Biomedical research at Oslo University Hospital

Publications (original articles or review articles) published in 2019 from OUS - Department of Cancer Genetics

49 publications found

Abravan A, Eide HA, Løndalen AM, Helland Å, Malinen E (2019)
Mapping Bone Marrow Response in the Vertebral Column by Positron Emission Tomography Following Radiotherapy and Erlotinib Therapy of Lung Cancer
Mol Imaging Biol, 21 (2), 391-398
DOI 10.1007/s11307-018-1226-7, PubMed 29916117

Alcala N, Leblay N, Gabriel AAG, Mangiante L, Hervas D, Giffon T, Sertier AS, Ferrari A, Derks J, Ghantous A, Delhomme TM, Chabrier A, Cuenin C, Abedi-Ardekani B, Boland A, Olaso R, Meyer V, Altmuller J, Le Calvez-Kelm F, Durand G, Voegele C, Boyault S, Moonen L, Lemaitre N, Lorimier P et al. (2019)
Integrative and comparative genomic analyses identify clinically relevant pulmonary carcinoid groups and unveil the supra-carcinoids
Nat Commun, 10 (1), 3407
DOI 10.1038/s41467-019-11276-9, PubMed 31431620

Bai B, Vodák D, Nakken S, Wise JF, Blaker YN, Lingjærde OC, Brodtkorb M, Hilden V, Trøen G, Lorenz S, Lawrence MS, Myklebost O, Meza-Zepeda L, Beiske K, Hovig E, Smeland EB, Holte H, Myklebust JH (2019)
Deep Profiling of Genetic Aberrations and Clonal Evolution in Follicular Lymphoma
Blood, 134 (Supplement_1), 20
DOI 10.1182/blood-2019-128403, PubMed 31723999

Bergholtz H, Lien TG, Ursin G, Holmen MM, Helland Å, Sørlie T, Haakensen VD (2019)
A Longitudinal Study of the Association between Mammographic Density and Gene Expression in Normal Breast Tissue
J Mammary Gland Biol Neoplasia, 24 (2), 163-175
DOI 10.1007/s10911-018-09423-x, PubMed 30613869

Bowitz Lothe IM, Kleive D, Pomianowska E, Cvancarova M, Kure E, Dueland S, Gladhaug IP, Labori KJ (2019)
Clinical relevance of pancreatobiliary and intestinal subtypes of ampullary and duodenal adenocarcinoma: Pattern of recurrence, chemotherapy, and survival after pancreatoduodenectomy
Pancreatology, 19 (2), 316-324
DOI 10.1016/j.pan.2019.01.019, PubMed 30713128

Brinkman AB, Nik-Zainal S, Simmer F, Rodríguez-González FG, Smid M, Alexandrov LB, Butler A, Martin S, Davies H, Glodzik D, Zou X, Ramakrishna M, Staaf J, Ringnér M, Sieuwerts A, Ferrari A, Morganella S, Fleischer T, Kristensen V, Gut M, van de Vijver MJ, Børresen-Dale AL, Richardson AL, Thomas G, Gut IG et al. (2019)
Partially methylated domains are hypervariable in breast cancer and fuel widespread CpG island hypermethylation
Nat Commun, 10 (1), 1749
DOI 10.1038/s41467-019-09828-0, PubMed 30988298

Dong X, Zhang R, He J, Lai L, Alolga RN, Shen S, Zhu Y, You D, Lin L, Chen C, Zhao Y, Duan W, Su L, Shafer A, Salama M, Fleischer T, Bjaanæs MM, Karlsson A, Planck M, Wang R, Staaf J, Helland Å, Esteller M, Wei Y, Chen F et al. (2019)
Trans-omics biomarker model improves prognostic prediction accuracy for early-stage lung adenocarcinoma
Aging (Albany NY), 11 (16), 6312-6335
DOI 10.18632/aging.102189, PubMed 31434796

Dörk T, Peterlongo P, Mannermaa A, Bolla MK, Wang Q, Dennis J, Ahearn T, Andrulis IL, Anton-Culver H, Arndt V, Aronson KJ, Augustinsson A, Freeman LEB, Beckmann MW, Beeghly-Fadiel A, Behrens S, Bermisheva M, Blomqvist C, Bogdanova NV, Bojesen SE, Brauch H, Brenner H, Burwinkel B, Canzian F, Chan TL et al. (2019)
Two truncating variants in FANCC and breast cancer risk
Sci Rep, 9 (1), 12524
DOI 10.1038/s41598-019-48804-y, PubMed 31467304

Escala-Garcia M, Guo Q, Dörk T, Canisius S, Keeman R, Dennis J, Beesley J, Lecarpentier J, Bolla MK, Wang Q, Abraham J, Andrulis IL, Anton-Culver H, Arndt V, Auer PL, Beckmann MW, Behrens S, Benitez J, Bermisheva M, Bernstein L, Blomqvist C, Boeckx B, Bojesen SE, Bonanni B, Børresen-Dale AL et al. (2019)
Genome-wide association study of germline variants and breast cancer-specific mortality
Br J Cancer, 120 (6), 647-657
DOI 10.1038/s41416-019-0393-x, PubMed 30787463

Ferreira MA, Gamazon ER, Al-Ejeh F, Aittomäki K, Andrulis IL, Anton-Culver H, Arason A, Arndt V, Aronson KJ, Arun BK, Asseryanis E, Azzollini J, Balmaña J, Barnes DR, Barrowdale D, Beckmann MW, Behrens S, Benitez J, Bermisheva M, Białkowska K, Blomqvist C, Bogdanova NV, Bojesen SE, Bolla MK, Borg A et al. (2019)
Genome-wide association and transcriptome studies identify target genes and risk loci for breast cancer
Nat Commun, 10 (1), 1741
DOI 10.1038/s41467-018-08053-5, PubMed 30988301

Flørenes VA, Flem-Karlsen K, McFadden E, Bergheim IR, Nygaard V, Nygård V, Farstad IN, Øy GF, Emilsen E, Giller-Fleten K, Ree AH, Flatmark K, Gullestad HP, Hermann R, Ryder T, Wernhoff P, Mælandsmo GM (2019)
A Three-dimensional Ex Vivo Viability Assay Reveals a Strong Correlation Between Response to Targeted Inhibitors and Mutation Status in Melanoma Lymph Node Metastases
Transl Oncol, 12 (7), 951-958
DOI 10.1016/j.tranon.2019.04.001, PubMed 31096111

Fornes O, Castro-Mondragon JA, Khan A, van der Lee R, Zhang X, Richmond PA, Modi BP, Correard S, Gheorghe M, Baranašić D, Santana-Garcia W, Tan G, Chèneby J, Ballester B, Parcy F, Sandelin A, Lenhard B, Wasserman WW, Mathelier A (2019)
JASPAR 2020: update of the open-access database of transcription factor binding profiles
Nucleic Acids Res (in press)
DOI 10.1093/nar/gkz1001, PubMed 31701148

Fougner C, Bergholtz H, Kuiper R, Norum JH, Sørlie T (2019)
Claudin-low-like mouse mammary tumors show distinct transcriptomic patterns uncoupled from genomic drivers
Breast Cancer Res, 21 (1), 85
DOI 10.1186/s13058-019-1170-8, PubMed 31366361

Fromm B, Domanska D, Høye E, Ovchinnikov V, Kang W, Aparicio-Puerta E, Johansen M, Flatmark K, Mathelier A, Hovig E, Hackenberg M, Friedländer MR, Peterson KJ (2019)
MirGeneDB 2.0: the metazoan microRNA complement
Nucleic Acids Res (in press)
DOI 10.1093/nar/gkz1016, PubMed 31642479

Fromm B, Domanska D, Høye E, Ovchinnikov V, Kang W, Aparicio-Puerta E, Johansen M, Flatmark K, Mathelier A, Hovig E, Hackenberg M, Friedländer MR, Peterson KJ (2019)
MirGeneDB 2.0: the metazoan microRNA complement
Nucleic Acids Res (in press)
DOI 10.1093/nar/gkz885, PubMed 31598695

Gheorghe M, Sandve GK, Khan A, Chèneby J, Ballester B, Mathelier A (2019)
A map of direct TF-DNA interactions in the human genome
Nucleic Acids Res, 47 (4), e21
DOI 10.1093/nar/gky1210, PubMed 30517703

Ha TJ, Zhang PGY, Robert R, Yeung J, Swanson DJ, Mathelier A, Wasserman WW, Im S, Itoh M, Kawaji H, Lassmann T, Daub CO, Arner E, FANTOM Consortium, Carninci P, Hayashizaki Y, Forrest ARR, Goldowitz D (2019)
Identification of novel cerebellar developmental transcriptional regulators with motif activity analysis
BMC Genomics, 20 (1), 718
DOI 10.1186/s12864-019-6063-9, PubMed 31533632

Halvorsen AR, Ragle Aure M, Õjlert ÅK, Brustugun OT, Solberg S, Nebdal D, Helland Å (2019)
Identification of microRNAs involved in pathways which characterize the expression subtypes of NSCLC
Mol Oncol, 13 (12), 2604-2615
DOI 10.1002/1878-0261.12571, PubMed 31505091

Hamfjord J, Guren TK, Dajani O, Johansen JS, Glimelius B, Sorbye H, Pfeiffer P, Lingjærde OC, Tveit KM, Kure EH, Pallisgaard N, Spindler KG (2019)
Total circulating cell-free DNA as a prognostic biomarker in metastatic colorectal cancer before first-line oxaliplatin-based chemotherapy
Ann Oncol, 30 (7), 1088-1095
DOI 10.1093/annonc/mdz139, PubMed 31046124

Itkonen HM, Urbanucci A, Martin SE, Khan A, Mathelier A, Thiede B, Walker S, Mills IG (2019)
High OGT activity is essential for MYC-driven proliferation of prostate cancer cells
Theranostics, 9 (8), 2183-2197
DOI 10.7150/thno.30834, PubMed 31149037

Jiang X, Finucane HK, Schumacher FR, Schmit SL, Tyrer JP, Han Y, Michailidou K, Lesseur C, Kuchenbaecker KB, Dennis J, Conti DV, Casey G, Gaudet MM, Huyghe JR, Albanes D, Aldrich MC, Andrew AS, Andrulis IL, Anton-Culver H, Antoniou AC, Antonenkova NN, Arnold SM, Aronson KJ, Arun BK, Bandera EV et al. (2019)
Shared heritability and functional enrichment across six solid cancers
Nat Commun, 10 (1), 431
DOI 10.1038/s41467-018-08054-4, PubMed 30683880

Johansson HJ, Socciarelli F, Vacanti NM, Haugen MH, Zhu Y, Siavelis I, Fernandez-Woodbridge A, Aure MR, Sennblad B, Vesterlund M, Branca RM, Orre LM, Huss M, Fredlund E, Beraki E, Garred Ø, Boekel J, Sauer T, Zhao W, Nord S, Höglander EK, Jans DC, Brismar H, Haukaas TH, Bathen TF et al. (2019)
Breast cancer quantitative proteome and proteogenomic landscape
Nat Commun, 10 (1), 1600
DOI 10.1038/s41467-019-09018-y, PubMed 30962452

Kraby MR, Opdahl S, Russnes HG, Bofin AM (2019)
Microvessel density in breast cancer: the impact of field area on prognostic informativeness
J Clin Pathol, 72 (4), 304-310
DOI 10.1136/jclinpath-2018-205536, PubMed 30630872

Lai X, Geier OM, Fleischer T, Garred Ø, Borgen E, Funke SW, Kumar S, Rognes ME, Seierstad T, Børresen-Dale AL, Kristensen VN, Engebraaten O, Köhn-Luque A, Frigessi A (2019)
Toward Personalized Computer Simulation of Breast Cancer Treatment: A Multiscale Pharmacokinetic and Pharmacodynamic Model Informed by Multitype Patient Data
Cancer Res, 79 (16), 4293-4304
DOI 10.1158/0008-5472.CAN-18-1804, PubMed 31118201

Lampignano R, Neumann MHD, Weber S, Kloten V, Herdean A, Voss T, Groelz D, Babayan A, Tibbesma M, Schlumpberger M, Chemi F, Rothwell DG, Wikman H, Galizzi JP, Bergheim IR, Russnes H, Mussolin B, Bonin S, Voigt C, Musa H, Pinzani P, Lianidou E, Brady G, Speicher MR, Pantel K et al. (2019)
Multicenter Evaluation of Circulating Cell-Free DNA Extraction and Downstream Analyses for the Development of Standardized (Pre)analytical Work Flows
Clin Chem (in press)
DOI 10.1373/clinchem.2019.306837, PubMed 31628139

Lee YS, Krishnan A, Oughtred R, Rust J, Chang CS, Ryu J, Kristensen VN, Dolinski K, Theesfeld CL, Troyanskaya OG (2019)
A Computational Framework for Genome-wide Characterization of the Human Disease Landscape
Cell Syst, 8 (2), 152-162.e6
DOI 10.1016/j.cels.2018.12.010, PubMed 30685436

Lindholm EM, Leivonen SK, Undlien E, Nebdal D, Git A, Caldas C, Børresen-Dale AL, Kleivi K (2019)
miR-342-5p as a Potential Regulator of HER2 Breast Cancer Cell Growth
Microrna, 8 (2), 155-165
DOI 10.2174/2211536608666181206124922, PubMed 30520388

Lindholm EM, Ragle Aure M, Haugen MH, Kleivi Sahlberg K, Kristensen VN, Nebdal D, Børresen-Dale AL, Lingjaerde OC, Engebraaten O (2019)
miRNA expression changes during the course of neoadjuvant bevacizumab and chemotherapy treatment in breast cancer
Mol Oncol, 13 (10), 2278-2296
DOI 10.1002/1878-0261.12561, PubMed 31402562

Madssen TS, Cao MD, Pladsen AV, Ottestad L, Sahlberg KK, Bathen TF, Giskeødegård GF (2019)
Historical Biobanks in Breast Cancer Metabolomics- Challenges and Opportunities
Metabolites, 9 (11)
DOI 10.3390/metabo9110278, PubMed 31766128

Mukhopadhyay UK, Oturkar CC, Adams C, Wickramasekera N, Bansal S, Medisetty R, Miller A, Swetzig WM, Silwal-Pandit L, Børresen-Dale AL, Creighton CJ, Park JH, Konduri SD, Mukhopadhyay A, Caradori A, Omilian A, Bshara W, Kaipparettu BA, Das GM (2019)
TP53 Status as a Determinant of Pro- vs Anti-Tumorigenic Effects of Estrogen Receptor-Beta in Breast Cancer
J Natl Cancer Inst, 111 (11), 1202-1215
DOI 10.1093/jnci/djz051, PubMed 30990221

Nik-Zainal S, Davies H, Staaf J, Ramakrishna M, Glodzik D, Zou X, Martincorena I, Alexandrov LB, Martin S, Wedge DC, Van Loo P, Ju YS, Smid M, Brinkman AB, Morganella S, Aure MR, Lingjærde OC, Langerød A, Ringnér M, Ahn SM, Boyault S, Brock JE, Broeks A, Butler A, Desmedt C et al. (2019)
Author Correction: Landscape of somatic mutations in 560 breast cancer whole-genome sequences
Nature, 566 (7742), E1
DOI 10.1038/s41586-019-0883-2, PubMed 30659290

Nome ME, Euceda LR, Jabeen S, Debik J, Bathen TF, Giskeødegård GF, Taskén KA, Maelandsmo GM, Halvorsen B, Yndestad A, Borgen E, Garred Ø, Aukrust P, Ueland T, Engebraaten O, Kristensen VN, Tekpli X (2019)
Serum levels of inflammation-related markers and metabolites predict response to neoadjuvant chemotherapy with and without bevacizumab in breast cancers
Int J Cancer, 146 (1), 223-235
DOI 10.1002/ijc.32638, PubMed 31444972

Norum JH, Frings O, Kasper M, Bergholtz H, Zell Thime H, Bergström Å, Andersson A, Kuiper R, Fredlund E, Sørlie T, Toftgård R (2019)
GLI1-induced mammary gland tumours are transplantable and maintain major molecular features
Int J Cancer
DOI 10.1002/ijc.32522, PubMed 31219615

Nygård S, Lingjærde OC, Caldas C, Hovig E, Børresen-Dale AL, Helland Å, Haakensen VD (2019)
PathTracer: High-sensitivity detection of differential pathway activity in tumours
Sci Rep, 9 (1), 16332
DOI 10.1038/s41598-019-52529-3, PubMed 31704995

Ree AH, Nygaard V, Russnes HG, Heinrich D, Nygaard V, Johansen C, Bergheim IR, Hovig E, Beiske K, Negård A, Børresen-Dale AL, Flatmark K, Mælandsmo GM (2019)
Responsiveness to PD-1 Blockade in End-Stage Colon Cancer with Gene Locus 9p24.1 Copy-Number Gain
Cancer Immunol Res, 7 (5), 701-706
DOI 10.1158/2326-6066.CIR-18-0777, PubMed 30804006

Salvatore S, Dagestad Rand K, Grytten I, Ferkingstad E, Domanska D, Holden L, Gheorghe M, Mathelier A, Glad I, Kjetil Sandve G (2019)
Beware the Jaccard: the choice of similarity measure is important and non-trivial in genomic colocalisation analysis
Brief Bioinform (in press)
DOI 10.1093/bib/bbz083, PubMed 31624847

Sandhu V, Labori KJ, Borgida A, Lungu I, Bartlett J, Hafezi-Bakhtiari S, Denroche RE, Jang GH, Pasternack D, Mbaabali F, Watson M, Wilson J, Kure EH, Gallinger S, Haibe-Kains B (2019)
Meta-Analysis of 1,200 Transcriptomic Profiles Identifies a Prognostic Model for Pancreatic Ductal Adenocarcinoma
JCO Clin Cancer Inform, 3, 1-16
DOI 10.1200/CCI.18.00102, PubMed 31070984

Shao B, Bjaanæs MM, Helland Å, Schütte C, Conrad T (2019)
EMT network-based feature selection improves prognosis prediction in lung adenocarcinoma
PLoS One, 14 (1), e0204186
DOI 10.1371/journal.pone.0204186, PubMed 30703089

Shu X, Wu L, Khankari NK, Shu XO, Wang TJ, Michailidou K, Bolla MK, Wang Q, Dennis J, Milne RL, Schmidt MK, Pharoah PDP, Andrulis IL, Hunter DJ, Simard J, Easton DF, Zheng W, Breast Cancer Association Consortium (2019)
Associations of obesity and circulating insulin and glucose with breast cancer risk: a Mendelian randomization analysis
Int J Epidemiol, 48 (3), 795-806
DOI 10.1093/ije/dyy201, PubMed 30277539

Smid M, Wilting SM, Uhr K, Rodríguez-González FG, de Weerd V, Prager-Van der Smissen WJC, van der Vlugt-Daane M, van Galen A, Nik-Zainal S, Butler A, Martin S, Davies HR, Staaf J, van de Vijver MJ, Richardson AL, MacGrogan G, Salgado R, van den Eynden GGGM, Purdie CA, Thompson AM, Caldas C, Span PN, Sweep FCGJ, Simpson PT, Lakhani SR et al. (2019)
The circular RNome of primary breast cancer
Genome Res, 29 (3), 356-366
DOI 10.1101/gr.238121.118, PubMed 30692147

Stankovic B, Bjørhovde HAK, Skarshaug R, Aamodt H, Frafjord A, Müller E, Hammarström C, Beraki K, Bækkevold ES, Woldbæk PR, Helland Å, Brustugun OT, Øynebråten I, Corthay A (2019)
Immune Cell Composition in Human Non-small Cell Lung Cancer
Front Immunol, 9, 3101
DOI 10.3389/fimmu.2018.03101, PubMed 30774636

Swanson DM, Lien T, Bergholtz H, Sørlie T, Frigessi A (2019)
A Bayesian two-way latent structure model for genomic data integration reveals few pan-genomic cluster subtypes in a breast cancer cohort
Bioinformatics, 35 (23), 4886-4897
DOI 10.1093/bioinformatics/btz381, PubMed 31077301

Taylor-King JP, Baratchart E, Dhawan A, Coker EA, Rye IH, Russnes H, Chapman SJ, Basanta D, Marusyk A (2019)
Simulated ablation for detection of cells impacting paracrine signalling in histology analysis
Math Med Biol, 36 (1), 93-112
DOI 10.1093/imammb/dqx022, PubMed 29452382

Tekpli X, Lien T, Røssevold AH, Nebdal D, Borgen E, Ohnstad HO, Kyte JA, Vallon-Christersson J, Fongaard M, Due EU, Svartdal LG, Sveli MAT, Garred Ø, OSBREAC, Frigessi A, Sahlberg KK, Sørlie T, Russnes HG, Naume B, Kristensen VN (2019)
An independent poor-prognosis subtype of breast cancer defined by a distinct tumor immune microenvironment
Nat Commun, 10 (1), 5499
DOI 10.1038/s41467-019-13329-5, PubMed 31796750

Vaclavikova R, Klajic J, Brynychova V, Elsnerova K, Alnaes GIG, Tost J, Kristensen VN, Rob L, Kodet R, Skapa P, Mrhalova M, Soucek P (2019)
Development of high‑resolution melting analysis for ABCB1 promoter methylation: Clinical consequences in breast and ovarian carcinoma
Oncol Rep, 42 (2), 763-774
DOI 10.3892/or.2019.7186, PubMed 31173253

Zhang R, Lai L, Dong X, He J, You D, Chen C, Lin L, Zhu Y, Huang H, Shen S, Wei L, Chen X, Guo Y, Liu L, Su L, Shafer A, Moran S, Fleischer T, Bjaanaes MM, Karlsson A, Planck M, Staaf J, Helland Å, Esteller M, Wei Y et al. (2019)
SIPA1L3 methylation modifies the benefit of smoking cessation on lung adenocarcinoma survival: an epigenomic-smoking interaction analysis
Mol Oncol, 13 (5), 1235-1248
DOI 10.1002/1878-0261.12482, PubMed 30924596

Zhang R, Lai L, He J, Chen C, You D, Duan W, Dong X, Zhu Y, Lin L, Shen S, Guo Y, Su L, Shafer A, Moran S, Fleischer T, Bjaanæs MM, Karlsson A, Planck M, Staaf J, Helland Å, Esteller M, Wei Y, Chen F, Christiani DC (2019)
EGLN2 DNA methylation and expression interact with HIF1A to affect survival of early-stage NSCLC
Epigenetics, 14 (2), 118-129
DOI 10.1080/15592294.2019.1573066, PubMed 30665327

Zhu Q, Tekpli X, Troyanskaya OG, Kristensen VN (2019)
Subtype-Specific Transcriptional Regulators in Breast Tumors Subjected to Genetic and Epigenetic Alterations
Bioinformatics (in press)
DOI 10.1093/bioinformatics/btz709, PubMed 31529022

Öjlert ÅK, Halvorsen AR, Nebdal D, Lund-Iversen M, Solberg S, Brustugun OT, Lingjaerde OC, Helland Å (2019)
The immune microenvironment in non-small cell lung cancer is predictive of prognosis after surgery
Mol Oncol, 13 (5), 1166-1179
DOI 10.1002/1878-0261.12475, PubMed 30854794