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1.  Copy Number Variation of the Beta-Defensin Genes in Europeans: No Supporting Evidence for Association with Lung Function, Chronic Obstructive Pulmonary Disease or Asthma 
PLoS ONE  2014;9(1):e84192.
Lung function measures are heritable, predict mortality and are relevant in diagnosis of chronic obstructive pulmonary disease (COPD). COPD and asthma are diseases of the airways with major public health impacts and each have a heritable component. Genome-wide association studies of SNPs have revealed novel genetic associations with both diseases but only account for a small proportion of the heritability. Complex copy number variation may account for some of the missing heritability. A well-characterised genomic region of complex copy number variation contains beta-defensin genes (DEFB103, DEFB104 and DEFB4), which have a role in the innate immune response. Previous studies have implicated these and related genes as being associated with asthma or COPD. We hypothesised that copy number variation of these genes may play a role in lung function in the general population and in COPD and asthma risk. We undertook copy number typing of this locus in 1149 adult and 689 children using a paralogue ratio test and investigated association with COPD, asthma and lung function. Replication of findings was assessed in a larger independent sample of COPD cases and smoking controls. We found evidence for an association of beta-defensin copy number with COPD in the adult cohort (OR = 1.4, 95%CI:1.02–1.92, P = 0.039) but this finding, and findings from a previous study, were not replicated in a larger follow-up sample(OR = 0.89, 95%CI:0.72–1.07, P = 0.217). No robust evidence of association with asthma in children was observed. We found no evidence for association between beta-defensin copy number and lung function in the general populations. Our findings suggest that previous reports of association of beta-defensin copy number with COPD should be viewed with caution. Suboptimal measurement of copy number can lead to spurious associations. Further beta-defensin copy number measurement in larger sample sizes of COPD cases and children with asthma are needed.
doi:10.1371/journal.pone.0084192
PMCID: PMC3880289  PMID: 24404154
2.  A multi-centre study of ACE and the risk of late-onset Alzheimer’s disease 
A key pathological feature of late-onset Alzheimer’s disease (LOAD) is the abnormal extracellular accumulation of the amyloid beta (Aβ) peptide. Thus altered Aβ degradation could be a major contributor to the development of LOAD. Variants in the gene encoding the Aβ-degrading enzyme, angiotensin-1 converting enzyme (ACE) therefore represent plausible candidates for association with LOAD pathology and risk. Following Alzgene meta-analyses of all published case-control studies, the ACE variants rs4291 and rs1800764 showed significant association with LOAD risk. Furthermore ACE haplotypes are associated with both plasma ACE levels and LOAD risk. We tested three ACE variants (rs4291, rs4343 and rs1800764) for association with LOAD in ten Caucasian case-control populations (n=8,212). No association was found using multiple logistic models (all p>0.09). We found no population heterogeneity (all p>0.38) or evidence for association with LOAD risk following meta-analysis of the ten populations for rs4343 (OR=1.00), rs4291 (OR=0.97) or rs1800764 (OR=0.99). Although we found no haplotypic association in our complete dataset (p=0.51), a significant global haplotypic p-value was observed in one population (p=0.007) due to an association of the H3 haplotype (OR=0.72, p=0.02) and a trend towards an association of H4 (OR=1.38, p=0.09) and H7 (OR=2.07, p=0.08) although these did not survive Bonferroni correction. Previously reported associations of ACE variants with LOAD will be diminished following this study. At best, ACE variants have modest effect sizes, which are likely part of a complex interaction between genetic, phenotypic and pharmacological effects that would be undetected in traditional case-control studies.
doi:10.3233/JAD-2011-101914
PMCID: PMC3655234  PMID: 21297258
Alzheimer Disease; Late Onset; Angiotensin-1 Converting Enzyme; Haplotype; Heterogeneity; Meta-Analysis
3.  Next generation sequencing of CLU, PICALM and CR1: pitfalls and potential solutions 
CLU, PICALM and CR1 were identified as genetic risk factors for late onset Alzheimer’s disease (AD) in two large genome wide association studies (GWAS) published in 2009, but the variants that convey this alteration in disease risk, and how the genes relate to AD pathology is yet to be discovered. A next generation sequencing (NGS) project was conducted targeting CLU, CR1 and PICALM, in 96 AD samples (8 pools of 12), in an attempt to discover rare variants within these AD associated genes. Inclusion of repetitive regions in the design of the SureSelect capture lead to significant issues in alignment of the data, leading to poor specificity and a lower than expected depth of coverage. A strong positive correlation (0.964, p<0.001) was seen between NGS and 1000 genome project frequency estimates. Of the ~170 “novel” variants detected in the genes, seven SNPs, all of which were present in multiple sample pools, were selected for validation by Sanger sequencing. Two SNPs were successfully validated by this method, and shown to be genuine variants, while five failed validation. These spurious SNP calls occurred as a result of the presence of small indels and mononucleotide repeats, indicating such features should be regarded with caution, and validation via an independent method is important for NGS variant calls.
PMCID: PMC3508540  PMID: 23205178
Next generation sequencing; Alzheimer’s disease; genes; CLU; PICALM; CR1
4.  Structural Dynamics Associated with Intermediate Formation in an Archetypal Conformational Disease 
Structure(London, England:1993)  2012;20-135(3-3):504-512.
Summary
In conformational diseases, native protein conformers convert to pathological intermediates that polymerize. Structural characterization of these key intermediates is challenging. They are unstable and minimally populated in dynamic equilibria that may be perturbed by many analytical techniques. We have characterized a forme fruste deficiency variant of α1-antitrypsin (Lys154Asn) that forms polymers recapitulating the conformer-specific neo-epitope observed in polymers that form in vivo. Lys154Asn α1-antitrypsin populates an intermediate ensemble along the polymerization pathway at physiological temperatures. Nuclear magnetic resonance spectroscopy was used to report the structural and dynamic changes associated with this. Our data highlight an interaction network likely to regulate conformational change and do not support the recent contention that the disease-relevant intermediate is substantially unfolded. Conformational disease intermediates may best be defined using powerful but minimally perturbing techniques, mild disease mutants, and physiological conditions.
Highlights
► An α1-antitrypsin deficiency mutant is a forme fruste model for the Z variant ► NMR spectroscopic and ion-mobility mass spectrometric characterization of the mutant ► Residue-specific discrimination of disease-relevant and denaturant-induced ensembles ► A “clasp” motif caps a network of stabilizing interactions in α1-antitrypsin
doi:10.1016/j.str.2012.01.012
PMCID: PMC3314904  PMID: 22405009
5.  A Comprehensive Evaluation of Potential Lung Function Associated Genes in the SpiroMeta General Population Sample 
PLoS ONE  2011;6(5):e19382.
Rationale
Lung function measures are heritable traits that predict population morbidity and mortality and are essential for the diagnosis of chronic obstructive pulmonary disease (COPD). Variations in many genes have been reported to affect these traits, but attempts at replication have provided conflicting results. Recently, we undertook a meta-analysis of Genome Wide Association Study (GWAS) results for lung function measures in 20,288 individuals from the general population (the SpiroMeta consortium).
Objectives
To comprehensively analyse previously reported genetic associations with lung function measures, and to investigate whether single nucleotide polymorphisms (SNPs) in these genomic regions are associated with lung function in a large population sample.
Methods
We analysed association for SNPs tagging 130 genes and 48 intergenic regions (+/−10 kb), after conducting a systematic review of the literature in the PubMed database for genetic association studies reporting lung function associations.
Results
The analysis included 16,936 genotyped and imputed SNPs. No loci showed overall significant association for FEV1 or FEV1/FVC traits using a carefully defined significance threshold of 1.3×10−5. The most significant loci associated with FEV1 include SNPs tagging MACROD2 (P = 6.81×10−5), CNTN5 (P = 4.37×10−4), and TRPV4 (P = 1.58×10−3). Among ever-smokers, SERPINA1 showed the most significant association with FEV1 (P = 8.41×10−5), followed by PDE4D (P = 1.22×10−4). The strongest association with FEV1/FVC ratio was observed with ABCC1 (P = 4.38×10−4), and ESR1 (P = 5.42×10−4) among ever-smokers.
Conclusions
Polymorphisms spanning previously associated lung function genes did not show strong evidence for association with lung function measures in the SpiroMeta consortium population. Common SERPINA1 polymorphisms may affect FEV1 among smokers in the general population.
doi:10.1371/journal.pone.0019382
PMCID: PMC3098839  PMID: 21625484
7.  The role of IREB2 and transforming growth factor beta-1 genetic variants in COPD: a replication case-control study 
BMC Medical Genetics  2011;12:24.
Background
Genetic factors are known to contribute to COPD susceptibility and these factors are not fully understood. Conflicting results have been reported for many genetic studies of candidate genes based on their role in the disease. Genome-wide association studies in combination with expression profiling have identified a number of new candidates including IREB2. A meta-analysis has implicated transforming growth factor beta-1 (TGFbeta1) as a contributor to disease susceptibility.
Methods
We have examined previously reported associations in both genes in a collection of 1017 white COPD patients and 912 non-diseased smoking controls. Genotype information was obtained for seven SNPs in the IREB2 gene, and for four SNPs in the TGFbeta1 gene. Allele and genotype frequencies were compared between COPD cases and controls, and odds ratios were calculated. The analysis was adjusted for age, sex, smoking and centre, including interactions of age, sex and smoking with centre.
Results
Our data replicate the association of IREB2 SNPs in association with COPD for SNP rs2568494, rs2656069 and rs12593229 with respective adjusted p-values of 0.0018, 0.0039 and 0.0053. No significant associations were identified for TGFbeta1.
Conclusions
These studies have therefore confirmed that the IREB2 locus is a contributor to COPD susceptibility and suggests a new pathway in COPD pathogenesis invoking iron homeostasis.
doi:10.1186/1471-2350-12-24
PMCID: PMC3047296  PMID: 21320324
8.  Using Fisher's method with PLINK ‘LD clumped’ output to compare SNP effects across Genome-wide Association Study (GWAS) datasets 
As the number of publically available GWAS datasets continues to grow, bioinformatic tools which enable routine manipulation of data are becoming increasingly useful. Meta-analysis using multiple GWAS datasets has become essential to elucidate novel SNP associations which may not be readily discovered in each GWAS individually due to insufficient power. Replication of GWAS findings is critical and is the ‘arbiter’ of genuine SNP associations. We have developed an ‘LD aware’ bioinformatics application which allows efficient comparison of SNP effects across multiple GWAS datasets using Fisher’s combined probability test from PLINK (v1.06) ‘LD clumped’ output. Availability: the application is freely available from the authors.
PMCID: PMC3077236  PMID: 21537399
Genome-wide Association Studies (GWAS); Fisher’s method; bioinformatic tools
9.  Using In silico LD clumping and meta-analysis of genome-wide datasets as a complementary tool to investigate and validate new candidate biomarkers in Alzheimer's disease 
Despite the recent wealth of genome-wide association studies, insufficient power may explain why much of the heritable contribution to common diseases remains hidden. As different SNP panels are genotyped by commercial chips, increasing study power through meta-analysis is made problematic. To address these power issues we suggest an approach which permits meta-analysis of candidate SNPs from multiple GWAS. By identifying correlated SNPs from different platforms (r2=1), using PLINK’s ‘clumping’ method, we generated combined p-values (using Fisher’s combined and random effects meta-analysis) for each clump. P-values were corrected for the number of clumps (representing the number of independent tests). We also explored to what extent commercial platforms tag HapMap SNPs within these candidate genes. To illustrate this approach, and to serve as ‘proof-of-principle’, we used 3 late-onset Alzheimer’s disease GWAS datasets to explore SNP-disease associations in 4 new candidate genes encoding cerebro-spinal fluid biomarkers for Alzheimer’s disease; Fibrinogen γ-chain (FGG), SPARC-like1 (SPARCL1), Contactin-1 (CNTN1) and Contactin-2 (CNTN2). Genes encoding current Alzheimer’s biomarkers; APP (Aβ), MAPT (Tau) and APOE were also included. This method identified two SNP ‘clumps’; one clump in APOE (rs4420638) and one downstream of CNTN2 (which harboured rs7523477 and rs4951168) which were significant following random effects meta-analysis (P < 0.05). The latter was linked to three conserved SNPs in the 3’-UTR of CNTN2. We cannot rule out that this result is a false positive due to the large number of statistical tests applied; nevertheless this approach is easily applied and might well have utility in future ‘–omics’ studies.
PMCID: PMC3076759  PMID: 21537386
PLINK; Clumping; Alzheimer's disease; genome-wide association study (GWAS); CNTN1; CNTN2; SPARCL1; FGG; APOE; meta-analysis
10.  Concordant Association of Insulin Degrading Enzyme Gene (IDE) Variants with IDE mRNA, Aß, and Alzheimer's Disease 
PLoS ONE  2010;5(1):e8764.
Background
The insulin-degrading enzyme gene (IDE) is a strong functional and positional candidate for late onset Alzheimer's disease (LOAD).
Methodology/Principal Findings
We examined conserved regions of IDE and its 10 kb flanks in 269 AD cases and 252 controls thereby identifying 17 putative functional polymorphisms. These variants formed eleven haplotypes that were tagged with ten variants. Four of these showed significant association with IDE transcript levels in samples from 194 LOAD cerebella. The strongest, rs6583817, which has not previously been reported, showed unequivocal association (p = 1.5×10−8, fold-increase = 2.12,); the eleven haplotypes were also significantly associated with transcript levels (global p = 0.003). Using an in vitro dual luciferase reporter assay, we found that rs6583817 increases reporter gene expression in Be(2)-C (p = 0.006) and HepG2 (p = 0.02) cell lines. Furthermore, using data from a recent genome-wide association study of two Croatian isolated populations (n = 1,879), we identified a proxy for rs6583817 that associated significantly with decreased plasma Aβ40 levels (ß = −0.124, p = 0.011) and total measured plasma Aβ levels (b = −0.130, p = 0.009). Finally, rs6583817 was associated with decreased risk of LOAD in 3,891 AD cases and 3,605 controls. (OR = 0.87, p = 0.03), and the eleven IDE haplotypes (global p = 0.02) also showed significant association.
Conclusions
Thus, a previously unreported variant unequivocally associated with increased IDE expression was also associated with reduced plasma Aß40 and decreased LOAD susceptibility. Genetic association between LOAD and IDE has been difficult to replicate. Our findings suggest that targeted testing of expression SNPs (eSNPs) strongly associated with altered transcript levels in autopsy brain samples may be a powerful way to identify genetic associations with LOAD that would otherwise be difficult to detect.
doi:10.1371/journal.pone.0008764
PMCID: PMC2808243  PMID: 20098734
11.  Association of MMP - 12 polymorphisms with severe and very severe COPD: A case control study of MMPs - 1, 9 and 12 in a European population 
BMC Medical Genetics  2010;11:7.
Background
Genetic factors play a role in chronic obstructive pulmonary disease (COPD) but are poorly understood. A number of candidate genes have been proposed on the basis of the pathogenesis of COPD. These include the matrix metalloproteinase (MMP) genes which play a role in tissue remodelling and fit in with the protease - antiprotease imbalance theory for the cause of COPD. Previous genetic studies of MMPs in COPD have had inadequate coverage of the genes, and have reported conflicting associations of both single nucleotide polymorphisms (SNPs) and SNP haplotypes, plausibly due to under-powered studies.
Methods
To address these issues we genotyped 26 SNPs, providing comprehensive coverage of reported SNP variation, in MMPs- 1, 9 and 12 from 977 COPD patients and 876 non-diseased smokers of European descent and evaluated their association with disease singly and in haplotype combinations. We used logistic regression to adjust for age, gender, centre and smoking history.
Results
Haplotypes of two SNPs in MMP-12 (rs652438 and rs2276109), showed an association with severe/very severe disease, corresponding to GOLD Stages III and IV.
Conclusions
Those with the common A-A haplotype for these two SNPs were at greater risk of developing severe/very severe disease (p = 0.0039) while possession of the minor G variants at either SNP locus had a protective effect (adjusted odds ratio of 0.76; 95% CI 0.61 - 0.94). The A-A haplotype was also associated with significantly lower predicted FEV1 (42.62% versus 44.79%; p = 0.0129). This implicates haplotypes of MMP-12 as modifiers of disease severity.
doi:10.1186/1471-2350-11-7
PMCID: PMC2820470  PMID: 20078883
12.  Analysis of Genome-Wide Association Study (GWAS) data looking for replicating signals in Alzheimer's disease (AD) 
We have performed cross-platform comparisons of output from 4 GWAS in late-onset Alzheimer's disease (LOAD) – Reiman et al., 2007; Li et al., 2008; Beecham et al., 2008 and Carrasquillo et al., 2009 to search for new association signals. The aim was to reveal genes that replicated across studies and hence merit further investigation. All SNPs with p-values ranging between 5×10−5 – 5×10−8 from each study were assessed across the other studies (either directly or by using a perfect proxy when comparing data from different chip platforms). This revealed only a single SNP (rs929156 in the tripartite motif-containing protein 15, TRIM15, gene) that was replicating across all studies at a level approaching genome-wide significance (P = 8.77×10−8) and where meta-analysis of odds ratios showed a significant effect on risk (OR 1.1, 95% Cl 1.0-1.2, P = 0.03). The vast majority of data analysed failed to replicate across these GWAS. The number of replicating association signals we observed is no higher than would be expected due to chance. However, increasing the power by using additional data from larger studies may enable this approach to identify potential LOAD candidate genes for confirmatory association studies.
PMCID: PMC3076755  PMID: 21537453
Late-onset Alzheimer's disease (LOAD); meta-analysis; genome-wide association analysis (GWAS); tripartite motif-containing protein 15 (TRIM15) gene; replication; single nucleotide polymorphism (SNP)
13.  Alpha1-antitrypsin deficiency: current perspective on research, diagnosis, and management 
The Alpha One International Registry (AIR), a multinational research program focused on alpha1-antitrypsin (AAT) deficiency, was formed in response to a World Health Organization recommendation. Each of the nearly 20 participating countries maintains a national registry of patients with AAT deficiency and contributes to an international database located in Malmö, Sweden. This database is designed to increase understanding of AAT deficiency. Additionally, AIR members are engaged in active, wide-ranging investigations to improve the diagnosis, monitoring, and treatment of the disease and meet biennially to exchange views and research findings. The fourth biennial meeting was held in Copenhagen, Denmark, on 2–3 June 2005. This review covers the wide range of AAT deficiency-related topics that were addressed encompassing advances in genetic characterization, risk factor identification, clinical epidemiology, inflammatory and signalling processes, therapeutic advances, and lung imaging techniques.
PMCID: PMC2706616  PMID: 18046892
alpha1-antitrypsin deficiency; epidemiology; polymorphism; genetics; augmentation therapy
14.  A rapid and efficient method for DNA extraction from paraffin wax embedded tissue for PCR amplification 
Clinical Molecular Pathology  1996;49(3):M179-M180.
DNA from archival, formaldehyde fixed, paraffin wax embedded human tissue, suitable for amplification by the polymerase chain reaction (PCR), was obtained using a microwave method based on the capture of DNA by magnetic beads. Fragments of the α-1-antitrypsin gene (AAT) and the apolipoprotein E gene (APOE) were amplified successfully from human liver and brain tissue, respectively. This procedure provides a more rapid, simple and efficient method for reproducibly obtaining DNA from preserved tissue that has been kept in storage for up to 30 years.
Images
PMCID: PMC408047  PMID: 16696069
PCR; DNA extraction; paraffin wax sections

Results 1-14 (14)