cM), where our group has reported a highly significant association finding with nearby alpha-2-macroglobulin (A2M ) (39), and follow-up analyses in the full NIMH sample used here remain strong (Saunders et al., submitted). Although this association finding has been controversial, and the great majority of follow-up studies have been negative (for example, see 40,41), several other groups have reported modest linkage signals in this general region (13–15) or association with A2M itself (for a recent review see 47). We report here the results of a high-resolution genome screen of a large, uniformly ascertained and evaluated sample of AD families. Although our results are only partially concordant with prior published reports, and the signals generated are not amenable to rapid gene discovery, this result is consistent with efforts to map other complex diseases. Our analyses reveal the expected strong signal for APOE on chromosome 19, and a number of more modest linkage peaks that deserve follow-up with linkage analysis of additional microsatellite markers as well as association testing of polymorphisms in positional candidate genes. If these analyses continue to provide support for the presence of AD susceptibility genes in these regions, systematic linkage disequilibrium mapping may be warranted. While some of the more marginal peaks in our study probably represent false-positive findings, others, particularly those with relatively stronger signals and/or prior reports (e.g. on chromosomes 9q and 10q), are more likely to harbor genuine AD susceptibility genes. The substantial effort required to identify and characterize as many of these genes as possible will greatly facilitate the development of strategies for treatment, early intervention, and prevention of this devastating disease. MATERIALS AND METHODS Sample Subjects were collected as part of the NIMH Genetics Initiative following a standardized protocol developed and tested by the three sites (42). Each site collected a wealth of information from family members, medical records and direct examination of the subjects in order to reach a diagnosis of AD by NINCDS/ADRDA criteria (26,43). Over the nearly 10 years of follow-up reflected in this dataset, autopsies were obtained on 326 affected subjects (48% of the deceased), and a clinical diagnosis of AD has been confirmed at autopsy by standard research criteria (44,45) in 94% of the cases. The NIMH sample constitutes a national archive for AD genetic research; all DNA samples are stored in a centralized cell repository at Rutgers University, and data are stored in a centralized data management center at Washington University in St Louis. Outside investigators (10–13,16,35,46) have used subsets of the first ∼60% of the samples collected. In order to select a sample more closely resembling more typical AD than had been studied previously, ascertainment criteria for the NIMH sample required only an affected relative pair, with no additional requirements regarding age of onset or family structure. The original sample included a total of 1527 subjects from 457 families. Six families (14 individuals) with only one sampled affected individual available were excluded. In addition, because onset prior to age 50 is strongly associated with PS1 (47), we excluded 14 additional families (with 74 individuals) in which any sampled individual had an onset age under 50 years. The total sample for the present analyses is comprised of 1439 individuals from 437 families, including 994 affected individuals (mean age of onset 72.4±7.7 years, range 50–97 years), 411 unaffected, and 34 with phenotype unknown. Families were classified as ‘late-onset’ (320 families) when all sampled affecteds had onset ages ≥65 years, and ‘early/mixed’ (117 families) otherwise. The family structure of the sample varies widely: 357 families are nuclear, 36 are extended families including one or more affected sibpairs, and 58 are extended families without an affected sibpair. Genotyping techniques Genotyping was performed at the Center for Inherited Disease Research (CIDR) using a modification of the CHLC version 9 marker set (381 markers, average spacing 9 cM, average heterozygosity 0.76, maximum gap 19 cM). Allele calls were reviewed by two technicians, blind to family structure and phenotype. Binning of all allele sizes for each marker was performed using the FASTCLUS procedure in SAS. Calls falling outside of bins and Mendelian inconsistencies, identified using GAS, were reviewed for obvious laboratory errors. Four blind duplicates, four positive and two negative control samples were run with every 86 study samples. The error rate for the genome scan, based on 28 023 paired genotypes from these blind duplicates, was 0.22%. The overall missing data rate was 3.6%. The rate of remaining Mendelian inconsistencies was 0.08%. See also www.cidr.jhmi.edu for details on the marker set and genotyping methods. Statistical techniques We initially calculated allele frequencies with maximum likelihood estimates using all available data with the program USERM13 (48) based on the program MENDEL (49), but for a fraction of the loci with greater than 20 alleles (six in total) we used a compression algorithm that we developed to reduce the number of alleles at a locus by combining the lowest frequency alleles into a single allele, and renumbering the remaining alleles to maintain consecutive numbering. Except for one marker (D2S2739) with 47 alleles, we were able to maintain the heterozygosity of the sample while compressing the most polymorphic loci to fewer than 20 alleles. When comparing linkage results using compressed versus non-compressed alleles, the differences in calculated lod scores never exceeded 0.05 in absolute value (data not shown). In order to protect our results against false-positive findings due to rare alleles (25), we rounded up rare allele frequencies to 0.01 while adjusting the most common alleles proportionally to compensate, and used these for our primary analyses. ‘Affecteds only’ parametric two-point analyses were performed in FASTLINK (19,20) using a dominant inheritance model with a disease gene frequency of 0.02. While affecteds only analysis can sometimes lead to inflation of the lod score, especially in the presence of missing data or misspecified allele frequencies (50,51), we felt that it was still preferable for the present analyses given the uncertainties regarding the true phenotype of ‘unaffected’ individuals and the shape of the age of onset distribution in a familial sample. Penetrance in affected individuals was set to correspond to phenocopy rates of 5% for definite AD (n=289), 10% for probable AD (n=640), and 20% for possible AD (n=65). Multipoint non-parametric analyses were performed in GENEHUNTER-PLUS using the ASM program (exponential model) to calculate MLS and Zlr scores (21,22). Genetic maps and intermarker distances were provided by CIDR (www.cidr.jhmi.edu) and are similar but not identical to those from the Marshfield Center for Medical Genetics (http://research.marshfieldclinic.org/genetics/), and thus use the Kosambi map function. Both parametric and non-parametric analyses were repeated limiting the sample to the 411 white families, and also limiting the sample to the 238 families not included in the analyses of Kehoe et al., and Myers et al. (11,13). In addition, we estimated two-point lod-scores under the assumption of heterogeneity across families (HLOD) in GENEHUNTER PLUS using the same inheritance models as in the TLS analyses (see above). GENEFINDER (29) was used to estimate the location and 95% confidence intervals around an underlying AD locus on chromosome 10q. The program utilizes multipoint marker information to approximate IBD sharing in affected sib pairs, using a robust, model-free approach similar to that used in GENEHUNTER. Based on the assumptions that a single disease locus exists in the map region being studied and that the true IBD sharing between affected siblings will be maximized at the trait locus, GENEFINDER employs generalized estimating equations to estimate the map location of the disease locus. ACKNOWLEDGEMENTS The authors thank all families for their participation, Drs Nan M. Laird and Ellen Wijsman for advice regarding statistical methodology, and Dr Steven Moldin and staff at NIMH and all three sites for assistance with all aspects of the project. This work was sponsored by grants from the NIMH and the National Institute on Aging. L.B. was a fellow of the Deutsche Forschungsgemeinschaft and is now recipient of a translational research fellowship of the Harvard Center for Neurodegeneration and Repair. A.J.S. was an NIA-NRSA recipient. Data and biomaterials were collected in three projects that participated in the National Institute of Mental Health (NIMH) Alzheimer Disease Genetics Initiative. From 1991–1998, the Principal Investigators and Co-Investigators were: Massachusetts General Hospital, Boston, MA, U01 MH46281, M.S.A and D.B.; Johns Hopkins University, Baltimore, MD, U01 MH46290, S.S.B., G.A.C. and M.F.F.; University of Alabama, Birmingham, AL, U01 MH46373, R.C.P.G. and L.E.H. Genotyping services were provided by the Center for Inherited Disease Research (CIDR), which is fully funded through a federal contract from the National Institutes of Health to The Johns Hopkins University, Contract Number N01-HG-65403. * To whom correspondence should be addressed at: Genetics and Aging Research Unit, Center for Aging, Genetics and Neurodegeneration, MGH East, 114 16th Street, Charlestown, MA 02129-4404, USA. Tel: +1 6177266845; Fax: +1 6177241949; Email: tanzi@helix.mgh.harvard.edu Open in new tabDownload slide Figure 1.Non-parametric multipoint lod score curves for each chromosome in the genome screen. Families were considered ‘late-onset’ if all sampled affected individuals had onset ages ≥65 years, and ‘early/mixed-onset’ otherwise. Marker locations are given in Kosambi centi-Morgans according to the map supplied by CIDR. Note that the scale used for chromosome 19 is different from that for the remainder of the genome. Table 1. MLS and Z-scores for the likelihood ratio (Zlr) plus TLS and recombination fractions (𝛉) for all chromosomal regions with MLS ≥1.0 plus those with ‘suggestive linkage’ (TLS≥1.9) in the two-point analysis alone. ‘Total’ refers to the full NIMH sample (n=437 families); families are ‘late-onset’ if all sampled affected individuals had onset ages ≥65 years, and ‘early/mixed’ otherwise. Chromosomal locations are given in Kosambi centi-Morgans according to the map provided by CIDR. Bold indicates regions of at least ‘suggestive linkage’ by Lander and Kruglyak criteria (23) in either the multipoint or two-point analyses or both Chromosome . Stratum . Multipoint analyses . Two-point analyses . . . cM . MLS . Zlr (P-value) . Marker (cM) . TLS (𝛉) . 1p36 Late 27 1.1 (2.3 (0.01) D1S1597 (30) (1.1 (0.25) 1p31 Early/mixed 121 1.6 (2.7 (0.0035) D1S551 (125) (0.4 (0.3) 1q23 Late 178 1.1 (2.2 (0.01) D1S1677 (178) 2.1 (0.2) 3p26 Early/mixed 9 2.0 3.0 (0.001) D3S2387 (6) 2.0 (0.1) 3p14 Total 88 1.1 2.2 (0.01) D3S4542 (90) 1.1 (0.25) 4q32 Total 158 1.8 2.9 (0.002) D4S1629 (158) 1.9 (0.25) 4q35 Late 204 1.8 2.9 (0.002) D4S1652 (209) 0.9 (0.25) 5p14 Late 37 1.4 2.6 (0.005) D5S2845 (37) 0.5 (0.3) 5q35 Total 182 1.3 2.4 (0.008) D5S211 (182) 1.1 (0.25) 6p21 Total 64 1.0 2.2 (0.01) D6S1017 (64) 1.9 (0.25) 6q27 Total 181 2.2 3.2 (0.0007) D6S1027 (187) 1.5 (0.25) 9p21 Total 55 1.3 2.5 (0.006) D9S1118 (58) 0.6 (0.3) 9q22 Late 101 2.9 3.6 (0.0002) D9S283 (95) 2.0 (0.2) 10p14 Early/mixed 19 1.1 2.3 (0.01) D10S189 (19) 0.3 (0.35) 10q22 Total 92 1.8 2.9 (0.002) D10S1432 (94) 1.1 (0.25) 10q24 Late 135 0.9 2.0 (0.02) D10S1237(135) 1.9 (0.25) 11q25 Total 148 2.1 3.1 (0.001) D11S968 (148) 1.7 (0.25) 13q32 Late 77 1.1 2.3 (0.01) D13S793 (77) 0.5 (0.3) 14q22 Early/mixed 55 2.2 3.2 (0.0007) D14S587 (55) 2.1 (0.15) 15q26 Early/mixed 123 1.3 2.5 (0.006) D15S642 (123) 2.1 (0.15) 16q23 Total 99 1.4 2.6 (0.005) D16S516 (99) 0.9 (0.3) 19q13 Early/mixed 70 7.7 5.9 (1.8×10−9) D19S178 (68) 3.9 (0.1) 21q22 Total 37 0.1 0.7 (0.24) D21S1440 (37) 2.5 (0.2) Xp21 Late 20 1.0 2.2 (0.01) DXS9902 (22) 1.6 (0.25) Chromosome . Stratum . Multipoint analyses . Two-point analyses . . . cM . MLS . Zlr (P-value) . Marker (cM) . TLS (𝛉) . 1p36 Late 27 1.1 (2.3 (0.01) D1S1597 (30) (1.1 (0.25) 1p31 Early/mixed 121 1.6 (2.7 (0.0035) D1S551 (125) (0.4 (0.3) 1q23 Late 178 1.1 (2.2 (0.01) D1S1677 (178) 2.1 (0.2) 3p26 Early/mixed 9 2.0 3.0 (0.001) D3S2387 (6) 2.0 (0.1) 3p14 Total 88 1.1 2.2 (0.01) D3S4542 (90) 1.1 (0.25) 4q32 Total 158 1.8 2.9 (0.002) D4S1629 (158) 1.9 (0.25) 4q35 Late 204 1.8 2.9 (0.002) D4S1652 (209) 0.9 (0.25) 5p14 Late 37 1.4 2.6 (0.005) D5S2845 (37) 0.5 (0.3) 5q35 Total 182 1.3 2.4 (0.008) D5S211 (182) 1.1 (0.25) 6p21 Total 64 1.0 2.2 (0.01) D6S1017 (64) 1.9 (0.25) 6q27 Total 181 2.2 3.2 (0.0007) D6S1027 (187) 1.5 (0.25) 9p21 Total 55 1.3 2.5 (0.006) D9S1118 (58) 0.6 (0.3) 9q22 Late 101 2.9 3.6 (0.0002) D9S283 (95) 2.0 (0.2) 10p14 Early/mixed 19 1.1 2.3 (0.01) D10S189 (19) 0.3 (0.35) 10q22 Total 92 1.8 2.9 (0.002) D10S1432 (94) 1.1 (0.25) 10q24 Late 135 0.9 2.0 (0.02) D10S1237(135) 1.9 (0.25) 11q25 Total 148 2.1 3.1 (0.001) D11S968 (148) 1.7 (0.25) 13q32 Late 77 1.1 2.3 (0.01) D13S793 (77) 0.5 (0.3) 14q22 Early/mixed 55 2.2 3.2 (0.0007) D14S587 (55) 2.1 (0.15) 15q26 Early/mixed 123 1.3 2.5 (0.006) D15S642 (123) 2.1 (0.15) 16q23 Total 99 1.4 2.6 (0.005) D16S516 (99) 0.9 (0.3) 19q13 Early/mixed 70 7.7 5.9 (1.8×10−9) D19S178 (68) 3.9 (0.1) 21q22 Total 37 0.1 0.7 (0.24) D21S1440 (37) 2.5 (0.2) Xp21 Late 20 1.0 2.2 (0.01) DXS9902 (22) 1.6 (0.25) Open in new tab Table 1. MLS and Z-scores for the likelihood ratio (Zlr) plus TLS and recombination fractions (𝛉) for all chromosomal regions with MLS ≥1.0 plus those with ‘suggestive linkage’ (TLS≥1.9) in the two-point analysis alone. ‘Total’ refers to the full NIMH sample (n=437 families); families are ‘late-onset’ if all sampled affected individuals had onset ages ≥65 years, and ‘early/mixed’ otherwise. Chromosomal locations are given in Kosambi centi-Morgans according to the map provided by CIDR. Bold indicates regions of at least ‘suggestive linkage’ by Lander and Kruglyak criteria (23) in either the multipoint or two-point analyses or both Chromosome . Stratum . Multipoint analyses . Two-point analyses . . . cM . MLS . Zlr (P-value) . Marker (cM) . TLS (𝛉) . 1p36 Late 27 1.1 (2.3 (0.01) D1S1597 (30) (1.1 (0.25) 1p31 Early/mixed 121 1.6 (2.7 (0.0035) D1S551 (125) (0.4 (0.3) 1q23 Late 178 1.1 (2.2 (0.01) D1S1677 (178) 2.1 (0.2) 3p26 Early/mixed 9 2.0 3.0 (0.001) D3S2387 (6) 2.0 (0.1) 3p14 Total 88 1.1 2.2 (0.01) D3S4542 (90) 1.1 (0.25) 4q32 Total 158 1.8 2.9 (0.002) D4S1629 (158) 1.9 (0.25) 4q35 Late 204 1.8 2.9 (0.002) D4S1652 (209) 0.9 (0.25) 5p14 Late 37 1.4 2.6 (0.005) D5S2845 (37) 0.5 (0.3) 5q35 Total 182 1.3 2.4 (0.008) D5S211 (182) 1.1 (0.25) 6p21 Total 64 1.0 2.2 (0.01) D6S1017 (64) 1.9 (0.25) 6q27 Total 181 2.2 3.2 (0.0007) D6S1027 (187) 1.5 (0.25) 9p21 Total 55 1.3 2.5 (0.006) D9S1118 (58) 0.6 (0.3) 9q22 Late 101 2.9 3.6 (0.0002) D9S283 (95) 2.0 (0.2) 10p14 Early/mixed 19 1.1 2.3 (0.01) D10S189 (19) 0.3 (0.35) 10q22 Total 92 1.8 2.9 (0.002) D10S1432 (94) 1.1 (0.25) 10q24 Late 135 0.9 2.0 (0.02) D10S1237(135) 1.9 (0.25) 11q25 Total 148 2.1 3.1 (0.001) D11S968 (148) 1.7 (0.25) 13q32 Late 77 1.1 2.3 (0.01) D13S793 (77) 0.5 (0.3) 14q22 Early/mixed 55 2.2 3.2 (0.0007) D14S587 (55) 2.1 (0.15) 15q26 Early/mixed 123 1.3 2.5 (0.006) D15S642 (123) 2.1 (0.15) 16q23 Total 99 1.4 2.6 (0.005) D16S516 (99) 0.9 (0.3) 19q13 Early/mixed 70 7.7 5.9 (1.8×10−9) D19S178 (68) 3.9 (0.1) 21q22 Total 37 0.1 0.7 (0.24) D21S1440 (37) 2.5 (0.2) Xp21 Late 20 1.0 2.2 (0.01) DXS9902 (22) 1.6 (0.25) Chromosome . Stratum . Multipoint analyses . Two-point analyses . . . cM . MLS . Zlr (P-value) . Marker (cM) . TLS (𝛉) . 1p36 Late 27 1.1 (2.3 (0.01) D1S1597 (30) (1.1 (0.25) 1p31 Early/mixed 121 1.6 (2.7 (0.0035) D1S551 (125) (0.4 (0.3) 1q23 Late 178 1.1 (2.2 (0.01) D1S1677 (178) 2.1 (0.2) 3p26 Early/mixed 9 2.0 3.0 (0.001) D3S2387 (6) 2.0 (0.1) 3p14 Total 88 1.1 2.2 (0.01) D3S4542 (90) 1.1 (0.25) 4q32 Total 158 1.8 2.9 (0.002) D4S1629 (158) 1.9 (0.25) 4q35 Late 204 1.8 2.9 (0.002) D4S1652 (209) 0.9 (0.25) 5p14 Late 37 1.4 2.6 (0.005) D5S2845 (37) 0.5 (0.3) 5q35 Total 182 1.3 2.4 (0.008) D5S211 (182) 1.1 (0.25) 6p21 Total 64 1.0 2.2 (0.01) D6S1017 (64) 1.9 (0.25) 6q27 Total 181 2.2 3.2 (0.0007) D6S1027 (187) 1.5 (0.25) 9p21 Total 55 1.3 2.5 (0.006) D9S1118 (58) 0.6 (0.3) 9q22 Late 101 2.9 3.6 (0.0002) D9S283 (95) 2.0 (0.2) 10p14 Early/mixed 19 1.1 2.3 (0.01) D10S189 (19) 0.3 (0.35) 10q22 Total 92 1.8 2.9 (0.002) D10S1432 (94) 1.1 (0.25) 10q24 Late 135 0.9 2.0 (0.02) D10S1237(135) 1.9 (0.25) 11q25 Total 148 2.1 3.1 (0.001) D11S968 (148) 1.7 (0.25) 13q32 Late 77 1.1 2.3 (0.01) D13S793 (77) 0.5 (0.3) 14q22 Early/mixed 55 2.2 3.2 (0.0007) D14S587 (55) 2.1 (0.15) 15q26 Early/mixed 123 1.3 2.5 (0.006) D15S642 (123) 2.1 (0.15) 16q23 Total 99 1.4 2.6 (0.005) D16S516 (99) 0.9 (0.3) 19q13 Early/mixed 70 7.7 5.9 (1.8×10−9) D19S178 (68) 3.9 (0.1) 21q22 Total 37 0.1 0.7 (0.24) D21S1440 (37) 2.5 (0.2) Xp21 Late 20 1.0 2.2 (0.01) DXS9902 (22) 1.6 (0.25) Open in new tab Table 2. Results for the ‘non-Kehoe’ families, those not included in the genome screen of Kehoe et al. (13). Multipoint non-parametric lod scores (MLS) and Z-scores for the likelihood ratio (Zlr) plus two-point parametric lod scores (TLS) and recombination fractions (𝛉) for all chromosomal regions appearing in Table 1 [i.e. those with MLS≥1.0 plus those with ‘suggestive linkage’ (TLS≥1.9) in the two-point analysis alone in the full NIMH sample]. ‘Total non-Kehoe’ refers to the entire non-Kehoe sample (n=238 families); families are ‘late-onset’ if all sampled affected individuals had onset ages ≥65 years, and ‘early/mixed’ otherwise. Chromosomal locations are given in Kosambi centi-Morgans according to the map provided by CIDR. Bold indicates regions of at least ‘suggestive linkage’ by Lander and Kruglyak criteria (23) in either the multipoint or two-point analyses or both. The shaded regions are those that appear in bold in Table 1 [i.e. those with at least ‘suggestive’ linkage by Lander and Kruglyak criteria (23) in either the multipoint or two point analyses or both in the full NIMH sample] Chromosome . Stratum . Multipoint analyses . Two-point analyses . . . cM . MLS . Zlr (P-value) . Marker (cM) . TLS (𝛉) . 1p36 Late 27 1.3 2.4 (0.008) D1S1597 (30) 1.6 (0.15) 1p31 Early/mixed 121 1.7 2.8 (0.003) D1S551 (125) 0.4 (0.2) 1q23 Late 178 0.8 1.9 (0.03) D1S1677 (178) 1.1 (0.15) 3p26 Early/mixed   9 2.9 3.7 (0.0001) D3S2387 (6) 2.0 (0.1) 3p14 Total  88 1.5 2.7 (0.004) D3S4542 (90) 2.1 (0.15) 4q32 Total 158 1.1 2.3 (0.01) D4S1629 (158) 1.9 (0.2) 4q35 Late 204 1.1 2.2 (0.01) D4S1652 (209) 0.6 (0.2) 5p14 Late 37 0.2 0.9 (0.18) D5S2845 (37) 0 (0.3) 5q35 Total 182 0.7 1.8 (0.04) D5S211 (182) 0.3 (0.25) 6p21 Total 64 0.2 0.9 (0.18) D6S1017 (64) 1.2 (0.2) 6q27 Total 181 2.7 3.5 (0.0002) D6S1027 (187) 1.8 (0.2) 9p21 Total  55 0.7 2.1 (0.02) D9S1118 (58) 0.2 (0.3) 9q22 Late 101 0.2 1.0 (0.16) D9S283 (95) 0.8 (0.2) 10p14 Early/mixed  19 1.2 2.3 (0.01) D10S189 (19) 0.9 (0.15) 10q22 Total 92 0.2 1.0 (0.16) D10S1432 (94) 0.1 (0.35) 10q24 Late 135 0.03 0.4 (0.34) D10S1237 (135) 0.4 (0.25) 11q25 Total 148 1.1 2.3 (0.01) D11S968 (148) 0.7 (0.25) 13q32 Late 77 1.4 2.5 (0.006) D13S793 (77) 0.5 (0.3) 14q22 Early/mixed 55 2.9 3.6 (0.0002) D14S587 (55) 2.7 (0.15) 15q26 Early/mixed 123 1.2 2.4 (0.008) D15S642 (123) 2.1 (0.15) 16q23 Total  99 0.6 1.6 (0.05) D16S516 (99) 0 (0.5) 19q13 Early/mixed 70 7.6 5.9 (1.8×10−9) D19S178 (68) 4.5 (0.05) 21q22 Total  37 0.1 0.5 (0.3) D21S1440 (37) 1.6 (0.2) Xp21 Late  20 0.2 1.0 (0.16) DXS9902 (22) 1.0 (0.2) Chromosome . Stratum . Multipoint analyses . Two-point analyses . . . cM . MLS . Zlr (P-value) . Marker (cM) . TLS (𝛉) . 1p36 Late 27 1.3 2.4 (0.008) D1S1597 (30) 1.6 (0.15) 1p31 Early/mixed 121 1.7 2.8 (0.003) D1S551 (125) 0.4 (0.2) 1q23 Late 178 0.8 1.9 (0.03) D1S1677 (178) 1.1 (0.15) 3p26 Early/mixed   9 2.9 3.7 (0.0001) D3S2387 (6) 2.0 (0.1) 3p14 Total  88 1.5 2.7 (0.004) D3S4542 (90) 2.1 (0.15) 4q32 Total 158 1.1 2.3 (0.01) D4S1629 (158) 1.9 (0.2) 4q35 Late 204 1.1 2.2 (0.01) D4S1652 (209) 0.6 (0.2) 5p14 Late 37 0.2 0.9 (0.18) D5S2845 (37) 0 (0.3) 5q35 Total 182 0.7 1.8 (0.04) D5S211 (182) 0.3 (0.25) 6p21 Total 64 0.2 0.9 (0.18) D6S1017 (64) 1.2 (0.2) 6q27 Total 181 2.7 3.5 (0.0002) D6S1027 (187) 1.8 (0.2) 9p21 Total  55 0.7 2.1 (0.02) D9S1118 (58) 0.2 (0.3) 9q22 Late 101 0.2 1.0 (0.16) D9S283 (95) 0.8 (0.2) 10p14 Early/mixed  19 1.2 2.3 (0.01) D10S189 (19) 0.9 (0.15) 10q22 Total 92 0.2 1.0 (0.16) D10S1432 (94) 0.1 (0.35) 10q24 Late 135 0.03 0.4 (0.34) D10S1237 (135) 0.4 (0.25) 11q25 Total 148 1.1 2.3 (0.01) D11S968 (148) 0.7 (0.25) 13q32 Late 77 1.4 2.5 (0.006) D13S793 (77) 0.5 (0.3) 14q22 Early/mixed 55 2.9 3.6 (0.0002) D14S587 (55) 2.7 (0.15) 15q26 Early/mixed 123 1.2 2.4 (0.008) D15S642 (123) 2.1 (0.15) 16q23 Total  99 0.6 1.6 (0.05) D16S516 (99) 0 (0.5) 19q13 Early/mixed 70 7.6 5.9 (1.8×10−9) D19S178 (68) 4.5 (0.05) 21q22 Total  37 0.1 0.5 (0.3) D21S1440 (37) 1.6 (0.2) Xp21 Late  20 0.2 1.0 (0.16) DXS9902 (22) 1.0 (0.2) Open in new tab Table 2. Results for the ‘non-Kehoe’ families, those not included in the genome screen of Kehoe et al. (13). Multipoint non-parametric lod scores (MLS) and Z-scores for the likelihood ratio (Zlr) plus two-point parametric lod scores (TLS) and recombination fractions (𝛉) for all chromosomal regions appearing in Table 1 [i.e. those with MLS≥1.0 plus those with ‘suggestive linkage’ (TLS≥1.9) in the two-point analysis alone in the full NIMH sample]. ‘Total non-Kehoe’ refers to the entire non-Kehoe sample (n=238 families); families are ‘late-onset’ if all sampled affected individuals had onset ages ≥65 years, and ‘early/mixed’ otherwise. Chromosomal locations are given in Kosambi centi-Morgans according to the map provided by CIDR. Bold indicates regions of at least ‘suggestive linkage’ by Lander and Kruglyak criteria (23) in either the multipoint or two-point analyses or both. The shaded regions are those that appear in bold in Table 1 [i.e. those with at least ‘suggestive’ linkage by Lander and Kruglyak criteria (23) in either the multipoint or two point analyses or both in the full NIMH sample] Chromosome . Stratum . Multipoint analyses . Two-point analyses . . . cM . MLS . Zlr (P-value) . Marker (cM) . TLS (𝛉) . 1p36 Late 27 1.3 2.4 (0.008) D1S1597 (30) 1.6 (0.15) 1p31 Early/mixed 121 1.7 2.8 (0.003) D1S551 (125) 0.4 (0.2) 1q23 Late 178 0.8 1.9 (0.03) D1S1677 (178) 1.1 (0.15) 3p26 Early/mixed   9 2.9 3.7 (0.0001) D3S2387 (6) 2.0 (0.1) 3p14 Total  88 1.5 2.7 (0.004) D3S4542 (90) 2.1 (0.15) 4q32 Total 158 1.1 2.3 (0.01) D4S1629 (158) 1.9 (0.2) 4q35 Late 204 1.1 2.2 (0.01) D4S1652 (209) 0.6 (0.2) 5p14 Late 37 0.2 0.9 (0.18) D5S2845 (37) 0 (0.3) 5q35 Total 182 0.7 1.8 (0.04) D5S211 (182) 0.3 (0.25) 6p21 Total 64 0.2 0.9 (0.18) D6S1017 (64) 1.2 (0.2) 6q27 Total 181 2.7 3.5 (0.0002) D6S1027 (187) 1.8 (0.2) 9p21 Total  55 0.7 2.1 (0.02) D9S1118 (58) 0.2 (0.3) 9q22 Late 101 0.2 1.0 (0.16) D9S283 (95) 0.8 (0.2) 10p14 Early/mixed  19 1.2 2.3 (0.01) D10S189 (19) 0.9 (0.15) 10q22 Total 92 0.2 1.0 (0.16) D10S1432 (94) 0.1 (0.35) 10q24 Late 135 0.03 0.4 (0.34) D10S1237 (135) 0.4 (0.25) 11q25 Total 148 1.1 2.3 (0.01) D11S968 (148) 0.7 (0.25) 13q32 Late 77 1.4 2.5 (0.006) D13S793 (77) 0.5 (0.3) 14q22 Early/mixed 55 2.9 3.6 (0.0002) D14S587 (55) 2.7 (0.15) 15q26 Early/mixed 123 1.2 2.4 (0.008) D15S642 (123) 2.1 (0.15) 16q23 Total  99 0.6 1.6 (0.05) D16S516 (99) 0 (0.5) 19q13 Early/mixed 70 7.6 5.9 (1.8×10−9) D19S178 (68) 4.5 (0.05) 21q22 Total  37 0.1 0.5 (0.3) D21S1440 (37) 1.6 (0.2) Xp21 Late  20 0.2 1.0 (0.16) DXS9902 (22) 1.0 (0.2) Chromosome . Stratum . Multipoint analyses . Two-point analyses . . . cM . MLS . Zlr (P-value) . Marker (cM) . TLS (𝛉) . 1p36 Late 27 1.3 2.4 (0.008) D1S1597 (30) 1.6 (0.15) 1p31 Early/mixed 121 1.7 2.8 (0.003) D1S551 (125) 0.4 (0.2) 1q23 Late 178 0.8 1.9 (0.03) D1S1677 (178) 1.1 (0.15) 3p26 Early/mixed   9 2.9 3.7 (0.0001) D3S2387 (6) 2.0 (0.1) 3p14 Total  88 1.5 2.7 (0.004) D3S4542 (90) 2.1 (0.15) 4q32 Total 158 1.1 2.3 (0.01) D4S1629 (158) 1.9 (0.2) 4q35 Late 204 1.1 2.2 (0.01) D4S1652 (209) 0.6 (0.2) 5p14 Late 37 0.2 0.9 (0.18) D5S2845 (37) 0 (0.3) 5q35 Total 182 0.7 1.8 (0.04) D5S211 (182) 0.3 (0.25) 6p21 Total 64 0.2 0.9 (0.18) D6S1017 (64) 1.2 (0.2) 6q27 Total 181 2.7 3.5 (0.0002) D6S1027 (187) 1.8 (0.2) 9p21 Total  55 0.7 2.1 (0.02) D9S1118 (58) 0.2 (0.3) 9q22 Late 101 0.2 1.0 (0.16) D9S283 (95) 0.8 (0.2) 10p14 Early/mixed  19 1.2 2.3 (0.01) D10S189 (19) 0.9 (0.15) 10q22 Total 92 0.2 1.0 (0.16) D10S1432 (94) 0.1 (0.35) 10q24 Late 135 0.03 0.4 (0.34) D10S1237 (135) 0.4 (0.25) 11q25 Total 148 1.1 2.3 (0.01) D11S968 (148) 0.7 (0.25) 13q32 Late 77 1.4 2.5 (0.006) D13S793 (77) 0.5 (0.3) 14q22 Early/mixed 55 2.9 3.6 (0.0002) D14S587 (55) 2.7 (0.15) 15q26 Early/mixed 123 1.2 2.4 (0.008) D15S642 (123) 2.1 (0.15) 16q23 Total  99 0.6 1.6 (0.05) D16S516 (99) 0 (0.5) 19q13 Early/mixed 70 7.6 5.9 (1.8×10−9) D19S178 (68) 4.5 (0.05) 21q22 Total  37 0.1 0.5 (0.3) D21S1440 (37) 1.6 (0.2) Xp21 Late  20 0.2 1.0 (0.16) DXS9902 (22) 1.0 (0.2) Open in new tab References 1 Tanzi, R.E. and Bertram, L. 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Results of a high-resolution genome screen of 437 Alzheimer's Disease families

Blacker, Deborah; (The NIMH Genetics Initiative Alzheimer's Disease Study Group); Bertram, Lars; (The NIMH Genetics Initiative Alzheimer's Disease Study Group); Saunders, Aleister J.; (The NIMH Genetics Initiative Alzheimer's Disease Study Group); Moscarillo, Thomas J.; (The NIMH Genetics Initiative Alzheimer's Disease Study Group); Albert, Marilyn S.; (The NIMH Genetics Initiative Alzheimer's Disease Study Group); Wiener, Howard; (The NIMH Genetics Initiative Alzheimer's Disease Study Group); Perry, Rodney T.; (The NIMH Genetics Initiative Alzheimer's Disease Study Group); Collins, Julianne S.; (The NIMH Genetics Initiative Alzheimer's Disease Study Group); Harrell, Lindy E.; (The NIMH Genetics Initiative Alzheimer's Disease Study Group); Go, Rodney C.P.; (The NIMH Genetics Initiative Alzheimer's Disease Study Group); Mahoney, Amy; (The NIMH Genetics Initiative Alzheimer's Disease Study Group); Beaty, Terri; (The NIMH Genetics Initiative Alzheimer's Disease Study Group); Fallin, M. Danielle; (The NIMH Genetics Initiative Alzheimer's Disease Study Group); Avramopoulos, Dimitrios; (The NIMH Genetics Initiative Alzheimer's Disease Study Group); Chase, Gary A.; (The NIMH Genetics Initiative Alzheimer's Disease Study Group); Folstein, Marshal F.; (The NIMH Genetics Initiative Alzheimer's Disease Study Group); McInnis, Melvin G.; (The NIMH Genetics Initiative Alzheimer's Disease Study Group); Bassett, Susan S.; (The NIMH Genetics Initiative Alzheimer's Disease Study Group); Doheny, Kimberly J.; (The NIMH Genetics Initiative Alzheimer's Disease Study Group); Pugh, Elizabeth W.; (The NIMH Genetics Initiative Alzheimer's Disease Study Group); Tanzi, Rudolph E.; (The NIMH Genetics Initiative Alzheimer's Disease Study Group)
Human Molecular Genetics , Volume 12 (1) – Jan 1, 2003

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Oxford University Press
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Copyright © 2022 Oxford University Press
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0964-6906
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1460-2083
DOI
10.1093/hmg/ddg007
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Abstract

Abstract Alzheimer's disease (AD) is a devastating neurodegenerative disorder of late life with complex inheritance. Mutations in three known genes lead to the rare early-onset autosomal dominant form of AD, while a common polymorphism (ε4) in the gene encoding apolipoprotein E (APOE ) is a risk factor for more typical late-onset (>60 years) AD. A recent study concluded that there are up to four additional genes with an equal or greater contribution to the disease. We performed a 9 cM genome screen of 437 families with AD, the full National Institute of Mental Health (NIMH) sample, which has been carefully ascertained, evaluated and followed by our group over the last decade. Performing standard parametric and non-parametric linkage analyses, we observed a ‘highly significant’ linkage peak by Lander and Kruglyak criteria on chromosome 19q13, which probably represents APOE. Twelve additional locations—on 1q23, 3p26, 4q32, 5p14, 6p21, 6q27, 9q22, 10q24, 11q25, 14q22, 15q26 and 21q22—met criteria for ‘suggestive’ linkage [i.e. two-point lod score (TLS) ≥1.9 and/or multipoint lod score (MLS) ≥2.2] in at least one of our analyses. Although some of these will surely prove to be false positives, these linkage signals should provide a valuable framework for future studies aimed at identifying additional susceptibility genes for late-onset AD. INTRODUCTION Alzheimer's disease (AD) is a devastating neurodegenerative disorder of late life with complex inheritance. A rare Mendelian subform with early onset exhibits autosomal dominant inheritance and both locus and allelic heterogeneity. This form can be caused by any of over 120 mutations in three known genes (reviewed in 1): the amyloid precursor protein (APP), presenilin 1 (PSEN1) and presenilin 2 (PSEN2). For the much more common late-onset form of AD, which shows complex inheritance, only one gene has been consistently associated with the disease. A common polymorphism (ε4) in the gene encoding apolipoprotein E (APOE) confers increased risk for late-onset AD (2, 3), and lowers the age of onset in a dose-dependent fashion (4–6). Although APOE plays a major role in the risk for late-onset AD, a variety of genetic and epidemiological studies have shown that genes beyond APOE are involved in disease etiology (7,8). A recent study (9) in which age of onset was examined as a quantitative trait estimated that up to four additional major genes as well as several minor AD genes remain to be identified. Although in theory age of onset is distinct from risk, for a late-onset disease like AD there is considerable overlap in practice, as has been observed in studies of APOE. In any case, efforts to find genes affecting risk and/or age of onset of AD have made limited progress. Genome screens for AD reported to date (10–12) have selected their samples in a variety of ways, have used both disease risk and age of onset as outcomes, and have employed a wide variety of analytic methods. Many studies use overlapping portions of the NIMH sample used here (10–13), which only adds to the difficulty in understanding the relationship among the various results. Beyond APOE, for which nearby markers have shown detectable (but not necessarily statistically significant) linkage on chromosome 19q13, the major linkage findings reported to date have been on chromosomes 12 (11,13–15), 10 (16–18), and 9 (10,13). In addition, there have been over three dozen reports of genetic association, mostly with genes thought to influence pathobiological pathways in AD (1). Here we report our parametric and non-parametric linkage analyses of a 9 cM genome screen of the 437 multiplex families in the full NIMH Genetics Initiative sample. RESULTS The results of our affecteds-only parametric two-point analyses in FASTLINK (19,20) and non-parametric multipoint analyses in GENEHUNTER-PLUS (21,22) on the full NIMH sample are summarized in Table 1. Our analyses were performed for the total sample (which includes the 437 families in which no sampled affected subject experienced disease onset before age 50; see Methods), and in strata based on age of onset—a ‘late-onset’ stratum (families in which all sampled affected subjects onset ≥65), and an ‘early/mixed-onset’ stratum (all others, i.e. at least one sampled affected subject onsets <65). Table 1 shows multipoint lod score (MLS; also shown in Figure 1 across the genome) and multipoint likelihood ratio Z-score (Zlr), as well as two-point lod score (TLS) and estimated recombination fraction (𝛉) for all loci with MLS>1.0 or ‘suggestive linkage’ in the two-point analyses alone. There is one region—on 19q13—that meets Lander and Kruglyak criteria for ‘highly significant’ linkage (23); this is presumed to represent APOE, as the best linked marker (D19S178) maps within ∼1 Mb upstream of this locus (24). There are 10 additional regions—1q23, 3p26, 4q32, 6p21, 6q27, 9q22, 10q24, 14q22, 15q26 and 21q22—that meet criteria for ‘suggestive’ linkage in the total sample and/or at least one onset-age stratum in at least one of the analyses (23). We chose to analyze the data rounding up all rare marker allele frequencies to at least 0.01 (and adjusting the frequencies of the most common alleles to compensate) in order to decrease the likelihood of false-positive linkage due to the effect of rare alleles (25). We also analyzed the data using ‘unrounded’ allele frequencies estimated from the data, and the results did not change appreciably, although several regions had slightly weaker linkage signals (data not shown). In addition, because of concerns about population heterogeneity, we also analyzed the data excluding the 26 non-Caucasian families; there were no appreciable differences in the results (data not shown). Last, we also analyzed the data allowing for heterogeneity using the two-point HLOD option in GENEHUNTER. Overall, the results were consistent with the regular two-point analyses. However, after accounting for heterogeneity, two new regions, on 5p14 [at 37 cM, HLOD (late-onset)=2.6, α=0.25] and 11q25 [at 148 cM, HLOD (total sample)=2.4, α=0.23], both of which gave modest signals previously, crossed the Lander and Kruglyak threshold, making a total of 12 ‘suggestive’ regions in at least one of our analyses. In addition, one new minor peak appeared on 3p12 [at 114 cM, HLOD (total sample)=1.6, α=0.16] where in the regular two-point analyses no linkage was observed, and one existing peak on 9q22 [at 101 cM, HLOD (late-onset)=2.6, α=0.29] had a notably stronger signal. Because of the overlap among our sample and these reported by other groups, we obtained a list of the NIMH subjects used in the report of Kehoe and colleagues from the NIMH Center for Genetic Studies (http://zork.wustl.edu/∼nimh), and repeated all analyses including only those individuals not used in the Kehoe report (13) or the follow-up Stage II screen of Myers and colleagues (11), which uses approximately the same sample. The remaining sample has markedly less power: it includes only 238 analyzable families with 808 individuals. Nonetheless, most of the observed peaks were still present, and were sometimes larger (1p36, 1p31, 3p26, 3p14, 6q27, 10p14, 13q32, 14q22, 19q13, and 21q22) in the smaller ‘non-Kehoe’ sample in at least one of the analyses (Table 2). DISCUSSION As expected, there is a ‘highly significant’ peak (TLS=3.9, MLS=7.7) in the early/mixed stratum on chromosome 19q13 at marker D19S178, which maps within ∼1 Mb of APOE (24). Interestingly, linkage evidence for late-onset families was less pronounced, and peaked 17 cM (∼14 Mb) proximal at marker D19S433 (TLS=2.3 at 𝛉=0.2, MLS=1.6), which is in agreement with previous reports in this and other samples, suggesting that APOE-ε4 acts in part through a decrease of onset age (6,26). Our findings are consistent with prior findings on chromosome 9, although, as is common in the analysis of complex diseases (27,28), the location information is indistinct within each study, and can vary considerably across studies. Our chromosome 9q22 linkage at ∼101 cM is ∼10 cM distal to a ‘suggestive’ peak (at ∼91 cM) reported in the Kehoe genome screen in a subset of the NIMH sample (13), and again in the Myers (11) screen (stage II of the Kehoe screen), which used the same subset of the NIMH sample plus additional families from the USA and UK. These ‘Kehoe’ families appear to be driving the linkage, since there is no peak observed in this region in the ‘non-Kehoe’ families. In addition, our 9q22 peak and a smaller 9p21 peak at ∼55 cM are flanked by two peaks reported by Pericak-Vance and colleagues (10): a ‘significant’ proximal peak (at ∼43 cM) in the autopsy-confirmed subset of an overlapping sample, and a less pronounced distal peak (at ∼151 cM). The Pericak-Vance genome screen pooled portions of the NIMH sample with other samples, and had access to approximately the same families as the Kehoe group. While both chromosome 9 peaks are absent in the non-Kehoe families, Pericak-Vance and colleagues specifically noted that their peaks were observed consistently across the various subsamples (10). The picture on chromosome 10 is also largely consistent with prior findings, and equally indistinct. The chromosome 10q24 finding at 134 cM was only marginally suggestive in the present analyses (Table 1), but we recently reported significant linkage nearby using a different set of markers in the same sample (18). Our findings were published in tandem with reports from two other groups demonstrating significant linkage ∼30–50 cM proximal (16,17). Very recently, Li and colleagues have reanalyzed their data using age of onset as a quantitative trait (12), and report a peak around 125 cM, i.e. closer to the linkage region that we had identified earlier (between 115 and 127 cM) (18). Interestingly, the multi-point peak in the present analyses (∼92 cM) lies between the peak observed by the latter two studies (16,17) (∼80 cM) and our earlier linkage region, while the two-point peak here (134 cM) lies beyond our earlier peak and close to the region identified in the age at onset analyses of Li and colleagues (12). Similar to the findings on chromosome 9, almost no linkage evidence was observed in the subset of ‘non-Kehoe’ families alone (Table 2). In order to gain a better understanding of the broad signal on chromosome 10, additional analyses of the chromosome 10 data were performed in GENEFINDER (29), which estimates the location and a 95% confidence interval for an unobserved trait locus using multipoint marker information to approximate identity by descent (IBD) sharing in affected sib pairs, yielded strong signals with overlapping confidence intervals across a very broad region from 62 to 131 cM in the late-onset stratum [with Z-scores ranging from 2.5 (P=0.006) to 3.1 (P=0.001)], while the early/mixed stratum had a weaker but somewhat narrower signal from 13 to 37 cM [Z-score 1.6 (P=0.054)]. Thus, it is still unclear whether there are one or two underlying genes located on the long arm of chromosome 10. Many of the remaining linkage peaks lie near interesting candidate genes for AD. Our ‘suggestive’ linkage peak in late-onset families on chromosome 1q23 [which falls in a region where Kehoe and colleagues reported an MLS of 2.7 (13), but we see virtually no signal in the non-Kehoe sample (see Table 2)] is immediately adjacent to the gene encoding nicastrin (NCSTN ), which binds presenilin and is required for γ-secretase activity and Aβ generation (30). The peak on 4q32 maps to a general region that also gave weak evidence for linkage in both genome scans by Pericak-Vance and colleagues (10,14). The gene encoding α-synuclein (SNCA, at 4q21), which has been suggested as an AD candidate gene (31), is more than 70 Mb proximal, and thus is unlikely to account for this signal. The suggestive two-point signal on 6p21, a region that has also only been weakly linked or associated in previous studies (12–14,32) lies within 15 Mb of the gene encoding the tumor necrosis factor-α (TNFA), for which a significant haplotype association has been reported in the NIMH dataset (33). The suggestive multipoint signal on 6q27 (see Table 1) maps within ∼8 Mb of the plasminogen gene (PLG), which is a protease implicated in cleavage of Aβ (34). This region also shows a fairly strong signal in the ‘non-Kehoe’ sample (Table 2). Moreover, a similar region has been implicated in a recent re-analysis of the Kehoe-subset of the NIMH dataset (35). The linked interval on chromosome 14q22 in the early/mixed onset stratum could reflect linkage to the early-onset AD gene PSEN1, which maps ∼20 Mb distal of the best linked marker (D14S587; TLS=2.1 at 𝛉=0.15) and only ∼3 Mb distal of the next best linked marker (D14S588; TLS=1.9 at 𝛉=0.15). This finding is consistent with recent reports that many early-onset AD patients carry mutations in this gene (36) and that a promoter polymorphism 48 bp upstream of PSEN1 increases risk for early onset AD (37). To our knowledge, there are no prior reports of linkage or association near chromosome 15q26, and it should be noted that this ‘suggestive’ peak is driven almost entirely by a single marker (D15S642) at the q-terminal and thus is less likely to be confirmed. Finally, it is of note that the suggestive two-point peak on chromosome 21q22 lies ∼12 Mb from the early-onset AD gene APP, but only 5 Mb from BACE2 [which has been reported to cleave APP near the α-secretase site within the Aβ-domain and is the homolog of the β-secretase (BACE)] (38). Interestingly, there is a linkage signal on chromosome 11q25 (HLOD=2.4, just over the Lander and Kruglyak threshold for suggestive linkage when accounting for heterogeneity, and MLS=2.1 in the regular multipoint analyses) that maps within ∼20 Mb of BACE itself. Of note, no evidence of linkage was observed in the analyses here on chromosome 12 (maximum MLS=0.2 at 57 cM for the early/mixed stratum; maximum TLS=0.8 for marker C12S916 at 57 cM), where our group has reported a highly significant association finding with nearby alpha-2-macroglobulin (A2M ) (39), and follow-up analyses in the full NIMH sample used here remain strong (Saunders et al., submitted). Although this association finding has been controversial, and the great majority of follow-up studies have been negative (for example, see 40,41), several other groups have reported modest linkage signals in this general region (13–15) or association with A2M itself (for a recent review see 47). We report here the results of a high-resolution genome screen of a large, uniformly ascertained and evaluated sample of AD families. Although our results are only partially concordant with prior published reports, and the signals generated are not amenable to rapid gene discovery, this result is consistent with efforts to map other complex diseases. Our analyses reveal the expected strong signal for APOE on chromosome 19, and a number of more modest linkage peaks that deserve follow-up with linkage analysis of additional microsatellite markers as well as association testing of polymorphisms in positional candidate genes. If these analyses continue to provide support for the presence of AD susceptibility genes in these regions, systematic linkage disequilibrium mapping may be warranted. While some of the more marginal peaks in our study probably represent false-positive findings, others, particularly those with relatively stronger signals and/or prior reports (e.g. on chromosomes 9q and 10q), are more likely to harbor genuine AD susceptibility genes. The substantial effort required to identify and characterize as many of these genes as possible will greatly facilitate the development of strategies for treatment, early intervention, and prevention of this devastating disease. MATERIALS AND METHODS Sample Subjects were collected as part of the NIMH Genetics Initiative following a standardized protocol developed and tested by the three sites (42). Each site collected a wealth of information from family members, medical records and direct examination of the subjects in order to reach a diagnosis of AD by NINCDS/ADRDA criteria (26,43). Over the nearly 10 years of follow-up reflected in this dataset, autopsies were obtained on 326 affected subjects (48% of the deceased), and a clinical diagnosis of AD has been confirmed at autopsy by standard research criteria (44,45) in 94% of the cases. The NIMH sample constitutes a national archive for AD genetic research; all DNA samples are stored in a centralized cell repository at Rutgers University, and data are stored in a centralized data management center at Washington University in St Louis. Outside investigators (10–13,16,35,46) have used subsets of the first ∼60% of the samples collected. In order to select a sample more closely resembling more typical AD than had been studied previously, ascertainment criteria for the NIMH sample required only an affected relative pair, with no additional requirements regarding age of onset or family structure. The original sample included a total of 1527 subjects from 457 families. Six families (14 individuals) with only one sampled affected individual available were excluded. In addition, because onset prior to age 50 is strongly associated with PS1 (47), we excluded 14 additional families (with 74 individuals) in which any sampled individual had an onset age under 50 years. The total sample for the present analyses is comprised of 1439 individuals from 437 families, including 994 affected individuals (mean age of onset 72.4±7.7 years, range 50–97 years), 411 unaffected, and 34 with phenotype unknown. Families were classified as ‘late-onset’ (320 families) when all sampled affecteds had onset ages ≥65 years, and ‘early/mixed’ (117 families) otherwise. The family structure of the sample varies widely: 357 families are nuclear, 36 are extended families including one or more affected sibpairs, and 58 are extended families without an affected sibpair. Genotyping techniques Genotyping was performed at the Center for Inherited Disease Research (CIDR) using a modification of the CHLC version 9 marker set (381 markers, average spacing 9 cM, average heterozygosity 0.76, maximum gap 19 cM). Allele calls were reviewed by two technicians, blind to family structure and phenotype. Binning of all allele sizes for each marker was performed using the FASTCLUS procedure in SAS. Calls falling outside of bins and Mendelian inconsistencies, identified using GAS, were reviewed for obvious laboratory errors. Four blind duplicates, four positive and two negative control samples were run with every 86 study samples. The error rate for the genome scan, based on 28 023 paired genotypes from these blind duplicates, was 0.22%. The overall missing data rate was 3.6%. The rate of remaining Mendelian inconsistencies was 0.08%. See also www.cidr.jhmi.edu for details on the marker set and genotyping methods. Statistical techniques We initially calculated allele frequencies with maximum likelihood estimates using all available data with the program USERM13 (48) based on the program MENDEL (49), but for a fraction of the loci with greater than 20 alleles (six in total) we used a compression algorithm that we developed to reduce the number of alleles at a locus by combining the lowest frequency alleles into a single allele, and renumbering the remaining alleles to maintain consecutive numbering. Except for one marker (D2S2739) with 47 alleles, we were able to maintain the heterozygosity of the sample while compressing the most polymorphic loci to fewer than 20 alleles. When comparing linkage results using compressed versus non-compressed alleles, the differences in calculated lod scores never exceeded 0.05 in absolute value (data not shown). In order to protect our results against false-positive findings due to rare alleles (25), we rounded up rare allele frequencies to 0.01 while adjusting the most common alleles proportionally to compensate, and used these for our primary analyses. ‘Affecteds only’ parametric two-point analyses were performed in FASTLINK (19,20) using a dominant inheritance model with a disease gene frequency of 0.02. While affecteds only analysis can sometimes lead to inflation of the lod score, especially in the presence of missing data or misspecified allele frequencies (50,51), we felt that it was still preferable for the present analyses given the uncertainties regarding the true phenotype of ‘unaffected’ individuals and the shape of the age of onset distribution in a familial sample. Penetrance in affected individuals was set to correspond to phenocopy rates of 5% for definite AD (n=289), 10% for probable AD (n=640), and 20% for possible AD (n=65). Multipoint non-parametric analyses were performed in GENEHUNTER-PLUS using the ASM program (exponential model) to calculate MLS and Zlr scores (21,22). Genetic maps and intermarker distances were provided by CIDR (www.cidr.jhmi.edu) and are similar but not identical to those from the Marshfield Center for Medical Genetics (http://research.marshfieldclinic.org/genetics/), and thus use the Kosambi map function. Both parametric and non-parametric analyses were repeated limiting the sample to the 411 white families, and also limiting the sample to the 238 families not included in the analyses of Kehoe et al., and Myers et al. (11,13). In addition, we estimated two-point lod-scores under the assumption of heterogeneity across families (HLOD) in GENEHUNTER PLUS using the same inheritance models as in the TLS analyses (see above). GENEFINDER (29) was used to estimate the location and 95% confidence intervals around an underlying AD locus on chromosome 10q. The program utilizes multipoint marker information to approximate IBD sharing in affected sib pairs, using a robust, model-free approach similar to that used in GENEHUNTER. Based on the assumptions that a single disease locus exists in the map region being studied and that the true IBD sharing between affected siblings will be maximized at the trait locus, GENEFINDER employs generalized estimating equations to estimate the map location of the disease locus. ACKNOWLEDGEMENTS The authors thank all families for their participation, Drs Nan M. Laird and Ellen Wijsman for advice regarding statistical methodology, and Dr Steven Moldin and staff at NIMH and all three sites for assistance with all aspects of the project. This work was sponsored by grants from the NIMH and the National Institute on Aging. L.B. was a fellow of the Deutsche Forschungsgemeinschaft and is now recipient of a translational research fellowship of the Harvard Center for Neurodegeneration and Repair. A.J.S. was an NIA-NRSA recipient. Data and biomaterials were collected in three projects that participated in the National Institute of Mental Health (NIMH) Alzheimer Disease Genetics Initiative. From 1991–1998, the Principal Investigators and Co-Investigators were: Massachusetts General Hospital, Boston, MA, U01 MH46281, M.S.A and D.B.; Johns Hopkins University, Baltimore, MD, U01 MH46290, S.S.B., G.A.C. and M.F.F.; University of Alabama, Birmingham, AL, U01 MH46373, R.C.P.G. and L.E.H. Genotyping services were provided by the Center for Inherited Disease Research (CIDR), which is fully funded through a federal contract from the National Institutes of Health to The Johns Hopkins University, Contract Number N01-HG-65403. * To whom correspondence should be addressed at: Genetics and Aging Research Unit, Center for Aging, Genetics and Neurodegeneration, MGH East, 114 16th Street, Charlestown, MA 02129-4404, USA. Tel: +1 6177266845; Fax: +1 6177241949; Email: tanzi@helix.mgh.harvard.edu Open in new tabDownload slide Figure 1.Non-parametric multipoint lod score curves for each chromosome in the genome screen. Families were considered ‘late-onset’ if all sampled affected individuals had onset ages ≥65 years, and ‘early/mixed-onset’ otherwise. Marker locations are given in Kosambi centi-Morgans according to the map supplied by CIDR. Note that the scale used for chromosome 19 is different from that for the remainder of the genome. Table 1. MLS and Z-scores for the likelihood ratio (Zlr) plus TLS and recombination fractions (𝛉) for all chromosomal regions with MLS ≥1.0 plus those with ‘suggestive linkage’ (TLS≥1.9) in the two-point analysis alone. ‘Total’ refers to the full NIMH sample (n=437 families); families are ‘late-onset’ if all sampled affected individuals had onset ages ≥65 years, and ‘early/mixed’ otherwise. Chromosomal locations are given in Kosambi centi-Morgans according to the map provided by CIDR. Bold indicates regions of at least ‘suggestive linkage’ by Lander and Kruglyak criteria (23) in either the multipoint or two-point analyses or both Chromosome . Stratum . Multipoint analyses . Two-point analyses . . . cM . MLS . Zlr (P-value) . Marker (cM) . TLS (𝛉) . 1p36 Late 27 1.1 (2.3 (0.01) D1S1597 (30) (1.1 (0.25) 1p31 Early/mixed 121 1.6 (2.7 (0.0035) D1S551 (125) (0.4 (0.3) 1q23 Late 178 1.1 (2.2 (0.01) D1S1677 (178) 2.1 (0.2) 3p26 Early/mixed 9 2.0 3.0 (0.001) D3S2387 (6) 2.0 (0.1) 3p14 Total 88 1.1 2.2 (0.01) D3S4542 (90) 1.1 (0.25) 4q32 Total 158 1.8 2.9 (0.002) D4S1629 (158) 1.9 (0.25) 4q35 Late 204 1.8 2.9 (0.002) D4S1652 (209) 0.9 (0.25) 5p14 Late 37 1.4 2.6 (0.005) D5S2845 (37) 0.5 (0.3) 5q35 Total 182 1.3 2.4 (0.008) D5S211 (182) 1.1 (0.25) 6p21 Total 64 1.0 2.2 (0.01) D6S1017 (64) 1.9 (0.25) 6q27 Total 181 2.2 3.2 (0.0007) D6S1027 (187) 1.5 (0.25) 9p21 Total 55 1.3 2.5 (0.006) D9S1118 (58) 0.6 (0.3) 9q22 Late 101 2.9 3.6 (0.0002) D9S283 (95) 2.0 (0.2) 10p14 Early/mixed 19 1.1 2.3 (0.01) D10S189 (19) 0.3 (0.35) 10q22 Total 92 1.8 2.9 (0.002) D10S1432 (94) 1.1 (0.25) 10q24 Late 135 0.9 2.0 (0.02) D10S1237(135) 1.9 (0.25) 11q25 Total 148 2.1 3.1 (0.001) D11S968 (148) 1.7 (0.25) 13q32 Late 77 1.1 2.3 (0.01) D13S793 (77) 0.5 (0.3) 14q22 Early/mixed 55 2.2 3.2 (0.0007) D14S587 (55) 2.1 (0.15) 15q26 Early/mixed 123 1.3 2.5 (0.006) D15S642 (123) 2.1 (0.15) 16q23 Total 99 1.4 2.6 (0.005) D16S516 (99) 0.9 (0.3) 19q13 Early/mixed 70 7.7 5.9 (1.8×10−9) D19S178 (68) 3.9 (0.1) 21q22 Total 37 0.1 0.7 (0.24) D21S1440 (37) 2.5 (0.2) Xp21 Late 20 1.0 2.2 (0.01) DXS9902 (22) 1.6 (0.25) Chromosome . Stratum . Multipoint analyses . Two-point analyses . . . cM . MLS . Zlr (P-value) . Marker (cM) . TLS (𝛉) . 1p36 Late 27 1.1 (2.3 (0.01) D1S1597 (30) (1.1 (0.25) 1p31 Early/mixed 121 1.6 (2.7 (0.0035) D1S551 (125) (0.4 (0.3) 1q23 Late 178 1.1 (2.2 (0.01) D1S1677 (178) 2.1 (0.2) 3p26 Early/mixed 9 2.0 3.0 (0.001) D3S2387 (6) 2.0 (0.1) 3p14 Total 88 1.1 2.2 (0.01) D3S4542 (90) 1.1 (0.25) 4q32 Total 158 1.8 2.9 (0.002) D4S1629 (158) 1.9 (0.25) 4q35 Late 204 1.8 2.9 (0.002) D4S1652 (209) 0.9 (0.25) 5p14 Late 37 1.4 2.6 (0.005) D5S2845 (37) 0.5 (0.3) 5q35 Total 182 1.3 2.4 (0.008) D5S211 (182) 1.1 (0.25) 6p21 Total 64 1.0 2.2 (0.01) D6S1017 (64) 1.9 (0.25) 6q27 Total 181 2.2 3.2 (0.0007) D6S1027 (187) 1.5 (0.25) 9p21 Total 55 1.3 2.5 (0.006) D9S1118 (58) 0.6 (0.3) 9q22 Late 101 2.9 3.6 (0.0002) D9S283 (95) 2.0 (0.2) 10p14 Early/mixed 19 1.1 2.3 (0.01) D10S189 (19) 0.3 (0.35) 10q22 Total 92 1.8 2.9 (0.002) D10S1432 (94) 1.1 (0.25) 10q24 Late 135 0.9 2.0 (0.02) D10S1237(135) 1.9 (0.25) 11q25 Total 148 2.1 3.1 (0.001) D11S968 (148) 1.7 (0.25) 13q32 Late 77 1.1 2.3 (0.01) D13S793 (77) 0.5 (0.3) 14q22 Early/mixed 55 2.2 3.2 (0.0007) D14S587 (55) 2.1 (0.15) 15q26 Early/mixed 123 1.3 2.5 (0.006) D15S642 (123) 2.1 (0.15) 16q23 Total 99 1.4 2.6 (0.005) D16S516 (99) 0.9 (0.3) 19q13 Early/mixed 70 7.7 5.9 (1.8×10−9) D19S178 (68) 3.9 (0.1) 21q22 Total 37 0.1 0.7 (0.24) D21S1440 (37) 2.5 (0.2) Xp21 Late 20 1.0 2.2 (0.01) DXS9902 (22) 1.6 (0.25) Open in new tab Table 1. MLS and Z-scores for the likelihood ratio (Zlr) plus TLS and recombination fractions (𝛉) for all chromosomal regions with MLS ≥1.0 plus those with ‘suggestive linkage’ (TLS≥1.9) in the two-point analysis alone. ‘Total’ refers to the full NIMH sample (n=437 families); families are ‘late-onset’ if all sampled affected individuals had onset ages ≥65 years, and ‘early/mixed’ otherwise. Chromosomal locations are given in Kosambi centi-Morgans according to the map provided by CIDR. Bold indicates regions of at least ‘suggestive linkage’ by Lander and Kruglyak criteria (23) in either the multipoint or two-point analyses or both Chromosome . Stratum . Multipoint analyses . Two-point analyses . . . cM . MLS . Zlr (P-value) . Marker (cM) . TLS (𝛉) . 1p36 Late 27 1.1 (2.3 (0.01) D1S1597 (30) (1.1 (0.25) 1p31 Early/mixed 121 1.6 (2.7 (0.0035) D1S551 (125) (0.4 (0.3) 1q23 Late 178 1.1 (2.2 (0.01) D1S1677 (178) 2.1 (0.2) 3p26 Early/mixed 9 2.0 3.0 (0.001) D3S2387 (6) 2.0 (0.1) 3p14 Total 88 1.1 2.2 (0.01) D3S4542 (90) 1.1 (0.25) 4q32 Total 158 1.8 2.9 (0.002) D4S1629 (158) 1.9 (0.25) 4q35 Late 204 1.8 2.9 (0.002) D4S1652 (209) 0.9 (0.25) 5p14 Late 37 1.4 2.6 (0.005) D5S2845 (37) 0.5 (0.3) 5q35 Total 182 1.3 2.4 (0.008) D5S211 (182) 1.1 (0.25) 6p21 Total 64 1.0 2.2 (0.01) D6S1017 (64) 1.9 (0.25) 6q27 Total 181 2.2 3.2 (0.0007) D6S1027 (187) 1.5 (0.25) 9p21 Total 55 1.3 2.5 (0.006) D9S1118 (58) 0.6 (0.3) 9q22 Late 101 2.9 3.6 (0.0002) D9S283 (95) 2.0 (0.2) 10p14 Early/mixed 19 1.1 2.3 (0.01) D10S189 (19) 0.3 (0.35) 10q22 Total 92 1.8 2.9 (0.002) D10S1432 (94) 1.1 (0.25) 10q24 Late 135 0.9 2.0 (0.02) D10S1237(135) 1.9 (0.25) 11q25 Total 148 2.1 3.1 (0.001) D11S968 (148) 1.7 (0.25) 13q32 Late 77 1.1 2.3 (0.01) D13S793 (77) 0.5 (0.3) 14q22 Early/mixed 55 2.2 3.2 (0.0007) D14S587 (55) 2.1 (0.15) 15q26 Early/mixed 123 1.3 2.5 (0.006) D15S642 (123) 2.1 (0.15) 16q23 Total 99 1.4 2.6 (0.005) D16S516 (99) 0.9 (0.3) 19q13 Early/mixed 70 7.7 5.9 (1.8×10−9) D19S178 (68) 3.9 (0.1) 21q22 Total 37 0.1 0.7 (0.24) D21S1440 (37) 2.5 (0.2) Xp21 Late 20 1.0 2.2 (0.01) DXS9902 (22) 1.6 (0.25) Chromosome . Stratum . Multipoint analyses . Two-point analyses . . . cM . MLS . Zlr (P-value) . Marker (cM) . TLS (𝛉) . 1p36 Late 27 1.1 (2.3 (0.01) D1S1597 (30) (1.1 (0.25) 1p31 Early/mixed 121 1.6 (2.7 (0.0035) D1S551 (125) (0.4 (0.3) 1q23 Late 178 1.1 (2.2 (0.01) D1S1677 (178) 2.1 (0.2) 3p26 Early/mixed 9 2.0 3.0 (0.001) D3S2387 (6) 2.0 (0.1) 3p14 Total 88 1.1 2.2 (0.01) D3S4542 (90) 1.1 (0.25) 4q32 Total 158 1.8 2.9 (0.002) D4S1629 (158) 1.9 (0.25) 4q35 Late 204 1.8 2.9 (0.002) D4S1652 (209) 0.9 (0.25) 5p14 Late 37 1.4 2.6 (0.005) D5S2845 (37) 0.5 (0.3) 5q35 Total 182 1.3 2.4 (0.008) D5S211 (182) 1.1 (0.25) 6p21 Total 64 1.0 2.2 (0.01) D6S1017 (64) 1.9 (0.25) 6q27 Total 181 2.2 3.2 (0.0007) D6S1027 (187) 1.5 (0.25) 9p21 Total 55 1.3 2.5 (0.006) D9S1118 (58) 0.6 (0.3) 9q22 Late 101 2.9 3.6 (0.0002) D9S283 (95) 2.0 (0.2) 10p14 Early/mixed 19 1.1 2.3 (0.01) D10S189 (19) 0.3 (0.35) 10q22 Total 92 1.8 2.9 (0.002) D10S1432 (94) 1.1 (0.25) 10q24 Late 135 0.9 2.0 (0.02) D10S1237(135) 1.9 (0.25) 11q25 Total 148 2.1 3.1 (0.001) D11S968 (148) 1.7 (0.25) 13q32 Late 77 1.1 2.3 (0.01) D13S793 (77) 0.5 (0.3) 14q22 Early/mixed 55 2.2 3.2 (0.0007) D14S587 (55) 2.1 (0.15) 15q26 Early/mixed 123 1.3 2.5 (0.006) D15S642 (123) 2.1 (0.15) 16q23 Total 99 1.4 2.6 (0.005) D16S516 (99) 0.9 (0.3) 19q13 Early/mixed 70 7.7 5.9 (1.8×10−9) D19S178 (68) 3.9 (0.1) 21q22 Total 37 0.1 0.7 (0.24) D21S1440 (37) 2.5 (0.2) Xp21 Late 20 1.0 2.2 (0.01) DXS9902 (22) 1.6 (0.25) Open in new tab Table 2. Results for the ‘non-Kehoe’ families, those not included in the genome screen of Kehoe et al. (13). Multipoint non-parametric lod scores (MLS) and Z-scores for the likelihood ratio (Zlr) plus two-point parametric lod scores (TLS) and recombination fractions (𝛉) for all chromosomal regions appearing in Table 1 [i.e. those with MLS≥1.0 plus those with ‘suggestive linkage’ (TLS≥1.9) in the two-point analysis alone in the full NIMH sample]. ‘Total non-Kehoe’ refers to the entire non-Kehoe sample (n=238 families); families are ‘late-onset’ if all sampled affected individuals had onset ages ≥65 years, and ‘early/mixed’ otherwise. Chromosomal locations are given in Kosambi centi-Morgans according to the map provided by CIDR. Bold indicates regions of at least ‘suggestive linkage’ by Lander and Kruglyak criteria (23) in either the multipoint or two-point analyses or both. The shaded regions are those that appear in bold in Table 1 [i.e. those with at least ‘suggestive’ linkage by Lander and Kruglyak criteria (23) in either the multipoint or two point analyses or both in the full NIMH sample] Chromosome . Stratum . Multipoint analyses . Two-point analyses . . . cM . MLS . Zlr (P-value) . Marker (cM) . TLS (𝛉) . 1p36 Late 27 1.3 2.4 (0.008) D1S1597 (30) 1.6 (0.15) 1p31 Early/mixed 121 1.7 2.8 (0.003) D1S551 (125) 0.4 (0.2) 1q23 Late 178 0.8 1.9 (0.03) D1S1677 (178) 1.1 (0.15) 3p26 Early/mixed   9 2.9 3.7 (0.0001) D3S2387 (6) 2.0 (0.1) 3p14 Total  88 1.5 2.7 (0.004) D3S4542 (90) 2.1 (0.15) 4q32 Total 158 1.1 2.3 (0.01) D4S1629 (158) 1.9 (0.2) 4q35 Late 204 1.1 2.2 (0.01) D4S1652 (209) 0.6 (0.2) 5p14 Late 37 0.2 0.9 (0.18) D5S2845 (37) 0 (0.3) 5q35 Total 182 0.7 1.8 (0.04) D5S211 (182) 0.3 (0.25) 6p21 Total 64 0.2 0.9 (0.18) D6S1017 (64) 1.2 (0.2) 6q27 Total 181 2.7 3.5 (0.0002) D6S1027 (187) 1.8 (0.2) 9p21 Total  55 0.7 2.1 (0.02) D9S1118 (58) 0.2 (0.3) 9q22 Late 101 0.2 1.0 (0.16) D9S283 (95) 0.8 (0.2) 10p14 Early/mixed  19 1.2 2.3 (0.01) D10S189 (19) 0.9 (0.15) 10q22 Total 92 0.2 1.0 (0.16) D10S1432 (94) 0.1 (0.35) 10q24 Late 135 0.03 0.4 (0.34) D10S1237 (135) 0.4 (0.25) 11q25 Total 148 1.1 2.3 (0.01) D11S968 (148) 0.7 (0.25) 13q32 Late 77 1.4 2.5 (0.006) D13S793 (77) 0.5 (0.3) 14q22 Early/mixed 55 2.9 3.6 (0.0002) D14S587 (55) 2.7 (0.15) 15q26 Early/mixed 123 1.2 2.4 (0.008) D15S642 (123) 2.1 (0.15) 16q23 Total  99 0.6 1.6 (0.05) D16S516 (99) 0 (0.5) 19q13 Early/mixed 70 7.6 5.9 (1.8×10−9) D19S178 (68) 4.5 (0.05) 21q22 Total  37 0.1 0.5 (0.3) D21S1440 (37) 1.6 (0.2) Xp21 Late  20 0.2 1.0 (0.16) DXS9902 (22) 1.0 (0.2) Chromosome . Stratum . Multipoint analyses . Two-point analyses . . . cM . MLS . Zlr (P-value) . Marker (cM) . TLS (𝛉) . 1p36 Late 27 1.3 2.4 (0.008) D1S1597 (30) 1.6 (0.15) 1p31 Early/mixed 121 1.7 2.8 (0.003) D1S551 (125) 0.4 (0.2) 1q23 Late 178 0.8 1.9 (0.03) D1S1677 (178) 1.1 (0.15) 3p26 Early/mixed   9 2.9 3.7 (0.0001) D3S2387 (6) 2.0 (0.1) 3p14 Total  88 1.5 2.7 (0.004) D3S4542 (90) 2.1 (0.15) 4q32 Total 158 1.1 2.3 (0.01) D4S1629 (158) 1.9 (0.2) 4q35 Late 204 1.1 2.2 (0.01) D4S1652 (209) 0.6 (0.2) 5p14 Late 37 0.2 0.9 (0.18) D5S2845 (37) 0 (0.3) 5q35 Total 182 0.7 1.8 (0.04) D5S211 (182) 0.3 (0.25) 6p21 Total 64 0.2 0.9 (0.18) D6S1017 (64) 1.2 (0.2) 6q27 Total 181 2.7 3.5 (0.0002) D6S1027 (187) 1.8 (0.2) 9p21 Total  55 0.7 2.1 (0.02) D9S1118 (58) 0.2 (0.3) 9q22 Late 101 0.2 1.0 (0.16) D9S283 (95) 0.8 (0.2) 10p14 Early/mixed  19 1.2 2.3 (0.01) D10S189 (19) 0.9 (0.15) 10q22 Total 92 0.2 1.0 (0.16) D10S1432 (94) 0.1 (0.35) 10q24 Late 135 0.03 0.4 (0.34) D10S1237 (135) 0.4 (0.25) 11q25 Total 148 1.1 2.3 (0.01) D11S968 (148) 0.7 (0.25) 13q32 Late 77 1.4 2.5 (0.006) D13S793 (77) 0.5 (0.3) 14q22 Early/mixed 55 2.9 3.6 (0.0002) D14S587 (55) 2.7 (0.15) 15q26 Early/mixed 123 1.2 2.4 (0.008) D15S642 (123) 2.1 (0.15) 16q23 Total  99 0.6 1.6 (0.05) D16S516 (99) 0 (0.5) 19q13 Early/mixed 70 7.6 5.9 (1.8×10−9) D19S178 (68) 4.5 (0.05) 21q22 Total  37 0.1 0.5 (0.3) D21S1440 (37) 1.6 (0.2) Xp21 Late  20 0.2 1.0 (0.16) DXS9902 (22) 1.0 (0.2) Open in new tab Table 2. Results for the ‘non-Kehoe’ families, those not included in the genome screen of Kehoe et al. (13). Multipoint non-parametric lod scores (MLS) and Z-scores for the likelihood ratio (Zlr) plus two-point parametric lod scores (TLS) and recombination fractions (𝛉) for all chromosomal regions appearing in Table 1 [i.e. those with MLS≥1.0 plus those with ‘suggestive linkage’ (TLS≥1.9) in the two-point analysis alone in the full NIMH sample]. ‘Total non-Kehoe’ refers to the entire non-Kehoe sample (n=238 families); families are ‘late-onset’ if all sampled affected individuals had onset ages ≥65 years, and ‘early/mixed’ otherwise. Chromosomal locations are given in Kosambi centi-Morgans according to the map provided by CIDR. Bold indicates regions of at least ‘suggestive linkage’ by Lander and Kruglyak criteria (23) in either the multipoint or two-point analyses or both. The shaded regions are those that appear in bold in Table 1 [i.e. those with at least ‘suggestive’ linkage by Lander and Kruglyak criteria (23) in either the multipoint or two point analyses or both in the full NIMH sample] Chromosome . Stratum . Multipoint analyses . Two-point analyses . . . cM . MLS . Zlr (P-value) . Marker (cM) . TLS (𝛉) . 1p36 Late 27 1.3 2.4 (0.008) D1S1597 (30) 1.6 (0.15) 1p31 Early/mixed 121 1.7 2.8 (0.003) D1S551 (125) 0.4 (0.2) 1q23 Late 178 0.8 1.9 (0.03) D1S1677 (178) 1.1 (0.15) 3p26 Early/mixed   9 2.9 3.7 (0.0001) D3S2387 (6) 2.0 (0.1) 3p14 Total  88 1.5 2.7 (0.004) D3S4542 (90) 2.1 (0.15) 4q32 Total 158 1.1 2.3 (0.01) D4S1629 (158) 1.9 (0.2) 4q35 Late 204 1.1 2.2 (0.01) D4S1652 (209) 0.6 (0.2) 5p14 Late 37 0.2 0.9 (0.18) D5S2845 (37) 0 (0.3) 5q35 Total 182 0.7 1.8 (0.04) D5S211 (182) 0.3 (0.25) 6p21 Total 64 0.2 0.9 (0.18) D6S1017 (64) 1.2 (0.2) 6q27 Total 181 2.7 3.5 (0.0002) D6S1027 (187) 1.8 (0.2) 9p21 Total  55 0.7 2.1 (0.02) D9S1118 (58) 0.2 (0.3) 9q22 Late 101 0.2 1.0 (0.16) D9S283 (95) 0.8 (0.2) 10p14 Early/mixed  19 1.2 2.3 (0.01) D10S189 (19) 0.9 (0.15) 10q22 Total 92 0.2 1.0 (0.16) D10S1432 (94) 0.1 (0.35) 10q24 Late 135 0.03 0.4 (0.34) D10S1237 (135) 0.4 (0.25) 11q25 Total 148 1.1 2.3 (0.01) D11S968 (148) 0.7 (0.25) 13q32 Late 77 1.4 2.5 (0.006) D13S793 (77) 0.5 (0.3) 14q22 Early/mixed 55 2.9 3.6 (0.0002) D14S587 (55) 2.7 (0.15) 15q26 Early/mixed 123 1.2 2.4 (0.008) D15S642 (123) 2.1 (0.15) 16q23 Total  99 0.6 1.6 (0.05) D16S516 (99) 0 (0.5) 19q13 Early/mixed 70 7.6 5.9 (1.8×10−9) D19S178 (68) 4.5 (0.05) 21q22 Total  37 0.1 0.5 (0.3) D21S1440 (37) 1.6 (0.2) Xp21 Late  20 0.2 1.0 (0.16) DXS9902 (22) 1.0 (0.2) Chromosome . Stratum . Multipoint analyses . Two-point analyses . . . cM . MLS . Zlr (P-value) . Marker (cM) . TLS (𝛉) . 1p36 Late 27 1.3 2.4 (0.008) D1S1597 (30) 1.6 (0.15) 1p31 Early/mixed 121 1.7 2.8 (0.003) D1S551 (125) 0.4 (0.2) 1q23 Late 178 0.8 1.9 (0.03) D1S1677 (178) 1.1 (0.15) 3p26 Early/mixed   9 2.9 3.7 (0.0001) D3S2387 (6) 2.0 (0.1) 3p14 Total  88 1.5 2.7 (0.004) D3S4542 (90) 2.1 (0.15) 4q32 Total 158 1.1 2.3 (0.01) D4S1629 (158) 1.9 (0.2) 4q35 Late 204 1.1 2.2 (0.01) D4S1652 (209) 0.6 (0.2) 5p14 Late 37 0.2 0.9 (0.18) D5S2845 (37) 0 (0.3) 5q35 Total 182 0.7 1.8 (0.04) D5S211 (182) 0.3 (0.25) 6p21 Total 64 0.2 0.9 (0.18) D6S1017 (64) 1.2 (0.2) 6q27 Total 181 2.7 3.5 (0.0002) D6S1027 (187) 1.8 (0.2) 9p21 Total  55 0.7 2.1 (0.02) D9S1118 (58) 0.2 (0.3) 9q22 Late 101 0.2 1.0 (0.16) D9S283 (95) 0.8 (0.2) 10p14 Early/mixed  19 1.2 2.3 (0.01) D10S189 (19) 0.9 (0.15) 10q22 Total 92 0.2 1.0 (0.16) D10S1432 (94) 0.1 (0.35) 10q24 Late 135 0.03 0.4 (0.34) D10S1237 (135) 0.4 (0.25) 11q25 Total 148 1.1 2.3 (0.01) D11S968 (148) 0.7 (0.25) 13q32 Late 77 1.4 2.5 (0.006) D13S793 (77) 0.5 (0.3) 14q22 Early/mixed 55 2.9 3.6 (0.0002) D14S587 (55) 2.7 (0.15) 15q26 Early/mixed 123 1.2 2.4 (0.008) D15S642 (123) 2.1 (0.15) 16q23 Total  99 0.6 1.6 (0.05) D16S516 (99) 0 (0.5) 19q13 Early/mixed 70 7.6 5.9 (1.8×10−9) D19S178 (68) 4.5 (0.05) 21q22 Total  37 0.1 0.5 (0.3) D21S1440 (37) 1.6 (0.2) Xp21 Late  20 0.2 1.0 (0.16) DXS9902 (22) 1.0 (0.2) Open in new tab References 1 Tanzi, R.E. and Bertram, L. 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Journal

Human Molecular GeneticsOxford University Press

Published: Jan 1, 2003

Keywords: alzheimer's disease; apolipoprotein e; genome; false-positive results; genetic inheritance

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