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Ioncopy: an R Shiny app to call copy number alterations in targeted NGS data.

Budczies J, Pfarr N, Romanovsky E, Endris V, Stenzinger A, Denkert C.

BMC Bioinformatics. 2018 Apr 24;19(1):157. doi: 10.1186/s12859-018-2159-5.


Pancreatic neuroendocrine carcinomas reveal a closer relationship to ductal adenocarcinomas than to neuroendocrine tumors G3.

Konukiewitz B, Jesinghaus M, Steiger K, Schlitter AM, Kasajima A, Sipos B, Zamboni G, Weichert W, Pfarr N, Klöppel G.

Hum Pathol. 2018 Jul;77:70-79. doi: 10.1016/j.humpath.2018.03.018. Epub 2018 Mar 26.


PICCA study: panitumumab in combination with cisplatin/gemcitabine chemotherapy in KRAS wild-type patients with biliary cancer-a randomised biomarker-driven clinical phase II AIO study.

Vogel A, Kasper S, Bitzer M, Block A, Sinn M, Schulze-Bergkamen H, Moehler M, Pfarr N, Endris V, Goeppert B, Merx K, Schnoy E, Siveke JT, Michl P, Waldschmidt D, Kuhlmann J, Geissler M, Kahl C, Evenkamp R, Schmidt T, Kuhlmann A, Weichert W, Kubicka S.

Eur J Cancer. 2018 Mar;92:11-19. doi: 10.1016/j.ejca.2017.12.028. Epub 2018 Feb 3.


Multicenter validation of cancer gene panel-based next-generation sequencing for translational research and molecular diagnostics.

Hirsch B, Endris V, Lassmann S, Weichert W, Pfarr N, Schirmacher P, Kovaleva V, Werner M, Bonzheim I, Fend F, Sperveslage J, Kaulich K, Zacher A, Reifenberger G, Köhrer K, Stepanow S, Lerke S, Mayr T, Aust DE, Baretton G, Weidner S, Jung A, Kirchner T, Hansmann ML, Burbat L, von der Wall E, Dietel M, Hummel M.

Virchows Arch. 2018 Apr;472(4):557-565. doi: 10.1007/s00428-017-2288-7. Epub 2018 Jan 27.


Appendiceal goblet cell carcinoids and adenocarcinomas ex-goblet cell carcinoid are genetically distinct from primary colorectal-type adenocarcinoma of the appendix.

Jesinghaus M, Konukiewitz B, Foersch S, Stenzinger A, Steiger K, Muckenhuber A, Groß C, Mollenhauer M, Roth W, Detlefsen S, Weichert W, Klöppel G, Pfarr N, Schlitter AM.

Mod Pathol. 2018 May;31(5):829-839. doi: 10.1038/modpathol.2017.184. Epub 2018 Jan 12.


Increased intraepithelial CD3+ T-lymphocytes and high PD-L1 expression on tumor cells are associated with a favorable prognosis in esophageal squamous cell carcinoma and allow prognostic immunogenic subgrouping.

Jesinghaus M, Steiger K, Slotta-Huspenina J, Drecoll E, Pfarr N, Meyer P, Konukiewitz B, Bettstetter M, Wieczorek K, Ott K, Feith M, Langer R, Weichert W, Specht K, Boxberg M.

Oncotarget. 2017 Jul 18;8(29):46756-46768. doi: 10.18632/oncotarget.18606.


Mutational profiles of Brenner tumors show distinctive features uncoupling urothelial carcinomas and ovarian carcinoma with transitional cell histology.

Pfarr N, Darb-Esfahani S, Leichsenring J, Taube E, Boxberg M, Braicu I, Jesinghaus M, Penzel R, Endris V, Noske A, Weichert W, Schirmacher P, Denkert C, Stenzinger A.

Genes Chromosomes Cancer. 2017 Oct;56(10):758-766. doi: 10.1002/gcc.22480. Epub 2017 Jul 25.


Prevalence of somatic mitochondrial mutations and spatial distribution of mitochondria in non-small cell lung cancer.

Kazdal D, Harms A, Endris V, Penzel R, Kriegsmann M, Eichhorn F, Muley T, Stenzinger A, Pfarr N, Weichert W, Warth A.

Br J Cancer. 2017 Jul 11;117(2):220-226. doi: 10.1038/bjc.2017.155. Epub 2017 May 30.


Molecular signaling in multiple myeloma: association of RAS/RAF mutations and MEK/ERK pathway activation.

Xu J, Pfarr N, Endris V, Mai EK, Md Hanafiah NH, Lehners N, Penzel R, Weichert W, Ho AD, Schirmacher P, Goldschmidt H, Andrulis M, Raab MS.

Oncogenesis. 2017 May 15;6(5):e337. doi: 10.1038/oncsis.2017.36.


Molecular, morphological and survival analysis of 177 resected pancreatic ductal adenocarcinomas (PDACs): Identification of prognostic subtypes.

Schlitter AM, Segler A, Steiger K, Michalski CW, Jäger C, Konukiewitz B, Pfarr N, Endris V, Bettstetter M, Kong B, Regel I, Kleeff J, Klöppel G, Esposito I.

Sci Rep. 2017 Feb 1;7:41064. doi: 10.1038/srep41064.


Somatostatin receptor expression related to TP53 and RB1 alterations in pancreatic and extrapancreatic neuroendocrine neoplasms with a Ki67-index above 20.

Konukiewitz B, Schlitter AM, Jesinghaus M, Pfister D, Steiger K, Segler A, Agaimy A, Sipos B, Zamboni G, Weichert W, Esposito I, Pfarr N, Klöppel G.

Mod Pathol. 2017 Apr;30(4):587-598. doi: 10.1038/modpathol.2016.217. Epub 2017 Jan 6.


Colorectal mixed adenoneuroendocrine carcinomas and neuroendocrine carcinomas are genetically closely related to colorectal adenocarcinomas.

Jesinghaus M, Konukiewitz B, Keller G, Kloor M, Steiger K, Reiche M, Penzel R, Endris V, Arsenic R, Hermann G, Stenzinger A, Weichert W, Pfarr N, Klöppel G.

Mod Pathol. 2017 Apr;30(4):610-619. doi: 10.1038/modpathol.2016.220. Epub 2017 Jan 6.


Influence of the HER receptor ligand system on sensitivity to cetuximab and trastuzumab in gastric cancer cell lines.

Kneissl J, Hartmann A, Pfarr N, Erlmeier F, Lorber T, Keller S, Zwingenberger G, Weichert W, Luber B.

J Cancer Res Clin Oncol. 2017 Apr;143(4):573-600. doi: 10.1007/s00432-016-2308-z. Epub 2016 Dec 8.


Integration of genomics and histology revises diagnosis and enables effective therapy of refractory cancer of unknown primary with PDL1 amplification.

Gröschel S, Bommer M, Hutter B, Budczies J, Bonekamp D, Heining C, Horak P, Fröhlich M, Uhrig S, Hübschmann D, Geörg C, Richter D, Pfarr N, Pfütze K, Wolf S, Schirmacher P, Jäger D, von Kalle C, Brors B, Glimm H, Weichert W, Stenzinger A, Fröhling S.

Cold Spring Harb Mol Case Stud. 2016 Nov;2(6):a001180.


Mutations of cancer-related genes in benign tumors: the example of hidradenoma papilliferum.

Pfarr N, Stenzinger A.

Hum Pathol. 2017 Apr;62:246-247. doi: 10.1016/j.humpath.2016.09.034. Epub 2016 Nov 16. No abstract available.


Targeted next-generation sequencing enables reliable detection of HER2 (ERBB2) status in breast cancer and provides ancillary information of clinical relevance.

Pfarr N, Penzel R, Endris V, Lier C, Flechtenmacher C, Volckmar AL, Kirchner M, Budczies J, Leichsenring J, Herpel E, Noske A, Weichert W, Schneeweiss A, Schirmacher P, Sinn HP, Stenzinger A.

Genes Chromosomes Cancer. 2017 Apr;56(4):255-265. doi: 10.1002/gcc.22431. Epub 2016 Nov 23.


Tubular, lactating, and ductal adenomas are devoid of MED12 Exon2 mutations, and ductal adenomas show recurrent mutations in GNAS and the PI3K-AKT pathway.

Volckmar AL, Leichsenring J, Flechtenmacher C, Pfarr N, Siebolts U, Kirchner M, Budczies J, Bockmayr M, Ridinger K, Lorenz K, Herpel E, Noske A, Weichert W, Klauschen F, Schirmacher P, Penzel R, Endris V, Stenzinger A.

Genes Chromosomes Cancer. 2017 Jan;56(1):11-17. doi: 10.1002/gcc.22396. Epub 2016 Aug 9.


Molecular driver alterations and their clinical relevance in cancer of unknown primary site.

Löffler H, Pfarr N, Kriegsmann M, Endris V, Hielscher T, Lohneis P, Folprecht G, Stenzinger A, Dietel M, Weichert W, Krämer A.

Oncotarget. 2016 Jul 12;7(28):44322-44329. doi: 10.18632/oncotarget.10035.


Copy number changes of clinically actionable genes in melanoma, non-small cell lung cancer and colorectal cancer-A survey across 822 routine diagnostic cases.

Pfarr N, Penzel R, Klauschen F, Heim D, Brandt R, Kazdal D, Jesinghaus M, Herpel E, Schirmacher P, Warth A, Weichert W, Endris V, Stenzinger A.

Genes Chromosomes Cancer. 2016 Nov;55(11):821-33. doi: 10.1002/gcc.22378. Epub 2016 Jun 27.


Isolation and characterization of circulating tumor cells using a novel workflow combining the CellSearch® system and the CellCelector.

Neumann MH, Schneck H, Decker Y, Schömer S, Franken A, Endris V, Pfarr N, Weichert W, Niederacher D, Fehm T, Neubauer H.

Biotechnol Prog. 2017 Jan;33(1):125-132. doi: 10.1002/btpr.2294. Epub 2016 May 17.


Pan-cancer analysis of copy number changes in programmed death-ligand 1 (PD-L1, CD274) - associations with gene expression, mutational load, and survival.

Budczies J, Bockmayr M, Denkert C, Klauschen F, Gröschel S, Darb-Esfahani S, Pfarr N, Leichsenring J, Onozato ML, Lennerz JK, Dietel M, Fröhling S, Schirmacher P, Iafrate AJ, Weichert W, Stenzinger A.

Genes Chromosomes Cancer. 2016 Aug;55(8):626-39. doi: 10.1002/gcc.22365. Epub 2016 May 30.


Genetic changes of non-small cell lung cancer under neoadjuvant therapy.

Warth A, Endris V, Stenzinger A, Penzel R, Harms A, Duell T, Abdollahi A, Lindner M, Schirmacher P, Muley T, Dienemann H, Fink L, Morresi-Hauf A, Pfarr N, Weichert W.

Oncotarget. 2016 May 17;7(20):29761-9. doi: 10.18632/oncotarget.8858.


NGS-based BRCA1/2 mutation testing of high-grade serous ovarian cancer tissue: results and conclusions of the first international round robin trial.

Endris V, Stenzinger A, Pfarr N, Penzel R, Möbs M, Lenze D, Darb-Esfahani S, Hummel M, Sabine-Merkelbach-Bruse, Jung A, Lehmann U, Kreipe H, Kirchner T, Büttner R, Jochum W, Höfler G, Dietel M, Weichert W, Schirmacher P.

Virchows Arch. 2016 Jun;468(6):697-705. doi: 10.1007/s00428-016-1919-8. Epub 2016 Mar 22.


CD274/PD-L1 gene amplification and PD-L1 protein expression are common events in squamous cell carcinoma of the oral cavity.

Straub M, Drecoll E, Pfarr N, Weichert W, Langer R, Hapfelmeier A, Götz C, Wolff KD, Kolk A, Specht K.

Oncotarget. 2016 Mar 15;7(11):12024-34. doi: 10.18632/oncotarget.7593.


Genotyping of colorectal cancer for cancer precision medicine: Results from the IPH Center for Molecular Pathology.

Jesinghaus M, Pfarr N, Endris V, Kloor M, Volckmar AL, Brandt R, Herpel E, Muckenhuber A, Lasitschka F, Schirmacher P, Penzel R, Weichert W, Stenzinger A.

Genes Chromosomes Cancer. 2016 Jun;55(6):505-21. doi: 10.1002/gcc.22352. Epub 2016 Mar 22.


Ioncopy: a novel method for calling copy number alterations in amplicon sequencing data including significance assessment.

Budczies J, Pfarr N, Stenzinger A, Treue D, Endris V, Ismaeel F, Bangemann N, Blohmer JU, Dietel M, Loibl S, Klauschen F, Weichert W, Denkert C.

Oncotarget. 2016 Mar 15;7(11):13236-47. doi: 10.18632/oncotarget.7451.


Genetic heterogeneity in synchronous colorectal cancers impacts genotyping approaches and therapeutic strategies.

Jesinghaus M, Pfarr N, Kloor M, Endris V, Tavernar L, Muckenhuber A, von Knebel Doeberitz M, Penzel R, Weichert W, Stenzinger A.

Genes Chromosomes Cancer. 2016 Mar;55(3):268-77. doi: 10.1002/gcc.22330. Epub 2015 Dec 9.


Mutations in genes encoding PI3K-AKT and MAPK signaling define anogenital papillary hidradenoma.

Pfarr N, Sinn HP, Klauschen F, Flechtenmacher C, Bockmayr M, Ridinger K, von Winterfeld M, Warth A, Lorenz K, Budczies J, Penzel R, Lennerz JK, Endris V, Weichert W, Stenzinger A.

Genes Chromosomes Cancer. 2016 Feb;55(2):113-9. doi: 10.1002/gcc.22315. Epub 2015 Oct 23.


NUT carcinoma of the thorax: Case report and review of the literature.

Harms A, Herpel E, Pfarr N, Penzel R, Heussel CP, Herth FJ, Dienemann H, Weichert W, Warth A.

Lung Cancer. 2015 Dec;90(3):484-91. doi: 10.1016/j.lungcan.2015.10.001. Epub 2015 Oct 9. Review.


High-throughput diagnostic profiling of clinically actionable gene fusions in lung cancer.

Pfarr N, Stenzinger A, Penzel R, Warth A, Dienemann H, Schirmacher P, Weichert W, Endris V.

Genes Chromosomes Cancer. 2016 Jan;55(1):30-44. doi: 10.1002/gcc.22297. Epub 2015 Sep 23.


Utility of different massive parallel sequencing platforms for mutation profiling in clinical samples and identification of pitfalls using FFPE tissue.

Fassunke J, Haller F, Hebele S, Moskalev EA, Penzel R, Pfarr N, Merkelbach-Bruse S, Endris V.

Int J Mol Med. 2015 Nov;36(5):1233-43. doi: 10.3892/ijmm.2015.2339. Epub 2015 Sep 7.


Distribution of MED12 mutations in fibroadenomas and phyllodes tumors of the breast--implications for tumor biology and pathological diagnosis.

Pfarr N, Kriegsmann M, Sinn P, Klauschen F, Endris V, Herpel E, Muckenhuber A, Jesinghaus M, Klosterhalfen B, Penzel R, Lennerz JK, Weichert W, Stenzinger A.

Genes Chromosomes Cancer. 2015 Jul;54(7):444-52. doi: 10.1002/gcc.22256. Epub 2015 Apr 30.


Semiconductor-based sequencing of formalin-fixed, paraffin-embedded colorectal cancer samples.

Stenzinger A, Pfarr N, Penzel R, Wolf T, Schirmacher P, Endris V, Weichert W.

Oncologist. 2015 May;20(5):e10-1. doi: 10.1634/theoncologist.2014-0280. Epub 2015 Apr 10. No abstract available.


[Molecular diagnostics of non-small cell lung cancer: New markers and technologies].

Warth A, Endris V, Kriegsmann M, Stenzinger A, Penzel R, Pfarr N, Weichert W.

Pathologe. 2015 Mar;36(2):154-63. doi: 10.1007/s00292-015-0004-4. Review. German.


Distinctive Spatiotemporal Stability of Somatic Mutations in Metastasized Microsatellite-stable Colorectal Cancer.

Jesinghaus M, Wolf T, Pfarr N, Muckenhuber A, Ahadova A, Warth A, Goeppert B, Sers C, Kloor M, Endris V, Stenzinger A, Weichert W.

Am J Surg Pathol. 2015 Aug;39(8):1140-7. doi: 10.1097/PAS.0000000000000423.


Mutational profiles in triple-negative breast cancer defined by ultradeep multigene sequencing show high rates of PI3K pathway alterations and clinically relevant entity subgroup specific differences.

Kriegsmann M, Endris V, Wolf T, Pfarr N, Stenzinger A, Loibl S, Denkert C, Schneeweiss A, Budczies J, Sinn P, Weichert W.

Oncotarget. 2014 Oct 30;5(20):9952-65.


Mutations in POLE and survival of colorectal cancer patients--link to disease stage and treatment.

Stenzinger A, Pfarr N, Endris V, Penzel R, Jansen L, Wolf T, Herpel E, Warth A, Klauschen F, Kloor M, Roth W, Bläker H, Chang-Claude J, Brenner H, Hoffmeister M, Weichert W.

Cancer Med. 2014 Dec;3(6):1527-38. doi: 10.1002/cam4.305. Epub 2014 Aug 1.


Targeted ultra-deep sequencing reveals recurrent and mutually exclusive mutations of cancer genes in blastic plasmacytoid dendritic cell neoplasm.

Stenzinger A, Endris V, Pfarr N, Andrulis M, Jöhrens K, Klauschen F, Siebolts U, Wolf T, Koch PS, Schulz M, Hartschuh W, Goerdt S, Lennerz JK, Wickenhauser C, Klapper W, Anagnostopoulos I, Weichert W.

Oncotarget. 2014 Aug 15;5(15):6404-13.


Identification of a new intronic BMPR2-mutation and early diagnosis of heritable pulmonary arterial hypertension in a large family with mean clinical follow-up of 12 years.

Hinderhofer K, Fischer C, Pfarr N, Szamalek-Hoegel J, Lichtblau M, Nagel C, Egenlauf B, Ehlken N, Grünig E.

PLoS One. 2014 Mar 12;9(3):e91374. doi: 10.1371/journal.pone.0091374. eCollection 2014.


Hemodynamic and genetic analysis in children with idiopathic, heritable, and congenital heart disease associated pulmonary arterial hypertension.

Pfarr N, Fischer C, Ehlken N, Becker-Grünig T, López-González V, Gorenflo M, Hager A, Hinderhofer K, Miera O, Nagel C, Schranz D, Grünig E.

Respir Res. 2013 Jan 9;14:3. doi: 10.1186/1465-9921-14-3.


Hemodynamic and clinical onset in patients with hereditary pulmonary arterial hypertension and BMPR2 mutations.

Pfarr N, Szamalek-Hoegel J, Fischer C, Hinderhofer K, Nagel C, Ehlken N, Tiede H, Olschewski H, Reichenberger F, Ghofrani AH, Seeger W, Grünig E.

Respir Res. 2011 Jul 29;12:99. doi: 10.1186/1465-9921-12-99.


Autonomous thyroid adenoma: only an adulthood disease?

Schwab KO, Pfarr N, van der Werf-Grohmann N, Pohl M, Rädecke J, Musholt T, Pohlenz J.

J Pediatr. 2009 Jun;154(6):931-3.e2. doi: 10.1016/j.jpeds.2008.12.019.


Two novel mutations in the human thyroid peroxidase (TPO) gene: genetics and clinical findings in four children.

Simm D, Pfarr N, Pohlenz J, Prawitt D, Dörr HG.

Acta Paediatr. 2009 Jun;98(6):1057-61. doi: 10.1111/j.1651-2227.2009.01236.x. Epub 2009 Feb 20.


Congenital hypothyroidism caused by a novel homozygous mutation in the thyroid peroxidase gene.

Fuchs O, Pfarr N, Pohlenz J, Thanner F, Schmidt H.

J Pediatr Endocrinol Metab. 2008 Nov;21(11):1093-7.


Elevated serum triiodothyronine and intellectual and motor disability with paroxysmal dyskinesia caused by a monocarboxylate transporter 8 gene mutation.

Fuchs O, Pfarr N, Pohlenz J, Schmidt H.

Dev Med Child Neurol. 2009 Mar;51(3):240-4. doi: 10.1111/j.1469-8749.2008.03125.x. Epub 2008 Oct 17.


Pseudodominant inheritance of goitrous congenital hypothyroidism caused by TPO mutations: molecular and in silico studies.

Deladoëy J, Pfarr N, Vuissoz JM, Parma J, Vassart G, Biesterfeld S, Pohlenz J, Van Vliet G.

J Clin Endocrinol Metab. 2008 Feb;93(2):627-33. Epub 2007 Nov 20.


Subclinical hyperthyroidism due to a thyrotropin receptor (TSHR) gene mutation (S505R).

Pohlenz J, Pfarr N, Krüger S, Hesse V.

Acta Paediatr. 2006 Dec;95(12):1685-7.


Congenital hypothyroidism caused by new mutations in the thyroid oxidase 2 (THOX2) gene.

Pfarr N, Korsch E, Kaspers S, Herbst A, Stach A, Zimmer C, Pohlenz J.

Clin Endocrinol (Oxf). 2006 Dec;65(6):810-5. Review.


Goitrous congenital hypothyroidism and hearing impairment associated with mutations in the TPO and SLC26A4/PDS genes.

Pfarr N, Borck G, Turk A, Napiontek U, Keilmann A, Müller-Forell W, Kopp P, Pohlenz J.

J Clin Endocrinol Metab. 2006 Jul;91(7):2678-81. Epub 2006 May 9.


Congenital primary hypothyroidism with subsequent adenomatous goiter in a Turkish patient caused by a homozygous 10-bp deletion in the thyroid peroxidase (TPO) gene.

Pfarr N, Musholt TJ, Musholt PB, Brzezinska R, Pohlenz J.

Clin Endocrinol (Oxf). 2006 May;64(5):514-8. Review.


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