Hi-C detects novel structural variants in HL-60 and HL-60/S4 cell lines.

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dc.contributor.author Jacobson, Elsie C en
dc.contributor.author Grand, Ralph S en
dc.contributor.author Perry, Johanna en
dc.contributor.author Vickers, Mark en
dc.contributor.author Olins, Ada L en
dc.contributor.author Olins, Donald E en
dc.contributor.author O'Sullivan, Justin en
dc.date.accessioned 2020-05-14T04:45:09Z en
dc.date.issued 2020-01 en
dc.identifier.issn 0888-7543 en
dc.identifier.uri http://hdl.handle.net/2292/50691 en
dc.description.abstract Cancer cell lines often have large structural variants (SVs) that evolve over time. There are many reported differences in large scale SVs between HL-60 and HL-60/S4, two cell lines derived from the same acute myeloid leukemia sample. However, the stability and variability of inter- and intra-chromosomal structural variants between different sources of the same cell line is unknown. Here, we used Hi-C and RNA-seq to identify and compare large SVs in HL-60 and HL-60/S4 cell lines. Comparisons with previously published karyotypes identified novel SVs in both cell lines. Hi-C was used to characterize the known expansion centered on the MYC locus. The MYC expansion was integrated into known locations in HL-60/S4, and a novel location (chr4) in HL-60. The HL-60 cell line has more within-line structural variation than the HL-60/S4 derivative cell line. Collectively we demonstrate the usefulness of Hi-C and with RNA-seq data for the identification and characterization of SVs. en
dc.format.medium Print-Electronic en
dc.language eng en
dc.relation.ispartofseries Genomics en
dc.rights Items in ResearchSpace are protected by copyright, with all rights reserved, unless otherwise indicated. Previously published items are made available in accordance with the copyright policy of the publisher. en
dc.rights.uri https://researchspace.auckland.ac.nz/docs/uoa-docs/rights.htm en
dc.subject HL-60 Cells en
dc.subject Chromosomes, Human en
dc.subject Chromatin en
dc.subject Humans en
dc.subject Proto-Oncogene Proteins c-myc en
dc.subject Gene Fusion en
dc.subject Protein Biosynthesis en
dc.subject Genome, Human en
dc.subject Genetic Variation en
dc.subject Karyotype en
dc.subject RNA-Seq en
dc.title Hi-C detects novel structural variants in HL-60 and HL-60/S4 cell lines. en
dc.type Journal Article en
dc.identifier.doi 10.1016/j.ygeno.2019.05.009 en
pubs.issue 1 en
pubs.begin-page 151 en
pubs.volume 112 en
dc.rights.holder Copyright: The author en
pubs.end-page 162 en
pubs.publication-status Published en
dc.rights.accessrights http://purl.org/eprint/accessRights/RestrictedAccess en
pubs.subtype Research Support, Non-U.S. Gov't en
pubs.subtype Journal Article en
pubs.elements-id 773777 en
pubs.org-id Liggins Institute en
dc.identifier.eissn 1089-8646 en
pubs.record-created-at-source-date 2019-05-17 en
pubs.dimensions-id 31095996 en


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