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dc.contributor.authorLópez-Knowles, E
dc.contributor.authorGao, Q
dc.contributor.authorCheang, MCU
dc.contributor.authorMorden, J
dc.contributor.authorParker, J
dc.contributor.authorMartin, L-A
dc.contributor.authorPinhel, I
dc.contributor.authorMcNeill, F
dc.contributor.authorHills, M
dc.contributor.authorDetre, S
dc.contributor.authorAfentakis, M
dc.contributor.authorZabaglo, L
dc.contributor.authorDodson, A
dc.contributor.authorSkene, A
dc.contributor.authorHolcombe, C
dc.contributor.authorRobertson, J
dc.contributor.authorSmith, I
dc.contributor.authorBliss, JM
dc.contributor.authorDowsett, M
dc.contributor.authorPOETIC trialists
dc.date.accessioned2016-08-17T11:15:34Z
dc.date.issued2016-04
dc.identifier.citationBreast cancer research : BCR, 2016, 18 (1), pp. 39 - ?
dc.identifier.issn1465-5411
dc.identifier.urihttps://repository.icr.ac.uk/handle/internal/54
dc.identifier.eissn1465-542X
dc.identifier.doi10.1186/s13058-016-0696-2
dc.description.abstractBackground Gene expression is widely used for the characterisation of breast cancers. Variability due to tissue heterogeneity or measurement error or systematic change due to peri-surgical procedures can affect measurements but is poorly documented. We studied the variability of global gene expression between core-cuts of primary ER+ breast cancers and the impact of delays to tissue stabilisation due to sample X-ray and of diagnostic core cutting.Methods Twenty-six paired core-cuts were taken immediately after tumour excision and up to 90 minutes delay due to sample X-ray; 57 paired core-cuts were taken at diagnosis and 2 weeks later at surgical excision. Whole genome expression analysis was conducted on extracted RNA. Correlations and differences were assessed between the expression of individual genes, gene sets/signatures and intrinsic subtypes.Results Twenty-three and 56 sample pairs, respectively, were suitable for analysis. The range of correlations for both sample sets were similar with the majority being >0.97 in both. Correlations between pairs for 18 commonly studied genes were also similar between the studies and mainly with Pearson correlation coefficients >0.6 except for a small number of genes, which had a narrow-dynamic range (e.g. MKI67, SNAI2). There was no systematic difference in intrinsic subtyping between the first and second sample of either set but there was c.15 % discordance between the subtype assignments between the pairs, mainly where the subtyping of individual samples was less certain. Increases in the expression of several stress/early-response genes (e.g. FOS, FOSB, JUN) were found in both studies and confirmed findings in earlier smaller studies. Increased expression of IL6, IGFBP2 and MYC (by 17 %, 14 % and 44 %, respectively) occurred between the samples taken 2 weeks apart and again confirmed findings from an earlier study.Conclusions There is generally good correlation in gene expression between pairs of core-cuts except where genes have a narrow dynamic range. Similar correlation coefficients to the average gene expression profiles of intrinsic subtype, particularly LumA and LumB, can lead to discordances between assigned subtypes. Substantial changes in expression of early-response genes occur within an hour after surgery and in IL6, IGFB2 and MYC as a result of diagnostic core-cut biopsy.Trial registration Trial number CRUK/07/015 . Study start date September 2008.
dc.formatElectronic
dc.format.extent39 - ?
dc.languageeng
dc.language.isoeng
dc.rights.urihttps://creativecommons.org/licenses/by/4.0
dc.subjectPOETIC trialists
dc.subjectHumans
dc.subjectBreast Neoplasms
dc.subjectInsulin-Like Growth Factor Binding Protein 2
dc.subjectProto-Oncogene Proteins c-myc
dc.subjectNeoplasm Proteins
dc.subjectKi-67 Antigen
dc.subjectInterleukin-6
dc.subjectBiopsy
dc.subjectPrognosis
dc.subjectOligonucleotide Array Sequence Analysis
dc.subjectGene Expression Regulation, Neoplastic
dc.subjectGenetic Heterogeneity
dc.subjectFemale
dc.subjectPerioperative Period
dc.subjectTranscriptome
dc.subjectBiomarkers, Tumor
dc.titleHeterogeneity in global gene expression profiles between biopsy specimens taken peri-surgically from primary ER-positive breast carcinomas.
dc.typeJournal Article
dcterms.dateAccepted2016-03-10
rioxxterms.versionofrecord10.1186/s13058-016-0696-2
rioxxterms.licenseref.urihttps://creativecommons.org/licenses/by/4.0
rioxxterms.licenseref.startdate2016-04
rioxxterms.typeJournal Article/Review
dc.relation.isPartOfBreast cancer research : BCR
pubs.issue1
pubs.notesNo embargo
pubs.organisational-group/ICR
pubs.organisational-group/ICR/Primary Group
pubs.organisational-group/ICR/Primary Group/ICR Divisions
pubs.organisational-group/ICR/Primary Group/ICR Divisions/Breast Cancer Research
pubs.organisational-group/ICR/Primary Group/ICR Divisions/Breast Cancer Research/Endocrinology
pubs.organisational-group/ICR/Primary Group/ICR Divisions/Clinical Studies
pubs.organisational-group/ICR/Primary Group/ICR Divisions/Clinical Studies/Clinical Trials & Statistics Unit
pubs.organisational-group/ICR/Primary Group/ICR Divisions/Clinical Studies/Genomic Analysis – Clinical Trials
pubs.organisational-group/ICR/Primary Group/ICR Divisions/Clinical Studies/Medicine (RMH Smith Cunningham)
pubs.organisational-group/ICR/Primary Group/ICR Divisions/Clinical Studies/Medicine (RMH Smith Cunningham)/Medicine (RMH Smith Cunningham) (hon.)
pubs.organisational-group/ICR/Primary Group/ICR Divisions/Molecular Pathology
pubs.organisational-group/ICR/Primary Group/ICR Divisions/Molecular Pathology/Endocrinology
pubs.organisational-group/ICR/Primary Group/ICR Divisions/Molecular Pathology/Endocrinology/Endocrinology (hon.)
pubs.organisational-group/ICR/Primary Group/Royal Marsden Clinical Units
pubs.organisational-group/ICR
pubs.organisational-group/ICR/Primary Group
pubs.organisational-group/ICR/Primary Group/ICR Divisions
pubs.organisational-group/ICR/Primary Group/ICR Divisions/Breast Cancer Research
pubs.organisational-group/ICR/Primary Group/ICR Divisions/Breast Cancer Research/Endocrinology
pubs.organisational-group/ICR/Primary Group/ICR Divisions/Clinical Studies
pubs.organisational-group/ICR/Primary Group/ICR Divisions/Clinical Studies/Clinical Trials & Statistics Unit
pubs.organisational-group/ICR/Primary Group/ICR Divisions/Clinical Studies/Genomic Analysis – Clinical Trials
pubs.organisational-group/ICR/Primary Group/ICR Divisions/Clinical Studies/Medicine (RMH Smith Cunningham)
pubs.organisational-group/ICR/Primary Group/ICR Divisions/Clinical Studies/Medicine (RMH Smith Cunningham)/Medicine (RMH Smith Cunningham) (hon.)
pubs.organisational-group/ICR/Primary Group/ICR Divisions/Molecular Pathology
pubs.organisational-group/ICR/Primary Group/ICR Divisions/Molecular Pathology/Endocrinology
pubs.organisational-group/ICR/Primary Group/ICR Divisions/Molecular Pathology/Endocrinology/Endocrinology (hon.)
pubs.organisational-group/ICR/Primary Group/Royal Marsden Clinical Units
pubs.publication-statusPublished
pubs.volume18
pubs.embargo.termsNo embargo
icr.researchteamClinical Trials & Statistics Uniten_US
icr.researchteamGenomic Analysis – Clinical Trialsen_US
icr.researchteamMedicine (RMH Smith Cunningham)en_US
icr.researchteamEndocrinologyen_US
dc.contributor.icrauthorMorden, James Peteren
dc.contributor.icrauthorSmith, Ianen
dc.contributor.icrauthorBliss, Judithen
dc.contributor.icrauthorMartin, Lesley-Annen
dc.contributor.icrauthorDowsett, Mitchen
dc.contributor.icrauthorCheang, Chonen
dc.contributor.icrauthorGao, Qiongen
dc.contributor.icrauthorLopez Knowles, Elenaen


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