CONTRA · Project

Software Tools That Predict Cancer Drug Resistance and Track Tumor Evolution

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Cancer drugs often work at first but then stop — the tumor evolves and finds a way around them, like bacteria becoming resistant to antibiotics. CONTRA trained 15 researchers across Europe to build software that traces how individual cancer cells mutate, spread, and develop resistance over time. Think of it as a family tree for tumor cells — once you see how they branch and evolve, you can predict which drug they'll dodge next. The project produced five working software tools that reconstruct these evolutionary paths from genetic sequencing data.

By the numbers

Early-stage researchers trained in computational oncology

Consortium partners across the network

Countries represented in the consortium

Working software tools delivered

Industry partners in the consortium

Total project deliverables

33%

Industry participation ratio in consortium

The business problem

What needed solving

Cancer drugs frequently fail after initial success because tumors evolve resistance — and today, oncology companies have limited ability to predict which tumors will resist which drugs and when. This blind spot leads to failed clinical trials, wasted R&D investment, and poor patient outcomes. Companies working on cancer therapeutics and diagnostics need computational tools that can map tumor evolution and forecast resistance before it happens.

The solution

What was built

CONTRA delivered 5 software tools: a resistance risk evaluation tool, a resistance onset prediction model, tumor phylogeny reconstruction software, progression inference software for multiple tumors, and software for analyzing phylogeny combined with migration patterns. The project also produced 14 total deliverables and trained 15 computational oncology researchers.

Audience

Who needs this

Pharma companies with oncology drug pipelines facing resistance failuresPrecision medicine companies developing tumor profiling servicesLiquid biopsy and companion diagnostics companiesBioinformatics platform providers serving oncology clientsCancer research hospitals building computational pathology capabilities

Business applications

Who can put this to work

Pharmaceutical R&D

enterprise

Target: Drug development companies working on oncology pipelines

If you are a pharma company losing millions when late-stage cancer drugs fail due to resistance — CONTRA built a resistance risk evaluation tool and a resistance onset prediction model that analyze tumor evolution patterns from sequencing data. These tools can flag which drug candidates face the highest resistance risk before you commit to expensive Phase III trials. The consortium included 5 industry partners across 7 countries specifically to bridge this gap between research and commercial drug development.

Precision Medicine / Diagnostics

mid-size

Target: Companies developing companion diagnostics or liquid biopsy platforms

If you are a diagnostics company analyzing circulating tumor cells or single-cell sequencing data — CONTRA developed software for tumor phylogeny reconstruction and progression inference for multiple tumors. These tools turn raw sequencing data into actionable evolutionary maps showing how a patient's cancer is likely to spread. With 15 trained computational oncology specialists now in the workforce, there is also a talent pool for hiring.

Biotech Software

SME

Target: Bioinformatics companies building clinical decision-support platforms

If you are a biotech software company that needs validated algorithms for analyzing tumor heterogeneity — CONTRA produced 5 dedicated software tools including phylogeny-with-migration analysis and progression inference across multiple tumors. These can be integrated into existing clinical bioinformatics pipelines. The project's 33% industry ratio in its 15-partner consortium means the tools were developed with commercial software standards in mind.

Frequently asked

Quick answers

What would it cost to license or access these software tools?

Based on available project data, CONTRA was funded as an MSCA-ITN training network, which typically results in open-source research software. Licensing terms would need to be discussed directly with the coordinator at KTH Royal Institute of Technology in Sweden. The 5 software deliverables were produced in an academic context, so commercial licensing may require a separate agreement.

Can these tools work at the scale our pharma pipeline needs?

The project produced 5 distinct software tools handling tumor phylogeny reconstruction, resistance prediction, and progression inference from single-cell sequencing data. These were developed as research-grade tools by 15 ESRs across 15 partner institutions. Scaling to production-grade clinical or commercial use would likely require engineering investment beyond the current prototypes.

Who owns the intellectual property for these tools?

IP from MSCA-ITN projects is typically shared between the host institutions and the training network. With 15 partners across 7 countries (including institutions in Sweden, Germany, UK, Spain, Poland, Switzerland, and Canada), IP ownership may be distributed. KTH as coordinator would be the first point of contact for licensing discussions.

Are these tools validated for clinical or regulatory use?

Based on available project data, the tools were developed in a research and training context, not a clinical validation setting. The resistance risk evaluation tool and resistance onset prediction model would need separate clinical validation studies before any regulatory submission. The consortium included 5 industry partners who may have contributed to validation planning.

How long would integration into our existing bioinformatics pipeline take?

CONTRA produced standalone software tools for specific tasks: phylogeny reconstruction, migration analysis, resistance prediction, and progression inference. Integration timeline depends on your existing data infrastructure and sequencing workflows. The tools work with single-cell sequencing data and mutation data, so compatibility with your data formats would be the first checkpoint.

Is there ongoing development and support for these tools?

The project officially closed in June 2022. However, the 15 trained ESRs and their host institutions may continue development independently. The project website at itn-contra.org and the coordinator at KTH would be the best sources for current status of each tool. With 7 university partners and 3 research organizations involved, some tools likely have active maintainers.

Consortium

Who built it

CONTRA's 15-partner consortium spans 7 countries (Sweden, Germany, UK, Spain, Poland, Switzerland, Canada) with a healthy 33% industry ratio — 5 industry partners alongside 7 universities and 3 research organizations, including 2 SMEs. The coordinator is KTH Royal Institute of Technology in Sweden, a top-tier technical university. The mix of academic and commercial partners suggests the software tools were built with some awareness of industry needs, though the primary mission was training 15 doctoral-level researchers. For a business looking to access these tools, the industry partners in the consortium may already have integration experience, and the 15 trained ESRs represent a ready talent pool of computational oncology specialists now entering the job market.

KUNGLIGA TEKNISKA HOEGSKOLANCoordinator · SE
UNIWERSYTET WARSZAWSKIparticipant · PL
THE CHANCELLOR MASTERS AND SCHOLARS OF THE UNIVERSITY OF CAMBRIDGEparticipant · UK
FUNDACION CENTRO TECNOLOXICO DE TELECOMUNICACIONS DE GALICIApartner · ES
MERCK KOMMANDITGESELLSCHAFT AUF AKTIENpartner · DE
FUNDACIO INSTITUT DE RECERCA BIOMEDICA (IRB BARCELONA)participant · ES
EIDGENOESSISCHE TECHNISCHE HOCHSCHULE ZUERICHparticipant · CH
INSTITUTE OF CANCER RESEARCH: THE ROYAL CANCER HOSPITAL LBGparticipant · UK
UNIVERSIDAD DE VIGOparticipant · ES
KING'S COLLEGE LONDONparticipant · UK

How to reach the team

KTH Royal Institute of Technology, Sweden — reach out via university technology transfer office for licensing inquiries

Order a report on this consortium See KUNGLIGA TEKNISKA HOEGSKOLAN profile →

Next steps

Talk to the team behind this work.

Want to connect with the CONTRA team about their resistance prediction or tumor phylogeny software? SciTransfer can arrange a direct introduction to the right people at KTH and their industry partners.

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