Clinical Genomics Lund

Amplification of ERBB2 (HER2) in embryonal rhabdomyosarcoma: A potential treatment target in rare cases?

Mitra S, Sydow S, Magnusson L, ..., Gisselsson D, Mertens F

Genes Chromosomes Cancer 61 (1) 5-9 [2022-01-00; online 2021-09-01]

Year 2021

CD105+CD90+CD13+ identifies a clonogenic subset of adventitial lung fibroblasts.

Kadefors M, Rolandsson Enes S, Åhrman E, ..., Scheding S, Westergren-Thorsson G

Sci Rep 11 (1) 24417 [2021-12-24; online 2021-12-24]

Early Pregnancy Exposure to Ambient Air Pollution among Late-Onset Preeclamptic Cases Is Associated with Placental DNA Hypomethylation of Specific Genes and Slower Placental Maturation.

Engström K, Mandakh Y, Garmire L, ..., Erlandsson L, Hansson SR

Toxics 9 (12) 338 [2021-12-06; online 2021-12-06]

Different Responses to Neoadjuvant Chemotherapy in Urothelial Carcinoma Molecular Subtypes.

Sjödahl G, Abrahamsson J, Holmsten K, ..., Ullén A, Liedberg F

Eur. Urol. - (-) - [2021-11-12; online 2021-11-12]

A comparison of rule-based and centroid single-sample multiclass predictors for transcriptomic classification.

Eriksson P, Marzouka NA, Sjödahl G, ..., Liedberg F, Höglund M

Bioinformatics - (-) - [2021-11-12; online 2021-11-12]

cGMP-PKG dependent transcriptome in normal and degenerating retinas: Novel insights into the retinitis pigmentosa pathology.

Zhou J, Rasmussen M, Ekström P

Exp. Eye Res. 212 (-) 108752 [2021-11-00; online 2021-08-31]

Transcriptomics paving the way for improved diagnostics and precision medicine of acute leukemia.

Lilljebjörn H, Orsmark-Pietras C, Mitelman F, Hagström-Andersson A, Fioretos T

Semin. Cancer Biol. - (-) - [2021-10-01; online 2021-10-01]

A cis-acting structural variation at the ZNF558 locus controls a gene regulatory network in human brain development.

Johansson PA, Brattås PL, Douse CH, ..., Eichler EE, Jakobsson J

Cell Stem Cell - (-) - [2021-10-01; online 2021-10-01]

Bioinformatics Compute and Storage [Service] Clinical Genomics Lund [Service]

Genomic and transcriptomic characterization of desmoplastic small round cell tumors.

Sydow S, Versleijen-Jonkers YMH, Hansson M, ..., Flucke UE, Mertens F

Genes Chromosomes Cancer 60 (9) 595-603 [2021-09-00; online 2021-05-17]

Bioinformatics Compute and Storage [Service] Clinical Genomics Lund [Service]

Anti-tumor effects of rigosertib in high-risk neuroblastoma.

Radke K, Hansson K, Sjölund J, ..., Gisselsson D, Bexell D

Transl Oncol 14 (8) 101149 [2021-08-00; online 2021-06-09]

Single-cell sequencing in translational cancer research and challenges to meet clinical diagnostic needs.

Pfisterer U, Bräunig J, Brattås P, ..., Karlsson G, Fioretos T

Genes Chromosomes Cancer 60 (7) 504-524 [2021-07-00; online 2021-03-15]

Human Primary Airway Basal Cells Display a Continuum of Molecular Phases from Health to Disease in Chronic Obstructive Pulmonary Disease.

Wijk SC, Prabhala P, Michaliková B, ..., Westergren-Thorsson G, Magnusson M

Am J Respir Cell Mol Biol 65 (1) 103-113 [2021-07-00; online 2021-04-01]

Genomic and Phenotypic Evolution of Achromobacter xylosoxidans during Chronic Airway Infections of Patients with Cystic Fibrosis.

Khademi SMH, Gabrielaite M, Paulsson M, ..., Marvig RL, Påhlman LI

mSystems - (-) e0052321 [2021-06-29; online 2021-06-29]

Bioinformatics Compute and Storage [Service] Clinical Genomics Lund [Service]

Trailblazing precision medicine in Europe: A joint view by Genomic Medicine Sweden and the Centers for Personalized Medicine, ZPM, in Germany.

Stenzinger A, Edsjö A, Ploeger C, ..., Rosenquist R, GMS working groups and ZPM working groups

Semin. Cancer Biol. - (-) - [2021-05-24; online 2021-05-24]

Clinical Genomics Lund [Service] Clinical Genomics Stockholm [Collaborative] Clinical Genomics Uppsala [Collaborative]

PubMed

[Precision diagnostics and therapy in hematological malignancies].

Hellström Lindberg E, Cavelier L, Cammenga J, ..., Fioretos T, Rosenquist R

Lakartidningen 118 (-) - [2021-05-10; online 2021-05-10]

Activation of endogenous retroviruses during brain development causes an inflammatory response.

Jönsson ME, Garza R, Sharma Y, ..., Jern P, Jakobsson J

EMBO J. 40 (9) e106423 [2021-05-03; online 2021-03-01]

Bioinformatics Compute and Storage [Service] Clinical Genomics Lund [Service]

High-Throughput and Automated Acoustic Trapping of Extracellular Vesicles to Identify microRNAs With Diagnostic Potential for Prostate Cancer.

Ku A, Fredsøe J, Sørensen KD, ..., Lilja H, Ceder Y

Front Oncol 11 (-) 631021 [2021-03-25; online 2021-03-25]

Bioinformatics Compute and Storage [Service] Clinical Genomics Lund [Service]

Prevalence of germline pathogenic variants in 22 cancer susceptibility genes in Swedish pediatric cancer patients.

von Stedingk K, Stjernfelt KJ, Kvist A, ..., Olsson H, Øra I

Sci Rep 11 (1) 5307 [2021-03-05; online 2021-03-05]

Distinct mechanisms of resistance to fulvestrant treatment dictate level of ER independence and selective response to CDK inhibitors in metastatic breast cancer.

Kaminska K, Akrap N, Staaf J, ..., Bosch A, Honeth G

Breast Cancer Res. 23 (1) 26 [2021-02-18; online 2021-02-18]

multiclassPairs: An R package to train multiclass pairbased classifier.

Marzouka NA, Eriksson P

Bioinformatics - (-) - [2021-02-05; online 2021-02-05]

Isolation of high-yield and -quality RNA from human precision-cut lung slices for RNA-sequencing and computational integration with larger patient cohorts.

Stegmayr J, Alsafadi HN, Langwiński W, ..., Leigh ND, Wagner DE

Am J Physiol Lung Cell Mol Physiol 320 (2) L232-L240 [2021-02-01; online 2020-10-28]

Bioinformatics Compute and Storage [Service] Clinical Genomics Lund [Service]

Hypoxia inducible factor-2α importance for migration, proliferation, and self-renewal of trunk neural crest cells.

Niklasson CU, Fredlund E, Monni E, ..., Bronner ME, Mohlin S

Dev. Dyn. 250 (2) 191-236 [2021-02-00; online 2020-09-26]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Clinical Genomics Lund [Service]

BL1391: an established cell line from a human malignant peripheral nerve sheath tumor with unique genomic features.

Tolomeo D, Agostini A, Macchia G, ..., Mertens F, Storlazzi CT

Hum Cell 34 (1) 238-245 [2021-01-00; online 2020-08-27]

Bioinformatics Compute and Storage [Service] Clinical Genomics Lund [Service]

Year 2020

Associations between serum concentrations of perfluoroalkyl substances and DNA methylation in women exposed through drinking water: A pilot study in Ronneby, Sweden.

Xu Y, Jurkovic-Mlakar S, Lindh CH, ..., Jakobsson K, Engström K

Environ Int 145 (-) 106148 [2020-12-00; online 2020-09-30]

Recurring urothelial carcinomas show genomic rearrangements incompatible with a direct relationship.

Marzouka NA, Lindgren D, Eriksson P, ..., Axelson H, Höglund M

Sci Rep 10 (1) 19539 [2020-11-11; online 2020-11-11]

Inducible Deletion of YAP and TAZ in Adult Mouse Smooth Muscle Causes Rapid and Lethal Colonic Pseudo-Obstruction.

Daoud F, Holmberg J, Alajbegovic A, ..., Swärd K, Albinsson S

Cellular and Molecular Gastroenterology and Hepatology 11 (2) 623-637 [2020-09-28; online 2020-09-28]

Therapeutic targeting of KSP in preclinical models of high-risk neuroblastoma.

Hansson K, Radke K, Aaltonen K, ..., Gisselsson D, Bexell D

Sci Transl Med 12 (562) - [2020-09-23; online 2020-09-25]

A dynamic mutational landscape associated with an inter-regionally diverse immune response in malignant rhabdoid tumour.

Yasui H, Valind A, Karlsson J, ..., Backman T, Gisselsson D

J. Pathol. 252 (1) 22-28 [2020-09-00; online 2020-07-22]

Clinical Genomics Lund

13q12.2 deletions in acute lymphoblastic leukemia lead to upregulation of FLT3 through enhancer hijacking.

Yang M, Safavi S, Woodward EL, ..., Nord KH, Paulsson K

Blood 136 (8) 946-956 [2020-08-20; online 2020-05-10]

Multiplex profiling of serum proteins in solution using barcoded antibody fragments and next generation sequencing.

Brofelth M, Ekstrand AI, Gour S, ..., Axelsson U, Borrebaeck CAK

Commun Biol 3 (1) 339 [2020-07-03; online 2020-07-03]

Clinical Genomics Lund

PHF1 fusions cause distinct gene expression and chromatin accessibility profiles in ossifying fibromyxoid tumors and mesenchymal cells.

Hofvander J, Jo VY, Fletcher CDM, ..., Magnusson L, Mertens F

Mod. Pathol. 33 (7) 1331-1340 [2020-07-00; online 2020-01-13]

Molecular changes during progression from nonmuscle invasive to advanced urothelial carcinoma.

Sjödahl G, Eriksson P, Patschan O, ..., Liedberg F, Höglund M

Int. J. Cancer 146 (9) 2636-2647 [2020-05-01; online 2019-11-14]

Recurrent Fusions Between YAP1 and KMT2A in Morphologically Distinct Neoplasms Within the Spectrum of Low-grade Fibromyxoid Sarcoma and Sclerosing Epithelioid Fibrosarcoma.

Puls F, Agaimy A, Flucke U, ..., Arbajian E, Mertens F

Am. J. Surg. Pathol. 44 (5) 594-606 [2020-05-00; online 2020-01-09]

Bioinformatics Compute and Storage [Service] Clinical Genomics Lund [Service]

Early growth response 1 regulates hematopoietic support and proliferation in human primary bone marrow stromal cells.

Li H, Lim HC, Zacharaki D, ..., Hansson J, Scheding S

Haematologica 105 (5) 1206-1215 [2020-05-00; online 2019-08-01]

Deep sequencing of myxoinflammatory fibroblastic sarcoma.

Arbajian E, Hofvander J, Magnusson L, Mertens F

Genes Chromosomes Cancer 59 (5) 309-317 [2020-05-00; online 2020-01-31]

Clonal competition within complex evolutionary hierarchies shapes AML over time.

Sandén C, Lilljebjörn H, Orsmark Pietras C, ..., Ågerstam H, Fioretos T

Nat Commun 11 (1) 579 [2020-02-05; online 2020-02-05]

Clinical Genomics Lund

Genomic and transcriptomic features of dermatofibrosarcoma protuberans: Unusual chromosomal origin of the COL1A1-PDGFB fusion gene and synergistic effects of amplified regions in tumor development.

Köster J, Arbajian E, Viklund B, ..., Mandahl N, Mertens F

Cancer Genet 241 (-) 34-41 [2020-02-00; online 2019-12-10]

Bioinformatics Compute and Storage [Service] Clinical Genomics Lund

Year 2019

Undifferentiated pleomorphic sarcomas with PRDM10 fusions have a distinct gene expression profile.

Hofvander J, Puls F, Pillay N, ..., Nilsson J, Mertens F

J. Pathol. 249 (4) 425-434 [2019-12-00; online 2019-08-27]

Bioinformatics Compute and Storage [Service] Clinical Genomics Lund [Service]

Molecular pathology of the luminal class of urothelial tumors.

Bernardo C, Eriksson P, Marzouka NA, ..., Sjödahl G, Höglund M

J. Pathol. 249 (3) 308-318 [2019-11-00; online 2019-08-27]

Molecular subtypes applied to a population-based modern cystectomy series do not predict cancer-specific survival.

Kollberg P, Chebil G, Eriksson P, Sjödahl G, Liedberg F

Urol Oncol 37 (10) 791-799 [2019-10-00; online 2019-05-02]

FLT3N676K drives acute myeloid leukemia in a xenograft model of KMT2A-MLLT3 leukemogenesis.

Hyrenius-Wittsten A, Pilheden M, Falqués-Costa A, ..., Järås M, Hagström-Andersson AK

Leukemia 33 (9) 2310-2314 [2019-09-00; online 2019-04-05]

Gene fusion involving the insulin-like growth factor 1 receptor in an ALK-negative inflammatory myofibroblastic tumour.

Piarulli G, Puls F, Wängberg B, ..., Arbajian E, Mertens F

Histopathology 74 (7) 1098-1102 [2019-06-00; online 2019-04-24]

Bioinformatics Compute and Storage [Service] Clinical Genomics Lund [Service]

A urinary extracellular vesicle microRNA biomarker discovery pipeline; from automated extracellular vesicle enrichment by acoustic trapping to microRNA sequencing.

Ku A, Ravi N, Yang M, ..., Lilja H, Ceder Y

PLoS ONE 14 (5) e0217507 [2019-05-29; online 2019-05-29]

Proteogenomics and Hi-C reveal transcriptional dysregulation in high hyperdiploid childhood acute lymphoblastic leukemia.

Yang M, Vesterlund M, Siavelis I, ..., Lehtiö J, Paulsson K

Nat Commun 10 (1) 1519 [2019-04-03; online 2019-04-03]

Bioinformatics Compute and Storage [Service] Clinical Genomics Lund [Service] Global Proteomics and Proteogenomics [Technology development]

Year 2018

Transcriptional landscape of B cell precursor acute lymphoblastic leukemia based on an international study of 1,223 cases.

Li JF, Dai YT, Lilljebjörn H, ..., Chen SJ, Huang JY

Proc. Natl. Acad. Sci. U.S.A. 115 (50) E11711-E11720 [2018-12-11; online 2018-11-28]

Convergent evolution of 11p allelic loss in multifocal Wilms tumors arising in WT1 mutation carriers.

Valind A, Wessman S, Pal N, ..., Sandstedt B, Gisselsson D

Pediatr Blood Cancer 65 (11) e27301 [2018-11-00; online 2018-07-03]

Neuroblastoma with flat genomic profile: a question of representativity?

Valind A, Öra I, Mertens F, Gisselsson D

BMJ Case Reports 2018 (-) bcr-2018-225568 [2018-09-08; online 2018-09-08]

Gastrointestinal microbiota contributes to the development of murine transfusion-related acute lung injury.

Kapur R, Kim M, Rebetz J, ..., Speck ER, Semple JW

Blood Adv 2 (13) 1651-1663 [2018-07-10; online 2018-07-12]

Microenvironmental control of breast cancer subtype elicited through paracrine platelet-derived growth factor-CC signaling.

Roswall P, Bocci M, Bartoschek M, ..., Eriksson U, Pietras K

Nat. Med. 24 (4) 463-473 [2018-05-00; online 2018-03-12]

Clinical Value of RNA Sequencing-Based Classifiers for Prediction of the Five Conventional Breast Cancer Biomarkers: A Report From the Population-Based Multicenter Sweden Cancerome Analysis Network-Breast Initiative.

Brueffer C, Vallon-Christersson J, Grabau D, ..., Borg Å, Saal LH

JCO Precision Oncology 2 (2) 1-18 [2018-03-09; online 2018-03-09]

Isolated myelosarcoma is characterized by recurrent NFE2 mutations and concurrent preleukemic clones in the bone marrow.

Lazarevic V, Orsmark-Pietras C, Lilljebjörn H, ..., Juliusson G, Fioretos T

Blood 131 (5) 577-581 [2018-02-01; online 2017-11-30]

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, ..., Saal LH, Borg Å

Br J Surg 105 (2) e158-e168 [2018-01-00; online 2018-01-18]

Bioinformatics Compute and Storage [Service] Clinical Genomics Lund [Collaborative]

Year 2017

New oncogenic subtypes in pediatric B-cell precursor acute lymphoblastic leukemia.

Lilljebjörn H, Fioretos T

Blood 130 (12) 1395-1401 [2017-09-21; online 2017-08-04]

Gene Expression Profiling of Large Cell Lung Cancer Links Transcriptional Phenotypes to the New Histological WHO 2015 Classification

Karlsson A, Brunnström H, Micke P, ..., Planck M, Staaf J

Journal of Thoracic Oncology 12 (8) 1257-1267 [2017-08-00; online 2017-08-00]

Clinical Genomics Lund [Service] Clinical Genomics Uppsala [Collaborative]

HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures.

Davies H, Glodzik D, Morganella S, ..., Stratton MR, Nik-Zainal S

Nat. Med. 23 (4) 517-525 [2017-04-00; online 2017-03-13]

Identification of two distinct mesenchymal stromal cell populations in human malignant glioma.

Svensson A, Ramos-Moreno T, Eberstål S, Scheding S, Bengzon J

J. Neurooncol. 131 (2) 245-254 [2017-01-00; online 2016-10-18]

Year 2016

Identification of ETV6-RUNX1-like and DUX4-rearranged subtypes in paediatric B-cell precursor acute lymphoblastic leukaemia.

Lilljebjörn H, Henningsson R, Hyrenius-Wittsten A, ..., Fontes M, Fioretos T

Nat Commun 7 (-) 11790 [2016-06-06; online 2016-06-06]