The Genome-wide methods platform consists of five nodes located at Helsinki, Turku and Oulu. The network provides state-of-the-art genomics and transcriptomics services using high throughput genetic methods. The service portfolio includes a broad range of sequencing services including whole genome, whole exome, targeted panel, cell free DNA, transcriptome, metagenome and methylation sequencing as well as Sanger sequencing and genotyping. We are constantly also setting up new applications and welcome collaborative development projects supporting molecular biology and biomedical research. Our core facilities are coordinated by professional personnel and experts in the field and our services are based on the focus areas and expertise of the units within the platform. The platform participates actively in teaching and training, bringing the latest knowledge in genomics research and state-of-the-art technologies to the research community.
Contact details
Nodes
Services
Recent user publications
Available instrumentation

Contact details

Platform Chair

Kati Donner
kati.donner@helsinki.fi

Nodes

Node/Host UniversityNode PI
FIMM Genomics, UH
Kati Donner, UH
kati.donner@helsinki.fi
DNA Sequencing and Genomics
Laboratory (BIDGEN), UH
Petri Auvinen, UH
petri.auvinen@helsinki.fi
Genome Biology Unit (GBU), UH
Saara Ollila, UH
saara.ollila@helsinki.fi
Finnish Functional Genomics
Centre (FFGC), UTU
Minna Kyläniemi & Riikka Lund, UTU
minna.kylaniemi@utu.fi
riikka.lund@utu.fi*
BCO Sequencing Center, UO
Tuomo Mantere, UO
tuomo.mantere@oulu.fi

UH: University of Helsinki; UO: University of Oulu; UTU: University of Turku; *Riikka Lund on partial leave of absence 2024

Services

FIMM Genomics

Whole genome, exome and targeted sequencing, transcriptomics, metagenomics and CRISPR screening, cfDNA and Sanger sequencing, fragment analysis, long read sequencing and enzymatic methyl sequencing, cell line authentication, primary data analysis e.g. RNA-seq and miRNA data analysis, CNV analysis and variant filtering and annotation. Bioinformatics services for analysis of the NGS data. Targeted gene and protein expression assays by NanoString and Olink systems.

DNA Sequencing and Genomics Laboratory

Sequencing of genomes and RNA samples from all kinds of origins using short read and long read approaches. Also Sanger sequencing of PCR fragments and plasmids preparations. Bioinformatics analysis for genomes when resources allow it.

Genome Biology Unit

Delivery of constructs from genome-wide collection of cDNA, shRNA and gRNA libraries, Gateway cloning and mutagenesis, gRNA and double gRNA design and cloning, pooled library construction and amplification.

Finnish Functional Genomics Centre

Human exome sequencing, whole genome sequencing, RRBS analysis, transcriptomics, metagenomics, bacterial 16S rRNA sequencing, sequencing of ready libraries.

BCO Sequencing Center

Human exome sequencing, transcriptomics, metabarcode, bacterial 16S rRNA, and fungal ITS region sequencing, sequencing of customer prepared libraries, capillary sequencing, automatic DNA/RNA extraction, automated electrophoresis, optical genome mapping.

Recent user publications

FIMM

Nygren P. J., Bouhlal J. O. V., Jokinen E., Forstén S., Laajala E., Dias D. A. A., Awad S. A., Ianevski A., Klievink J., Lähteenmäki H., Kuusanmäki H., Myllymäki M., Kasanen T., Saeed K., Lee D. A., iCAN Flagship, Hjorth-Hansen H., Aittokallio T., Dufva O., Mustjoki S. High-throughput drug screening identifies SMAC mimetics as enhancers of NK cell cytotoxicity in chronic myeloid leukemia. Blood. 2025. Apr 10;145(15):1670-1686. doi: 10.1182/blood.2024025286. Sequencing and primary data analysis were performed at FIMM.

BIDGEN

Löytynoja A, Pohjoismäki J, Valtonen M, Laakkonen J, Morita W, Kunnasranta M, Väinölä R, Olsen MT, Auvinen P, Jernvall J. Deep origins, distinct adaptations, and species-level status indicated for a glacial relict seal. Proc Natl Acad Sci U S A. 2025 Jun 24;122(25):e2503368122. doi: 10.1073/pnas.2503368122.

BIDGEN was designing the sampling and performed the sequencing part of the samples treated in Helsinki. This publication led to distinction of the Saimaa ringed seal as a species. The Finnish Association for Nature Conservation gave the 2025 environmental price to the authors of this publication due to the elevation to species.

GBU

Monteuuis G, Awadhpersad R, van der Kolk D, Singh SK, Nyman TA, Malyutina A, Zamboni N, Moisio K, Juutila J, Hietakangas V, Seneca S, Carroll CJ, Jackson CB. Vacuolar-type H+-ATPase-mediated extra-organellar buffering resolves mitochondrial dysfunction. Nat Commun. 2025 Dec 3;17(1):67. doi: 10.1038/s41467-025-66656-1. PMID: 41339359; PMCID: PMC12769673.

sgRNAs used in this were distributed by Genome Biology Unit core facility supported by HiLIFE and the Faculty of Medicine, University of Helsinki, and Biocenter Finland.

FFGC

Suomi T, Kalim UU, Rasool O, Laiho A, Kallionpää H, Vähä-Mäkilä M, Nurmio M, Mykkänen J, Härkönen T, Hyöty H, Ilonen J, Veijola R, Toppari J, Knip M, Elo LL, Lahesmaa R. Type 1 Diabetes in Children With Genetic Risk May Be Predicted Very Early With a Blood miRNA. Diabetes Care. 2022 Apr 1;45(4):e77-e79. DOI: 10.2337/dc21-2120. FFGC small RNAseq library preparation and NGS.

BCO

Kaisanlahti A , Turunen J , Byts N, Samoylenko A, Bart G, Virtanen N, Tejesvi MV, Zhyvolozhnyi A , Sarfraz S , Kumpula S, Hekkala J, Salmi S , Will O, Korvala J, Paalanne N, Erawijantari PP, Suokas M, Peñate Medina T , Vainio S, Peñate Medina O, Lahti L, Tapiainen T, Reunanen J. Maternal microbiota communicates with the fetus through microbiota-derived extracellular vesicles. Microbiome. 2023;11(1):249. doi: 10.1186/s40168−023−01694−9. BCO: NGS (16S rRNA) and data analysis.
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NovaSeq 6000 flow cells and the sequencer

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Available instrumentation

FIMM

NovaSeq X plus, NextSeq500, MiSeq i100 Plus (Illumina), AVITI24 (Element Biosciences), PromethION 2 Solo, MinION (ONT), ABI3730xl DNA Analyzer (Thermo), Fragment analyser, TapeStation 4200 (Agilent), VictorNivo (Revvity), NanoString nCounter FLEX (nanoString), Olink Signature Q 100 (Thermo), FemtoPulse (Agilent)

BIDGEN

Miseq, Iseq (Illumina), Revio (Pacific Biociences), AVITI 24 (Element Biosciences), PromethION 2 Solo (Oxford Nanopore), ABI Sanger sequencer ABI3500xL (Thermo), qPCR and ddPCR, Fragment analyser (Agilent), Bioanalyzer (Agilent), Ionic (Purigen)

GBU

ORFeome cDNA library, TRC1 shRNA library, Sanger gRNA library

FFGC

Novaseq X, Novaseq 6000, MiSeq (Illumina), Fragment Analyzer, Bioanalyzer, Quantstudio 12K Flex, Pyromark Q24 (Qiagen)

BCO

Illumina NextSeq550, Ion Torrent PG, ABI 3500xL Genetic Analyzer, Bionano Genomics Saphyr, QIASymphony, QIAqility, BioRad CFX96 Touch Real-Time PCR, Agilent 2100 Bioanalyzer