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...
- 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)
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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 |
_version_ |
1814167509975171072 |