Suvi Mäkeläinen

My work combines bioinformatics, molecular genetics, and experimental approaches to reveal how different genetic mechanisms influence health and disease. I collaborate widely across veterinary medicine, genomics, and biomedical sciences, and my research contributes both to improved animal health and to translational insights relevant for human medicine.

I did my bachelor studies at the Helsinki university concentrating on animal genetics and made my BSc thesis in linear description in riding horse breeding evaluation, after which i worked at Suomen Hippos, an organisation responsible for horse breeding and registration in Finland. During my BSc education I made an intership at Göttingen university in Germany and got interested in molecular biology while working on a project aiming to find a candidate gene for visual problems in cows. I did my MSc studies in the Netherlands at Wageningen university and wrote my major thesis in equine osteochondrosis and minor thesis in bioinformatics and cancer research, including an internship at the Netherlands Cancer Institute working on human in vitro cancer studies.

After my MSc I moved to Sweden for my doctoral studies. I finished my doctoral thesis in 2020 with the title Canine inherited retinal degenerations: a model for visual impairment in humans. After my PhD I continued as a post-doctoral researcher in cancer genomics and bioinformatics at Kerstin Lindblad-Toh's and Karin Forsberg-Nilssons research group at Uppsala university, focusing on the non-coding cancer genome.

I then received a grant to continue as a researcher working on inherited retinal degeneration and divided my time between Uppsala University, Department of Immunology, Genetics and Pathology, Neuro-oncology and Neurodegeneration as well as SLU, Department of Clinal Sciences. Since September 2025 I am working as a researcher at HBIO, Molecular Genetics and Bioinformatics.

My main research interests include the genetic mechanisms underlying inherited retinal degeneration (IRD), skeletal dysplasia, and immune-mediated diseases.

Many different dog breeds are affected by one or several forms of inherited retinal degeneration (IRD) that leads to visual impairment and blindness. Both dogs and humans are affected by IRDs, and the comparative value of the canine studies has proven essential for advancing modern therapeutic approaches such as gene therapy for human patients. Our research also results in the development of diagnostic genetic tests, helping reduce the number of affected dogs and improving canine health. Our IRD research group at SLU includes both veterinarians, geneticists, bioinformaticians and doctoral students.

The Major Histocompatibility Complex (MHC) is a group of genes present in most vertebrates and is the most variable region of the genome. MHC plays a central role in the adaptive immune system, where MHC class I and II molecules bind foreign peptides from pathogens such as viruses, bacteria, and parasites, and present them to T-cells, triggering a specific immune response to combat invading pathogens. 

Compared to human MHC, our understanding of MHC in domestic animals is limited. The number of MHC genes likely varies between individuals of the same species, and MHC polymorphism is crucial for a broad and effective immune response. Using advanced long-read DNA and RNA sequencing technology, we are studying the structure of the MHC region in cattle, sheep, dogs, and horses. The goal is to develop a system to accurately identify polymorphisms in MHC class I and II genes and to study how these genes are linked to resistance to parasites and other pathogens. The results will not only enhance our understanding of genetic diversity and immune defense in domestic animals but may also reduce reliance on pharmaceuticals, improve animal health and welfare, and strengthen resilience against future threats.

I am also working on several projects on other inherited conditions in dogs, cats, and horses, with the aim of identifying disease-causing genetic variants.

I am currently lecturing on cancer genomics and bioinformatics on courses at SLU and Uppsala university, including Comparative Genomics (UU), Bioinformatics (UU), Veterinary Medical Genetics (SLU) and Genome Analysis (SLU).

I'm happy to supervise degree projects. Please see the list of Available degree projects or contact me directly if interested.

Previous degree projects:

Handledare till Nazanin Sayad – Advanced Research Training (3MR001) 2024, Uppsala universitet, 2024, Canine model for human retinal ciliopathy

Bihandledare till Melina Martin – MSc i bioinformatik, Uppsala universitet, 2023 Developing a reproducible bioinformatics workflow for canine inherited retinal disease Länk till examensarbete

Bihandledare till Emma Hjorth – Veterinärprogrammets examensarbete, SLU, 2021 Genetisk bakgrund till ärftlig retinal degeneration hos lagotto romagnolo
Länk till examensarbete

Bihandledare till Anna Darlene van der Heiden – MSc in Animal Science, SLU, 2019 Establishing a canine genome sequencing protocol using Oxford Nanopore
Länk till examensarbete

Bihandledare till Dilovan Kamil – BSc i biologi, Uppsala universitet, 2018

Bihandledare till Skrollan Hasse Kampling – BSc i biologi, Uppsala universitet, 2018

Current grants supporting my research:

Agria SKK forskningsfond - Machine Learning Based Identification and Validation of Disease-causing Mutations. Main applicant.

Thure F. och Karin Forsbergs Stiftelse - Genetic causes of canine inherited retinal diseases. Main applicant.

Sällskapsdjurens forskningsfond - Higher resolution for canine vision. Main applicant.

FORMAS - The Major Histocompability Complex (MHC) - Genetic variation and its impact on endoparsite susceptibility in cattle, sheep, horses and dogs. Co-applicant.

Stiftelsen Hästforskning - Why are some horses more prone to infections while others in the group develop immunity? Co-applicant.

Thure F. och Karin Forsbergs Stiftelse- The role of Major Histocompatibility Complex (MHC) in canine health. Co-applicant.

Sällskapsdjurens forskningsfond - MHC in dogs. Co-applicant.

Previous grants:

Sällskapsdjurens forskningsfond - DNA sekvensering med ny teknik kan visa den genetiska orsaken till blindhet hos hund. Main applicant.

Full list of publications in SLU publication database (SLUpub)

A nonsense mutation in the PRKG2 gene in dalmatian dogs with chondrodysplasia Mäkeläinen, S.; Ekman, S.; Hytönen, M.K. et al. PLoS One. 2025 Nov 26;20(11):e0322107. https://doi.org/10.1371/journal.pone.0322107

A canine model of Stargardt Disease 1 develops early cone dysfunction recapitulating the human phenotype Azarkevich, Alexandra J.; Winkler, Paige A.; Daggy, Alexis M. et al. Conference abstract, Investigative Ophthalmology & Visual Science 2025, volume: 66, number: 8
 
Working dog-like chorioretinopathy in 5 Swedish Elkhounds Goncalves, Daniel; Lindström, Lisa; Mäkeläinen, Suvi et al. Conference abstract, Veterinary Ophthalmology
2024

Using evolutionary constraint to define novel candidate driver genes in medulloblastoma Roy, Ananya; Sakthikumar, Sharadha; Kozyrev, Sergey V. et al.
Proceedings of the National Academy of Sciences of the United States of America
2023, volume: 120, number: 33, article number: e2300984120 https://doi.org/10.1073/pnas.2300984120
 
Abnormal Appearance of the Area Centralis in Labrador Retrievers With an ABCA4 Loss-of-function Mutation Ekesten, Bjorn; Makelainen, Suvi; Ellis, Stuart et al. Translational Vision Science & Technology 2022, volume: 11, number: 2, article number: 36 https://doi.org/10.1167/tvst.11.2.36
 
A novel canine reference genome resolves genomic architecture and uncovers transcript complexity Wang, Chao; Wallerman, Ola; Arendt, Maja-Louise et al.
Communications biology 2021, volume: 4, number: 1, article number: 185 https://doi.org/10.1038/s42003-021-01698-x
 
Canine inherited retinal degenerations: a model for visual impairment in humans
Mäkeläinen, Suvi. Doctoral thesis, Acta Universitatis Agriculturae Sueciae
2020, number: 2020:54, https://pub.epsilon.slu.se/17778/1/makelainen_s_201012.pdf

Fundus autofluorescence and foveal appearance in Labrador Retriever dogs with an ABCA4 loss-of-function mutation Ekesten, Bjorn; Makelainen, Suvi; Kjellstrom, Ulrika et al. Conference abstract Investigative Ophthalmology & Visual Science
2020, volume: 61, number: 7

Deletion in the Bardet-Biedl syndrome gene TTC8 results in a syndromic retinal degeneration in dogs Mäkeläinen, Suvi; Hellsand, Minas; Van Der Heiden, Anna Darlene et al. Genes 2020, volume: 11, number: 9, article number: 1090 https://doi.org/10.3390/genes11091090

Whole Genome Sequencing of Bengal Cat Trios with Thoracic Malformations
Mäkeläinen, Suvi; Ley, Cecilia; Ström Holst, Bodil et al. Conference abstract 2019

An early onset retinopathy in Golden retriever dogs Mäkeläinen, Suvi; Narfström, Kristina; Ekesten, Björn et al. Conference abstract 2019

An ABCA4 loss-of-function mutation causes a canine form of Stargardt disease
Makelainen, Suvi; Godia, Marta; Hellsand, Minas et al. PLoS Genetics
2019, volume: 15, number: 3, article number: e1007873 https://doi.org/10.1371/journal.pgen.1007873

Oncopig Soft-Tissue Sarcomas Recapitulate Key Transcriptional Features of Human Sarcomas Schachtschneider, Kyle M.; Liu, Yingkai; Makelainen, Suvi et al. Scientific Reports
2017, volume: 7, article number: 2624 https://doi.org/10.1038/s41598-017-02912-9