Exploring potential functional variants in the Alzheimer’s disease associated genes, CD2AP, EPHA1 and CD33

Little is known about the molecular biology of late onset Alzheimer’s disease (LOAD), the most common dementia in the elderly. Genetic loci associated with LOAD have been identified through genome-wide association studies (GWAS). However, the functional variants responsible for the observed GWAS association at each of the loci remain unknown. The aim of this project was to identify and assess potential functional rare variants at three associated loci, CD2AP, EPHA1 and CD33. Target enriched, pooled sequencing of 96 post-mortem confirmed LOAD patient samples was used to identify 1273 variants within the three GWAS loci. Variants were prioritised using a combination of in silico functional annotation and putative disease association. Disease association was assessed through comparison to an independent, imputed LOAD GWAS dataset (2067 cases, 7376 controls). 18 coding and untranslated region variants and 9 noncoding variants were prioritised for further investigation. Potential splicing variants in CD2AP (6:47544253A>G) and EPHA1 (rs6967117) were assessed using minigene assays, although neither were found to influence splicing products in vivo. Five untranslated variants from the three genes and a frameshift variant in CD33 (rs201074739) were assessed for potential cis-regulatory consequences using allelic expression imbalance in brain tissues and B-lymphoblast cell lines. Only the frameshift variant displayed significant allelic expression imbalance and was found to be targeted for nonsense-mediated decay. None of the prioritised variants investigated were both functional and significantly associated with LOAD. However, pooled next generation sequencing using target enrichment successfully identified potential functional rare variants in CD2AP, EPHA1 and CD33. Rare variants do have a role to play in late onset Alzheimer’s disease. With the development of additional functional databases and improvements imputing rare variants from GWAS datasets, the combined prioritisation strategy used in this thesis will be useful for similar studies investigating causal GWAS variants

The Risk of Cancer Among Patients Previously Hospitalized for Atopic Dermatitis

In treatment of severe atopic dermatitis, drugs with carcinogenic potentials are used to manage the disease. We therefore analyzed whether patients having severe atopic eczema had an increased cancer risk. The study population included all individuals hospitalized in Denmark with a primary diagnosis of atopic dermatitis during 1977–1996. Follow-up was conducted in 1996 in the Danish Cancer Register. A total of 6275 persons were included. Among 2030 adult patients, an increased risk of cancer was observed, standard morbidity ratio (SMR)=1.5 (95% CI: 1.2–1.9). Half the excess cases of cancer was keratinocyte carcinomas of the skin diagnosed within the first 9 y of follow–up, SMR=2.4 (95% CI: 1.4–3.9). For men, SMR=2.7 (95%CI: 1.2–5.4). In conclusion, earlier hospitalized adult atopic dermatitis patients had an increased risk of cancer. Half the excess cases of cancer were keratinocyte carcinomas. This may be a result of a detection bias or due to the carcinogenic potentials of some of the therapies of severe atopic dermatitis

The Risk of Cancer Among Patients Previously Hospitalized for Atopic Dermatitis

In treatment of severe atopic dermatitis, drugs with carcinogenic potentials are used to manage the disease. We therefore analyzed whether patients having severe atopic eczema had an increased cancer risk. The study population included all individuals hospitalized in Denmark with a primary diagnosis of atopic dermatitis during 1977–1996. Follow-up was conducted in 1996 in the Danish Cancer Register. A total of 6275 persons were included. Among 2030 adult patients, an increased risk of cancer was observed, standard morbidity ratio (SMR)=1.5 (95% CI: 1.2–1.9). Half the excess cases of cancer was keratinocyte carcinomas of the skin diagnosed within the first 9 y of follow–up, SMR=2.4 (95% CI: 1.4–3.9). For men, SMR=2.7 (95%CI: 1.2–5.4). In conclusion, earlier hospitalized adult atopic dermatitis patients had an increased risk of cancer. Half the excess cases of cancer were keratinocyte carcinomas. This may be a result of a detection bias or due to the carcinogenic potentials of some of the therapies of severe atopic dermatitis

Blood type gene locus has no influence on ACE association with Alzheimer's disease

The ABO blood group locus was recently found to contribute independently as well as via interactions with ACE gene variation to plasma levels of angiotensin converting enzyme (ACE). Variation in ACE has also previously been implicated as conferring susceptibility for Alzheimer’s disease (AD), but has also been proposed to confer risk via interactions with other as yet unknown genes. More recently, larger studies have not supported ACE as a risk factor for AD, while the role of ACE pathway in AD has come under increased levels of scrutiny with respect to various aspects of AD pathology and possible therapies. We explored the potential combined involvement of ABO and ACE variation in the genetic susceptibility of 2067 AD cases compared to 1376 non-demented elderly. Including the effects of ABO haplotype did not provide any evidence for the genetic association of ACE with AD

How "benign" is cutaneous mastocytosis? A Danish registry-based matched cohort study.

BACKGROUND: There are limited estimates of the incidence rates (IRs) of mastocytosis, and only a few studies have addressed the long-term consequences of living with these diagnoses. Previous reports have shown that systemic mastocytosis is associated with leukemic transformations and an increased risk of death as opposed to cutaneous mastocytosis (CM) and indolent systemic mastocytosis (ISM), which have benign diagnoses with life expectancy rates similar to those of the background population. OBJECTIVE: This study aimed to analyze the incidence and mortality of mastocytosis. METHODS: A population-based matched cohort study of patients with mastocytosis between 1 January 1, 1977 and 31 December 31, 2014 was identified from the Danish National Health Registries. IRs of CM, ISM, and pediatric mastocytosis were highlighted. Survival estimates were compared with those of a healthy background population, using a Cox proportional hazard model. RESULTS: A total of 1461 patients with mastocytosis were identified. The annual IR of overall mastocytosis was 1.1 per 100,000 person years (95% confidence interval [CI], 1.0-1.2). Among children, the IR was 1.8 per 100,000 person years (95% CI, 1.6-2.1). The prevalence of any comorbidity was twice as high among patients with mastocytosis compared with the population without mastocytosis (odds ratio: 2.1; 95% CI, 1.8-2.5). The Charlson Comorbidity Index-adjusted mortality among adult patients with mastocytosis was HRCutaneous Mastocytosis 1.2 (95% CI, 0.8-1.9), HRIndolent Systemic Mastocytosis 1.9 (95% CI 1.4-2.5), and HRSystemic Mastocytosis 4.2 (95%, CI 1.9-9.4), respectively. CONCLUSION: Based on an entire nation, with free health care at the point of access, we estimated an annual IR of mastocytosis and its subgroups. We discovered that patients with ISM had an increased risk of death compared with the general population. Our data supported the overall benign nature of CM diagnosed after age 2 years

Investigating splicing variants uncovered by next-generation sequencing the Alzheimer’s disease candidate genes, CLU, PICALM, CR1, ABCA7, BIN1, the MS4A locus, CD2AP, EPHA1 and CD33

Late onset Alzheimer’s disease (LOAD), the most common cause of late onset dementia, has a strong genetic component. To date, 21 disease-risk loci have been identified through genome wide association studies (GWAS). However, the causative functional variant(s) within these loci are yet to be discovered. This study aimed to identify potential functional splicing mutations in the nine original GWAS-risk genes: CLU, PICALM, CR1, ABCA7, BIN1, the MS4A locus, CD2AP, EPHA1 and CD33. Target enriched next generation sequencing (NGS) was used to resequence the entire genetic region for each of these GWAS-risk loci in 96 LOAD patients and in silico databases were used to annotate the variants for functionality. Predicted splicing variants were further functionally characterised using splicing prediction software and minigene splicing assays. Following in silico annotation, 21 variants were predicted to influence splicing and, upon further annotation, four of these were examined utilising the in vitro minigene assay. Two variants, rs881768 A>G in ABCA7 and a novel variant 11: 60179827 T>G in MS4A6A were shown, in these cell assays, to affect the splicing of these genes. The method employed in the paper successfully identified potential splicing variants in GWAS-risk genes. Further investigation will be needed to understand the full effect of these variants on LOAD risk. However, these results suggest a possible pipeline in order to identify putative functional variants as a result of NGS in disease-associated loci although improvements are needed within the current prediction programme in order to reduce the number of false positives

Investigating the genetic architecture of dementia with Lewy bodies: a two-stage genome-wide association study

Background Dementia with Lewy bodies is the second most common form of dementia in elderly people but has been overshadowed in the research field, partly because of similarities between dementia with Lewy bodies, Parkinson’s disease, and Alzheimer’s disease. So far, to our knowledge, no large-scale genetic study of dementia with Lewy bodies has been done. To better understand the genetic basis of dementia with Lewy bodies, we have done a genome-wide association study with the aim of identifying genetic risk factors for this disorder. Methods In this two-stage genome-wide association study, we collected samples from white participants of European ancestry who had been diagnosed with dementia with Lewy bodies according to established clinical or pathological criteria. In the discovery stage (with the case cohort recruited from 22 centres in ten countries and the controls derived from two publicly available database of Genotypes and Phenotypes studies [phs000404.v1.p1 and phs000982.v1.p1] in the USA), we performed genotyping and exploited the recently established Haplotype Reference Consortium panel as the basis for imputation. Pathological samples were ascertained following autopsy in each individual brain bank, whereas clinical samples were collected by clinical teams after clinical examination. There was no specific timeframe for collection of samples. We did association analyses in all participants with dementia with Lewy bodies, and also in only participants with pathological diagnosis. In the replication stage, we performed genotyping of significant and suggestive results from the discovery stage. Lastly, we did a meta-analysis of both stages under a fixed-effects model and used logistic regression to test for association in each stage. Findings This study included 1743 patients with dementia with Lewy bodies (1324 with pathological diagnosis) and 4454 controls (1216 patients with dementia with Lewy bodies vs 3791 controls in the discovery stage; 527 vs 663 in the replication stage). Results confirm previously reported associations: APOE (rs429358; odds ratio [OR] 2·40, 95% CI 2·14–2·70; p=1·05 × 10–⁴⁸), SNCA (rs7681440; OR 0·73, 0·66–0·81; p=6·39 × 10–¹⁰), and GBA (rs35749011; OR 2·55, 1·88–3·46; p=1·78 × 10–⁹). They also provide some evidence for a novel candidate locus, namely CNTN1 (rs7314908; OR 1·51, 1·27–1·79; p=2·21 × 10–⁶); further replication will be important. Additionally, we estimate the heritable component of dementia with Lewy bodies to be about 36%. Interpretation Despite the small sample size for a genome-wide association study, and acknowledging the potential biases from ascertaining samples from multiple locations, we present the most comprehensive and well powered genetic study in dementia with Lewy bodies so far. These data show that common genetic variability has a role in the disease

Analysis of C9orf72 repeat expansions in a large international cohort of dementia with Lewy bodies

C9orf72 repeat expansions are a common cause of amyotrophic lateral sclerosis and frontotemporal dementia. To date, no large-scale study of dementia with Lewy bodies (DLB) has been undertaken to assess the role of C9orf72 repeat expansions in the disease. Here, we investigated the prevalence of C9orf72 repeat expansions in a large cohort of DLB cases and identified no pathogenic repeat expansions in neuropathologically or clinically defined cases, showing that C9orf72 repeat expansions are not causally associated with DLB. (C) 2016 Elsevier Inc. All rights reserved.Peer reviewe

A comprehensive screening of copy number variability in dementia with Lewy bodies

The role of genetic variability in dementia with Lewy bodies (DLB) is now indisputable; however, data regarding copy number variation (CNV) in this disease has been lacking. Here, we used whole-genome genotyping of 1454 DLB cases and 1525 controls to assess copy number variability. We used 2 algorithms to confidently detect CNVs, performed a case-control association analysis, screened for candidate CNVs previously associated with DLB-related diseases, and performed a candidate gene approach to fully explore the data. We identified 5 CNV regions with a significant genome-wide association to DLB; 2 of these were only present in cases and absent from publicly available databases: one of the regions overlapped LAPTM4B, a known lysosomal protein, whereas the other overlapped the NME1 locus and SPAG9. We also identified DLB cases presenting rare CNVs in genes previously associated with DLB or related neurodegenerative diseases, such as SNCA, APP, and MAPT. To our knowledge, this is the first study reporting genome-wide CNVs in a large DLB cohort. These results provide preliminary evidence for the contribution of CNVs in DLB risk. (C) 2019 Elsevier Inc. All rights reserved.Peer reviewe