Cancer researchers have unveiled a standardized pathology and molecular workflow designed to solve one of the most difficult problems in international genomics: turning frozen tumor samples collected across different countries, hospitals and environmental settings into reliable whole-genome data. The protocol, developed for the seven-year Mutographs project led by the Wellcome Sanger Institute and funded by Cancer Research UK, establishes a centralized process for evaluating, enriching and extracting DNA from cancer tissues before sequencing. Its goal is to investigate why the incidence of particular cancers varies dramatically around the world, including cancers for which the environmental or biological causes remain unclear. By linking pathology with genomic analysis from the earliest stages, the workflow achieved an overall success rate of 88% in producing DNA suitable for whole-genome sequencing.
The Mutographs project focuses on the idea that cancers preserve a molecular record of the damage that contributed to their development. Every tumor contains patterns of mutations, known as mutational signatures, that can reveal the effects of carcinogens, infections, dietary exposures, DNA repair defects or other biological processes. These signatures are not always visible through conventional clinical examination, and they may differ between populations even when tumors appear similar under the microscope. Whole-genome sequencing allows scientists to examine mutations across coding and noncoding regions of DNA, structural rearrangements and other genomic changes. However, such analysis is only as reliable as the tissue entering the sequencing pipeline. Poor preservation, low tumor content or contamination by normal cells can obscure the signals researchers are trying to detect.
The new protocol addresses this challenge by treating pathology assessment as an integrated component of genomics rather than as a separate preliminary step. The International Agency for Research on Cancer coordinated the pathology work and paired extraction of DNA from tumor and blood specimens. Blood provides a source of constitutional, or germline, DNA, allowing researchers to distinguish inherited genetic variation from mutations acquired by tumor cells. The comparison is essential for identifying somatic mutations, which arise during a person’s lifetime and may reflect cancer-causing exposures. It also helps prevent normal genetic differences between individuals from being misinterpreted as tumor-specific alterations during whole-genome analysis.
Frozen tissue presents particular technical difficulties. Unlike formalin-fixed, paraffin-embedded material, which is widely used for routine histopathology, frozen samples can be challenging to section, stain and interpret. Their morphology may be less familiar to laboratories, and freezing artifacts can distort cellular structures or make the boundaries between tumor and normal tissue difficult to recognize. The workflow therefore requires practical experience in handling frozen specimens and assessing their morphology through digital pathology. Tissue is examined through multiple pathology stages, with quality-control checks used to verify the diagnosis, estimate the proportion of tumor cells and determine whether the material meets eligibility requirements for sequencing.
A central issue is tumor purity. A piece of tissue that appears adequate by volume may contain large areas of connective tissue, blood, necrosis or healthy cells, leaving too little cancer DNA for accurate analysis. When tumor cells are diluted by normal tissue, mutations may appear at a lower frequency and can fall below detection thresholds. The Mutographs workflow uses tumor-enrichment procedures to improve this balance. In some cases, pathologists perform macrodissection, manually removing selected regions from a tissue section to concentrate the tumor. For more complex specimens, laser-capture microdissection can isolate microscopic groups of cancer cells with high precision. The method uses a focused laser to separate marked regions from surrounding tissue, enabling molecular analysis of areas that would otherwise be overwhelmed by noncancerous material.
The protocol also describes manual and automated approaches for DNA extraction from both tumor and blood. Extraction from frozen cancer tissue must recover DNA that is sufficiently intact and free of substances that interfere with downstream enzymatic reactions or library preparation. Automated systems can improve consistency and throughput, particularly when processing large numbers of samples, while manual procedures may offer greater flexibility for unusual or limited specimens. Regardless of the method, the resulting DNA undergoes quality assessment before it is accepted for sequencing. These checks help determine whether the quantity, purity and integrity of the material are compatible with the demands of whole-genome library construction and high-throughput sequencing.
The reported 88% overall success rate is significant because the samples originated from a multinational research effort involving difficult and variable collection conditions. International studies often face differences in local pathology practices, transport times, freezing procedures, storage systems and available laboratory infrastructure. Even small variations can affect tissue morphology or DNA quality, making it difficult to compare data across locations. A centralized and reproducible workflow reduces this variability by applying the same decision points and quality criteria to specimens from different regions. It also creates a documented basis for excluding samples that are low quality, noneligible or unlikely to produce interpretable genomic data, protecting the final analysis from misleading results.
The decision to exclude a sample is not a failure of the project but an essential part of quality control. Sequencing a specimen with insufficient tumor content or severely degraded DNA can generate large quantities of data without producing dependable biological conclusions. In a study investigating differences in cancer incidence across populations, such errors could be particularly damaging because technical artifacts might be mistaken for genuine geographic patterns. Pathology review allows researchers to identify these risks before substantial sequencing resources are used. It also makes it possible to select the most informative tissue region, enrich tumor cells when necessary and preserve a clear record of why each sample was included or rejected.
The Mutographs workflow is expected to support comparisons of mutational signatures across selected cancers with unexplained differences in incidence worldwide. If recurring mutation patterns are found in tumors from particular regions, researchers can investigate whether they are associated with environmental exposures, infectious agents, occupational risks, lifestyle factors or local genetic backgrounds. The protocol does not itself identify a specific cause of cancer, but it provides the technical foundation required to search for those causes with confidence. Its broader value lies in connecting morphology, tissue processing, DNA quality control and genomic interpretation into a single pipeline. In settings where frozen tissues are difficult to process and laboratory resources vary, that integration could become a model for future international cancer-genomics initiatives. The study, published in Nature Protocols, demonstrates that carefully standardized pathology can turn geographically diverse and technically challenging samples into robust evidence about how cancers arise and why their burden differs around the world.
Subject of Research: Global cancer genomics, frozen tumor tissue processing, pathology quality control and mutational signature analysis
Article Title: Centralized processing of frozen tumor tissues for global cancer genomics
Article References: Abedi-Ardekani, B., Nikmanesh, A., Sotoudeh, M. et al. Centralized processing of frozen tumor tissues for global cancer genomics. Nat Protoc (2026). https://doi.org/10.1038/s41596-026-01426-x
Image Credits: AI Generated
DOI: https://doi.org/10.1038/s41596-026-01426-x
Keywords: Mutographs project, cancer genomics, frozen tumor tissue, whole-genome sequencing, mutational signatures, pathology, tumor enrichment, macrodissection, laser-capture microdissection, DNA extraction, global cancer research
Tags: cancer genomicscancer incidence variability worldwidecentralized tissue sample evaluationenvironmental and biological cancer factorsfrozen tumor tissue processinginternational cancer researchmolecular tumor profilingmutational signatures analysisMutographs projectstandardized pathology workflowtumor DNA extraction protocolsWhole genome sequencing in cancer
