Clinical Genomics Lund

Transcriptomic profiles of myxofibrosarcoma and undifferentiated pleomorphic sarcoma correlate with clinical and genomic features.

Mitra S, Farswan A, Piccinelli P, ..., Pillay N, Mertens F

J. Pathol. 264 (3) 293-304 [2024-11-00; online 2024-09-11]

In vivo dendritic cell reprogramming for cancer immunotherapy.

Ascic E, Åkerström F, Sreekumar Nair M, ..., Rosa FF, Pereira CF

Science 386 (6719) eadn9083 [2024-10-18; online 2024-10-18]

Early evolutionary branching across spatial domains predisposes to clonal replacement under chemotherapy in neuroblastoma.

Karlsson J, Yasui H, Mañas A, ..., Bexell D, Gisselsson D

Nat Commun 15 (1) 8992 [2024-10-18; online 2024-10-18]

Molecular Subtypes Are Associated With Clinical Benefit in Cisplatin-Treated Metastatic Urothelial Cancer Patients.

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

JCO Precision Oncology 8 (-) e2400209 [2024-10-00; online 2024-10-02]

Mini-heterochromatin domains constrain the cis-regulatory impact of SVA transposons in human brain development and disease.

Horváth V, Garza R, Jönsson ME, ..., Douse CH, Jakobsson J

Nat. Struct. Mol. Biol. 31 (10) 1543-1556 [2024-10-00; online 2024-06-04]

Clinical Genomics Lund [Service] NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Single-cell genomics details the maturation block in BCP-ALL and identifies therapeutic vulnerabilities in DUX4-r cases.

Thorsson H, Henningsson R, Puente-Moncada N, ..., Lilljebjörn H, Fioretos T

Blood 144 (13) 1399-1411 [2024-09-26; online 2024-07-05]

Hematopoietic cells emerging from hemogenic endothelium exhibit lineage-specific oxidative stress responses.

Biezeman H, Nubiè M, Oburoglu L

J. Biol. Chem. 300 (11) 107815 [2024-09-24; online 2024-09-24]

A Versatile and Upgraded Version of the LundTax Classification Algorithm Applied to Independent Cohorts.

Cotillas EA, Bernardo C, Veerla S, ..., Sjödahl G, Eriksson P

J Mol Diagn - (-) - [2024-09-24; online 2024-09-24]

Activating mutations remodel the chromatin accessibility landscape to drive distinct regulatory networks in KMT2A-rearranged acute leukemia.

Zhang Q, Falqués-Costa T, Pilheden M, ..., Hyrenius-Wittsten A, Hagström-Andersson AK

Hemasphere 8 (9) e70006 [2024-09-00; online 2024-09-26]

DNA methylation governs the sensitivity of repeats to restriction by the HUSH-MORC2 corepressor.

Pandiloski N, Horváth V, Karlsson O, ..., Jakobsson J, Douse CH

Nat Commun 15 (1) 7534 [2024-08-30; online 2024-08-30]

Bioinformatics Support for Computational Resources [Service] Clinical Genomics Lund [Service] NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Escherichia coli in urban marine sediments: interpreting virulence, biofilm formation, halotolerance, and antibiotic resistance to infer contamination or naturalization.

Erb IK, Suarez C, Frank EM, ..., Lindberg E, Paul CJ

FEMS Microbes 5 (-) xtae024 [2024-08-14; online 2024-08-14]

Bioinformatics Support for Computational Resources [Service] Clinical Genomics Lund [Service]

Micro-costing of genetic diagnostics in acute leukemia in Sweden: from standard-of-care to whole-genome sequencing.

Thangavelu T, Wirta V, Orsmark-Pietras C, ..., Rosenquist R, Levin LÅ

J Med Econ 27 (1) 1053-1060 [2024-08-08; online 2024-08-08]

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

A cancer immunotherapy modality based on dendritic cell reprogrammingin vivo

Ascic E, Åkerström F, Sreekumar Nair M, ..., Rosa FF, Pereira CF

- - (-) - [2024-07-11; online 2024-07-11]

Precision Diagnostics in Myeloid Malignancies: Development and Validation of a National Capture-Based Gene Panel.

Orsmark-Pietras C, Lyander A, Ladenvall C, ..., Fioretos T, SciLifeLab Clinical Genomics Platform and Genomic Medicine Sweden

Genes Chromosomes Cancer 63 (7) e23257 [2024-07-00; online 2024-07-20]

Clinical Genomics Lund [Service] Clinical Genomics Stockholm [Service] Clinical Genomics Uppsala [Technology development]

The annotation of GBA1 has been concealed by its protein-coding pseudogene GBAP1.

Gustavsson EK, Sethi S, Gao Y, ..., Hardy J, Ryten M

Sci Adv 10 (26) eadk1296 [2024-06-28; online 2024-06-26]

MOXD1 is a lineage-specific gene and a tumor suppressor in neuroblastoma

Fredlund E, Andersson S, Hilgert E, ..., van Nes J, Mohlin S

Sci Adv 10 (25) - [2024-06-21; online 2024-06-21]

Sequential drug treatment targeting cell cycle and cell fate regulatory programs blocks non-genetic cancer evolution in acute lymphoblastic leukemia.

Malyukova A, Lahnalampi M, Falqués-Costa T, ..., Heinäniemi M, Sangfelt O

Genome Biol. 25 (1) 143 [2024-05-31; online 2024-05-31]

Distinct Infiltration of T Cell Populations in Bladder Cancer Molecular Subtypes.

Sincic V, Arlenhold KF, Richtmann S, ..., Liedberg F, Lundberg K

Cells 13 (11) - [2024-05-28; online 2024-05-28]

MDM2 amplification in rod-shaped chromosomes provides clues to early stages of circularized gene amplification in liposarcoma.

Sydow S, Piccinelli P, Mitra S, ..., Spierings D, Mertens F

Commun Biol 7 (1) 606 [2024-05-20; online 2024-05-20]

Clinical Genomics Lund [Service] NGI Long read [Collaborative] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

Genomic alterations in ovarian endometriosis and subsequently diagnosed ovarian carcinoma.

Linder A, Westbom-Fremer S, Mateoiu C, ..., Hedenfalk I, Sundfeldt K

Hum. Reprod. 39 (5) 1141-1154 [2024-05-02; online 2024-03-09]

Clinical Genomics Gothenburg [Service] Clinical Genomics Lund [Service]

Current and emerging sequencing-based tools for precision cancer medicine.

Edsjö A, Gisselsson D, Staaf J, ..., Cavelier L, Rosenquist R

Mol Aspects Med 96 (-) 101250 [2024-04-00; online 2024-02-07]

Analysis of genetic variant associated with heart failure mortality implicates thymic stromal lymphopoietin as mediator of strain‐induced myocardial fibroblast‐mast cell crosstalk and fibrosis

Pimpalwar N, Celik S, Karbalaei Sadegh M, ..., Gidlöf O, Smith JG

The FASEB Journal 38 (4) - [2024-02-29; online 2024-02-26]

Metastasis and recurrence patterns in the molecular subtypes of urothelial bladder cancer.

Sjödahl G, Eriksson P, Holmsten K, ..., Ullén A, Liedberg F

Int. J. Cancer 154 (1) 180-190 [2024-01-01; online 2023-09-06]

Year 2023

A Gradual Transition Toward Anaplasia in Wilms Tumor Through Tolerance to Genetic Damage.

Uno K, Rastegar B, Jansson C, ..., Mengelbier LH, Gisselsson D

Mod. Pathol. 37 (1) 100382 [2023-11-10; online 2023-11-10]

Single-cell transcriptomics of human traumatic brain injury reveals activation of endogenous retroviruses in oligodendroglia.

Garza R, Sharma Y, Atacho DAM, ..., Jakobsson J, Marklund N

Cell Rep - (-) 113395 [2023-11-08; online 2023-11-08]

LINE-1 retrotransposons drive human neuronal transcriptome complexity and functional diversification.

Garza R, Atacho DAM, Adami A, ..., Douse CH, Jakobsson J

Sci Adv 9 (44) eadh9543 [2023-11-03; online 2023-11-01]

Clinical Genomics Lund [Service] NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

UROSCAN and UROSCANSEQ: a large-scale multicenter effort towards translation of molecular bladder cancer subtypes into clinical practice – from biobank to RNA-sequencing in real time

Liedberg F, Abrahamsson J, Bernardo C, ..., Sjödahl G, Eriksson P

Scandinavian Journal of Urology 57 (1-6) 2-9 [2023-11-02; online 2022-12-20]

Clinical and genetic analyses of a Swedish patient series diagnosed with ataxia.

Gorcenco S, Kafantari E, Wallenius J, ..., Karrman K, Puschmann A

J. Neurol. - (-) - [2023-10-03; online 2023-10-03]

Targeting Toll-like receptor-driven systemic inflammation by engineering an innate structural fold into drugs.

Petruk G, Puthia M, Samsudin F, ..., Lindstedt S, Schmidtchen A

Nat Commun 14 (1) 6097 [2023-09-29; online 2023-09-29]

Clinical Genomics Lund [Service] Structural Proteomics [Collaborative]

Single-cell multiomics of human fetal hematopoiesis define a developmental-specific population and a fetal signature.

Sommarin MNE, Olofzon R, Palo S, ..., Karlsson G, Böiers C

Blood Adv 7 (18) 5325-5340 [2023-09-26; online 2023-06-28]

Combined GLUT1 and OXPHOS inhibition eliminates acute myeloid leukemia cells by restraining their metabolic plasticity.

Rodriguez-Zabala M, Ramakrishnan R, Reinbach K, ..., Woods NB, Järås M

Blood Adv 7 (18) 5382-5395 [2023-09-26; online 2023-07-28]

Clinical Genomics Lund [Service] Swedish Metabolomics Centre (SMC) [Service]

In vivo gene expression profile of Haemophilus influenzae during human pneumonia.

Polland L, Rydén H, Su Y, Paulsson M

Microbiol Spectr 11 (5) e0163923 [2023-09-14; online 2023-09-14]

Bioinformatics Support and Infrastructure [Service] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service] Clinical Genomics Lund [Service]

Trunk neural crest gene MOXD1 affects embryonic development

Fredlund E, Andersson S, Ferreira M, Mohlin S

- - (-) - [2023-08-31; online 2023-08-31]

GATA2 mitotic bookmarking is required for definitive haematopoiesis.

Silvério-Alves R, Kurochkin I, Rydström A, ..., Martin-Gonzalez J, Pereira CF

Nat Commun 14 (1) 4645 [2023-08-14; online 2023-08-14]

Restoring tumor immunogenicity with dendritic cell reprogramming.

Zimmermannova O, Ferreira AG, Ascic E, ..., Svane IM, Pereira CF

Sci Immunol 8 (85) eadd4817 [2023-07-14; online 2023-07-07]

Resolving the Pathogenesis of Anaplastic Wilms Tumors through Spatial Mapping of Cancer Cell Evolution.

Rastegar B, Andersson N, Petersson A, ..., Holmquist Mengelbier L, Gisselsson D

Clin. Cancer Res. 29 (14) 2668-2677 [2023-07-14; online 2023-05-04]

Urodrill - a novel MRI-guided endoscopic biopsy technique to sample and molecularly classify muscle-invasive bladder cancer without fractionating the specimen during transurethral resection.

Eriksson P, Berg J, Bernardo C, ..., Zackrisson S, Liedberg F

Eur Urol Open Sci 53 (-) 78-82 [2023-07-00; online 2023-06-02]

Temporal multimodal single-cell profiling of native hematopoiesis illuminates altered differentiation trajectories with age.

Konturek-Ciesla A, Dhapola P, Zhang Q, ..., Karlsson G, Bryder D

Cell Rep 42 (4) 112304 [2023-04-25; online 2023-03-23]

Enhanced protein synthesis is a defining requirement for neonatal B cell development

Åkerstrand H, Boldrin E, Montano G, ..., Bellodi C, Yuan J

Front Immunol 14 (-) - [2023-04-17; online 2023-04-17]

The complement receptor C3AR constitutes a novel therapeutic target in NPM1-mutated AML.

von Palffy S, Thorsson H, Peña-Martínez P, ..., Lilljebjörn H, Fioretos T

Blood Adv 7 (7) 1204-1218 [2023-04-11; online 2022-11-17]

Clonal origin and development of high hyperdiploidy in childhood acute lymphoblastic leukaemia.

Woodward EL, Yang M, Moura-Castro LH, ..., Foijer F, Paulsson K

Nat Commun 14 (1) 1658 [2023-03-25; online 2023-03-25]

Identification of phenotypically, functionally, and anatomically distinct stromal niche populations in human bone marrow based on single-cell RNA sequencing.

Li H, Bräunig S, Dhapolar P, ..., Lang S, Scheding S

Elife 12 (-) - [2023-03-06; online 2023-03-06]

Venetoclax-Resistant T-ALL Cells Display Distinct Cancer Stem Cell Signatures and Enrichment of Cytokine Signaling.

Shah K, Al Ashiri L, Nasimian A, Ahmed M, Kazi JU

Int J Mol Sci 24 (5) - [2023-03-05; online 2023-03-05]

Inactivation of RB1, CDKN2A, and TP53 have distinct effects on genomic stability at side-by-side comparison in karyotypically normal cells.

Andersson N, Saba KH, Magnusson L, ..., Nord KH, Gisselsson D

Genes Chromosomes Cancer 62 (2) 93-100 [2023-02-00; online 2022-09-30]

Single-cell analysis of myeloid cells in HPV+ tonsillar cancer.

Jimenez DG, Altunbulakli C, Swoboda S, ..., Greiff L, Lindstedt M

Front Immunol 13 (-) 1087843 [2023-01-19; online 2023-01-19]

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

MOXD1 is a gate-keeper of organ homeostasis and functions as a tumor-suppressor in neuroblastoma

Fredlund E, Andersson S, Hilgert E, ..., van Nes J, Mohlin S

- - (-) - [2023-01-19; online 2023-01-19]

The injury-induced transcription factor SOX9 alters the expression of LBR, HMGA2, and HIPK3 in the human kidney.

Kha M, Krawczyk K, Choong OK, ..., Swärd K, Johansson ME

Am. J. Physiol. Renal Physiol. 324 (1) F75-F90 [2023-01-01; online 2022-12-01]

Clinical Genomics Gothenburg [Service] Clinical Genomics Lund [Service]

Cerebral small vessel disease: Recent advances and future directions.

Markus HS, de Leeuw FE

Int J Stroke 18 (1) 4-14 [2023-01-00; online 2022-12-29]

Year 2022

Developmental cues license megakaryocyte priming in murine hematopoietic stem cells.

Kristiansen TA, Zhang Q, Vergani S, ..., Ungerbäck J, Yuan J

Blood Adv 6 (24) 6228-6241 [2022-12-27; online 2022-05-19]

Clinically relevant treatment of PDX models reveals patterns of neuroblastoma chemoresistance.

Mañas A, Aaltonen K, Andersson N, ..., Gisselsson D, Bexell D

Sci Adv 8 (43) eabq4617 [2022-10-28; online 2022-10-28]

Engineering human mini-bones for the standardized modeling of healthy hematopoiesis, leukemia, and solid tumor metastasis.

Grigoryan A, Zacharaki D, Balhuizen A, ..., Bexell D, Bourgine PE

Sci Transl Med 14 (666) eabm6391 [2022-10-12; online 2022-10-12]

DNA promoter hypermethylation of melanocyte lineage genes determines melanoma phenotype.

Sanna A, Phung B, Mitra S, ..., Pietras K, Jönsson G

JCI Insight 7 (19) - [2022-10-10; online 2022-10-10]

Duplex Sequencing Uncovers Recurrent Low-frequency Cancer-associated Mutations in Infant and Childhood KMT2A-rearranged Acute Leukemia.

Pilheden M, Ahlgren L, Hyrenius-Wittsten A, ..., Gawad C, Hagström-Andersson AK

Hemasphere 6 (10) e785 [2022-10-00; online 2022-09-30]

Bacteraemia and infective endocarditis with Streptococcus bovis-Streptococcus equinus-complex: a retrospective cohort study.

Öberg J, Nilson B, Gilje P, Rasmussen M, Inghammar M

Infect Dis (Lond) 54 (10) 760-765 [2022-10-00; online 2022-06-22]

Distinct subcellular autophagy impairments in induced neurons from patients with Huntington's disease.

Pircs K, Drouin-Ouellet J, Horváth V, ..., Barker RA, Jakobsson J

Brain 145 (9) 3035-3057 [2022-09-14; online 2021-12-23]

Glioblastoma CD105+ cells define a SOX2- cancer stem cell-like subpopulation in the pre-invasive niche.

Li J, Ek F, Olsson R, Belting M, Bengzon J

Acta Neuropathol Commun 10 (1) 126 [2022-08-29; online 2022-08-29]

Chemical Biology Consortium Sweden (CBCS) [Collaborative] Clinical Genomics Lund [Service]

Scarf enables a highly memory-efficient analysis of large-scale single-cell genomics data.

Dhapola P, Rodhe J, Olofzon R, ..., Soneji S, Karlsson G

Nat Commun 13 (1) 4616 [2022-08-08; online 2022-08-08]

Concurrent stem- and lineage-affiliated chromatin programs precede hematopoietic lineage restriction.

Safi F, Dhapola P, Warsi S, ..., Thakur RK, Karlsson G

Cell Rep 39 (6) 110798 [2022-05-10; online 2022-05-12]

Single-cell transcriptional profiling informs efficient reprogramming of human somatic cells to cross-presenting dendritic cells.

Rosa FF, Pires CF, Kurochkin I, ..., Scheding S, Pereira CF

Sci Immunol 7 (69) eabg5539 [2022-03-04; online 2022-03-04]

Pyruvate metabolism guides definitive lineage specification during hematopoietic emergence.

Oburoglu L, Mansell E, Canals I, ..., Soneji S, Woods NB

EMBO Rep. 23 (2) e54384 [2022-02-03; online 2021-12-16]

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 29 (1) 52-69.e8 [2022-01-06; online 2021-10-07]

Bioinformatics Support for Computational Resources [Service] Clinical Genomics Lund [Service]

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]

<i>Streptococcus bovis</i>-bacteremia: subspecies distribution and association with colorectal cancer: a retrospective cohort study

Öberg J, Rasmussen M, Buchwald P, Nilson B, Inghammar M

Epidemiol. Infect. 150 (-) - [2022-00-00; online 2021-11-26]

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]

Targeted genomic investigations in a population-based cohort of mantle cell lymphoma reveal novel clinically relevant targets.

Rodrigues JM, Porwit A, Hassan M, Ek S, Jerkeman M

Leuk. Lymphoma 62 (11) 2637-2647 [2021-11-00; online 2021-06-03]

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]

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 Support for Computational Resources [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 Support for Computational Resources [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 Support for Computational Resources [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 Support for Computational Resources [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 Support for Computational Resources [Service] Clinical Genomics Lund [Service]

MAP3K6 Mutations in a Neurovascular Disease Causing Stroke, Cognitive Impairment, and Tremor.

Ilinca A, Englund E, Samuelsson S, ..., Lindgren AG, Puschmann A

Neurol Genet 7 (1) e548 [2021-02-00; online 2021-01-21]

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 Support for Computational Resources [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 Support for Computational Resources [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 Support for Computational Resources [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 Support for Computational Resources [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 Support for Computational Resources [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 Support for Computational Resources [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 Support for Computational Resources [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]

Evaluating the effectiveness of clinical medical librarian programs: a systematic review of the literature. J Med Libr Assoc 92(1) January 2004.

Year 2012

PubMed

Wagner KC, Byrd GD

J Med Libr Assoc 100 (4 Suppl) J [2012-10-00; online 2013-03-21]