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dc.contributor.authorFerrarini, A
dc.contributor.authorForcato, C
dc.contributor.authorBuson, G
dc.contributor.authorTononi, P
dc.contributor.authorDel Monaco, V
dc.contributor.authorTerracciano, M
dc.contributor.authorBolognesi, C
dc.contributor.authorFontana, F
dc.contributor.authorMedoro, G
dc.contributor.authorNeves, R
dc.contributor.authorMöhlendick, B
dc.contributor.authorRihawi, K
dc.contributor.authorArdizzoni, A
dc.contributor.authorSumanasuriya, S
dc.contributor.authorFlohr, P
dc.contributor.authorLambros, M
dc.contributor.authorde Bono, J
dc.contributor.authorStoecklein, NH
dc.contributor.authorManaresi, N
dc.date.accessioned2019-02-25T16:24:54Z
dc.date.issued2018-03-01
dc.identifier.citationPloS one, 2018, 13 (3), pp. e0193689 - ?
dc.identifier.issn1932-6203
dc.identifier.urihttps://repository.icr.ac.uk/handle/internal/3091
dc.identifier.eissn1932-6203
dc.identifier.doi10.1371/journal.pone.0193689
dc.description.abstractChromosomal instability and associated chromosomal aberrations are hallmarks of cancer and play a critical role in disease progression and development of resistance to drugs. Single-cell genome analysis has gained interest in latest years as a source of biomarkers for targeted-therapy selection and drug resistance, and several methods have been developed to amplify the genomic DNA and to produce libraries suitable for Whole Genome Sequencing (WGS). However, most protocols require several enzymatic and cleanup steps, thus increasing the complexity and length of protocols, while robustness and speed are key factors for clinical applications. To tackle this issue, we developed a single-tube, single-step, streamlined protocol, exploiting ligation mediated PCR (LM-PCR) Whole Genome Amplification (WGA) method, for low-pass genome sequencing with the Ion Torrent™ platform and copy number alterations (CNAs) calling from single cells. The method was evaluated on single cells isolated from 6 aberrant cell lines of the NCI-H series. In addition, to demonstrate the feasibility of the workflow on clinical samples, we analyzed single circulating tumor cells (CTCs) and white blood cells (WBCs) isolated from the blood of patients affected by prostate cancer or lung adenocarcinoma. The results obtained show that the developed workflow generates data accurately representing whole genome absolute copy number profiles of single cell and allows alterations calling at resolutions down to 100 Kbp with as few as 200,000 reads. The presented data demonstrate the feasibility of the Ampli1™ WGA-based low-pass workflow for detection of CNAs in single tumor cells which would be of particular interest for genome-driven targeted therapy selection and for monitoring of disease progression.
dc.formatElectronic-eCollection
dc.format.extente0193689 - ?
dc.languageeng
dc.language.isoeng
dc.publisherPUBLIC LIBRARY SCIENCE
dc.rights.urihttps://creativecommons.org/licenses/by/4.0
dc.subjectCell Line, Tumor
dc.subjectHumans
dc.subjectNeoplasms
dc.subjectAdenocarcinoma
dc.subjectLung Neoplasms
dc.subjectProstatic Neoplasms
dc.subjectPolymerase Chain Reaction
dc.subjectFemale
dc.subjectMale
dc.subjectNeoplastic Cells, Circulating
dc.subjectDNA Copy Number Variations
dc.subjectWorkflow
dc.subjectSingle-Cell Analysis
dc.subjectHigh-Throughput Nucleotide Sequencing
dc.subjectWhole Genome Sequencing
dc.subjectAdenocarcinoma of Lung
dc.titleA streamlined workflow for single-cells genome-wide copy-number profiling by low-pass sequencing of LM-PCR whole-genome amplification products.
dc.typeJournal Article
dcterms.dateAccepted2018-02-19
rioxxterms.versionofrecord10.1371/journal.pone.0193689
rioxxterms.licenseref.urihttps://creativecommons.org/licenses/by/4.0
rioxxterms.licenseref.startdate2018-01
rioxxterms.typeJournal Article/Review
dc.relation.isPartOfPloS one
pubs.issue3
pubs.notesNot known
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/Cancer Therapeutics
pubs.organisational-group/ICR/Primary Group/ICR Divisions/Cancer Therapeutics/Cancer Biomarkers
pubs.organisational-group/ICR/Primary Group/ICR Divisions/Clinical Studies
pubs.organisational-group/ICR/Primary Group/ICR Divisions/Clinical Studies/Cancer Biomarkers
pubs.organisational-group/ICR/Primary Group/ICR Divisions/Clinical Studies/Prostate Cancer Targeted Therapy Group
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/Cancer Therapeutics
pubs.organisational-group/ICR/Primary Group/ICR Divisions/Cancer Therapeutics/Cancer Biomarkers
pubs.organisational-group/ICR/Primary Group/ICR Divisions/Clinical Studies
pubs.organisational-group/ICR/Primary Group/ICR Divisions/Clinical Studies/Cancer Biomarkers
pubs.organisational-group/ICR/Primary Group/ICR Divisions/Clinical Studies/Prostate Cancer Targeted Therapy Group
pubs.publication-statusPublished
pubs.volume13
pubs.embargo.termsNot known
icr.researchteamCancer Biomarkers
icr.researchteamProstate Cancer Targeted Therapy Group
dc.contributor.icrauthorSumanasuriya, Semini
dc.contributor.icrauthorDe Bono, Johann


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