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

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 Genotypin...

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Autores:
Tipo de recurso:
Fecha de publicación:
2014
Institución:
Universidad del Rosario
Repositorio:
Repositorio EdocUR - U. Rosario
Idioma:
eng
OAI Identifier:
oai:repository.urosario.edu.co:10336/22308
Acceso en línea:
https://doi.org/10.1136/jclinpath-2014-202597
https://repository.urosario.edu.co/handle/10336/22308
Palabra clave:
Genomic DNA
Transcription factor
Transcriptome
Adult
Allele
Article
Asian
Binding site
Blood donor
Caucasian
Chronic fatigue syndrome
Controlled study
Diagnostic test
Endogenous depression
Female
Gene expression
Genetic association
Genotype
Human
Major clinical study
Male
Phenotype
Sequence analysis
Single nucleotide polymorphism
Chronic fatigue syndrome
Classification
Cluster analysis
Depression
Genetic predisposition
Genetics
Middle aged
Single nucleotide polymorphism
Adult
Cluster Analysis
Depression
Female
Genetic Predisposition to Disease
Genotype
Humans
Male
Middle Aged
Transcriptome
Chronic
Single Nucleotide
Fatigue Syndrome
Polymorphism
Rights
License
Abierto (Texto Completo)
id EDOCUR2_90aee0b258e48c767682e326edafe8d2
oai_identifier_str oai:repository.urosario.edu.co:10336/22308
network_acronym_str EDOCUR2
network_name_str Repositorio EdocUR - U. Rosario
repository_id_str
spelling 4626d36c-687d-4733-8db1-14adabc8f13f-1404187f1-16b5-496a-a7db-5918a0c5e4c6-12020-05-25T23:56:03Z2020-05-25T23:56:03Z2014Methods 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.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.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.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.application/pdfhttps://doi.org/10.1136/jclinpath-2014-202597https://repository.urosario.edu.co/handle/10336/22308engBMJ Publishing Group1083No. 121078Journal of Clinical PathologyVol. 67Journal of Clinical Pathology, Vol.67, No.12 (2014); pp. 1078-1083https://www.scopus.com/inward/record.uri?eid=2-s2.0-84910138360&doi=10.1136%2fjclinpath-2014-202597&partnerID=40&md5=6a498d197e6fb737ad0ce00d34d37d32Abierto (Texto Completo)http://purl.org/coar/access_right/c_abf2instname:Universidad del Rosarioreponame:Repositorio Institucional EdocURGenomic DNATranscription factorTranscriptomeAdultAlleleArticleAsianBinding siteBlood donorCaucasianChronic fatigue syndromeControlled studyDiagnostic testEndogenous depressionFemaleGene expressionGenetic associationGenotypeHumanMajor clinical studyMalePhenotypeSequence analysisSingle nucleotide polymorphismChronic fatigue syndromeClassificationCluster analysisDepressionGenetic predispositionGeneticsMiddle agedSingle nucleotide polymorphismAdultCluster AnalysisDepressionFemaleGenetic Predisposition to DiseaseGenotypeHumansMaleMiddle AgedTranscriptomeChronicSingle NucleotideFatigue SyndromePolymorphismUse of single-nucleotide polymorphisms (SNPs) to distinguish gene expression subtypes of chronic fatigue syndrome/myalgic encephalomyelitis (CFS/ME)articleArtículohttp://purl.org/coar/version/c_970fb48d4fbd8a85http://purl.org/coar/resource_type/c_6501Shimosako, NanaKerr, Jonathan R10336/22308oai:repository.urosario.edu.co:10336/223082022-05-02 07:37:13.986787https://repository.urosario.edu.coRepositorio institucional EdocURedocur@urosario.edu.co
dc.title.spa.fl_str_mv Use of single-nucleotide polymorphisms (SNPs) to distinguish gene expression subtypes of chronic fatigue syndrome/myalgic encephalomyelitis (CFS/ME)
title Use of single-nucleotide polymorphisms (SNPs) to distinguish gene expression subtypes of chronic fatigue syndrome/myalgic encephalomyelitis (CFS/ME)
spellingShingle Use of single-nucleotide polymorphisms (SNPs) to distinguish gene expression subtypes of chronic fatigue syndrome/myalgic encephalomyelitis (CFS/ME)
Genomic DNA
Transcription factor
Transcriptome
Adult
Allele
Article
Asian
Binding site
Blood donor
Caucasian
Chronic fatigue syndrome
Controlled study
Diagnostic test
Endogenous depression
Female
Gene expression
Genetic association
Genotype
Human
Major clinical study
Male
Phenotype
Sequence analysis
Single nucleotide polymorphism
Chronic fatigue syndrome
Classification
Cluster analysis
Depression
Genetic predisposition
Genetics
Middle aged
Single nucleotide polymorphism
Adult
Cluster Analysis
Depression
Female
Genetic Predisposition to Disease
Genotype
Humans
Male
Middle Aged
Transcriptome
Chronic
Single Nucleotide
Fatigue Syndrome
Polymorphism
title_short Use of single-nucleotide polymorphisms (SNPs) to distinguish gene expression subtypes of chronic fatigue syndrome/myalgic encephalomyelitis (CFS/ME)
title_full Use of single-nucleotide polymorphisms (SNPs) to distinguish gene expression subtypes of chronic fatigue syndrome/myalgic encephalomyelitis (CFS/ME)
title_fullStr Use of single-nucleotide polymorphisms (SNPs) to distinguish gene expression subtypes of chronic fatigue syndrome/myalgic encephalomyelitis (CFS/ME)
title_full_unstemmed Use of single-nucleotide polymorphisms (SNPs) to distinguish gene expression subtypes of chronic fatigue syndrome/myalgic encephalomyelitis (CFS/ME)
title_sort Use of single-nucleotide polymorphisms (SNPs) to distinguish gene expression subtypes of chronic fatigue syndrome/myalgic encephalomyelitis (CFS/ME)
dc.subject.keyword.spa.fl_str_mv Genomic DNA
Transcription factor
Transcriptome
Adult
Allele
Article
Asian
Binding site
Blood donor
Caucasian
Chronic fatigue syndrome
Controlled study
Diagnostic test
Endogenous depression
Female
Gene expression
Genetic association
Genotype
Human
Major clinical study
Male
Phenotype
Sequence analysis
Single nucleotide polymorphism
Chronic fatigue syndrome
Classification
Cluster analysis
Depression
Genetic predisposition
Genetics
Middle aged
Single nucleotide polymorphism
Adult
Cluster Analysis
Depression
Female
Genetic Predisposition to Disease
Genotype
Humans
Male
Middle Aged
Transcriptome
topic Genomic DNA
Transcription factor
Transcriptome
Adult
Allele
Article
Asian
Binding site
Blood donor
Caucasian
Chronic fatigue syndrome
Controlled study
Diagnostic test
Endogenous depression
Female
Gene expression
Genetic association
Genotype
Human
Major clinical study
Male
Phenotype
Sequence analysis
Single nucleotide polymorphism
Chronic fatigue syndrome
Classification
Cluster analysis
Depression
Genetic predisposition
Genetics
Middle aged
Single nucleotide polymorphism
Adult
Cluster Analysis
Depression
Female
Genetic Predisposition to Disease
Genotype
Humans
Male
Middle Aged
Transcriptome
Chronic
Single Nucleotide
Fatigue Syndrome
Polymorphism
dc.subject.keyword.eng.fl_str_mv Chronic
Single Nucleotide
Fatigue Syndrome
Polymorphism
description 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.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.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.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.
publishDate 2014
dc.date.created.spa.fl_str_mv 2014
dc.date.accessioned.none.fl_str_mv 2020-05-25T23:56:03Z
dc.date.available.none.fl_str_mv 2020-05-25T23:56:03Z
dc.type.eng.fl_str_mv article
dc.type.coarversion.fl_str_mv http://purl.org/coar/version/c_970fb48d4fbd8a85
dc.type.coar.fl_str_mv http://purl.org/coar/resource_type/c_6501
dc.type.spa.spa.fl_str_mv Artículo
dc.identifier.doi.none.fl_str_mv https://doi.org/10.1136/jclinpath-2014-202597
dc.identifier.uri.none.fl_str_mv https://repository.urosario.edu.co/handle/10336/22308
url https://doi.org/10.1136/jclinpath-2014-202597
https://repository.urosario.edu.co/handle/10336/22308
dc.language.iso.spa.fl_str_mv eng
language eng
dc.relation.citationEndPage.none.fl_str_mv 1083
dc.relation.citationIssue.none.fl_str_mv No. 12
dc.relation.citationStartPage.none.fl_str_mv 1078
dc.relation.citationTitle.none.fl_str_mv Journal of Clinical Pathology
dc.relation.citationVolume.none.fl_str_mv Vol. 67
dc.relation.ispartof.spa.fl_str_mv Journal of Clinical Pathology, Vol.67, No.12 (2014); pp. 1078-1083
dc.relation.uri.spa.fl_str_mv https://www.scopus.com/inward/record.uri?eid=2-s2.0-84910138360&doi=10.1136%2fjclinpath-2014-202597&partnerID=40&md5=6a498d197e6fb737ad0ce00d34d37d32
dc.rights.coar.fl_str_mv http://purl.org/coar/access_right/c_abf2
dc.rights.acceso.spa.fl_str_mv Abierto (Texto Completo)
rights_invalid_str_mv Abierto (Texto Completo)
http://purl.org/coar/access_right/c_abf2
dc.format.mimetype.none.fl_str_mv application/pdf
dc.publisher.spa.fl_str_mv BMJ Publishing Group
institution Universidad del Rosario
dc.source.instname.spa.fl_str_mv instname:Universidad del Rosario
dc.source.reponame.spa.fl_str_mv reponame:Repositorio Institucional EdocUR
repository.name.fl_str_mv Repositorio institucional EdocUR
repository.mail.fl_str_mv edocur@urosario.edu.co
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