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J Clin Pathol. 2014 Dec;67(12):1078-83. doi: 10.1136/jclinpath-2014-202597. Epub 2014 Sep 19.

Use of single-nucleotide polymorphisms (SNPs) to distinguish gene expression subtypes of chronic fatigue syndrome/myalgic encephalomyelitis (CFS/ME).

Author information

1
CFS Group, Department of Cellular & Molecular Medicine, St George's University of London, London, UK.
2
CFS Group, Department of Cellular & Molecular Medicine, St George's University of London, London, UK Escuela de Medicina y Ciencias de Salud, Universidad del Rosario, Bogota, Colombia.

Abstract

AIMS:

We have reported gene expression changes in patients with chronic fatigue syndrome/myalgic encephalomyelitis (CFS/ME) and the fact that such gene expression data can be used to identify subtypes of CFS/ME with distinct clinical phenotypes. Due to the difficulties in using a comparative gene expression method as an aid to CFS/ME disease and subtype-specific diagnosis, we have attempted to develop such a method based on single-nucleotide polymorphism (SNP) analysis.

METHODS:

To identify SNP allele associations with CFS/ME and CFS/ME subtypes, we tested genomic DNA of patients with CFS/ME (n=108), patients with endogenous depression (n=17) and normal blood donors (n=68) for 504 human SNP alleles located within 88 CFS-associated human genes using the SNP Genotyping GoldenGate Assay (Illumina, San Diego, California, USA). 360 ancestry informative markers (AIM) were also examined.

RESULTS:

21 SNPs were significantly associated with CFS/ME compared with depression and 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 Caucasian. Hierarchical clustering of AIM data revealed the relatedness between 2 couples of patients with CFS only and confirmed the overall heterogeneity of all subjects.

CONCLUSIONS:

This study provides evidence that human SNPs located within CFS/ME associated genes are associated with particular genomic subtypes of CFS/ME. Further work is required to develop this into a clinically useful subtype-specific diagnostic test.

KEYWORDS:

BIOLOGICAL SCIENCES; EPIDEMIOLOGY; GENETICS

PMID:
25240059
DOI:
10.1136/jclinpath-2014-202597
[Indexed for MEDLINE]

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