Show simple item record

dc.contributor.authorRoddy, AC
dc.contributor.authorJurek-Loughrey, A
dc.contributor.authorSouza, J
dc.contributor.authorGilmore, A
dc.contributor.authorO'Reilly, PG
dc.contributor.authorStupnikov, A
dc.contributor.authorGonzalez de Castro, D
dc.contributor.authorPrise, KM
dc.contributor.authorSalto-Tellez, M
dc.contributor.authorMcArt, DG
dc.date.accessioned2020-08-28T09:00:52Z
dc.date.issued2019-12
dc.identifier.citationMolecular biology and evolution, 2019, 36 (12), pp. 2883 - 2889
dc.identifier.issn0737-4038
dc.identifier.urihttps://repository.icr.ac.uk/handle/internal/4046
dc.identifier.eissn1537-1719
dc.identifier.doi10.1093/molbev/msz182
dc.description.abstractLongitudinal next-generation sequencing of cancer patient samples has enhanced our understanding of the evolution and progression of various cancers. As a result, and due to our increasing knowledge of heterogeneity, such sampling is becoming increasingly common in research and clinical trial sample collections. Traditionally, the evolutionary analysis of these cohorts involves the use of an aligner followed by subsequent stringent downstream analyses. However, this can lead to large levels of information loss due to the vast mutational landscape that characterizes tumor samples. Here, we propose an alignment-free approach for sequence comparison-a well-established approach in a range of biological applications including typical phylogenetic classification. Such methods could be used to compare information collated in raw sequence files to allow an unsupervised assessment of the evolutionary trajectory of patient genomic profiles. In order to highlight this utility in cancer research we have applied our alignment-free approach using a previously established metric, Jensen-Shannon divergence, and a metric novel to this area, Hellinger distance, to two longitudinal cancer patient cohorts in glioma and clear cell renal cell carcinoma using our software, NUQA. We hypothesize that this approach has the potential to reveal novel information about the heterogeneity and evolutionary trajectory of spatiotemporal tumor samples, potentially revealing early events in tumorigenesis and the origins of metastases and recurrences. Key words: alignment-free, Hellinger distance, exome-seq, evolution, phylogenetics, longitudinal.
dc.formatPrint
dc.format.extent2883 - 2889
dc.languageeng
dc.language.isoeng
dc.rights.urihttps://creativecommons.org/licenses/by/4.0
dc.subjectHumans
dc.subjectNeoplasms
dc.subjectGenetic Techniques
dc.subjectGenetic Heterogeneity
dc.subjectSoftware
dc.subjectBiological Evolution
dc.titleNUQA: Estimating Cancer Spatial and Temporal Heterogeneity and Evolution through Alignment-Free Methods.
dc.typeJournal Article
rioxxterms.versionofrecord10.1093/molbev/msz182
rioxxterms.licenseref.urihttps://creativecommons.org/licenses/by/4.0
rioxxterms.licenseref.startdate2019-12
rioxxterms.typeJournal Article/Review
dc.relation.isPartOfMolecular biology and evolution
pubs.issue12
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/Molecular Pathology
pubs.organisational-group/ICR/Primary Group/ICR Divisions/Molecular Pathology/Integrated Pathology
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/Molecular Pathology
pubs.organisational-group/ICR/Primary Group/ICR Divisions/Molecular Pathology/Integrated Pathology
pubs.publication-statusPublished
pubs.volume36
pubs.embargo.termsNot known
icr.researchteamIntegrated Pathologyen_US
dc.contributor.icrauthorSalto-Tellez, Manuelen


Files in this item

Thumbnail

This item appears in the following collection(s)

Show simple item record

https://creativecommons.org/licenses/by/4.0
Except where otherwise noted, this item's license is described as https://creativecommons.org/licenses/by/4.0