Browsing Institutt for informatikk by Author "Nakken, Sigve"

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  • Automated amplicon design suitable for analysis of DNA variants by melting techniques 
    Ekstrøm, Per O; Nakken, Sigve; Johansen, Morten; Hovig, Eivind (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2015)
    Background The technological development of DNA analysis has had tremendous development in recent years, and the present deep sequencing techniques present unprecedented opportunities for detailed and ...
  • BRAF V600E mutation in early-stage multiple myeloma: good response to broad acting drugs and no relation to prognosis 
    Rustad, Even Holth; Dai, Hong Yan; Hov, Håkon; Coward, Eivind; Beisvag, Vidar; Myklebost, Ola; Hovig, Eivind; Nakken, Sigve; Vodak, Daniel; Meza-Zepeda, Leonardo A.; Sandvik, Arne Kristian; Wader, Karin Fahl; Misund, Kristine; Sundan, Anders; Aarset, Harald; Waage, Anders (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2015)
    In this study, we analyzed the prevalence and clone size of BRAF V600E mutation in 209 patients with multiple myeloma and related the results to clinical phenotype, response and survival. Biopsies were screened for BRAF ...
  • Cancer Predisposition Sequencing Reporter (CPSR): A flexible variant report engine for high-throughput germline screening in cancer 
    Nakken, Sigve; Saveliev, Vladislav; Hofmann, Oliver; Møller, Pål; Myklebost, Ola; Hovig, Eivind (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2021)
    The value of high-throughput germline genetic testing is increasingly recognized inclinical cancer care. Disease-associated germline variants in cancer patients areimportant for risk management and surveillance, surgical ...
  • Cancer risk and survival in path_MMR carriers by gene and gender up to 75 years of age: a report from the Prospective Lynch Syndrome Database 
    Møller, Pål; Seppälä, Toni T.; Bernstein, Inge; Holinski-Feder, Elke; Sala, Paulo; Evans, D. Gareth; Lindblom, Annika; Macrae, Finlay; Blanco, Ignacio; Sijmons, Rolf H.; Jeffries, Jacqueline; Vasen, Hans F.A.; Burn, John; Nakken, Sigve; Hovig, Eivind; Rødland, Einar Andreas; Tharmaratnam, Kukatharmini; de Vos tot Nederveen Cappel, Wouter H.; Hill, James; Wijnen, Juul T.; Jenkins, Mark A.; Green, Kate; Lalloo, Fiona; Sunde, Lone; Mints, Miriam; Bertario, Lucio; Pineda, Marta; Navarro, Matilde; Morak, Monika; Renkonen-Sinisalo, Laura; Dominguez-Valentin, Mev; Frayling, Ian M.; Plazzer, John-Paul; Pylvanainen, Kirsi; Genuardi, Maurizio; Mecklin, Jukka-Pekka; Möslein, Gabriela; Sampson, Julian R.; Capella, Gabriel (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2018)
    Background Most patients with path_MMR gene variants (Lynch syndrome (LS)) now survive both their first and subsequent cancers, resulting in a growing number of older patients with LS for whom limited information exists ...
  • Chromosomal instability and a deregulated cell cycle are intrinsic features of high-risk gastrointestinal stromal tumours with a metastatic potential 
    Namløs, Heidi Maria; Khelik, Ksenia; Nakken, Sigve; Vodak, Daniel; Hovig, Eivind; Myklebost, Ola; Pedersen, Kjetil Boye; Meza, Leonardo Zepeda (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2023)
    Patients with localised, high‐risk gastrointestinal stromal tumours (GIST) benefit from adjuvant imatinib treatment. Still, approximately 40% of patients relapse within 3 years after adjuvant therapy and the clinical and ...
  • Clonal evolution in primary breast cancers under sequential epirubicin and docetaxel monotherapy 
    Venizelos, Andreas; Engebrethsen, Christina; Deng, Wei; Geisler, Jürgen; Geisler, Stephanie; Iversen, Gjertrud T.; Aas, Turid; Aase, Hildegunn S.; Seyedzadeh, Manouchehr; Steinskog, Eli S.; Myklebost, Ola; Nakken, Sigve; Vodak, Daniel; Hovig, Eivind; Meza-Zepeda, Leonardo A.; Lønning, Per E.; Knappskog, Stian; Eikesdal, Hans P. (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2022)
    Background Subclonal evolution during primary breast cancer treatment is largely unexplored. We aimed to assess the dynamic changes in subclonal composition of treatment-naïve breast cancers during neoadjuvant ...
  • Colorectal cancer incidence in path_MLH1 carriers subjected to different follow-up protocols: a Prospective Lynch Syndrome Database report 
    Seppälä, Toni; Pylvänäinen, Kirsi; Evans, Dafydd G; Järvinen, Heikki; Renkonen-Sinisalo, Laura; Bernstein, Inge; Holinski-Feder, Elke; Sala, Paola; Lindblom, Annika; Macrae, Finlay; Blanco, Ignacio; Sijmons, Rolf; Jeffries, Jacqueline; Vasen, Hans; Burn, John; Nakken, Sigve; Hovig, Eivind; Rødland, Einar A; Tharmaratnam, Kukatharmini; de Vos tot Nederveen Cappel, Wouter H; Hill, James; Wijnen, Juul; Jenkins, Mark; Genuardi, Maurizio; Green, Kate; Lalloo, Fiona; Sunde, Lone; Mints, Miriam; Bertario, Lucio; Pineda, Marta; Navarro, Matilde; Morak, Monika; Frayling, Ian M; Plazzer, John-Paul; Sampson, Julian R; Capella, Gabriel; Möslein, Gabriela; Mecklin, Jukka-Pekka; Møller, Pål (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2017)
    Background We have previously reported a high incidence of colorectal cancer (CRC) in carriers of pathogenic MLH1 variants (path_MLH1) despite follow-up with colonoscopy including polypectomy. ...
  • Colorectal cancer incidences in Lynch syndrome: a comparison of results from the prospective lynch syndrome database and the international mismatch repair consortium 
    Møller, Pål; Seppälä, Toni; Dowty, James G.; Haupt, Saskia; Dominguez-Valentin, Mev; Sunde, Lone; Bernstein, Inge; Engel, Christoph; Aretz, Stefan; Nielsen, Maartje; Capella, Gabriel; Evans, Dafydd G.; Burn, John; Holinski-Feder, Elke; Bertario, Lucio; Bonanni, Bernardo; Lindblom, Annika; Levi, Zohar; Macrae, Finlay; Winship, Ingrid; Plazzer, John-Paul; Sijmons, Rolf; Laghi, Luigi; Valle, Adriana D.; Heinimann, Karl; Half, Elizabeth; Lopez-Koestner, Francisco; Alvarez-Valenzuela, Karin; Scott, Rodney J.; Katz, Lior; Laish, Ido; Vainer, Elez; Vaccaro, Carlos A.; Carraro, Dirce M.; Gluck, Nathan; Abu-Freha, Naim; Stakelum, Aine; Kennelly, Rory; Winter, Des; Rossi, Benedito M.; Greenblatt, Marc; Bohorquez, Mabel; Sheth, Harsh; Tibiletti, Maria G.; Lino-Silva, Leonardo S.; Horisberger, Karoline; Portenkirchner, Carmen; Nascimento, Ivana; Rossi, Norma T.; da Silva, Leandro A.; Thomas, Huw; Zaránd, Attila; Mecklin, Jukka-Pekka; Pylvänäinen, Kirsi; Renkonen-Sinisalo, Laura; Lepisto, Anna; Peltomäki, Päivi; Therkildsen, Christina; Lindberg, Lars J.; Thorlacius-Ussing, Ole; von Knebel Doeberitz, Magnus; Loeffler, Markus; Rahner, Nils; Steinke-Lange, Verena; Schmiegel, Wolff; Vangala, Deepak; Perne, Claudia; Hüneburg, Robert; de Vargas, Aída F.; Latchford, Andrew; Gerdes, Anne-Marie; Backman, Ann-Sofie; Guillén-Ponce, Carmen; Snyder, Carrie; Lautrup, Charlotte K.; Amor, David; Palmero, Edenir; Stoffel, Elena; Duijkers, Floor; Hall, Michael J.; Hampel, Heather; Williams, Heinric; Okkels, Henrik; Lubiński, Jan; Reece, Jeanette; Ngeow, Joanne; Guillem, Jose G.; Arnold, Julie; Wadt, Karin; Monahan, Kevin; Senter, Leigha; Rasmussen, Lene J.; van Hest, Liselotte P.; Ricciardiello, Luigi; Kohonen-Corish, Maija R. J.; Ligtenberg, Marjolijn J. L.; Southey, Melissa; Aronson, Melyssa; Zahary, Mohd N.; Samadder, N. J.; Poplawski, Nicola; Hoogerbrugge, Nicoline; Morrison, Patrick J.; James, Paul; Lee, Grant; Chen-Shtoyerman, Rakefet; Ankathil, Ravindran; Pai, Rish; Ward, Robyn; Parry, Susan; Dębniak, Tadeusz; John, Thomas; van Overeem Hansen, Thomas; Caldés, Trinidad; Yamaguchi, Tatsuro; Barca-Tierno, Verónica; Garre, Pilar; Cavestro, Giulia M.; Weitz, Jürgen; Redler, Silke; Büttner, Reinhard; Heuveline, Vincent; Hopper, John L.; Win, Aung K.; Lindor, Noralane; Gallinger, Steven; Le Marchand, Loïc; Newcomb, Polly A.; Figueiredo, Jane; Buchanan, Daniel D.; Thibodeau, Stephen N.; ten Broeke, Sanne W.; Hovig, Eivind; Nakken, Sigve; Pineda, Marta; Dueñas, Nuria; Brunet, Joan; Green, Kate; Lalloo, Fiona; Newton, Katie; Crosbie, Emma J.; Mints, Miriam; Tjandra, Douglas; Neffa, Florencia; Esperon, Patricia; Kariv, Revital; Rosner, Guy; Pavicic, Walter H.; Kalfayan, Pablo; Torrezan, Giovana T.; Bassaneze, Thiago; Martin, Claudia; Moslein, Gabriela; Ahadova, Aysel; Kloor, Matthias; Sampson, Julian R.; Jenkins, Mark A. (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2022)
    Objective To compare colorectal cancer (CRC) incidences in carriers of pathogenic variants of the MMR genes in the PLSD and IMRC cohorts, of which only the former included mandatory colonoscopy surveillance ...
  • Combining a universal telomerase based cancer vaccine with ipilimumab in patients with metastatic melanoma - Five-year follow up of a phase I/IIa trial 
    Aamdal, Elin; Inderberg, Else Marit; Ellingsen, Espen Basmo; Rasch, Wenche; Brunsvig, Paal Fr.; Aamdal, Steinar; Heintz, Karen Marie; Vodák, Daniel; Nakken, Sigve; Hovig, Eivind; Nyakas, Marta Sølvi; Guren, Tormod Kyrre; Gaudernack, Gustav (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2021)
    Background Ipilimumab improves survival for patients with metastatic malignant melanoma. Combining a therapeutic cancer vaccine with ipilimumab may increase efficacy by providing enhanced anti-tumor immune responses. UV1 ...
  • The disruptive positions in human G-quadruplex motifs are less polymorphic and more conserved than their neutral counterparts 
    Nakken, Sigve; Rognes, Torbjørn; Hovig, Eivind (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2009)
    Specific guanine-rich sequence motifs in the human genome have considerable potential to form four-stranded structures known as G-quadruplexes or G4 DNA. The enrichment of these motifs in key chromosomal regions has suggested ...
  • Dominantly inherited micro-satellite instable cancer – the four Lynch syndromes - an EHTG, PLSD position statement 
    Møller, Pal; Seppälä, Toni T.; Ahadova, Aysel; Crosbie, Emma J.; Holinski-Feder, Elke; Scott, Rodney; Haupt, Saskia; Möslein, Gabriela; Winship, Ingrid; Broeke, Sanne W. B.; Kohut, Kelly E.; Ryan, Neil; Bauerfeind, Peter; Thomas, Laura E.; Evans, D. G.; Aretz, Stefan; Sijmons, Rolf H.; Half, Elizabeth; Heinimann, Karl; Horisberger, Karoline; Monahan, Kevin; Engel, Christoph; Cavestro, Giulia M.; Fruscio, Robert; Abu-Freha, Naim; Zohar, Levi; Laghi, Luigi; Bertario, Lucio; Bonanni, Bernardo; Tibiletti, Maria G.; Lino-Silva, Leonardo S.; Vaccaro, Carlos; Valle, Adriana D.; Rossi, Benedito M.; da Silva, Leandro A.; de Oliveira Nascimento, Ivana L.; Rossi, Norma T.; Dębniak, Tadeusz; Mecklin, Jukka-Pekka; Bernstein, Inge; Lindblom, Annika; Sunde, Lone; Nakken, Sigve; Heuveline, Vincent; Burn, John; Hovig, Eivind; Kloor, Matthias; Sampson, Julian R.; Dominguez-Valentin, Mev (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2023)
    The recognition of dominantly inherited micro-satellite instable (MSI) cancers caused by pathogenic variants in one of the four mismatch repair (MMR) genes MSH2, MLH1, MSH6 and PMS2 has modified our understanding of ...
  • Genetic Characterization in High-Risk Individuals from a Low-Resource City of Peru 
    Zavaleta, Elizabeth; Solis, Nelly; Palacios, Maria Isabel; Zevallos-Escobar, Liz Elva; Corales, Edison Vasquez; Bazo-Alvarez, Juan Carlos; Dominguez-Barrera, Constantino; Campos, Anthony; Wernhoff, Patrik; Ekstrøm, Per Olaf; Møller, Pål; Visnovska, Martina; Hovig, Eivind; Balazar-Palacios, Janina; Alvarez-Valenzuela, Karin; Nakken, Sigve; Dominguez-Valentin, Mev (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2022)
    Background: Genetic testing for hereditary cancers is inconsistently applied within the healthcare systems in Latin America. In Peru, the prevalence and spectrum of cancer-predisposing germline variants is thus poorly ...
  • Genetic variants of prospectively demonstrated phenocopies in BRCA1/2 kindreds 
    Dominguez-Valentin, Mev; Evans, D. G R; Nakken, Sigve; Tubeuf, Hélène; Vodak, Daniel; Ekstrøm, Per O; Nissen, Anke M; Morak, Monika; Holinski-Feder, Elke; Martins, Alexandra; Møller, Pål; Hovig, Eivind (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2018)
    Background In kindreds carrying path_BRCA1/2 variants, some women in these families will develop cancer despite testing negative for the family’s pathogenic variant. These families may have additional ...
  • GSuite HyperBrowser: integrative analysis of dataset collections across the genome and epigenome 
    Simovski, Boris; Vodak, Daniel; Gundersen, Sveinung; Domanska, Diana Ewa; Azab, Abdulrahman; Holden, Lars; Holden, Marit; Grytten, Ivar; Rand, Knut Dagestad; Drabløs, Finn Sverre; Johansen, Morten; Mora, Antonio M.; Lund-Andersen, Christin; Fromm, Bastian; Eskeland, Ragnhild; Gabrielsen, Odd Stokke; Ferkingstad, Egil; Nakken, Sigve; Bengtsen, Mads; Nederbragt, Alexander Johan; Thorarensen, Hildur Sif; Andreas Akse, Johannes; Glad, Ingrid Kristine; Hovig, Johannes Eivind; Sandve, Geir Kjetil (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2017)
    Background: Recent large-scale undertakings such as ENCODE and Roadmap Epigenomics have generated experimental data mapped to the human reference genome (as genomic tracks) representing a variety of functional elements ...
  • Identification of genetic variants for clinical management of familial colorectal tumors 
    Dominguez-Valentin, Mev; Nakken, Sigve; Tubeuf, Hélène; Vodak, Daniel; Ekstrøm, Per O; Nissen, Anke M; Morak, Monika; Holinski-Feder, Elke; Martins, Alexandra; Møller, Pål; Hovig, Eivind (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2018)
    Background The genetic mechanisms for families who meet the clinical criteria for Lynch syndrome (LS) but do not carry pathogenic variants in the mismatch repair (MMR) genes are still undetermined. We aimed ...
  • Implementing precision cancer medicine in the public health services of Norway: the diagnostic infrastructure and a cost estimate 
    Ree, Anne Hansen; Russnes, Hege Elisabeth Giercksky; Heinrich, Daniel; Dueland, Svein; Pedersen, Kjetil Boye; Nygaard, Vigdis; Silwal-Pandit, Laxmi; Østrup, Olga; Hovig, Eivind; Nygaard, Vegard; Rødland, Einar Andreas; Nakken, Sigve; Øien, Janne T; Johansen, Christin; Bergheim, Inger; Skarpeteig, Veronica; Sathermugathevan, Menaka; Sauer, Torill; Lund-Iversen, Marius; Beiske, Klaus; Nasser, Salah; Julsrud, Lars; Reisse, Claudius; Ruud, Espen Asak; Flørenes, Vivi Ann; Hagene, Kirsten T; Aas, Eline; Lurås, Hilde; Soriano, Siv Johnsen; Geitvik, Gry Aarum; Lingjærde, Ole Christian; Børresen-Dale, Anne-Lise; Mælandsmo, Gunhild; Flatmark, Kjersti (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2017)
    Objective Through the conduct of an individual-based intervention study, the main purpose of this project was to build and evaluate the required infrastructure that may enable routine practice of precision cancer medicine ...
  • Incidence of and survival after subsequent cancers in carriers of pathogenic MMR variants with previous cancer: A report from the prospective Lynch syndrome database 
    Møller, Pål; Seppälä, Toni; Bernstein, Inge; Holinski-Feder, Elke; Sala, Paola; Evans, D. Gareth; Lindblom, Annika; MacRae, Finlay; Blanco, Ignacio; Sijmons, Rolf; Jeffries, Jacqueline; Vasen, Hans; Burn, John; Nakken, Sigve; Hovig, Eivind; Rødland, Einar Andreas; Tharmaratnam, Kukatharmini; De Vos Tot Nederveen Cappel, Wouter H.; Hill, James; Wijnen, Juul; Jenkins, Mark; Green, Kate; Lalloo, Fiona; Sunde, Lone; Mints, Miriam; Bertario, Lucio; Pineda, Marta; Navarro, Matilde; Morak, Monika; Renkonen-Sinisalo, Laura; Frayling, Ian M.; Plazzer, John-Paul; Pylvanainen, Kirsi; Genuardi, Maurizio; Mecklin, Jukka-Pekka; Möslein, Gabriela; Sampson, Julian R.; Capella, Gabriel (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2017)
    Objective: Today most patients with Lynch syndrome (LS) survive their first cancer. There is limited information on the incidences and outcome of subsequent cancers. The present study addresses three questions: (i) what ...
  • Integrative genomic analysis of peritoneal malignant mesothelioma: Understanding a case with extraordinary chemotherapy response 
    Lund-Andersen, Christin; Nakken, Sigve; Nygård, Ståle; Fromm, Bastian; Aasheim, Lars Birger; Davidson, Ben; Julsrud, Lars; Abrahamsen, Torveig Weum; Kristensen, Annette Torgunrud; Dybdahl, Brit; Larsen, Stein Gunnar; Hovig, Eivind; Flatmark, Kjersti (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2019)
    Peritoneal malignant mesothelioma is a rare disease with a generally poor prognosis and poor response to chemotherapy. To improve survival there is a need for increased molecular understanding of the disease, including ...
  • Lack of association between screening interval and cancer stage in Lynch syndrome may be accounted for by over-diagnosis; a prospective Lynch syndrome database report 
    Seppälä, Toni T; Ahadova, Aysel; Dominguez-Valentin, Mev; Macrae, Finlay; Evans, D. G; Therkildsen, Christina; Sampson, Julian; Scott, Rodney; Burn, John; Möslein, Gabriela; Bernstein, Inge; Holinski-Feder, Elke; Pylvänäinen, Kirsi; Renkonen-Sinisalo, Laura; Lepistö, Anna; Lautrup, Charlotte K; Lindblom, Annika; Plazzer, John-Paul; Winship, Ingrid; Tjandra, Douglas; Katz, Lior H; Aretz, Stefan; Hüneburg, Robert; Holzapfel, Stefanie; Heinimann, Karl; Valle, Adriana D; Neffa, Florencia; Gluck, Nathan; de Vos tot Nederveen Cappel, Wouter H; Vasen, Hans; Morak, Monika; Steinke-Lange, Verena; Engel, Christoph; Rahner, Nils; Schmiegel, Wolff; Vangala, Deepak; Thomas, Huw; Green, Kate; Lalloo, Fiona; Crosbie, Emma J; Hill, James; Capella, Gabriel; Pineda, Marta; Navarro, Matilde; Blanco, Ignacio; ten Broeke, Sanne; Nielsen, Maartje; Ljungmann, Ken; Nakken, Sigve; Lindor, Noralane; Frayling, Ian; Hovig, Eivind; Sunde, Lone; Kloor, Matthias; Mecklin, Jukka-Pekka; Kalager, Mette; Møller, Pål (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2019)
    Background Recent epidemiological evidence shows that colorectal cancer (CRC) continues to occur in carriers of pathogenic mismatch repair (path_MMR) variants despite frequent colonoscopy surveillance in ...
  • Large-scale inference of the point mutational spectrum in human segmental duplications 
    Nakken, Sigve; Rødland, Einar A; Rognes, Torbjørn; Hovig, Eivind (Journal article / Tidsskriftartikkel / PublishedVersion; Peer reviewed, 2009)
    Background Recent segmental duplications are relatively large (≥ 1 kb) genomic regions of high sequence identity (≥ 90%). They cover approximately 4–5% of the human genome and play important roles in gene ...