Fast track — ArticlesITPR2 as a susceptibility gene in sporadic amyotrophic lateral sclerosis: a genome-wide association study
Introduction
Amyotrophic lateral sclerosis (ALS), a form of motor neuron disease, is a neurodegenerative disorder characterised by progressive wasting and weakness of limb, bulbar, and respiratory muscles. The disease is caused by loss of motor neurons in the spinal cord, brainstem, and motor cortex and can occur at any time in adulthood, with a median age of onset in the mid-fifties. About half of patients die within 3 years of symptom onset, usually because of respiratory failure.1, 2, 3 The only therapeutic strategy to slow progression of ALS is currently riluzole, which delays disease development by 3–6 months.4
Almost one tenth of cases of ALS are familial. 12–23% of familial ALS is linked to mutations in the superoxide dismutase 1 gene (SOD1),5 and rare cases are associated with mutations in the genes that encode alsin, dynactin, VAMP-associated protein B and C (VAPB), and angiogenin ribonuclease RNase A family 5 (ANG).6, 7 The remaining 90% or more of ALS cases are sporadic, and are thought to be multifactorial, with both environmental and genetic components.8, 9, 10 On the basis of concordance rates in twin studies, estimates of the heritability of ALS range from 0·38 to 0·85.11
The cause of motor neuron degeneration in sporadic ALS is unknown, but the many possible mechanisms include oxidative stress, glutamate-mediated excitotoxicity, and apoptosis.1, 12, 13 Several candidate-gene studies have investigated these possibilities, and have reported associations with variants of genes that include ANG, vascular endothelial growth factor (VEGF), hemochromatosis (HFE), and paraoxonase 1 (PON1), and with variations in copy number for the genes that encode survival of motor neuron proteins 1 and 2 (SMN1 and SMN2).6, 14, 15, 16, 17, 18, 19, 20
In the candidate approach, a gene is selected on the basis of its function and is subsequently tested for association with a disease. An alternative approach, made possible by progress such as completion of the International Haplotype Map (HapMap) project and the development of high-throughput, high-density genotyping technology, is that of genome-wide association. In this approach, nearly all common variation in the genome can be screened for association with disease in an unbiased way,21, 22 in contrast to the candidate-gene approach, which is based on pathophysiological hypotheses. Indeed, genome-wide association studies have successfully identified genetic risk factors for diseases that include age-related macular degeneration, diabetes mellitus types 1 and 2, coeliac disease, and breast cancer.23, 24, 25, 26
Most variation in human DNA is caused by single nucleotide polymorphisms (SNPs). More than 10 million SNPs have been identified and these common variants are thought to contribute to disease susceptibility (the common disease, common variant hypothesis). The HapMap project has shown that genetic variants that are near each other are often inherited together, meaning that SNPs are inherited in groups or haplotypes. Tag SNPs can be used to identify these haplotypes, and roughly 300 000 tag SNPs contain most of the information about patterns of genetic variation for all 10 million common SNPs. High-density, high-throughput genotyping technology has made genome-wide association studies possible by enabling researchers to test all tag SNPs for association with a disease in a single experiment.27
To identify genetic factors for sporadic ALS, we did a genome-wide association study in patients and healthy controls from The Netherlands, and we replicated our most significant findings in two independent sample series. We also investigated the possible pathological functions of associated genes using expression data from peripheral whole blood in patients with sporadic ALS and in control individuals who were included in the genome-wide association study. Such studies have previously shown that changes in gene expression in peripheral blood can be associated with diseases that do not have obvious blood phenotypes, including cerebral infarction, Huntington's disease, Alzheimer's disease, and Parkinson's disease.28, 29, 30, 31
Section snippets
Participants
We analysed populations from The Netherlands, Belgium, and Sweden. All samples from Belgian and Swedish patients were screened for SOD1 mutations, and the Swedish samples were also screened for ANG mutations. No samples with mutations in these genes were included in this study. Because no SOD1 mutation has been reported in patients with sporadic ALS or familial ALS in The Netherlands (Baas F and Andersen PM, unpublished), no SOD1 screening was done in these samples.
Patients were included in the
Results
Figure 1 shows the numbers of people and SNPs tested after exclusions at each genotyping stage, and table 1 shows characteristics of the study populations. In the genome-wide study, we genotyped samples from 477 patients with sporadic ALS and 472 control volunteers. We subsequently excluded 12 patients and 22 controls because the genotyping was of a poor quality (proportion of all genotypes successfully identified [call rate]<95%), and two pairs of patients were excluded because they were
Discussion
In our three-stage genome-wide association study, rs2306677 was associated with ALS after correction for multiple testing (table 3). Re-evaluation of stage-two results for this SNP by population showed a consistent pattern of association with ALS in the two independent Dutch series and the Swedish series, but contrasting results for the Belgian population (table 3). This difference might be due to the relatively small size of the sample (which could have caused inaccurate estimates of the
References (49)
- et al.
Amyotrophic lateral sclerosis
Lancet
(2007) - et al.
A mutation in the vesicle-trafficking protein VAPB causes late-onset spinal muscular atrophy and amyotrophic lateral sclerosis
Am J Hum Genet
(2004) - et al.
The complex genetics of amyotrophic lateral sclerosis
Lancet Neurol
(2007) - et al.
Amyotrophic lateral sclerosis as a complex genetic disease
Biochim Biophys Acta
(2006) - et al.
The role of excitotoxicity in the pathogenesis of amyotrophic lateral sclerosis
Biochim Biophys Acta
(2006) - et al.
Genetic association studies
Lancet
(2005) El Escorial World Federation of Neurology criteria for the diagnosis of amyotrophic lateral sclerosis
J Neurol Sci
(1994)- et al.
Capture-recapture methods
Lancet
(1992) - et al.
PLINK: a toolset for whole-genome association and population based linkage analysis
Am J Hum Genet
(2007) - et al.
Genome-wide genotyping in amyotrophic lateral sclerosis and neurologically normal controls: first stage analysis and public release of data
Lancet Neurol
(2007)