dc.contributor.advisor | Russnes, Hege G. | |
dc.contributor.advisor | Rye, Inga H. | |
dc.contributor.author | Kongelf, Geir Andre | |
dc.date.accessioned | 2020-05-12T08:13:22Z | |
dc.date.available | 2020-05-12T08:13:22Z | |
dc.date.issued | 2018 | |
dc.identifier.uri | https://hdl.handle.net/10642/8563 | |
dc.description | Master i biomedisin | en |
dc.description.abstract | Breast cancer is a disease dominated by copy number alterations, but only HER2 copy number
assessment analyzed by fluorescence in situ hybridization (FISH) is today included in the guidelines for
breast cancer diagnostics. The anticipated inclusion of copy number estimation for additional DNA
segments would be time consuming and cumbersome if analyzed with FISH. The development of Next
Generation Sequencing (NGS) has opened the possibility of copy number assessment in multiple regions
by targeted sequencing. Introduction of a panel aiming at detecting copy number alterations in breast
cancer would need validation. We employed FISH analysis and designed and validated 17 bacterial
artificial chromosomes (BAC) probes for selected chromosomal regions which are often subject to copy
number alterations in breast cancer. Copy number analysis performed on formalin-fixes paraffin-embedded
(FFPE) samples are subject to potential loss of chromosomal material due to sectioning artefacts. NGS
uses bulk tumor samples and does not suffer from this effect. We therefore wanted to see if there is a
systematic relationship in copy number difference between estimates using FFPE (i.e. sectioned cells) and
estimates using whole cell imprints to identify a possible adjusting factor. Linear regression generated
coefficients of large variation for the cell lines. We performed FISH analysis with the 17 probes on both
imprints and FFPE sections of the breast cancer cell lines HCC1954 and HCC2218 and found that there
were in general lower copy number estimates from FFPE sections. The average difference was about one
copy number for the most heterogeneous cell line and somewhat less for the other, but there were large
variations between the different regions in both cell lines so no specific adjusting factor was found. We then
used the same validated probes in FISH analysis of FFPE tumor samples from 12 patients diagnosed with
breast cancer and compared the copy number estimates with NGS estimates for the same regions. The
copy number estimates by NGS largely aligned with estimates by FISH, but with certain notable
discrepancies, reflecting the NGS test still being in a state of development. Further validation of the NGS
test against the current gold standard for copy number assessment, FISH, combined with improved data
analysis, is a crucial step preceding implementation in routine diagnostics. | en |
dc.language.iso | en | en |
dc.publisher | OsloMet - storbyuniversitetet. Institutt for naturvitenskapelige helsefag | en |
dc.relation.ispartofseries | MABIOD;2018 | |
dc.subject | Heterogeneity | en |
dc.subject | Copy number | en |
dc.subject | Fluorescence in situ hybridization | en |
dc.subject | Next Generation Sequencing | en |
dc.title | Copy number alterations in breast carcinomas: Comparison of different methods for assessment | en |
dc.type | Master thesis | en |
dc.description.version | publishedVersion | en |