Uppsala University

Contact

Head of the facility	Ann-Christine Syvänen

Expertise

Technologies	NGS-Whole genome sequencing (WGS) NGS-Exome sequencing(WES) NGS-other Fluorescence in situ hybridization (FISH) Array comparative genomic hybridization (aCGH) Genotyping qPCR Droplet Digital PCR (ddPCR) Genome editing - CRISP/cas9
Purposes	Research Clinical use Service
Applications	Biomarkers discovery and development Diagnostics and personalised disease profiling Disease processes research Epidemiology Infection medicine Microbial Genomics Single cells studies Therapeutic development

Features

Collaboration with industry where the institute collaborated with Genomics expertise (in the last 5 years)	>10
% of TIME involved in technology/methods development/innovation/intellectual property related to Genomics	10%
Certifications	ISO17025

Track record

Key opinion leaders

Ulf Gyllensten, Professor in Medical Genetics and Genomics, Platform Director of SciLifeLab Genomics: Expertise in human genomics and molecular epidemiology Lars Feuk, Professor in Medical Genetics and Genomics, Facility Director of the Uppsala Genome Center: Expertise in genetic variation and gene expression in human disease Ann-Christine Syvänen, Professor in Molecular Medicine, former Director of the SNP&SEQ Technology Platform: Expertise in medical genetics and technologies genome-wide analysis. Leif Andersson, Professor in Comparative genetics and functional genomics; Expertise in functional genomics in domestic animals. Kerstin Lindblad Toh, Professor in Comparative Genetics and Genomics; Expertise in comparative genomics to identify genes in canine and human disease. Tove Fall, Professor in Epidemiology, expertise in genomics analysis in diabetes and heart disease

Publications

Anava et al, 2020, Illuminating Genetic Mysteries of the Dead Sea Scrolls, Cell Halvorsen M et al, 2020, Increased burden of ultra-rare structural variants localizing to boundaries of topologically associated domains in schizophrenia, Nature Communications Sakthikumar S et al, 2020, Whole-genome sequencing of glioblastoma reveals enrichment of non-coding constraint mutations in known and novel genes. Genome Biology Sayadi A et al, 2019, The genomic footprint of sexual conflict, NatureNat Ecol Evol: 10.1038/s41559-019-1041-9

Contact

Head of the facility	Ann-Christine Syvänen

Expertise

Technologies	Serial analysis of gene expression (SAGE) RT-PCR Microarrays NGS- RNA sequencing
Purposes	Research Clinical use Service
Applications	Biomarkers discovery and development Diagnostics and personalised disease profiling Disease processes research Human and pathogen transcriptomes Non coding RNA analysis (miRNA, lncRNA, sRNA..) Responses to environment Single cells studies Therapeutic development

Features

Collaboration with industry where the institute collaborated with Transcriptomics expertise (in the last 5 years)	>10
Certifications	ISO17025

Track record

Key opinion leaders

Lars Feuk, Professor in Medical Genetics and Genomics, Facility Director of the Uppsala Genome Center: Expertise in genetic variation and gene expression in human disease Lars Forsberg, Associate Professor. The role of loss of chromosome Y (LOY) in human health and disease Leif Kirsebom, Professor. biology of RNA and its role in various cellular processes. Johan Elf, Professor in physical biology. central processes in bacterial cells as transcriptional regulation, protein synthesis and cell division Fredrik Pontén, Professor and Dr. Cecilia Lindskog from the Human Proteome Atlas. Lars Lind, Professor in Clinical Epidemiology.

Publications

Thompson DJ et al, 2019, Genetic predisposition to mosaic Y chromosome loss in blood Balliu B, et al, 2019, Genetic regulation of gene expression and splicing during a 10-year period of human aging, Genome Biol: 10.1186/s13059-019-1840-y Sjöstedt E, et al, 2020, An atlas of the protein-coding genes in the human, pig, and mouse brain. Science. DOI: 10.1126/science.aay5947

Contact

Head of the facility	Ann-Christine Syvänen

Expertise

Technologies	DNA Methylation Analysis - High resolution melt (HRM) DNA Methylation Analysis - Whole Genome Bisulfite Sequencing (WGBS) DNA Methylation Analysis – Reduced Representation Bisulfite Sequencing (RRBS) DNA Methylation Analysis – single-cell WGBS DNA Methylation Analysis – Genome-wide methylome analysis by long-read sequencing ChIP (including ChIP-chip, ChIP-seq) Single-cell ATAC-seq ATAC-seq
Purposes	Research Clinical use
Applications	Biomarkers discovery and development Diagnostics and personalised disease profiling Disease processes research Personalised "regulomes" Responses to environment Single cells studies Therapeutic development

Features

Collaboration with industry where the institute collaborated with Epigenomics expertise (in the last 5 years)	<10
% of TIME involved in technology/methods development/innovation/intellectual property related to Epigenomics	10%
Certifications	ISO17025

Track record

Key opinion leaders

Åsa Johansson, Assistant Professor. Expert in the role of genetics and epigenetics on human health Ann-Christine Syvänen, Professor in Molecular Medicine.Expertise in medical genetics and technologies genome-wide analysis including epigenetics. Helena Jernberg-Wiklund, Professor in Genetics and Pathology. Epigenetics of multiple myeloma

Publications

Moreno-Romero J et al, 2019, Epigenetic Signatures Associated With Imprinted Paternally Expressed Genes in the Arabidopsis Endosperm. Genome Biology: DOI: 10.1186/s13059-019-1652-0 Raine et al, 2017, SPlinted Ligation Adapter Tagging (SPLAT), a novel library preparation method for whole genome bisulphite sequencing. NAR. Nordlund et al, 2013.Genome-wide signatures of differential DNA methylation in pediatric acute lymphoblastic leukemia. Genome Biology.

Contact

Head of the facility	Ann-Christine Syvänen

Expertise

Technologies	Western Blot Isoelectric focusing (IEF) Capillary electrophoresis(EC) ELISA Luminex MesoScale Discovery(MSD) MALDI-MS LC-MS Liquid chromatography (HPLC, UHPLC) Olink panels
Purposes	Research Clinical use
Applications	Biomarkers discovery and development Diagnostics and personalised disease profiling Disease processes research Expression proteomics Interaction proteomics and protein networks Post-translational modifications Therapeutic development

Features

Collaboration with industry where the institute collaborated with Proteomics expertise (in the last 5 years)	>10

Track record

Key opinion leaders

Ulf Landegren, professor at the Immunology, Genetics and Pathology department. A pioneer the develpoment of methods such as oligonucleotide ligation assays, padlock, selector, and proximity probes. Jonas Bergquist, professor and Facility Director and Head of the mass spectrometry-based proteomics facility at Uppsala University. Per Andrén, associate Professor at the Dept. of Pharmaceutical Biosciences. Director of the National Center for Mass Spectrometry Imaging (NCMSI) infrastructure at Uppsala University. His research group works with imaging mass spectrometry and Peptidomics in neurodegenerative disorders and drug discovery.

Contact

Head of the facility	Ann-Christine Syvänen

Expertise

Technologies	High performance liquid chromatography (HPLC,UHPLC) LC-MS Nuclear magnetic resonance (NMR) Untargeted metabolomics assays
Purposes	Research
Applications	Biomarkers discovery and development Diagnostics and personalised disease profiling Disease processes research

Track record

Key opinion leaders	Mikael Hedeland, Professor at Department of Medicinal Chemistry, Analytical Pharmaceutical Chemistry. Group leader of the Metabolomics resarch group

DATA ANALYSIS for

• Genomics

DATA INTERPRETATION for

• Genomics

 DATA MANAGEMENT for:

• FAIR data

STATISTICS

• Molecular profiling (omics and others)
• Expertise in clinical design of experiments, clinical statistics
• Metadata (patient/sample information)
• Methods and policies for information infrastructure, including privacy and security

BIOINFORMATICS

• Genes and proteins annotation
• Expression profiling with omics, microarray and others (e.g. PCR) for RNAseq, microRNA, other RNA species and proteins
• Methylation profiling with NGS and array-types
• Data integration (“Systems biology”)
• Genetic analysis for Structural variation detection (Genome, Exome) and prediction of protein function from sequence information
• Drug-target interaction analysis
• Drug screening analysis
• Bio-Imaging informatics
• Development of new algorithms, e.g. new decision algorithms, new sequence aligners for NGS data, etc.
• Development of semantic analysis tools
• Informatics methods to support clinical decisions (diagnostic, predictive tests)