Andrew Grupe

Identification of complement factor 5 as a susceptibility locus for experimental allergic asthma

The prevalence and severity of allergic asthma continue to rise, lending urgency to the search for environmental triggers and genetic substrates. Using microarray analysis of pulmonary gene expression and single nucleotide polymorphism–based genotyping, combined with quantitative trait locus analysis, we identified the gene encoding complement factor 5 (C5) as a susceptibility locus for allergen-induced airway hyperresponsiveness in a murine model of asthma. A deletion in the coding sequence of C5 leads to C5-deficiency and susceptibility. Interleukin 12 (IL-12) is able to prevent or reverse experimental allergic asthma. Blockade of the C5a receptor rendered human monocytes unable to produce IL-12, mimicking blunted IL-12 production by macrophages from C5-deficient mice and providing a mechanism for the regulation of susceptibility to asthma by C5. The role of complement in modulating susceptibility to asthma highlights the importance of immunoregulatory events at the interface of innate and adaptive immunity in disease pathogenesis.

Sexually dimorphic effect of the Val66Met polymorphism of BDNF on susceptibility to Alzheimer's disease: New data and meta-analysis.

Conflicting results have been reported as to whether genetic variations (Val66Met and C270T) of the brain‐derived neurotrophic factor gene (BDNF) confer susceptibility to Alzheimers disease (AD). We genotyped these polymorphisms in a Japanese sample of 657 patients with AD and 525 controls, and obtained weak evidence of association for Val66Met (P = 0.063), but not for C270T. After stratification by sex, we found a significant allelic association between Val66Met and AD in women (P = 0.017), but not in men. To confirm these observations, we collected genotyping data for each sex from 16 research centers worldwide (4,711 patients and 4,537 controls in total). The meta‐analysis revealed that there was a clear sex difference in the allelic association; the Met66 allele confers susceptibility to AD in women (odds ratio = 1.14, 95% CI 1.05–1.24, P = 0.002), but not in men. Our results provide evidence that the Met66 allele of BDNF has a sexually dimorphic effect on susceptibility to AD.

SORL1 variants and risk of late-onset Alzheimer's disease

A recent study reported significant association of late-onset Alzheimers disease (LOAD) with multiple single nucleotide polymorphisms (SNPs) and haplotypes in SORL1, a neuronal sortilin-related receptor protein known to be involved in the trafficking and processing of amyloid precursor protein. Here we attempted to validate this finding in three large, well characterized case-control series. Approximately 2000 samples from the three series were individually genotyped for 12 SNPs, including the 10 reported significant SNPs and 2 that constitute the reported significant haplotypes. A total of 25 allelic and haplotypic association tests were performed. One SNP rs2070045 was marginally replicated in the three sample sets combined (nominal P=0.035); however, this result does not remain significant when accounting for multiple comparisons. Further validation in other sample sets will be required to assess the true effects of SORL1 variants in LOAD.

OncoKB: A Precision Oncology Knowledge Base

PURPOSE With prospective clinical sequencing of tumors emerging as a mainstay in cancer care, there is an urgent need for a clinical support tool that distills the clinical implications associated with specific mutation events into a standardized and easily interpretable format. To this end, we developed OncoKB, an expert-guided precision oncology knowledge base. METHODS OncoKB annotates the biological and oncogenic effect and the prognostic and predictive significance of somatic molecular alterations. Potential treatment implications are stratified by the level of evidence that a specific molecular alteration is predictive of drug response based on US Food and Drug Administration (FDA) labeling, National Comprehensive Cancer Network (NCCN) guidelines, disease-focused expert group recommendations and the scientific literature. RESULTS To date, over 3000 unique mutations, fusions, and copy number alterations in 418 cancer-associated genes have been annotated. To test the utility of OncoKB, we annotated all genomic events in 5983 primary tumor samples in 19 cancer types. Forty-one percent of samples harbored at least one potentially actionable alteration, of which 7.5% were predictive of clinical benefit from a standard treatment. OncoKB annotations are available through a public web resource (http://oncokb.org/) and are also incorporated into the cBioPortal for Cancer Genomics to facilitate the interpretation of genomic alterations by physicians and researchers. CONCLUSION OncoKB, a comprehensive and curated precision oncology knowledge base, offers oncologists detailed, evidence-based information about individual somatic mutations and structural alterations present in patient tumors with the goal of supporting optimal treatment decisions.

Apolipoprotein E levels in cerebrospinal fluid and the effects of ABCA1 polymorphisms

BackgroundAnimal studies suggest that brain apolipoprotein E (apoE) levels influence amyloid-β (Aβ) deposition and thus risk for Alzheimers disease (AD). We have previously demonstrated that deletion of the ATP-binding cassette A1 transporter (ABCA1) in mice causes dramatic reductions in brain and cerebrospinal fluid (CSF) apoE levels and lipidation. To examine whether polymorphisms in ABCA1 affect CSF apoE levels in humans, we measured apoE in CSF taken from 168 subjects who were 43 to 91 years old and were either cognitively normal or who had mild AD. We then genotyped the subjects for ten previously identified ABCA1 single nucleotide polymorphisms (SNPs).ResultsIn all subjects, the mean CSF apoE level was 9.09 μg/ml with a standard deviation of 2.70 μg/ml. Levels of apoE in CSF samples taken from the same individual two weeks apart were strongly correlated (r2 = 0.93, p < 0.01). In contrast, CSF apoE levels in different individuals varied widely (coefficient of variation = 46%). CSF apoE levels did not vary according to AD status, APOE genotype, gender or race. Average apoE levels increased with age by ~0.5 μg/ml per 10 years (r2 = 0.05, p = 0.003). We found no significant associations between CSF apoE levels and the ten ABCA1 SNPs we genotyped. Moreover, in a separate sample of 1225 AD cases and 1431 controls, we found no association between the ABCA1 SNP rs2230806 and AD as has been previously reported.ConclusionWe found that CSF apoE levels vary widely between individuals, but are stable within individuals over a two-week interval. AD status, APOE genotype, gender and race do not affect CSF apoE levels, but average CSF apoE levels increase with age. Given the lack of association between CSF apoE levels and genotypes for the ABCA1 SNPs we examined, either these SNPs do not affect ABCA1 function or if they do, they do not have strong effects in the CNS. Finally, we find no evidence for an association between the ABCA1 SNP rs2230806 and AD in a large sample set.

Association of ABCA1 with late-onset Alzheimer's disease is not observed in a case-control study.

Genetic association of ABCA1 or the ATP-binding cassette A1 transporter with late-onset Alzheimers disease (LOAD) has recently been proposed for a haplotype comprised of three single nucleotide polymorphisms (SNPs). We have genotyped these and other ABCA1 SNPs in a LOAD case-control series of 796 individuals (419 cases versus 377 controls) collected at Washington University. While our sample series is larger and thus presumably has greater power than any of the series used to implicate ABCA1, we were unable to replicate the published association, using either single markers or multiple marker haplotypes. Further, we did not observe significant and replicated association of other ABCA1 SNPs we examined with the disease, thus these ABCA1 variants do not appear to influence the risk of LOAD in this study.

A Case-Control Association Study of the 12 Single-Nucleotide Polymorphisms Implicated in Parkinson Disease by a Recent Genome Scan

To the Editor: To validate associations of SNPs that Maraganore et al.1 reported as associated with Parkinson disease (PD [MIM 168600]), we constructed a case-control series from PD cases and matched population/convenience controls that are available through the National Institute of Neurological Disorders and Stroke (NINDS) Human Genetics Resources at the Coriell Institute. Cases met United Kingdom Brain Bank criteria for idiopathic PD,2 and controls were neurologically normal. This series comprises 311 pairs of age- and sex-matched cases and controls. Cases had an age at disease onset ranging from 50 to 87 years (average [±SD] 63.8 ± 8.9 years) and were sampled at the age of 52–92 years (average [±SD] 70.1 ± 8.5 years). Controls were also sampled at the age of 52–92 years (average [±SD] 70.2 ± 8.5 years). All cases and controls are white, and each group includes 165 females (53.1%) and 146 males (46.9%), respectively. Cases in this series do not carry the Gly2019Ser mutation in LRRK2 [MIM 609007], which may occur in idiopathic PD,3 and several tests did not reveal evidence of significant population stratification for 78 individually genotyped null markers (data not shown). We individually genotyped the 11 SNPs that were reported significant and one of the two SNPs that map to the PARK10 [MIM 606852] locus (the two reported-significant SNPs are highly correlated: r2=0.99), using allele-specific real-time PCR in our PD case-control sample set. Cases and controls were run on the same plate in a blinded fashion. Our genotyping method has an overall accuracy of >99%.4 As an additional indication of genotyping quality, we calculated deviation from Hardy-Weinberg equilibrium (HWE) in cases and controls. One marker had an HWE exact P value of <.05 (.017 for rs2245218 in cases), but further examination of our genotype data did not reveal questionable calls. Therefore, these data were included in our analysis. All SNPs were tested for allelic association with PD with the use of χ2 statistics to calculate two-sided P values (table 1). Power calculations were done for a sample size of 311 pairs for each SNP, with the use of a one-sided allelic χ2-hypothesis test at a significance level of 0.05 and with the assumption that the control-allele frequencies of the unrelated controls and odds ratios (ORs) in table 4 in Maraganore et al.1 are true population parameters. Power calculation for rs7520966 was based on the tier 2 OR given in the text of Maraganore et al.,1 since it did not appear in their table 4. Table 1 Allelic Tests of SNPs Associated with Late-Onset PD Two markers, rs10200894 and rs17329669, were replicated in our sample set at P 50 years, whereas the study by Maraganore et al. included both early- and late-onset cases.1 Thus, it is possible that nonreplicated markers are associated with early-onset PD but make a lesser contribution to the more common, late-onset form of the disease. Additional studies are required to further assess the association of these markers with PD.

Association studies between risk for late-onset Alzheimer's disease and variants in insulin degrading enzyme.

Linkage studies have suggested there is a susceptibility gene for late onset Alzheimers disease (LOAD) in a broad region of chromosome 10. A strong positional and biological candidate is the gene encoding the insulin‐degrading enzyme (IDE), a protease involved in the catabolism of Aβ. However, previous association studies have produced inconsistent results. To systematically evaluate the role of variation in IDE in the risk for LOAD, we genotyped 18 SNPs spanning a 276 kb region in and around IDE, including three “tagging” SNPs identified in an earlier study. We used four case‐control series with a total of 1,217 cases and 1,257 controls. One SNP (IDE_7) showed association in two samples (P‐value = 0.0066, and P = 0.026, respectively), but this result was not replicated in the other two series. None of the other SNPs showed association with LOAD in any of the tested samples. Haplotypes, constructed from the three tagging SNPs, showed no globally significant association. In the UK2 series, the CTA haplotype was over‐represented in cases (P = 0.046), and in the combined data set, the CCG haplotype was more frequent in controls (P = 0.015). However, these weak associations observed in our series were in the opposite direction to the results in previous studies. Although our results are not universally negative, we were unable to replicate the results of previous studies and conclude that common variants or haplotypes of these variants in IDE are not major risk factors for LOAD.

Alpha-T-catenin is expressed in human brain and interacts with the Wnt signaling pathway but is not responsible for linkage to chromosome 10 in Alzheimer's disease.

The gene encoding α-T-catenin, CTNNA3, is positioned within a region on chromosome 10, showing strong evidence of linkage to Alzheimer’s disease (AD), and is therefore a good positional candidate gene for this disorder. We have demonstrated that α-T-catenin is expressed in human brain, and like other α-catenins, it inhibits Wnt signaling and is therefore also a functional candidate. We initially genotyped two single-nucleotide polymorphisms (SNPs) in the gene, in four independent samples comprising over 1200 cases and controls but failed to detect an association with either SNP. Similarly, we found no evidence for association between CTNNA3 and AD in a sample of subjects showing linkage to chromosome 10, nor were these SNPs associated with Aβ deposition in brain. To comprehensively screen the gene, we genotyped 30 additional SNPs in a subset of the cases and controls (n>700). None of these SNPs was associated with disease. Although an excellent candidate, we conclude that CTNNA3 is unlikely to account for the AD susceptibility locus on chromosome 10.

Ubiquilin 1 polymorphisms are not associated with late-onset Alzheimer's disease

Several studies have reported evidence for linkage of late‐onset Alzheimers disease (LOAD) to chromosome 9. Recently, an intronic polymorphism affecting alternative splicing of exon 8 of ubiquilin 1 (UBQLN1) was reported to be associated with LOAD. We attempted to replicate this observation by genotyping this polymorphism, rs12344615 (also known as UBQ‐8i), in a large sample of 1,544 LOAD cases and 1,642 nondemented controls. We did not find any evidence that this single nucleotide polymorphism, or any of six others tested in UBQLN1, increases risk for LOAD. Ann Neurol 2005