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author:("hardman, Orla")
1.  Analysis of amyotrophic lateral sclerosis as a multistep process: a population-based modelling study 
The Lancet. Neurology  2014;13(11):1108-1113.
Summary
Background
Amyotrophic lateral sclerosis shares characteristics with some cancers, such as onset being more common in later life, progression usually being rapid, the disease affecting a particular cell type, and showing complex inheritance. We used a model originally applied to cancer epidemiology to investigate the hypothesis that amyotrophic lateral sclerosis is a multistep process.
Methods
We generated incidence data by age and sex from amyotrophic lateral sclerosis population registers in Ireland (registration dates 1995–2012), the Netherlands (2006–12), Italy (1995–2004), Scotland (1989–98), and England (2002–09), and calculated age and sex-adjusted incidences for each register. We regressed the log of age-specific incidence against the log of age with least squares regression. We did the analyses within each register, and also did a combined analysis, adjusting for register.
Findings
We identified 6274 cases of amyotrophic lateral sclerosis from a catchment population of about 34 million people. We noted a linear relationship between log incidence and log age in all five registers: England r2=0·95, Ireland r2=0·99, Italy r2=0·95, the Netherlands r2=0·99, and Scotland r2=0·97; overall r2=0·99. All five registers gave similar estimates of the linear slope ranging from 4·5 to 5·1, with overlapping confidence intervals. The combination of all five registers gave an overall slope of 4·8 (95% CI 4·5–5·0), with similar estimates for men (4·6, 4·3–4·9) and women (5·0, 4·5–5·5).
Interpretation
A linear relationship between the log incidence and log age of onset of amyotrophic lateral sclerosis is consistent with a multistage model of disease. The slope estimate suggests that amyotrophic lateral sclerosis is a six-step process. Identification of these steps could lead to preventive and therapeutic avenues.
Funding
UK Medical Research Council; UK Economic and Social Research Council; Ireland Health Research Board; The Netherlands Organisation for Health Research and Development (ZonMw); the Ministry of Health and Ministry of Education, University, and Research in Italy; the Motor Neurone Disease Association of England, Wales, and Northern Ireland; and the European Commission (Seventh Framework Programme).
doi:10.1016/S1474-4422(14)70219-4
PMCID: PMC4197338  PMID: 25300936
2.  Multiparametric MRI study of ALS stratified for the C9orf72 genotype 
Neurology  2013;81(4):361-369.
Objective:
To describe the patterns of cortical and subcortical changes in amyotrophic lateral sclerosis (ALS) stratified for the C9orf72 genotype.
Methods:
A prospective, single-center, single-protocol, gray and white matter magnetic resonance case-control imaging study was undertaken with 30 C9orf72-negative patients with ALS, 9 patients with ALS carrying the C9orf72 hexanucleotide repeat expansion, and 44 healthy controls. Tract-based spatial statistics of multiple white matter diffusion parameters, cortical thickness measurements, and voxel-based morphometry analyses were carried out. All patients underwent comprehensive genetic and neuropsychological profiling.
Results:
A congruent pattern of cortical and subcortical involvement was identified in those with the C9orf72 genotype, affecting fusiform, thalamic, supramarginal, and orbitofrontal regions and the Broca area. White matter abnormalities in the C9orf72-negative group were relatively confined to corticospinal and cerebellar pathways with limited extramotor expansion. The body of the corpus callosum and superior motor tracts were affected in both ALS genotypes.
Conclusions:
Extensive cortical and subcortical frontotemporal involvement was identified in association with the C9orf72 genotype, compared to the relatively limited extramotor pathology in patients with C9orf72-negative ALS. The distinctive, genotype-specific pathoanatomical patterns are consistent with the neuropsychological profile of the 2 ALS cohorts. Our findings suggest that previously described extramotor changes in ALS could be largely driven by those with the C9orf72 genotype.
doi:10.1212/WNL.0b013e31829c5eee
PMCID: PMC3772833  PMID: 23771489
3.  An Exploratory Spatial Analysis of ALS Incidence in Ireland over 17.5 Years (1995 – July 2013) 
PLoS ONE  2014;9(5):e96556.
Introduction
There has been much interest in spatial analysis of ALS to identify potential environmental or genetically caused clusters of disease. Results to date have been inconclusive. The Irish ALS register has been recently geocoded, presenting opportunity to perform a spatial analysis on national prospectively gathered data of incident cases over an 18-year period.
Methods
1,645 cases of ALS in Ireland from January 1995 to July 2013 were identified from the Irish ALS register. 1,638 cases were successfully geocoded. Census data from four censuses: 1996, 2002, 2006 & 2011 were used to calculate an average population for the period and standardized incidence rates (SIRs) were calculated for 3,355 areas (Electoral Divisions). Bayesian conditional auto-regression was applied to produce smoothed relative risks (RR). These were then mapped for all cases, males & females separately, and those under 55 vs over 55 at diagnosis. Bayesian and linear regression were used to examine the relationship between population density and RR.
Results
Smoothed maps revealed no overall geographical pattern to ALS incidence in Ireland, although several areas of localized increased risk were identified. Stratified maps also suggested localized areas of increased RR, while dual analysis of the relationship between population density and RR of ALS yielded conflicting results, linear regression revealed a weak relationship.
Discussion
In contrast to some previous studies our analysis did not reveal any large-scale geographic patterns of incidence, yet localized areas of moderately high risk were found in both urban and rural areas. Stratified maps by age revealed a larger number of cases in younger people in the area of County Cork - possibly of genetic cause. Bayesian auto-regression of population density failed to find a significant association with risk, however weighted linear regression of post Bayesian smoothed Risk revealed an association between population density and increased ALS risk.
doi:10.1371/journal.pone.0096556
PMCID: PMC4035264  PMID: 24867594
4.  Lessons of ALS imaging: Pitfalls and future directions — A critical review 
NeuroImage : Clinical  2014;4:436-443.
Background
While neuroimaging in ALS has gained unprecedented momentum in recent years, little progress has been made in the development of viable diagnostic, prognostic and monitoring markers.
Objectives
To identify and discuss the common pitfalls in ALS imaging studies and to reflect on optimal study designs based on pioneering studies.
Methods
A “PubMed”-based literature search on ALS was performed based on neuroimaging-related keywords. Study limitations were systematically reviewed and classified so that stereotypical trends could be identified.
Results
Common shortcomings, such as relatively small sample sizes, statistically underpowered study designs, lack of disease controls, poorly characterised patient cohorts and a large number of conflicting studies, remain a significant challenge to the field. Imaging data of ALS continue to be interpreted at a group-level, as opposed to meaningful individual-patient inferences.
Conclusions
A systematic, critical review of ALS imaging has identified stereotypical shortcomings, the lessons of which should be considered in the design of future prospective MRI studies. At a time when large multicentre studies are underway a candid discussion of these factors is particularly timely.
Highlights
•Stereotypical shortcomings can be identified in ALS neuroimaging studies.•A systematic discussion of ALS study limitations is particularly timely.•Individual patient data meta-analyses and multicentre studies are urgently required.•The gaps identified in ALS imaging indicate exciting research opportunities.
doi:10.1016/j.nicl.2014.02.011
PMCID: PMC3950559  PMID: 24624329
Amyotrophic lateral sclerosis; Biomarker; MRI; PET; Spectroscopy; AD, axial diffusivity; C9orf72, chromosome 9 open reading frame 72; DTI, diffusion tensor imaging; FA, fractional anisotropy; MD, mean diffusivity; MEG, magnetoencephalography; MRS, magnetic resonance spectroscopy; MUNE, motor unit number estimation; PET, positron emission tomography; PNS, peripheral nervous system; RD, radial diffusivity; ROI, region of interest; SPECT, single photon emission computed tomography; TMS, transcranial magnetic stimulation; VBM, voxel-based morphometry
5.  Survival Analysis of Irish Amyotrophic Lateral Sclerosis Patients Diagnosed from 1995–2010 
PLoS ONE  2013;8(9):e74733.
Introduction
The Irish ALS register is a valuable resource for examining survival factors in Irish ALS patients. Cox regression has become the default tool for survival analysis, but recently new classes of flexible parametric survival analysis tools known as Royston-Parmar models have become available.
Methods
We employed Cox proportional hazards and Royston-Parmar flexible parametric modeling to examine factors affecting survival in Irish ALS patients. We further examined the effect of choice of timescale on Cox models and the proportional hazards assumption, and extended both Cox and Royston-Parmar models with time varying components.
Results
On comparison of models we chose a Royston-Parmar proportional hazards model without time varying covariates as the best fit. Using this model we confirmed the association of known survival markers in ALS including age at diagnosis (Hazard Ratio (HR) 1.34 per 10 year increase; 95% CI 1.26–1.42), diagnostic delay (HR 0.96 per 12 weeks delay; 95% CI 0.94–0.97), Definite ALS (HR 1.47 95% CI 1.17–1.84), bulbar onset disease (HR 1.58 95% CI 1.33–1.87), riluzole use (HR 0.72 95% CI 0.61–0.85) and attendance at an ALS clinic (HR 0.74 95% CI 0.64–0.86).
Discussion
Our analysis explored the strengths and weaknesses of Cox proportional hazard and Royston-Parmar flexible parametric methods. By including time varying components we were able to gain deeper understanding of the dataset. Variation in survival between time periods appears to be due to missing data in the first time period. The use of age as timescale to account for confounding by age resolved breaches of the proportional hazards assumption, but in doing so may have obscured deficiencies in the data. Our study demonstrates the need to test for, and fully explore, breaches of the Cox proportional hazards assumption. Royston-Parmar flexible parametric modeling proved a powerful method for achieving this.
doi:10.1371/journal.pone.0074733
PMCID: PMC3786977  PMID: 24098664
6.  The effects of a home-based arm ergometry exercise programme on physical fitness, fatigue and activity in polio survivors: protocol for a randomised controlled trial 
BMC Neurology  2012;12:157.
Background
Many Polio survivors have reduced mobility, pain and fatigue, which make access to conventional forms of aerobic exercise difficult. Inactivity leads to increased risk of health problems, many of which are prevalent among Polio survivors. Aerobic exercise programmes in Polio survivors should utilise stable muscle groups and should be designed to minimise exacerbation of pain and fatigue. A home-based arm ergometry aerobic exercise programme may represent an affordable and accessible exercise modality, incorporating exercise prescription principles in this group.
Methods/design
This is a prospective, single blinded, randomised controlled trial. There are two arms; exercise intervention using arm ergometers and control. Polio survivors meeting eligibility criteria will be recruited and randomly allocated to intervention or control groups. Participants allocated to the intervention group will receive a small arm ergometer and a polar heart rate monitor. They will carry out a home-based moderate intensity (50-70% HRMax) aerobic exercise programme for eight weeks, following instruction by the treating physiotherapist. Assessments will occur at baseline and after eight weeks and will include tests of physical fitness, activity, energy cost of walking, fatigue and quality of life. Clinically feasible assessment tools including the Six Minute Arm Test, the Physical Activity Scale for People with Physical Disabilities questionnaire, the Physiological Cost Index, Fatigue Severity Scale and the SF-36v2 will be utilised.
Discussion
The efficacy of a home-based arm ergometry programme in Polio survivors will be examined. No previous trial has examined such a programme using a wide range of outcome measures pertinent to Polio survivors. This study will provide new information on the impact of arm ergometry on physical fitness, activity, body composition, fatigue, pain, muscle strength, and health related quality of life. Also, the study will provide information, which at present is lacking, on safety of aerobic exercise in Polio, as potential negative outcomes of activity including loss of muscle strength, increased pain and fatigue will be closely monitored.
Trial registration
Clinicaltrials.gov identifier: NCT01271530
doi:10.1186/1471-2377-12-157
PMCID: PMC3553047  PMID: 23234560
Poliomyelitis; Arm Ergometry; Physical fitness; Fatigue
7.  Prognostic factors in ALS: A critical review 
We have performed a systematic review to summarize current knowledge concerning factors related to survival in ALS and to evaluate the implications of these data for clinical trials design. The median survival time from onset to death ranges from 20 to 48 months, but 10–20% of ALS patients have a survival longer than 10 years. Older age and bulbar onset are consistently reported to have a worse outcome. There are conflicting data on gender, diagnostic delay and El Escorial criteria. The rate of symptom progression was revealed to be an independent prognostic factor. Psychosocial factors, FTD, nutritional status, and respiratory function are also related to ALS outcome. The effect of enteral nutrition on survival is still unclear, while NIPPV has been found to improve survival. There are no well established biological markers of progression, although some are likely to emerge in the near future. These findings have relevant implications for the design of future trials. Randomization, besides the type of onset, should take into account age, respiratory status at entry, and a measure of disease progression pre-entry. Alternative trial designs can include the use of natural history controls, the so-called minimization method for treatment allocation, and the futility approach.
doi:10.3109/17482960802566824
PMCID: PMC3515205  PMID: 19922118
8.  Amyotrophic lateral sclerosis, physical exercise, trauma and sports: Results of a population-based pilot case-control study 
Our objective was to investigate exposure to physical exercise and trauma in patients with amyotrophic lateral sclerosis (ALS) compared to the general population. Previous studies in this area have yielded conflicting results. Using population-based ALS registries from Italy, the UK and Ireland, newly diagnosed patients with definite, probable or possible ALS were enrolled in a case-control study with two age- and sex-matched controls for each patient. Source, intensity and duration of physical activity and history of trauma were recorded. We here present the results of a pilot investigation. We studied 61 patients and 112 controls. Forty-one per cent of cases and 17.0% of controls (p = 0.001) had blue-collar occupations; 13.1% versus 3.6% reported strenuous physical activity at work (p = 0.05). Compared with controls, ALS patients had a longer exposure to work-related (10.7 vs. 7.3 years; p = 0.02) and sport-related physical exercise (9.6 vs. 5.2 years; p = 0.005). Three patients (0 controls) reported professional sports (p < 0.04). Traumatic events were similar. Blue collar occupation (OR 4.27; 95% CI 1.68–10.88) and duration of sport-related physical exercise (OR 1.03; 95% CI 1.00–1.05) were independent variables in multivariate analysis. We concluded that ALS is associated with physical exercise but not with traumatic events.
doi:10.3109/17482960903384283
PMCID: PMC3513269  PMID: 20433412
9.  The epidemiology and treatment of ALS: Focus on the heterogeneity of the disease and critical appraisal of therapeutic trials 
Effective treatments for amyotrophic lateral sclerosis (ALS) have remained elusive. Only riluzole, a drug thought to affect glutamate metabolism, improves survival albeit to modest extent. Explanations for the negative results of therapeutic trials include a likely heterogeneity, both in disease susceptibility and pathogenic mechanisms, and faulty methodology of clinical trials. Further understanding of these factors will lead to improvements in patient stratification, and in the design of future clinical trials.
doi:10.3109/17482968.2010.502940
PMCID: PMC3513399  PMID: 20698807
10.  Mapping of Gene Expression Reveals CYP27A1 as a Susceptibility Gene for Sporadic ALS 
PLoS ONE  2012;7(4):e35333.
Amyotrophic lateral sclerosis (ALS) is a progressive, neurodegenerative disease characterized by loss of upper and lower motor neurons. ALS is considered to be a complex trait and genome-wide association studies (GWAS) have implicated a few susceptibility loci. However, many more causal loci remain to be discovered. Since it has been shown that genetic variants associated with complex traits are more likely to be eQTLs than frequency-matched variants from GWAS platforms, we conducted a two-stage genome-wide screening for eQTLs associated with ALS. In addition, we applied an eQTL analysis to finemap association loci. Expression profiles using peripheral blood of 323 sporadic ALS patients and 413 controls were mapped to genome-wide genotyping data. Subsequently, data from a two-stage GWAS (3,568 patients and 10,163 controls) were used to prioritize eQTLs identified in the first stage (162 ALS, 207 controls). These prioritized eQTLs were carried forward to the second sample with both gene-expression and genotyping data (161 ALS, 206 controls). Replicated eQTL SNPs were then tested for association in the second-stage GWAS data to find SNPs associated with disease, that survived correction for multiple testing. We thus identified twelve cis eQTLs with nominally significant associations in the second-stage GWAS data. Eight SNP-transcript pairs of highest significance (lowest p = 1.27×10−51) withstood multiple-testing correction in the second stage and modulated CYP27A1 gene expression. Additionally, we show that C9orf72 appears to be the only gene in the 9p21.2 locus that is regulated in cis, showing the potential of this approach in identifying causative genes in association loci in ALS. This study has identified candidate genes for sporadic ALS, most notably CYP27A1. Mutations in CYP27A1 are causal to cerebrotendinous xanthomatosis which can present as a clinical mimic of ALS with progressive upper motor neuron loss, making it a plausible susceptibility gene for ALS.
doi:10.1371/journal.pone.0035333
PMCID: PMC3324559  PMID: 22509407
11.  Cognitive and clinical characteristics of patients with amyotrophic lateral sclerosis carrying a C9orf72 repeat expansion: a population-based cohort study 
Lancet Neurology  2012;11(3):232-240.
Summary
Background
Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease of upper and lower motor neurons, associated with frontotemporal dementia (FTD) in about 14% of incident cases. We assessed the frequency of the recently identified C9orf72 repeat expansion in familial and apparently sporadic cases of ALS and characterised the cognitive and clinical phenotype of patients with this expansion.
Methods
A population-based register of patients with ALS has been in operation in Ireland since 1995, and an associated DNA bank has been in place since 1999. 435 representative DNA samples from the bank were screened using repeat-primed PCR for the presence of a GGGGCC repeat expansion in C9orf72. We assessed clinical, cognitive, behavioural, MRI, and survival data from 191 (44%) of these patients, who comprised a population-based incident group and had previously participated in a longitudinal study of cognitive and behavioural changes in ALS.
Findings
Samples from the DNA bank included 49 cases of known familial ALS and 386 apparently sporadic cases. Of these samples, 20 (41%) cases of familial ALS and 19 (5%) cases of apparently sporadic ALS had the C9orf72 repeat expansion. Of the 191 patients for whom phenotype data were available, 21 (11%) had the repeat expansion. Age at disease onset was lower in patients with the repeat expansion (mean 56·3 [SD 8·3] years) than in those without (61·3 [10·6] years; p=0·043). A family history of ALS or FTD was present in 18 (86%) of those with the repeat expansion. Patients with the repeat expansion had significantly more co-morbid FTD than patients without the repeat (50% vs 12%), and a distinct pattern of non-motor cortex changes on high-resolution 3 T magnetic resonance structural neuroimaging. Age-matched univariate analysis showed shorter survival (20 months vs 26 months) in patients with the repeat expansion. Multivariable analysis showed an increased hazard rate of 1·9 (95% 1·1–3·7; p=0·035) in those patients with the repeat expansion compared with patients without the expansion
Interpretation
Patients with ALS and the C9orf72 repeat expansion seem to present a recognisable phenotype characterised by earlier disease onset, the presence of cognitive and behavioural impairment, specific neuroimaging changes, a family history of neurodegeneration with autosomal dominant inheritance, and reduced survival. Recognition of patients with ALS who carry an expanded repeat is likely to be important in the context of appropriate disease management, stratification in clinical trials, and in recognition of other related phenotypes in family members.
Funding
Health Seventh Framework Programme, Health Research Board, Research Motor Neuron, Irish Motor Neuron Disease Association, The Motor Neurone Disease Association of Great Britain and Northern Ireland, ALS Association.
doi:10.1016/S1474-4422(12)70014-5
PMCID: PMC3315021  PMID: 22305801
12.  Incidence of Amyotrophic Lateral Sclerosis in Europe 
Background
Geographical differences in amyotrophic lateral sclerosis (ALS) incidence have been reported in the literature, but comparisons across previous studies are limited by different methods in case ascertainment and by the relatively small size of the studied populations. To address these issues, the authors undertook a pooled-analysis of European population-based ALS registries.
Methods
All new incident ALS cases in subjects 18 years old and older were identified prospectively in six population-based registries in three European countries (Ireland, United Kingdom, Italy) in the two year period 1998-1999 with a reference population of almost 24 million.
Results
Based on 1,028 identified incident cases, the crude annual incidence rate of ALS in the general European population was 2.16 per 100,000 person-years; 95% CI 2.0-2.3), with similar incidence rates across all registries. The incidence was higher among men (3.0 per 100,000 person-years; 95% CI = 2.8 to 3.3) than among women (2.4 per 100,000 person-years; 95% CI=2.2 to 2.6). Spinal onset ALS was more common among men compared to women, particularly in the 70-80 year age group. Disease occurrence decreases rapidly after 80 years of age.
Conclusions
ALS incidence is homogeneous across Europe. Sex differences in incidence may be explained by the higher incidence of spinal onset ALS among males and the age-related disease pattern suggests that ALS occurs within a susceptible group within the population rather than being a disease of aging.
doi:10.1136/jnnp.2009.183525
PMCID: PMC2850819  PMID: 19710046
13.  Angiogenin Levels and ANG Genotypes: Dysregulation in Amyotrophic Lateral Sclerosis 
PLoS ONE  2010;5(11):e15402.
Objective
To determine whether 5 single nucleotide polymorphisms (SNPs) associate with ALS in 3 different populations. We also assessed the contribution of genotype to angiogenin levels in plasma and CSF.
Methods
Allelic association statistics were calculated for polymorphisms in the ANG gene in 859 patients and 1047 controls from Sweden, Ireland and Poland. Plasma, serum and CSF angiogenin levels were quantified and stratified according to genotypes across the ANG gene. The contribution of SNP genotypes to variance in circulating angiogenin levels was estimated in patients and controls.
Results
All SNPs showed association with ALS in the Irish group. The SNP rs17114699 replicated in the Swedish cohort. No SNP associated in the Polish cohort. Age- and sex-corrected circulating angiogenin levels were significantly lower in patients than in controls (p<0.001). An allele dose-dependent regulation of angiogenin levels was observed in controls. This regulation was attenuated in the ALS cohort. A significant positive correlation between CSF plasma angiogenin levels was present in controls and abolished in ALS.
Conclusions
ANG variants associate with ALS in the Irish and Swedish populations, but not in the Polish. There is evidence of dysregulation of angiogenin expression in plasma and CSF in sporadic ALS. Angiogenin expression is likely to be important in the pathogenesis of ALS.
doi:10.1371/journal.pone.0015402
PMCID: PMC2978104  PMID: 21085671
14.  Chromosome 9p21 in sporadic amyotrophic lateral sclerosis in the UK and seven other countries: a genome-wide association study 
Lancet Neurology  2010;9(10):986-994.
Summary
Background
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease of motor neurons that results in progressive weakness and death from respiratory failure, commonly within about 3 years. Previous studies have shown association of a locus on chromosome 9p with ALS and linkage with ALS–frontotemporal dementia. We aimed to test whether this genomic region is also associated with ALS in an independent set of UK samples, and to identify risk factors associated with ALS in a further genome-wide association study that combined data from the independent analysis with those from other countries.
Methods
We collected samples from patients with sporadic ALS from 20 UK hospitals and obtained UK control samples from the control groups of the Depression Case Control study, the Bipolar Affective Case Control Study, and the British 1958 birth cohort DNA collection. Genotyping of DNA in this independent analysis was done with Illumina HumanHap550 BeadChips. We then undertook a joint genome-wide analysis that combined data from the independent set with published data from the UK, USA, Netherlands, Ireland, Italy, France, Sweden, and Belgium. The threshold for significance was p=0·05 in the independent analysis, because we were interested in replicating a small number of previously reported associations, whereas the Bonferroni-corrected threshold for significance in the joint analysis was p=2·20×10−7
Findings
After quality control, samples were available from 599 patients and 4144 control individuals in the independent set. In this analysis, two single nucleotide polymorphisms in a locus on chromosome 9p21.2 were associated with ALS: rs3849942 (p=2·22×10−6; odds ratio [OR] 1·39, 95% CI 1·21–1·59) and rs2814707 (p=3·32×10−6; 1·38, 1·20–1·58). In the joint analysis, which included samples from 4312 patients with ALS and 8425 control individuals, rs3849942 (p=4·64×10−10; OR 1·22, 95% CI 1·15–1·30) and rs2814707 (p=4·72×10−10; 1·22, 1·15–1·30) were associated with ALS.
Interpretation
We have found strong evidence of a genetic association of two single nucleotide polymorphisms on chromosome 9 with sporadic ALS, in line with findings from previous independent GWAS of ALS and linkage studies of ALS–frontotemporal dementia. Our findings together with these earlier findings suggest that genetic variation at this locus on chromosome 9 causes sporadic ALS and familial ALS–frontotemporal dementia. Resequencing studies and then functional analysis should be done to identify the defective gene.
Funding
ALS Therapy Alliance, the Angel Fund, the Medical Research Council, the Motor Neurone Disease Association of Great Britain and Northern Ireland, the Wellcome Trust, and the National Institute for Health Research Dementias and Neurodegenerative Diseases Research Network (DeNDRoN).
doi:10.1016/S1474-4422(10)70197-6
PMCID: PMC3257853  PMID: 20801717
15.  Sequencing and analysis of an Irish human genome 
Genome Biology  2010;11(9):R91.
Background
Recent studies generating complete human sequences from Asian, African and European subgroups have revealed population-specific variation and disease susceptibility loci. Here, choosing a DNA sample from a population of interest due to its relative geographical isolation and genetic impact on further populations, we extend the above studies through the generation of 11-fold coverage of the first Irish human genome sequence.
Results
Using sequence data from a branch of the European ancestral tree as yet unsequenced, we identify variants that may be specific to this population. Through comparisons with HapMap and previous genetic association studies, we identified novel disease-associated variants, including a novel nonsense variant putatively associated with inflammatory bowel disease. We describe a novel method for improving SNP calling accuracy at low genome coverage using haplotype information. This analysis has implications for future re-sequencing studies and validates the imputation of Irish haplotypes using data from the current Human Genome Diversity Cell Line Panel (HGDP-CEPH). Finally, we identify gene duplication events as constituting significant targets of recent positive selection in the human lineage.
Conclusions
Our findings show that there remains utility in generating whole genome sequences to illustrate both general principles and reveal specific instances of human biology. With increasing access to low cost sequencing we would predict that even armed with the resources of a small research group a number of similar initiatives geared towards answering specific biological questions will emerge.
doi:10.1186/gb-2010-11-9-r91
PMCID: PMC2965383  PMID: 20822512
16.  Paraoxonase promoter and intronic variants modify risk of sporadic amyotrophic lateral sclerosis 
Background
The paraoxonases, PON1–3, play a major protective role both against environmental toxins and as part of the antioxidant defence system. Recently, non‐synonymous coding single nucleotide polymorphisms (SNPs), known to lower serum PON activity, have been associated with sporadic ALS (SALS) in a Polish population. A separate trio based study described a detrimental allele at the PON3 intronic variant INS2+3651 (rs10487132). Association between PON gene cluster variants and SALS requires external validation in an independent dataset.
Aims
To examine the association of the promoter SNPs PON1−162G>A and PON1−108T>C; the non‐synonymous functional SNPs PON1Q192R and L55M and PON2C311S and A148G; and the intronic marker PON3INS2+3651A>G, with SALS in a genetically homogenous population.
Methods
221 Irish patients with SALS and 202 unrelated control subjects were genotyped using KASPar chemistries. Statistical analyses and haplotype estimations were conducted using Haploview and Unphased software. Multiple permutation testing, as implemented in Unphased, was applied to haplotype p values to correct for multiple hypotheses.
Results
Two of the seven SNPs were associated with SALS in the Irish population: PON155M (OR 1.52, p = 0.006) and PON3INS2+3651 G (OR 1.36, p = 0.03). Two locus haplotype analysis showed association only when both of these risk alleles were present (OR 1.7, p = 0.005), suggesting a potential effect modification. Low functioning promoter variants were observed to influence this effect when compared with wild‐type.
Conclusions
These data provide additional evidence that genetic variation across the paroxanase loci may be common susceptibility factors for SALS.
doi:10.1136/jnnp.2006.112581
PMCID: PMC2117866  PMID: 17702780
17.  Screening for replication of genome-wide SNP associations in sporadic ALS 
We recently reported a joint analysis of genome-wide association (GWA) data on 958 sporadic amyotrophic lateral sclerosis (ALS) cases and 932 controls from Ireland and the publicly available data sets from the United States and the Netherlands. The strongest pooled association was rs10260404 in the dipeptidyl-peptidase 6 (DPP6) gene. Here, we sought confirmation of joint analysis signals in both an expanded Irish and a Polish ALS cohort. Among 287 522 autosomal single-nucleotide polymorphisms (SNPs), 27 were commonly associated on joint analysis of the Irish, US and Dutch GWAs. These 27 SNPs were genotyped in an expanded Irish cohort (312 patients with SALS; 259 controls) and an additional Polish cohort (218 patients; 356 controls). Eleven SNPs, including rs10260404, reached a final P-value below 0.05 in the Irish cohort. In the Polish cohort, only one SNP, rs6299711, showed nominal association with ALS. Pooling of data for 1267 patients with ALS and 1336 control subjects did not identify any association reaching Bonferroni significance (P<1.74 × 10−7). The present strategy did not reveal any consistently associated SNP across four populations. The result for DPP6 is surprising, as it has been replicated elsewhere. We discuss the possible interpretations and implications of these findings for future ALS GWA studies both within and between populations.
doi:10.1038/ejhg.2008.194
PMCID: PMC2986065  PMID: 18987618
amyotrophic lateral sclerosis; genome-wide study; DPP6; genetics
18.  Timeliness of diagnosis in Motor Neurone Disease: a population-based study 
The Ulster Medical Journal  2008;77(1):18-21.
Following the observation from our experience with the Northern Ireland Motor Neurone Disease (MND) register that excessive delays appeared to exist in the diagnosis of patients with MND, we performed a population-based study of the length and factors involved in the diagnostic process. In 73 patients we found that the median time to diagnosis from symptom onset was 15.6 months, being shorter in bulbar onset patients and longer in females or those presenting with non-specific gait disturbance. We divided this interval into three time periods – symptom onset to first medical contact, first medical contact to neurology referral and neurology referral to diagnosis. The time period from first medical contact to neurology referral was the longest of the three periods studied indicating that appropriate timely referral of patients to neurologists was responsible for the greatest delay in making a diagnosis of MND. We propose that improving the accessibility of neurological services could potentially reduce the time to diagnosis by at least three months.
PMCID: PMC2397016  PMID: 18269112
19.  Analysis of IFT74 as a candidate gene for chromosome 9p-linked ALS-FTD 
BMC Neurology  2006;6:44.
Background
A new locus for amyotrophic lateral sclerosis – frontotemporal dementia (ALS-FTD) has recently been ascribed to chromosome 9p.
Methods
We identified chromosome 9p segregating haplotypes within two families with ALS-FTD (F476 and F2) and undertook mutational screening of candidate genes within this locus.
Results
Candidate gene sequencing at this locus revealed the presence of a disease segregating stop mutation (Q342X) in the intraflagellar transport 74 (IFT74) gene in family 476 (F476), but no mutation was detected within IFT74 in family 2 (F2). While neither family was sufficiently informative to definitively implicate or exclude IFT74 mutations as a cause of chromosome 9-linked ALS-FTD, the nature of the mutation observed within F476 (predicted to truncate the protein by 258 amino acids) led us to sequence the open reading frame of this gene in a large number of ALS and FTD cases (n = 420). An additional sequence variant (G58D) was found in a case of sporadic semantic dementia. I55L sequence variants were found in three other unrelated affected individuals, but this was also found in a single individual among 800 Human Diversity Gene Panel samples.
Conclusion
Confirmation of the pathogenicity of IFT74 sequence variants will require screening of other chromosome 9p-linked families.
doi:10.1186/1471-2377-6-44
PMCID: PMC1764752  PMID: 17166276
20.  Delineating the genetic heterogeneity of ALS using targeted high-throughput sequencing 
Journal of Medical Genetics  2013;50(11):776-783.
Background
Over 100 genes have been implicated in the aetiology of amyotrophic lateral sclerosis (ALS). A detailed understanding of their independent and cumulative contributions to disease burden may help guide various clinical and research efforts.
Methods
Using targeted high-throughput sequencing, we characterised the variation of 10 Mendelian and 23 low penetrance/tentative ALS genes within a population-based cohort of 444 Irish ALS cases (50 fALS, 394 sALS) and 311 age-matched and geographically matched controls.
Results
Known or potential high-penetrance ALS variants were identified within 17.1% of patients (38% of fALS, 14.5% of sALS). 12.8% carried variants of Mendelian disease genes (C9orf72 8.78%; SETX 2.48%; ALS2 1.58%; FUS 0.45%; TARDBP 0.45%; OPTN 0.23%; VCP 0.23%. ANG, SOD1, VAPB 0%), 4.7% carried variants of low penetrance/tentative ALS genes and 9.7% (30% of fALS, 7.1% of sALS) carried previously described ALS variants (C9orf72 8.78%; FUS 0.45%; TARDBP 0.45%). 1.6% of patients carried multiple known/potential disease variants, including all identified carriers of an established ALS variant (p<0.01); TARDBP:c.859G>A(p.[G287S]) (n=2/2 sALS). Comparison of our results with those from studies of other European populations revealed significant differences in the spectrum of disease variation (p=1.7×10−4).
Conclusions
Up to 17% of Irish ALS cases may carry high-penetrance variants within the investigated genes. However, the precise nature of genetic susceptibility differs significantly from that reported within other European populations. Certain variants may not cause disease in isolation and concomitant analysis of disease genes may prove highly important.
doi:10.1136/jmedgenet-2013-101795
PMCID: PMC3812897  PMID: 23881933
Genetic Epidemiology; Motor Neurone Disease

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