The paper above seems to be this "completed study" funded by ME Research UK back in 2010, which I presume wasn't published at the time?
http://www.meresearch.org.uk/our-research/completed-studies/single-nucleotide-polymorphisms/
Authors
Shimosako N, Kerr JR
Institution
George’s University of London, London UK
Abstract
We have recently reported gene expression changes in patients with Chronic Fatigue Syndrome/Myalgic Encephalomyelitis and the utility of gene expression data to identify subtypes of CFS/ME with distinct clinical phenotypes (
J Infect Dis, 2008). Due to the difficulties in using a comparative gene expression method as an aid to CFS/ME disease and subtype-specific diagnosis, we attempted to achieve such a method based on single nucleotide polymorphisms (SNP) alleles.
To identify SNP allele associations with CFS/ME and CFS/ME subtypes, we tested genomic DNA of CFS/ME patients (n=108), endogenous depression patients (n=17), 13 and normal blood donors (n=68) for 454–504 human SNP alleles based within 88 CFS-associated human genes using the SNP Genotyping GoldenGate Assay (Illumina, San Diego, CA, USA). Ancestry informative markers (AIM) were also examined.
21 SNPs were significantly associated with CFS/ME, when compared with depression, & normal groups. 148 SNP alleles had a significant association with one or more CFS/ME subtypes. For each subtype, associated SNPs tended to be grouped together within particular genes. AIM SNPs indicated that 4 subjects were of asian origin while the remainder were Western European. Hierarchical clustering of AIM data confirmed the overall heterogeneity of all subjects.
This study provides evidence that human SNPs located within CFS/ME associated genes are associated with particular gene expression subtypes of CFS/ME. Further work is required to develop this into a clinically useful aid to subtype-specific diagnosis.
Comment by ME Research UK
The information inherited from our parents (usually in the form of a gene, a sequence of DNA) has to be translated into a product, such as an RNA molecule or a protein, before it can be used by the body, and this process is called gene expression. Over the past few years, a number of research groups worldwide have investigated gene expression in people with ME/CFS, and the number of scientific reports published has steadily increased. Overall, the genes identified in the illness seem related to ‘‘immunity and defense’’, supporting what is already known about the role of the immune system.
Dr Jonathan Kerr’s group at St George’s Hospital, University of London was one of the most active in defining the molecular basis of ME/CFS. Initially, the researchers performed a pilot study of gene expression in patients compared with controls, and have demonstrated marked human gene dysregulation, principally affecting the immune system. Their subsequent work on protein biomarkers (the backbone of any diagnostic test) identified several molecules which seemed to be specific to ME/CFS. In late 2007, the group published a paper (
Journal of Clinical Pathology) outlining their identification of a putative “gene signature” for the illness consisting of 88 human genes. As the box below shows, these genes can be subdivided into categories by, say, diseases and disorders or by molecular and cellular functions. The research team said that three of the genes identified are directly linked with mitochondrial metabolism, and a further ten had indirect links with mitochondrial metabolism.
Important disorders and functions associated with some of the genes in the putative ME/CFS gene “signature”
Diseases: Haematological (22 genes), Immunological (14), Cancer (31), Dermatological (3), Endocrine system (9)
Molecular & cellular function: Cellular development (26), Cell death (33), Gene expression (31), Cellular growth & proliferation (31), Cellular assembly & organisation (15)
Physiological system development & function: Haematological system (22), Nervous, immune & lymphatic system (18), Tissue morphology (18), Survival (17), Immunity (20)
As these 88 genes had been linked directly to the pathogenesis of ME/CFS, the logical next step was to begin the study of inherited determinants of susceptibility by examining single nucleotide polymorphisms (SNPs) – pronounced “snips” – within these genes. SNPs within some of these genes have been linked with features and complications which might be associated with CFS (eg. IL10RA SNPs are associated with development of lymphoma, a disease which some have speculated occurs increased frequency in CFS patients).
With funding from ME Research UK, the St George’s group began work on identifying the key SNPs for each of the 88 genes. As there are hundreds of SNPs within each gene and the cost of studying all of them would be prohibitive, the team focussed on “determinative” SNPs (ie. those which are known to predict all or most of the others within one gene); the number of determinative SNPs per gene typically varies between 3 and 7 (mean = ~5). Once these determinative SNPs had been identified for each gene, the researchers designed a low density array cards to contain their respective assays, had these manufactured, and then used these to test genomic DNA samples of 105 patients in the initial sample group. After comparing allele frequencies between the CFS and normal groups, the allele frequencies were then be related to the gene expression levels for each gene.
The results indicated that 21 SNP alleles could be significantly associated with CFS/ME patients as compared with Depression and Normal controls, and 148 SNP alleles which are associated with one or more CFS/ME subtypes. Assuming these results could be replicated, the authors believed that it might be possible to develop a subtype-specific diagnostic test using a subset of subtype-specific SNPs, to aid in the investigation and ultimately, the clinical management of CFS/ME patients.
In 2011, a study was designed to assess whether the “gene signature” for ME/CFS (reported above) was sensitive enough to correctly classify a separate blind dataset of ‘mRNA relative quantities’ from a new population of ME/CFS patients and healthy persons. The results (
published in PloS One) showed that the metric used was able to successfully classify roughly two-thirds of both ME/CFS and healthy samples, but – unfortunately – that the level of misclassification was high, leading the authors to conclude that the “gene signature” suggested in published scientific reports could not be used as a broad diagnostic test for ME/CFS.
What are SNPs?
Single nucleotide polymorphisms (SNPs) are small genetic changes in DNA that vary between individuals. In fact, humans are 99% identical as regards their gene sequences, and the 1% which remains is mostly accounted for SNPs, of which there are approx. 10 million in the human genome. This makes SNPs very useful – they can serve as helpful landmarks for population genetic maps, but their greatest importance is in biomedical research for comparing specific regions of the genome between groups or individuals with and without a disease.
While most SNPs are silent, some can have important consequences for individual susceptibility to disease and reactions to treatment. An example is the
apoE gene which is associated with an increased risk of Alzheimer’s disease. It is also thought that certain SNP combinations can contribute to a predisposition to developing medical conditions.
At present, an enormous literature exists reporting possible associations between SNPs and diseases. for instance, the SNP500Cancer project is examining samples to locate important SNPs, and there are many such examples in a range of illnesses.
The challenge in ME/CFS is to identify SNPs which will ultimately allow patients to be quickly and simply “diagnosed” from a sample, and possibly assigned to illness subgroups for specific therapies.
