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Whole-genome sequencing of triple-negative breast cancers in a population-based clinical study.

Staaf J, Glodzik D, Bosch A, Vallon-Christersson J, Reuterswärd C, Häkkinen J, Degasperi A, Amarante TD, Saal LH, Hegardt C, Stobart H, Ehinger A, Larsson C, Rydén L, Loman N, Malmberg M, Kvist A, Ehrencrona H, Davies HR, Borg Å, Nik-Zainal S.

Nat Med. 2019 Sep 30. doi: 10.1038/s41591-019-0582-4. [Epub ahead of print]


Cross comparison and prognostic assessment of breast cancer multigene signatures in a large population-based contemporary clinical series.

Vallon-Christersson J, Häkkinen J, Hegardt C, Saal LH, Larsson C, Ehinger A, Lindman H, Olofsson H, Sjöblom T, Wärnberg F, Ryden L, Loman N, Malmberg M, Borg Å, Staaf J.

Sci Rep. 2019 Aug 21;9(1):12184. doi: 10.1038/s41598-019-48570-x.


Agreement between molecular subtyping and surrogate subtype classification: a contemporary population-based study of ER-positive/HER2-negative primary breast cancer.

Lundgren C, Bendahl PO, Borg Å, Ehinger A, Hegardt C, Larsson C, Loman N, Malmberg M, Olofsson H, Saal LH, Sjöblom T, Lindman H, Klintman M, Häkkinen J, Vallon-Christersson J, Fernö M, Rydén L, Ekholm M.

Breast Cancer Res Treat. 2019 Aug 20. doi: 10.1007/s10549-019-05378-7. [Epub ahead of print]


Prediction of Lymph Node Metastasis in Breast Cancer by Gene Expression and Clinicopathological Models: Development and Validation within a Population-Based Cohort.

Dihge L, Vallon-Christersson J, Hegardt C, Saal LH, Häkkinen J, Larsson C, Ehinger A, Loman N, Malmberg M, Bendahl PO, Borg Å, Staaf J, Rydén L.

Clin Cancer Res. 2019 Jul 24. doi: 10.1158/1078-0432.CCR-19-0075. [Epub ahead of print]


Glucocorticoid-resistant B cell acute lymphoblastic leukemia displays receptor tyrosine kinase activation.

Chougule RA, Shah K, Moharram SA, Vallon-Christersson J, Kazi JU.

NPJ Genom Med. 2019 Apr 4;4:7. doi: 10.1038/s41525-019-0082-y. eCollection 2019.


Alternative splicing and ACMG-AMP-2015-based classification of PALB2 genetic variants: an ENIGMA report.

Lopez-Perolio I, Leman R, Behar R, Lattimore V, Pearson JF, Castéra L, Martins A, Vaur D, Goardon N, Davy G, Garre P, García-Barberán V, Llovet P, Pérez-Segura P, Díaz-Rubio E, Caldés T, Hruska KS, Hsuan V, Wu S, Pesaran T, Karam R, Vallon-Christersson J, Borg A, Investigators K, Valenzuela-Palomo A, Velasco EA, Southey M, Vreeswijk MPG, Devilee P, Kvist A, Spurdle AB, Walker LC, Krieger S, de la Hoya M.

J Med Genet. 2019 Jul;56(7):453-460. doi: 10.1136/jmedgenet-2018-105834. Epub 2019 Mar 19.


Performance of gene expression-based single sample predictors for assessment of clinicopathological subgroups and molecular subtypes in cancers: a case comparison study in non-small cell lung cancer.

Cirenajwis H, Lauss M, Planck M, Vallon-Christersson J, Staaf J.

Brief Bioinform. 2019 Feb 4. doi: 10.1093/bib/bbz008. [Epub ahead of print]


Minimizing inequality in access to precision medicine in breast cancer by real-time population-based molecular analysis in the SCAN-B initiative.

Rydén L, Loman N, Larsson C, Hegardt C, Vallon-Christersson J, Malmberg M, Lindman H, Ehinger A, Saal LH, Borg Å.

Br J Surg. 2018 Jan;105(2):e158-e168. doi: 10.1002/bjs.10741.


Mutational and putative neoantigen load predict clinical benefit of adoptive T cell therapy in melanoma.

Lauss M, Donia M, Harbst K, Andersen R, Mitra S, Rosengren F, Salim M, Vallon-Christersson J, Törngren T, Kvist A, Ringnér M, Svane IM, Jönsson G.

Nat Commun. 2017 Nov 23;8(1):1738. doi: 10.1038/s41467-017-01460-0.


Frequent miRNA-convergent fusion gene events in breast cancer.

Persson H, Søkilde R, Häkkinen J, Pirona AC, Vallon-Christersson J, Kvist A, Mertens F, Borg Å, Mitelman F, Höglund M, Rovira C.

Nat Commun. 2017 Oct 5;8(1):788. doi: 10.1038/s41467-017-01176-1.


Multiregion Whole-Exome Sequencing Uncovers the Genetic Evolution and Mutational Heterogeneity of Early-Stage Metastatic Melanoma.

Harbst K, Lauss M, Cirenajwis H, Isaksson K, Rosengren F, Törngren T, Kvist A, Johansson MC, Vallon-Christersson J, Baldetorp B, Borg Å, Olsson H, Ingvar C, Carneiro A, Jönsson G.

Cancer Res. 2016 Aug 15;76(16):4765-74. doi: 10.1158/0008-5472.CAN-15-3476. Epub 2016 May 23.


Targeted sequencing of BRCA1 and BRCA2 across a large unselected breast cancer cohort suggests that one-third of mutations are somatic.

Winter C, Nilsson MP, Olsson E, George AM, Chen Y, Kvist A, Törngren T, Vallon-Christersson J, Hegardt C, Häkkinen J, Jönsson G, Grabau D, Malmberg M, Kristoffersson U, Rehn M, Gruvberger-Saal SK, Larsson C, Borg Å, Loman N, Saal LH.

Ann Oncol. 2016 Aug;27(8):1532-8. doi: 10.1093/annonc/mdw209. Epub 2016 May 18.


Aberrant activation of the PI3K/mTOR pathway promotes resistance to sorafenib in AML.

Lindblad O, Cordero E, Puissant A, Macaulay L, Ramos A, Kabir NN, Sun J, Vallon-Christersson J, Haraldsson K, Hemann MT, Borg Å, Levander F, Stegmaier K, Pietras K, Rönnstrand L, Kazi JU.

Oncogene. 2016 Sep 29;35(39):5119-31. doi: 10.1038/onc.2016.41. Epub 2016 Mar 21.


An integrated genomics analysis of epigenetic subtypes in human breast tumors links DNA methylation patterns to chromatin states in normal mammary cells.

Holm K, Staaf J, Lauss M, Aine M, Lindgren D, Bendahl PO, Vallon-Christersson J, Barkardottir RB, Höglund M, Borg Å, Jönsson G, Ringnér M.

Breast Cancer Res. 2016 Feb 29;18(1):27. doi: 10.1186/s13058-016-0685-5.


The Sweden Cancerome Analysis Network - Breast (SCAN-B) Initiative: a large-scale multicenter infrastructure towards implementation of breast cancer genomic analyses in the clinical routine.

Saal LH, Vallon-Christersson J, Häkkinen J, Hegardt C, Grabau D, Winter C, Brueffer C, Tang MH, Reuterswärd C, Schulz R, Karlsson A, Ehinger A, Malina J, Manjer J, Malmberg M, Larsson C, Rydén L, Loman N, Borg Å.

Genome Med. 2015 Feb 2;7(1):20. doi: 10.1186/s13073-015-0131-9. eCollection 2015.


Erythropoietin suppresses the activation of pro-apoptotic genes in head and neck squamous cell carcinoma xenografts exposed to surgical trauma.

Lindgren G, Ekblad L, Vallon-Christersson J, Kjellén E, Gebre-Medhin M, Wennerberg J.

BMC Cancer. 2014 Sep 2;14:648. doi: 10.1186/1471-2407-14-648.


The HER2-encoded miR-4728-3p regulates ESR1 through a non-canonical internal seed interaction.

Newie I, Søkilde R, Persson H, Grabau D, Rego N, Kvist A, von Stedingk K, Axelson H, Borg Å, Vallon-Christersson J, Rovira C.

PLoS One. 2014 May 14;9(5):e97200. doi: 10.1371/journal.pone.0097200. eCollection 2014.


High expression of ZNF703 independent of amplification indicates worse prognosis in patients with luminal B breast cancer.

Reynisdottir I, Arason A, Einarsdottir BO, Gunnarsson H, Staaf J, Vallon-Christersson J, Jonsson G, Ringnér M, Agnarsson BA, Olafsdottir K, Fagerholm R, Einarsdottir T, Johannesdottir G, Johannsson OT, Nevanlinna H, Borg A, Barkardottir RB.

Cancer Med. 2013 Aug;2(4):437-46. doi: 10.1002/cam4.88. Epub 2013 May 22.


The retinoblastoma gene undergoes rearrangements in BRCA1-deficient basal-like breast cancer.

Jönsson G, Staaf J, Vallon-Christersson J, Ringnér M, Gruvberger-Saal SK, Saal LH, Holm K, Hegardt C, Arason A, Fagerholm R, Persson C, Grabau D, Johnsson E, Lövgren K, Magnusson L, Heikkilä P, Agnarsson BA, Johannsson OT, Malmström P, Fernö M, Olsson H, Loman N, Nevanlinna H, Barkardottir RB, Borg Å.

Cancer Res. 2012 Aug 15;72(16):4028-36. Epub 2012 Jun 15.


Molecular profiling reveals low- and high-grade forms of primary melanoma.

Harbst K, Staaf J, Lauss M, Karlsson A, Måsbäck A, Johansson I, Bendahl PO, Vallon-Christersson J, Törngren T, Ekedahl H, Geisler J, Höglund M, Ringnér M, Lundgren L, Jirström K, Olsson H, Ingvar C, Borg Å, Tsao H, Jönsson G.

Clin Cancer Res. 2012 Aug 1;18(15):4026-36. doi: 10.1158/1078-0432.CCR-12-0343. Epub 2012 Jun 6. Erratum in: Clin Cancer Res. 2012 Oct 15;18(20):5829. Höglund, Markus [corrected to Höglund, Mattias]; Ringnér, Mattias [corrected to Ringnér, Markus].


Characterisation of amplification patterns and target genes at chromosome 11q13 in CCND1-amplified sporadic and familial breast tumours.

Holm K, Staaf J, Jönsson G, Vallon-Christersson J, Gunnarsson H, Arason A, Magnusson L, Barkardottir RB, Hegardt C, Ringnér M, Borg A.

Breast Cancer Res Treat. 2012 Jun;133(2):583-94. doi: 10.1007/s10549-011-1817-3. Epub 2011 Oct 16.


CD44 isoforms are heterogeneously expressed in breast cancer and correlate with tumor subtypes and cancer stem cell markers.

Olsson E, Honeth G, Bendahl PO, Saal LH, Gruvberger-Saal S, Ringnér M, Vallon-Christersson J, Jönsson G, Holm K, Lövgren K, Fernö M, Grabau D, Borg A, Hegardt C.

BMC Cancer. 2011 Sep 29;11:418. doi: 10.1186/1471-2407-11-418.


Genotyping techniques to address diversity in tumors.

Lindgren D, Höglund M, Vallon-Christersson J.

Adv Cancer Res. 2011;112:151-82. doi: 10.1016/B978-0-12-387688-1.00006-5. Review.


Identification of new microRNAs in paired normal and tumor breast tissue suggests a dual role for the ERBB2/Her2 gene.

Persson H, Kvist A, Rego N, Staaf J, Vallon-Christersson J, Luts L, Loman N, Jonsson G, Naya H, Hoglund M, Borg A, Rovira C.

Cancer Res. 2011 Jan 1;71(1):78-86. doi: 10.1158/0008-5472.CAN-10-1869.


Multiple metastases from cutaneous malignant melanoma patients may display heterogeneous genomic and epigenomic patterns.

Harbst K, Staaf J, Måsbäck A, Olsson H, Ingvar C, Vallon-Christersson J, Ringnér M, Borg A, Jönsson G.

Melanoma Res. 2010 Oct;20(5):381-91.


Genomic subtypes of breast cancer identified by array-comparative genomic hybridization display distinct molecular and clinical characteristics.

Jönsson G, Staaf J, Vallon-Christersson J, Ringnér M, Holm K, Hegardt C, Gunnarsson H, Fagerholm R, Strand C, Agnarsson BA, Kilpivaara O, Luts L, Heikkilä P, Aittomäki K, Blomqvist C, Loman N, Malmström P, Olsson H, Johannsson OT, Arason A, Nevanlinna H, Barkardottir RB, Borg A.

Breast Cancer Res. 2010;12(3):R42. doi: 10.1186/bcr2596. Epub 2010 Jun 24.


Molecular subtypes of breast cancer are associated with characteristic DNA methylation patterns.

Holm K, Hegardt C, Staaf J, Vallon-Christersson J, Jönsson G, Olsson H, Borg A, Ringnér M.

Breast Cancer Res. 2010;12(3):R36. doi: 10.1186/bcr2590. Epub 2010 Jun 18.


Tasquinimod (ABR-215050), a quinoline-3-carboxamide anti-angiogenic agent, modulates the expression of thrombospondin-1 in human prostate tumors.

Olsson A, Björk A, Vallon-Christersson J, Isaacs JT, Leanderson T.

Mol Cancer. 2010 May 17;9:107. doi: 10.1186/1476-4598-9-107.


High-resolution genomic and expression analyses of copy number alterations in HER2-amplified breast cancer.

Staaf J, Jönsson G, Ringnér M, Vallon-Christersson J, Grabau D, Arason A, Gunnarsson H, Agnarsson BA, Malmström PO, Johannsson OT, Loman N, Barkardottir RB, Borg A.

Breast Cancer Res. 2010;12(3):R25. doi: 10.1186/bcr2568. Epub 2010 May 6.


Identification of subtypes in human epidermal growth factor receptor 2--positive breast cancer reveals a gene signature prognostic of outcome.

Staaf J, Ringnér M, Vallon-Christersson J, Jönsson G, Bendahl PO, Holm K, Arason A, Gunnarsson H, Hegardt C, Agnarsson BA, Luts L, Grabau D, Fernö M, Malmström PO, Johannsson OT, Loman N, Barkardottir RB, Borg A.

J Clin Oncol. 2010 Apr 10;28(11):1813-20. doi: 10.1200/JCO.2009.22.8775. Epub 2010 Mar 15.


BASE--2nd generation software for microarray data management and analysis.

Vallon-Christersson J, Nordborg N, Svensson M, Häkkinen J.

BMC Bioinformatics. 2009 Oct 12;10:330. doi: 10.1186/1471-2105-10-330.


The non-coding RNA of the multidrug resistance-linked vault particle encodes multiple regulatory small RNAs.

Persson H, Kvist A, Vallon-Christersson J, Medstrand P, Borg A, Rovira C.

Nat Cell Biol. 2009 Oct;11(10):1268-71. doi: 10.1038/ncb1972. Epub 2009 Sep 13.


Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios.

Staaf J, Vallon-Christersson J, Lindgren D, Juliusson G, Rosenquist R, Höglund M, Borg A, Ringnér M.

BMC Bioinformatics. 2008 Oct 2;9:409. doi: 10.1186/1471-2105-9-409.


Segmentation-based detection of allelic imbalance and loss-of-heterozygosity in cancer cells using whole genome SNP arrays.

Staaf J, Lindgren D, Vallon-Christersson J, Isaksson A, Göransson H, Juliusson G, Rosenquist R, Höglund M, Borg A, Ringnér M.

Genome Biol. 2008;9(9):R136. doi: 10.1186/gb-2008-9-9-r136. Epub 2008 Sep 16.


Recurrent gross mutations of the PTEN tumor suppressor gene in breast cancers with deficient DSB repair.

Saal LH, Gruvberger-Saal SK, Persson C, Lövgren K, Jumppanen M, Staaf J, Jönsson G, Pires MM, Maurer M, Holm K, Koujak S, Subramaniyam S, Vallon-Christersson J, Olsson H, Su T, Memeo L, Ludwig T, Ethier SP, Krogh M, Szabolcs M, Murty VV, Isola J, Hibshoosh H, Parsons R, Borg A.

Nat Genet. 2008 Jan;40(1):102-7. Epub 2007 Dec 9.


Normalization of array-CGH data: influence of copy number imbalances.

Staaf J, Jönsson G, Ringnér M, Vallon-Christersson J.

BMC Genomics. 2007 Oct 22;8:382.


Non-coding antisense transcription detected by conventional and single-stranded cDNA microarray.

Vallon-Christersson J, Staaf J, Kvist A, Medstrand P, Borg A, Rovira C.

BMC Genomics. 2007 Aug 29;8:295.


The Wilms' tumor gene 1 (WT1) induces expression of the N-myc downstream regulated gene 2 (NDRG2).

Svensson E, Vidovic K, Olofsson T, Vallon-Christersson J, Borg A, Gullberg U.

DNA Cell Biol. 2007 Aug;26(8):589-97.


High-resolution genomic profiles of breast cancer cell lines assessed by tiling BAC array comparative genomic hybridization.

Jönsson G, Staaf J, Olsson E, Heidenblad M, Vallon-Christersson J, Osoegawa K, de Jong P, Oredsson S, Ringnér M, Höglund M, Borg A.

Genes Chromosomes Cancer. 2007 Jun;46(6):543-58.


Recruitment of HIF-1alpha and HIF-2alpha to common target genes is differentially regulated in neuroblastoma: HIF-2alpha promotes an aggressive phenotype.

Holmquist-Mengelbier L, Fredlund E, Löfstedt T, Noguera R, Navarro S, Nilsson H, Pietras A, Vallon-Christersson J, Borg A, Gradin K, Poellinger L, Påhlman S.

Cancer Cell. 2006 Nov;10(5):413-23.


An introduction to BioArray Software Environment.

Troein C, Vallon-Christersson J, Saal LH.

Methods Enzymol. 2006;411:99-119. Review.


Gene expression profiles relate to SS18/SSX fusion type in synovial sarcoma.

Fernebro J, Francis P, Edén P, Borg A, Panagopoulos I, Mertens F, Vallon-Christersson J, Akerman M, Rydholm A, Bauer HC, Mandahl N, Nilbert M.

Int J Cancer. 2006 Mar 1;118(5):1165-72.


Distinct genomic profiles in hereditary breast tumors identified by array-based comparative genomic hybridization.

Jönsson G, Naylor TL, Vallon-Christersson J, Staaf J, Huang J, Ward MR, Greshock JD, Luts L, Olsson H, Rahman N, Stratton M, Ringnér M, Borg A, Weber BL.

Cancer Res. 2005 Sep 1;65(17):7612-21.


Calibration and assessment of channel-specific biases in microarray data with extended dynamical range.

Bengtsson H, Jönsson G, Vallon-Christersson J.

BMC Bioinformatics. 2004 Nov 12;5:177.


Nonsense-mediated mRNA decay in barley mutants allows the cloning of mutated genes by a microarray approach.

Gadjieva R, Axelsson E, Olsson U, Vallon-Christersson J, Hansson M.

Plant Physiol Biochem. 2004 Jul-Aug;42(7-8):681-5.


Human neuroblastoma cells exposed to hypoxia: induction of genes associated with growth, survival, and aggressive behavior.

Jögi A, Vallon-Christersson J, Holmquist L, Axelson H, Borg A, Påhlman S.

Exp Cell Res. 2004 May 1;295(2):469-87.


Staf50 is a novel p53 target gene conferring reduced clonogenic growth of leukemic U-937 cells.

Obad S, Brunnström H, Vallon-Christersson J, Borg A, Drott K, Gullberg U.

Oncogene. 2004 May 20;23(23):4050-9.


Characterization of a novel breast carcinoma xenograft and cell line derived from a BRCA1 germ-line mutation carrier.

Johannsson OT, Staff S, Vallon-Christersson J, Kytöla S, Gudjonsson T, Rennstam K, Hedenfalk IA, Adeyinka A, Kjellén E, Wennerberg J, Baldetorp B, Petersen OW, Olsson H, Oredsson S, Isola J, Borg A.

Lab Invest. 2003 Mar;83(3):387-96.


A naturally occurring allele of BRCA1 coding for a temperature-sensitive mutant protein.

Worley T, Vallon-Christersson J, Billack B, Borg A, Monteiro AN.

Cancer Biol Ther. 2002 Sep-Oct;1(5):497-501.


BioArray Software Environment (BASE): a platform for comprehensive management and analysis of microarray data.

Saal LH, Troein C, Vallon-Christersson J, Gruvberger S, Borg A, Peterson C.

Genome Biol. 2002 Jul 15;3(8):SOFTWARE0003. Epub 2002 Jul 15.

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