Molekylär precisionsmedicin

Comparison of high-throughput single-cell RNA-seq methods for ex vivo drug screening

Gezelius, Henrik; Enblad, Anna Pia; Lundmark, Anders; Åberg, Martin et al.

Ingår i NAR Genomics and Bioinformatics, 2024

• DOI för Comparison of high-throughput single-cell RNA-seq methods for ex vivo drug screening
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A multiomic characterization of the leukemia cell line REH using short- and long-read sequencing

Lysenkova, Mariya; Arvidsson, Gustav; Bunikis, Ignas; Lundmark, Anders et al.

Ingår i Life Science Alliance, 2024

• DOI för A multiomic characterization of the leukemia cell line REH using short- and long-read sequencing

Refining risk prediction in pediatric acute lymphoblastic leukemia through DNA methylation profiling

Orgueira, Adrian Mosquera; Krali, Olga; Miguez, Carlos Perez; Raindo, Andres Peleteiro et al.

Ingår i Clinical Epigenetics, 2024

• DOI för Refining risk prediction in pediatric acute lymphoblastic leukemia through DNA methylation profiling
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Multi-modal single cell sequencing of B cells in primary Sjögren's Syndrome.

Arvidsson, Gustav; Czarnewski, Paulo; Johansson, Alina; Raine, Amanda et al.

Ingår i Arthritis & Rheumatology, 2023

• DOI för Multi-modal single cell sequencing of B cells in primary Sjögren's Syndrome.

Increased MYB alternative promoter usage is associated with relapse in acute lymphoblastic leukemia

Fehr, André; Arvidsson, Gustav; Nordlund, Jessica; Lönnerholm, Gudmar et al.

Ingår i Genes, Chromosomes and Cancer, s. 597-606, 2023

• DOI för Increased MYB alternative promoter usage is associated with relapse in acute lymphoblastic leukemia
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Long-read whole-genome analysis of human single cells

Hård, Joanna; Mold, Jeff E; Eisfeldt, Jesper; Tellgren-Roth, Christian et al.

Ingår i Nature Communications, 2023

• DOI för Long-read whole-genome analysis of human single cells
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Multimodal classification of molecular subtypes in pediatric acute lymphoblastic leukemia

Krali, Olga; Marincevic-Zuniga, Yanara; Arvidsson, Gustav; Enblad, Anna Pia et al.

Ingår i npj Precision Oncology, 2023

• DOI för Multimodal classification of molecular subtypes in pediatric acute lymphoblastic leukemia
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Distinct HLA associations with autoantibody-defined subgroups in idiopathic inflammatory myopathies

Leclair, Valerie; Galindo-Feria, Angeles S.; Rothwell, Simon; Krystufkova, Olga et al.

Ingår i EBioMedicine, 2023

• DOI för Distinct HLA associations with autoantibody-defined subgroups in idiopathic inflammatory myopathies
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Genomic, transcriptomic and epigenomic sequencing data of the B-cell leukemia cell line REH

Lysenkova Wiklander, Mariya; Övernäs, Elin; Lagensjö, Johanna; Raine, Amanda et al.

Ingår i BMC Research Notes, 2023

• DOI för Genomic, transcriptomic and epigenomic sequencing data of the B-cell leukemia cell line REH
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Quartet DNA reference materials and datasets for comprehensively evaluating germline variant calling performance

Ren, Luyao; Duan, Xiaoke; Dong, Lianhua; Zhang, Rui et al.

Ingår i Genome Biology, 2023

• DOI för Quartet DNA reference materials and datasets for comprehensively evaluating germline variant calling performance
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Feasibility to use whole-genome sequencing as a sole diagnostic method to detect genomic aberrations in pediatric B-cell acute lymphoblastic leukemia

Rezayee, Fatemah; Eisfeldt, Jesper; Skaftason, Aron; Ofverholm, Ingegerd et al.

Ingår i Frontiers in Oncology, 2023

• DOI för Feasibility to use whole-genome sequencing as a sole diagnostic method to detect genomic aberrations in pediatric B-cell acute lymphoblastic leukemia
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Single-cell transcriptomics delineates the immune cell landscape in equine lower airways and reveals upregulation of FKBP5 in horses with asthma.

Riihimäki, Miia; Fegraeus, K. Jaderkvist; Nordlund, Jessica; Waern, Ida et al.

Ingår i Scientific Reports, s. 16261, 2023

• DOI för Single-cell transcriptomics delineates the immune cell landscape in equine lower airways and reveals upregulation of FKBP5 in horses with asthma.
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Exome-wide association study to identify rare variants influencing COVID-19 outcomes: Results from the Host Genetics Initiative

Butler-Laporte, Guillaume; Povysil, Gundula; Kosmicki, Jack A; Cirulli, Elizabeth T et al.

Ingår i PLOS Genetics, 2022

• DOI för Exome-wide association study to identify rare variants influencing COVID-19 outcomes: Results from the Host Genetics Initiative
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Complement C4 Copy Number Variation is Linked to SSA/Ro and SSB/La Autoantibodies in Systemic Inflammatory Autoimmune Diseases

Lundtoft, Christian; Pucholt, Pascal; Martin, Myriam; Bianchi, Matteo et al.

Ingår i Arthritis & Rheumatology, s. 1440-1450, 2022

• DOI för Complement C4 Copy Number Variation is Linked to SSA/Ro and SSB/La Autoantibodies in Systemic Inflammatory Autoimmune Diseases
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Tackling the translational challenges of multi-omics research in the realm of European personalised medicine: A workshop report

Oldoni, Emanuela; Saunders, Gary; Bietrix, Florence; Garcia Bermejo, Maria Laura et al.

Ingår i Frontiers in Molecular Biosciences, 2022

• DOI för Tackling the translational challenges of multi-omics research in the realm of European personalised medicine: A workshop report
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scSPLAT, a scalable plate-based protocol for single cell WGBS library preparation

Raine, Amanda; Lundmark, Anders; Annett, Alva; Wiman, Ann-Christin et al.

Ingår i Scientific Reports, 2022

• DOI för scSPLAT, a scalable plate-based protocol for single cell WGBS library preparation
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Transcriptome sequencing of archived lymphoma specimens is feasible and clinically relevant using exome capture technology

Skaftason, Aron; Qu, Ying; Abdulla, Maysaa; Nordlund, Jessica et al.

Ingår i Genes, Chromosomes and Cancer, s. 27-36, 2022

• DOI för Transcriptome sequencing of archived lymphoma specimens is feasible and clinically relevant using exome capture technology
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Variants in BANK1 are associated with lupus nephritis of European ancestry.

Bolin, Karin; Imgenberg-Kreuz, Juliana; Leonard, Dag; Sandling, Johanna K. et al.

Ingår i Genes and Immunity, s. 194-202, 2021

• DOI för Variants in BANK1 are associated with lupus nephritis of European ancestry.
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Contributions of de novo variants to systemic lupus erythematosus

Carlsson Almlöf, Jonas; Nystedt, Sara; Mechtidou, Aikaterini; Leonard, Dag et al.

Ingår i European Journal of Human Genetics, s. 184-193, 2021

• DOI för Contributions of de novo variants to systemic lupus erythematosus
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RAG1 co-expression signature identifies ETV6-RUNX1-like B-cell precursor acute lymphoblastic leukemia in children

Chen, Dongfeng; Camponeschi, Alessandro; Nordlund, Jessica; Marincevic-Zuniga, Yanara et al.

Ingår i Cancer Medicine, s. 3997-4003, 2021

• DOI för RAG1 co-expression signature identifies ETV6-RUNX1-like B-cell precursor acute lymphoblastic leukemia in children
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Single nucleus transcriptomics data integration recapitulates the major cell types in human liver

Diamanti, Klev; Inda Díaz, Juan Salvador; Raine, Amanda; Pan, Gang et al.

Ingår i Hepatology Research, s. 233-238, 2021

• DOI för Single nucleus transcriptomics data integration recapitulates the major cell types in human liver
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Immune cells lacking Y chromosome show dysregulation of autosomal gene expression

Dumanski, Jan P.; Halvardson, Jonatan; Davies, Hanna; Rychlicka-Buniowska, Edyta et al.

Ingår i Cellular and Molecular Life Sciences (CMLS), s. 4019-4033, 2021

• DOI för Immune cells lacking Y chromosome show dysregulation of autosomal gene expression
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Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing

Fang, Li Tai; Zhu, Bin; Zhao, Yongmei; Chen, Wanqiu et al.

Ingår i Nature Biotechnology, s. 1151-1160, 2021

• DOI för Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing

The SEQC2 epigenomics quality control (EpiQC) study

Foox, Jonathan; Nordlund, Jessica; Lalancette, Claudia; Gong, Ting et al.

Ingår i Genome Biology, 2021

• DOI för The SEQC2 epigenomics quality control (EpiQC) study
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DNA Methylation-Based Interferon Scores Associate With Sub-Phenotypes in Primary Sjögren's Syndrome

Imgenberg-Kreuz, Juliana; Sandling, Johanna K.; Norheim, Katrine Braekke; Johnsen, Svein Joar Auglaend et al.

Ingår i Frontiers in Immunology, 2021

• DOI för DNA Methylation-Based Interferon Scores Associate With Sub-Phenotypes in Primary Sjögren's Syndrome
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DNA Methylation Signatures Predict Cytogenetic Subtype and Outcome in Pediatric Acute Myeloid Leukemia (AML)

Krali, Olga; Palle, J; Bäcklin, Christofer; Abrahamsson, Jonas et al.

Ingår i Genes, 2021

• DOI för DNA Methylation Signatures Predict Cytogenetic Subtype and Outcome in Pediatric Acute Myeloid Leukemia (AML)
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Leukocytes with chromosome Y loss have reduced abundance of the cell surface immunoprotein CD99

Mattisson, Jonas; Danielsson, Marcus; Hammond, Maria; Davies, Hanna et al.

Ingår i Scientific Reports, 2021

• DOI för Leukocytes with chromosome Y loss have reduced abundance of the cell surface immunoprotein CD99
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Expression of BCL6 in paediatric B-cell acute lymphoblastic leukaemia and association with prognosis

Mäkinen, Artturi; Nikkilä, Atte; Mehtonen, Juha; Teppo, Susanna et al.

Ingår i Pathology, s. 875-882, 2021

• DOI för Expression of BCL6 in paediatric B-cell acute lymphoblastic leukaemia and association with prognosis
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Molecular pathways in patients with systemic lupus erythematosus revealed by gene-centred DNA sequencing

Sandling, Johanna K.; Pucholt, Pascal; Hultin-Rosenberg, Lina; Farias, Fabiana H. G. et al.

Ingår i Annals of the Rheumatic Diseases, s. 109-117, 2021

• DOI för Molecular pathways in patients with systemic lupus erythematosus revealed by gene-centred DNA sequencing
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Mutational patterns and clonal evolution from diagnosis to relapse in pediatric acute lymphoblastic leukemia

Sayyab, Shumaila; Lundmark, Anders; Larsson, Malin; Ringner, Markus et al.

Ingår i Scientific Reports, 2021

• DOI för Mutational patterns and clonal evolution from diagnosis to relapse in pediatric acute lymphoblastic leukemia
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Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing

Xiao, Wenming; Ren, Luyao; Chen, Zhong; Fang, Li Tai et al.

Ingår i Nature Biotechnology, s. 1141-1150, 2021

• DOI för Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing

Whole genome and exome sequencing reference datasets from a multi-center and cross-platform benchmark study

Zhao, Yongmei; Fang, Li Tai; Shen, Tsai-wei; Choudhari, Sulbha et al.

Ingår i Scientific Data, 2021

• DOI för Whole genome and exome sequencing reference datasets from a multi-center and cross-platform benchmark study
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Genome assembly of the basket willow, Salix viminalis, reveals earliest stages of sex chromosome expansion

Almeida, Pedro; Proux-Wera, Estelle; Churcher, Allison; Soler, Lucile et al.

Ingår i BMC Biology, 2020

• DOI för Genome assembly of the basket willow, Salix viminalis, reveals earliest stages of sex chromosome expansion
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Recent advances in single-molecule fluorescence microscopy render structural biology dynamic

Bacic, Luka; Sabantsev, Anton; Deindl, Sebastian

Ingår i Current opinion in structural biology, s. 61-68, 2020

• DOI för Recent advances in single-molecule fluorescence microscopy render structural biology dynamic
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Protein and DNA methylation-based scores as surrogate markers for interferon system activation in patients with primary Sjögren's syndrome

Björk, Albin; Andersson, Elina Richardsdotter; Imgenberg-Kreuz, Juliana; Thorlacius, Gudny Ella et al.

Ingår i RMD Open, 2020

• DOI för Protein and DNA methylation-based scores as surrogate markers for interferon system activation in patients with primary Sjögren's syndrome
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The proliferative history shapes the DNA methylome of B-cell tumors and predicts clinical outcome

Duran-Ferrer, Marti; Clot, Guillem; Nadeu, Ferran; Beekman, Renee et al.

Ingår i NATURE CANCER, s. 1066-1081, 2020

• DOI för The proliferative history shapes the DNA methylome of B-cell tumors and predicts clinical outcome

Clinicopathological features and prognostic value of SOX11 in childhood acute lymphoblastic leukemia

Gronroos, Toni; Makinen, Artturi; Laukkanen, Saara; Mehtonen, Juha et al.

Ingår i Scientific Reports, 2020

• DOI för Clinicopathological features and prognostic value of SOX11 in childhood acute lymphoblastic leukemia
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Overexpression of chromatin remodeling and tyrosine kinase genes in iAMP21-positive acute lymphoblastic leukemia

Ivanov Öfverholm, I.; Zachariadis, V.; Taylan, F.; Marincevic-Zuniga, Yanara et al.

Ingår i Leukemia and Lymphoma, s. 604-613, 2020

• DOI för Overexpression of chromatin remodeling and tyrosine kinase genes in iAMP21-positive acute lymphoblastic leukemia
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Function of multiple sclerosis-protective HLA class I alleles revealed by genome-wide protein-quantitative trait loci mapping of interferon signalling

Lundtoft, Christian; Pucholt, Pascal; Imgenberg-Kreuz, Juliana; Carlsson Almlöf, Jonas et al.

Ingår i PLOS Genetics, 2020

• DOI för Function of multiple sclerosis-protective HLA class I alleles revealed by genome-wide protein-quantitative trait loci mapping of interferon signalling
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Chapter Eleven: Advances in whole genome methylomic sequencing

Nordlund, Jessica

Ingår i Epigenetics Methods, s. 213-233, 2020

• DOI för Chapter Eleven: Advances in whole genome methylomic sequencing

Refined detection and phasing of structural aberrations in pediatric acute lymphoblastic leukemia by linked-read whole-genome sequencing

Nordlund, Jessica; Marincevic-Zuniga, Yanara; Cavelier, Lucia; Raine, Amanda et al.

Ingår i Scientific Reports, 2020

• DOI för Refined detection and phasing of structural aberrations in pediatric acute lymphoblastic leukemia by linked-read whole-genome sequencing
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High genetic risk score is associated with early disease onset, damage accrual and decreased survival in systemic lupus erythematosus

Reid, Sarah; Alexsson, Andrei; Frodlund, Martina; Morris, David et al.

Ingår i Annals of the Rheumatic Diseases, s. 363-369, 2020

• DOI för High genetic risk score is associated with early disease onset, damage accrual and decreased survival in systemic lupus erythematosus
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Association of aberrant ASNS imprinting with asparaginase sensitivity and chromosomal abnormality in childhood BCP-ALL

Watanabe, A.; Miyake, K.; Nordlund, Jessica; Syvänen, Ann-Christine et al.

Ingår i Blood, s. 2319-2333, 2020

• DOI för Association of aberrant ASNS imprinting with asparaginase sensitivity and chromosomal abnormality in childhood BCP-ALL

Whole-genome sequencing identifies complex contributions to genetic risk by variants in genes causing monogenic systemic lupus erythematosus

Almlöf, Jonas Carlsson; Nystedt, Sara; Leonard, Dag; Eloranta, Maija-Leena et al.

Ingår i Human Genetics, s. 141-150, 2019

• DOI för Whole-genome sequencing identifies complex contributions to genetic risk by variants in genes causing monogenic systemic lupus erythematosus
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CD99 expression is strongly associated with clinical outcome in children with B-cell precursor acute lymphoblastic leukaemia

Chen, Dongfeng; Camponeschi, Alessandro; Wu, Qingqing; Gerasimcik, Natalija et al.

Ingår i British Journal of Haematology, s. 418-423, 2019

• DOI för CD99 expression is strongly associated with clinical outcome in children with B-cell precursor acute lymphoblastic leukaemia

Arteria: An automation system for a sequencing core facility

Dahlberg, Johan; Hermansson, Johan; Sturlaugsson, Steinar; Lysenkova, Mariya et al.

Ingår i GigaScience, 2019

• DOI för Arteria: An automation system for a sequencing core facility
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A rare regulatory variant in the MEF2D gene affects gene regulation and splicing and is associated with a SLE sub-phenotype in Swedish cohorts

Farias, Fabiana H. G.; Dahlqvist, Johanna; Kozyrev, Sergey V.; Leonard, Dag et al.

Ingår i European Journal of Human Genetics, s. 432-441, 2019

• DOI för A rare regulatory variant in the MEF2D gene affects gene regulation and splicing and is associated with a SLE sub-phenotype in Swedish cohorts
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Circulating Levels of Interferon Regulatory Factor-5 Associates With Subgroups of Systemic Lupus Erythematosus Patients.

Idborg, Helena; Zandian, Arash; Ossipova, Elena; Wigren, Edvard et al.

Ingår i Frontiers in Immunology, 2019

• DOI för Circulating Levels of Interferon Regulatory Factor-5 Associates With Subgroups of Systemic Lupus Erythematosus Patients.
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Shared and Unique Patterns of DNA Methylation in Systemic Lupus Erythematosus and Primary Sjogren's Syndrome

Imgenberg-Kreuz, Juliana; Carlsson Almlöf, Jonas; Leonard, Dag; Sjöwall, Christopher et al.

Ingår i Frontiers in Immunology, 2019

• DOI för Shared and Unique Patterns of DNA Methylation in Systemic Lupus Erythematosus and Primary Sjogren's Syndrome
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Interferon signature in patients with STAT1 gain-of-function mutation is epigenetically determined

Kaleviste, Epp; Saare, Mario; Leahy, Timothy Ronan; Bondet, Vincent et al.

Ingår i European Journal of Immunology, s. 790-800, 2019

• DOI för Interferon signature in patients with STAT1 gain-of-function mutation is epigenetically determined