Publications

2017

Assembly and analysis of 100 full MHC haplotypes from the Danish population.
Jensen JM, Villesen P, Friborg RM; Danish Pan-Genome Consortium, Mailund T, Besenbacher S, Schierup MH.
Genome Res. 2017 Sep;27(9):1597-1607. doi: 10.1101/gr.218891.116. Epub 2017 Aug 3. PubMed

Whole genome characterization of sequence diversity of 15,220 Icelanders.
Jónsson H, Sulem P, Kehr B, Kristmundsdottir S, Zink F, Hjartarson E, Hardarson MT, Hjorleifsson KE, Eggertsson HP, Gudjonsson SA, Ward LD, Arnadottir GA, Helgason EA, Helgason H, Gylfason A, Jonasdottir A, Jonasdottir A, Rafnar T, Besenbacher S, Frigge ML, Stacey SN, Magnusson OT, Thorsteinsdottir U, Masson G, Kong A, Halldorsson BV, Helgason A, Gudbjartsson DF, Stefansson K.
Sci Data. 2017 Sep 21;4:170115. doi: 10.1038/sdata.2017.115. PubMed

Comprehensive Evaluation of TFF3 Promoter Hypomethylation and Molecular Biomarker Potential for Prostate Cancer Diagnosis and Prognosis.
Nørgaard M, Haldrup C, Storebjerg TM, Vestergaard EM, Wild PJ, Høyer S, Borre M, Ørntoft TF, Sørensen KD
Int J Mol Sci. 2017 Sep 20;18(9). pii: E2017. doi: 10.3390/ijms18092017. PubMed

Comprehensive multiregional analysis of molecular heterogeneity in bladder cancer.
Thomsen MBH, Nordentoft I, Lamy P, Vang S, Reinert L, Mapendano CK, Høyer S, Ørntoft TF, Jensen JB, Dyrskjøt L.
Sci Rep. 2017 Sep 15;7(1):11702. doi: 10.1038/s41598-017-11291-0. PubMed

A genetically inducible porcine model of intestinal cancer.
Callesen MM, Árnadóttir SS, Lyskjaer I, Ørntoft MW, Høyer S, Dagnaes-Hansen F, Liu Y, Li R, Callesen H, Rasmussen MH, Berthelsen MF, Thomsen MK, Schweiger PJ, Jensen KB, Laurberg S, Ørntoft TF, Elverløv-Jakobsen JE, Lindbjerg Andersen C.
Mol Oncol. 2017 Sep 7. doi: 10.1002/1878-0261.12136. [Epub ahead of print] PubMed

Direct detection of early-stage cancers using circulating tumor DNA.
Phallen J, Sausen M, Adleff V, Leal A, Hruban C, White J, Anagnostou V, Fiksel J, Cristiano S, Papp E, Speir S, Reinert T, Orntoft MW, Woodward BD, Murphy D, Parpart-Li S, Riley D, Nesselbush M, Sengamalay N, Georgiadis A, Li QK, Madsen MR, Mortensen FV, Huiskens J, Punt C, van Grieken N, Fijneman R, Meijer G, Husain H, Scharpf RB, Diaz LA Jr, Jones S, Angiuoli S, Ørntoft T, Nielsen HJ, Andersen CL, Velculescu VE.Sci Transl Med. 2017 Aug 16;9(403). pii: eaan2415. doi: 10.1126/scitranslmed.aan2415. PubMed

Sequencing and de novo assembly of 150 genomes from Denmark as a population reference.
Maretty L, Jensen JM, Petersen B, Sibbesen JA, Liu S, Villesen P, Skov L, Belling K, Theil Have C, Izarzugaza JMG, Grosjean M, Bork-Jensen J, Grove J, Als TD, Huang S, Chang Y, Xu R, Ye W, Rao J, Guo X, Sun J, Cao H, Ye C, van Beusekom J, Espeseth T, Flindt E, Friborg RM, Halager AE, Le Hellard S, Hultman CM, Lescai F, Li S, Lund O, Løngren P, Mailund T, Matey-Hernandez ML, Mors O, Pedersen CNS, Sicheritz-Pontén T, Sullivan P, Syed A, Westergaard D, Yadav R, Li N, Xu X, Hansen T, Krogh A, Bolund L, Sørensen TIA, Pedersen O, Gupta R, Rasmussen S, Besenbacher S, Børglum AD, Wang J, Eiberg H, Kristiansen K, Brunak S, Schierup MH.
Nature. 2017 Aug 3;548(7665):87-91. doi: 10.1038/nature23264. Epub 2017 Jul 26. PubMed

Prediction of Primary Tumors in Cancers of Unknown Primary.
Søndergaard D, Nielsen S, Pedersen CNS, Besenbacher S.
J Integr Bioinform. 2017 Jul 7;14(2). pii: /j/jib.2017.14.issue-2/jib-2017-0013/jib-2017-0013.xml. doi: 10.1515/jib-2017-0013. PubMed

Clinical implications of monitoring circulating tumor DNA in patients with colorectal cancer.Schøler LV, Reinert T, Ørntoft MW, Kassentoft CG, Árnadóttir SS, Vang S, Nordentoft I, Knudsen M, Lamy P, Andreasen D, Mortensen FV, Knudsen AR, Stribolt K, Sivesgaard K, Mouritzen P, Nielsen HJ, Laurberg S, Ørntoft TF, Andersen CL.
Clin Cancer Res. 2017 Jun 9. pii: clincanres.0510.2017. doi: 10.1158/1078-0432.CCR-17-0510. [Epub ahead of print] PubMed

An Optimized Shotgun Strategy for the Rapid Generation of Comprehensive Human Proteomes.
Bekker-Jensen DB, Kelstrup CD, Batth TS, Larsen SC, Haldrup C, Bramsen JB, Sørensen KD, Høyer S, Ørntoft TF, Andersen CL, Nielsen ML, Olsen JV.
Cell Syst. 2017 Jun 28;4(6):587-599.e4. doi: 10.1016/j.cels.2017.05.009. Epub 2017 Jun 7. PubMed

Prognostic Impact of a 12-gene Progression Score in Non-muscle-invasive Bladder Cancer: A Prospective Multicentre Validation Study.
Dyrskjøt L, Reinert T, Algaba F, Christensen E, Nieboer D, Hermann GG, Mogensen K, Beukers W, Marquez M, Segersten U, Høyer S, Ulhøi BP, Hartmann A, Stöhr R, Wach S, Nawroth R, Schwamborn K, Tulic C, Simic T, Junker K, Harving N, Petersen AC, Jensen JB, Keck B, Grimm MO, Horstmann M, Maurer T, Steyerberg EW, Zwarthoff EC, Real FX, Malats N, Malmström PU, Ørntoft TF.
Eur Urol. 2017 Jun 2. pii: S0302-2838(17)30475-X. doi: 10.1016/j.eururo.2017.05.040. [Epub ahead of print] PubMed

Molecular-Subtype-Specific Biomarkers Improve Prediction of Prognosis in Colorectal Cancer.
Bramsen JB, Rasmussen MH, Ongen H, Mattesen TB, Ørntoft MW, Árnadóttir SS, Sandoval J, Laguna T, Vang S, Øster B, Lamy P, Madsen MR, Laurberg S, Esteller M, Dermitzakis ET, Ørntoft TF, Andersen CL.
Cell Rep. 2017 May 9;19(6):1268-1280. doi: 10.1016/j.celrep.2017.04.045. PubMed

Incidence and prevalence of multiple endocrine neoplasia 2B in Denmark: a nationwide study.
Mathiesen JS, Kroustrup JP, Vestergaard P, Madsen M, Stochholm K, Poulsen PL, Krogh Rasmussen Å, Feldt-Rasmussen U, Schytte S, Pedersen HB, Hahn CH, Bentzen J, Gaustadnes M, Ørntoft TF, Hansen TVO, Nielsen FC, Brixen K, Frederiksen AL, Godballe C.
Endocr Relat Cancer. 2017 Apr 24. pii: ERC-17-0122. doi: 10.1530/ERC-17-0122. [Epub ahead of print] PubMed

Profiling of long non-coding RNAs identifies LINC00958 and LINC01296 as candidate oncogenes in bladder cancer.
Seitz AK, Christensen LL, Christensen E, Faarkrog K, Ostenfeld MS, Hedegaard J, Nordentoft I, Nielsen MM, Palmfeldt J, Thomson M, Jensen MT, Nawroth R, Maurer T, Ørntoft TF, Jensen JB, Damgaard CK, Dyrskjøt L.
Sci Rep. 2017 Mar 24;7(1):395. doi: 10.1038/s41598-017-00327-0. PubMed

epiG: statistical inference and profiling of DNA methylation from whole-genome bisulfite sequencing data.
Vincent M, Mundbjerg K, Skou Pedersen J, Liang G, Jones PA, Ørntoft TF, Dalsgaard Sørensen K, Wiuf C.
Genome Biol. 2017 Feb 21;18(1):38. doi: 10.1186/s13059-017-1168-4. PubMed

Heterogeneous patterns of DNA methylation-based field effects in histologically normal prostate tissue from cancer patients.
Møller M, Strand SH, Mundbjerg K, Liang G, Gill I, Haldrup C, Borre M, Høyer S, Ørntoft TF, Sørensen KD.
Sci Rep. 2017 Jan 13;7:40636. doi: 10.1038/srep40636. PubMed

Identifying aggressive prostate cancer foci using a DNA methylation classifier.
Mundbjerg K, Chopra S, Alemozaffar M, Duymich C, Lakshminarasimhan R, Nichols PW, Aron M, Siegmund KD, Ukimura O, Aron M, Stern M, Gill P, Carpten JD, Ørntoft TF, Sørensen KD, Weisenberger DJ, Jones PA, Duddalwar V, Gill I, Liang G.
Genome Biol. 2017 Jan 12;18(1):3. doi: 10.1186/s13059-016-1129-3. PubMed

Liquid Biopsy Analysis of FGFR3 and PIK3CA Hotspot Mutations for Disease Surveillance in Bladder Cancer.
Christensen E, Birkenkamp-Demtröder K, Nordentoft I, Høyer S, van der Keur K, van Kessel K, Zwarthoff E, Agerbæk M, Ørntoft TF, Jensen JB, Dyrskjøt L.
Eur Urol. 2017 Jan 6. pii: S0302-2838(16)30920-4. doi: 10.1016/j.eururo.2016.12.016. [Epub ahead of print] PubMed