Regulatory compliant software for mutation analysis in clinical diagnostics


the software for high quality mutational analyses in cancer precision medicine

ALTOmate is an integrated software for mutation analysis in the cancer precision medicine workflow. Targeting solid tumor applications, ALTOmate is CE marked for in vitro diagnostics (IVD) based on next-generation sequencing data. ALTOmate produces an accurate, highly selective list of tumor-specific mutations in gene panel and exome data at a fast turnaround time.

Encapsulated in a Singularity container for instant deployment within your IT infrastructure, ALTOmate delives results out of the box without configuration or interruption of your routine work. As a diagnostic specialist, you can rely on reproducible results, based on deterministic, fast and assumption free statistics.

ALTOmate consists of proprietary algorithms for read-trimming, read-alignment and mutation calling, based on our patented pattern recognition metrics (PBR). The single executable can handle sequencing data from various platform providers. ALTOmate will report nucleotide substitutions, small insertions and deletions in an industry standard VCF file, together with an audit trail of the analysis and relevant quality control metrics.


the accurate and efficient software for NGS analysis of tumor and patient-matched normal sample, assisting in the choice of personalized cancer therapy

VARify is a medical device software for reporting somatic SNVs and InDels in NGS-sequenced tumor and patient-matched samples with broad sequencing platform compatibility, CE marked for in vitro diagnostics (IVD).

VARify uses a patented, completely deterministic and assumption-free statistical model to produce a small, clinically relevant VCF file. Oncodia’s proprietary algorithms trim, align and identify the actionable somatic mutations with high sensitivity and substantially reduced false-positive calls

VARify is distributed as a single-file Singularity container, easily deployable and highly portable – from desktop PCs to computing clusters. VARify is among the fastest pipelines on the market, benefiting from full and smooth integration of all components in a monolithic executable, without any third-party dependencies. VARify is an efficient, reliable and highly selective software for precision oncology.

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Publications and patents

Defining eligible patients for allele-selective chemotherapies targeting NAT2 in colorectal cancer

Rendo, V., Kundu, S., Rameika, N., Ljungström, V., Svensson, R., Palin, K., Aaltonen, L., Stoimenov, I., Sjöblom, T.

Scientific Reports, Volume 10 (1), 2020, December 31. doi:10.1038/s41598-020-80288-z

Somatic ephrin receptor mutations are associated with metastasis in primary colorectal cancer

Mathot, L., Kundu, S., Viktor Ljungström, V., Svedlund, J., Moens, L., Adlerteg, T., … Sjöblom T.

Cancer Research  Volume 77 (7), 2017, April 1. doi: 10.1158/0008-5472.CAN-16-1921 

A new distance measure for non-identical data with application to image classification

Swaminathan, M., Yadav, P., Piloto, O., Sjöblom T. and Cheong I.

Pattern Recognition, Volume 63, 2017, Mar 17. doi: 10.1016/j.patcog.2016.10.018