The central quantitative finding of the study is striking in its own right: across every organ examined, cancer cells carried approximately four times as many DNA mutations as the normal cells surrounding them. That cancer genomes are more heavily mutated than healthy genomes has long been known, but the mechanisms behind this elevation have remained contested. The traditional view held that the extra mutations arise largely because cancer-driving genes, once activated, destabilize the genome and generate further damage, or because rare catastrophic events shred the DNA of a developing tumor. The City of Hope and TGen team set out to test these ideas rigorously, and their results point toward a different and, in some ways, more unsettling explanation rooted in variation between people rather than within tumors.

To conduct the analysis, the researchers examined DNA from healthy and cancerous tissues in seven human organs: the bladder, colon, esophagus, liver, lung, prostate and stomach. They mined publicly available whole-genome and whole-exome sequencing data, drawing on hundreds of normal tissue samples and thousands of cancer samples. This scale makes the work one of the largest cross-organ comparisons of somatic mutation burden ever assembled. By applying consistent statistical methods across such a broad dataset, the team could ask not only whether tumors carry more mutations than healthy tissue, which they do in every organ studied with a median increase of more than fourfold, but also how mutation counts are distributed among apparently healthy people.

The answer to that second question surprised the investigators. Even after statistically accounting for age, which is well known to drive mutation accumulation, some healthy individuals had up to eight times more mutations in their organs than others. In other words, mutations do not build up at a uniform pace across the population. Instead, people appear to accumulate genetic changes in their tissues at markedly different rates, and those at the high end of this distribution can, while remaining cancer-free, carry mutation loads comparable to those found in patients diagnosed with the disease. Senior author Cristian Tomasetti, director of City of Hope’s Center for Cancer Prevention, Early Detection and Monitoring and a professor in the Early Detection and Prevention Division at TGen, said the research helps answer why some individuals get cancer, noting that these differences in mutations play a bigger role in cancer development than previously thought.

To make sense of the elevated mutation burden in tumors, the study formally evaluated three competing hypotheses. The first, which the authors call the classical hypothesis, proposes that cancer-driving mutations themselves lead to additional mutations, for example by impairing DNA repair machinery once key tumor suppressor genes are disabled. The second, the catastrophic hypothesis, invokes rare but extreme genomic events, such as chromothripsis, in which chromosomes shatter and reassemble in a single crisis, rapidly generating large numbers of mutations at once. The third, termed the tail hypothesis, shifts the focus from the tumor to the person: individuals whose tissues naturally accumulate mutations at higher rates sit in the tail of the population distribution and are therefore more likely to develop cancer in the first place.

When the researchers tested these explanations against the data, the tail hypothesis most consistently accounted for both observations that matter: the higher mutation burden seen inside tumors and the elevated mutation burden found in the normal tissues of people who went on to develop cancer. This pattern helps explain a long-standing puzzle in cancer genomics, namely why patients often carry more mutations not only in their tumors but also in their healthy cells. If a high personal mutation rate precedes the disease rather than resulting from it, the excess mutations in normal tissue are not a byproduct of the tumor but a signature of the underlying predisposition that made the tumor more likely to arise.

First author Sophie Pénisson, an associate professor in TGen’s Early Detection and Prevention Division, explained that instead of most extra mutations being caused only by cancer-driving genes or rare DNA damage, the findings suggest that some people accumulate mutations at a higher rate in their tissues. That reframing matters because it changes the target of inquiry. Rather than focusing exclusively on what happens inside a tumor after it begins to grow, researchers may need to understand the biological processes, from DNA repair efficiency to environmental exposures to stem cell division dynamics, that determine how quickly any given person’s cells accrue genetic damage over a lifetime.

The practical implications could be far-reaching. If mutation rate can be measured reliably in normal tissue, it could serve as a biomarker of cancer predisposition, complementing existing risk models based on family history, genetics and lifestyle. Tomasetti suggested that measuring a person’s mutation rate could become a critical way to identify those at higher risk and to develop more personalized strategies to prevent cancer. Such strategies might include intensified screening schedules, earlier and more frequent detection efforts, or preventive interventions tailored to individuals whose tissues show unusually rapid mutation accumulation. The study also underscores the value of large sequencing datasets generated for other purposes, since the analysis relied on publicly available data from hundreds of normal samples and thousands of tumors.

The work arrives amid growing interest in the field sometimes described as somatic mosaicism in healthy tissue, where sequencing of ostensibly normal organs has revealed that mutations are far more widespread than once assumed. What this study adds is a population-level perspective: the variation in mutation burden among healthy people is not a narrow technical footnote but a potentially decisive factor in who crosses the threshold into malignancy. The finding that some apparently healthy individuals carry cancer-level mutation burdens suggests that risk assessment could, in principle, move upstream, identifying high-risk profiles before tumors form and opening a window for prevention that current clinical practice rarely provides.

The study, titled Comprehensive Genomic Analysis of Normal and Cancer Cells Elucidates the Elevated Mutational Burden in Cancer, was supported by the Virginia Piper Charitable Trust, the Robert and Lynda Carter Altman Family Foundation Research Fund, the John Templeton Foundation and the National Cancer Institute. Several of the authors disclosed relationships with biotechnology and diagnostics companies outside the submitted work, including patents and consulting arrangements, as detailed in the journal’s conflict of interest statement. For now, the message for the field is conceptual rather than clinical: the race to cancer may be run at very different speeds in different people, and the pace of mutation accumulation in ordinary, healthy tissue may be one of the most important variables determining who ultimately reaches the finish line.

Subject of Research: Variation in somatic mutation rates in normal human tissues and its role in cancer risk

Article Title: City of Hope and TGen study finds hidden mutation rates may shape cancer risk

Article References: City of Hope and TGen study finds hidden mutation rates may shape cancer risk. (n.d.). Original publication

Image Credits: AI Generated

DOI: Not provided

Keywords: cancer research, somatic mutations, mutation rate, genomics, cancer risk, TGen, City of Hope, Cancer Research journal, tail hypothesis, DNA damage, cancer prevention, whole-genome sequencing

Loss of heterozygosity, or LOH, is a familiar concept in genetics. In a diploid organism, each gene normally exists in two copies, one inherited from each parent. Errors during mitosis, the process by which a cell duplicates and divides, can eliminate one of those copies, either through recombination, chromosome loss or segmental deletion. Previous work had established that mitotic errors alter the allelic composition of a gene roughly a thousand times more often than replication errors produce point mutations. This means that when selection favors the loss of a gene’s function, it will frequently be achieved by discarding the chromosome or chromosomal segment that carries it, rather than by mutating the gene itself. Aneuploidy, the state of having an abnormal number of chromosomes, is found in up to a quarter of newly isolated wild strains of Saccharomyces cerevisiae, a striking testament to how common these events are.

What remained unclear was whether complex rearrangements, those affecting multiple chromosomes at once, accumulate gradually through a series of independent steps or emerge suddenly in coordinated bursts. To find out, the team built an experimental system in which genome rearrangements could be generated de novo and their frequency, triggers, architecture and stability all measured. They compiled a list of 454 yeast genes whose deletion had been shown, in earlier screens using two well-established but distinct methods, one detecting gross chromosomal rearrangements and one detecting chromosome instability, to increase LOH. After accounting for strains that could not be manipulated successfully, 392 diploid deletion strains remained, each carrying a homozygous deletion of a different gene together with two heterozygous marker loci: CAN1 on the left arm of chromosome V and ade2::URA3 in the middle of the right arm of chromosome XV.

The researchers propagated 20 replicate mutation-accumulation cultures of each strain and plated cells onto selective media containing canavanine or 5-fluoroorotic acid, which only cells that had lost the functional allele at the corresponding marker could colonize. These assays yielded robust, strain-specific estimates of the single LOH rate per cell division, with 95 percent confidence limits typically spanning only a narrow range around the central value. A substantial majority of the deletion strains, 68 percent at the CAN1 locus and 82 percent at the URA3 locus, showed higher single LOH rates than the wild-type control, confirming that the mutations compiled from earlier qualitative screens indeed destabilize the genome in quantitative assays. The team then scored how frequently double mutants, resistant to both drugs simultaneously, appeared. Deletion strains varied enormously, and the most unstable strains under double selection were also among the most unstable under single selection, with a Spearman rank correlation of 0.61.

The critical question was whether these double events could be explained as two independent single events occurring in sequence. Because the experimental data alone could not distinguish one-step from two-step origins, the team turned to computer simulations. Using the empirically measured single LOH rates, they modeled mutation accumulation across colony growth, allowing cells to become single mutants at their measured rates and double mutants either sequentially or coincidentally at a rate equal to the product of the two single rates. Even under the deliberately conservative assumption that neither single nor double mutants paid any fitness penalty, an assumption that would maximize the survival and spread of sequentially derived double mutants, the simulated frequencies fell far short of what was observed. When fitness costs of 10 and 20 percent were applied, as is more realistic, the gap widened further. The observed double LOH frequencies exceeded the coincidental predictions by tens or even hundreds of times in the most unstable strains, and after subtracting the predicted sequential component, the residual coincidental events remained 26 times more frequent than expected.

What kinds of cellular defects produce such explosive instability? The answer emerged from Gene Ontology analysis of the deleted genes in the most unstable strains. Nearly half of the genes carry annotations related to cell cycle checkpoints, the surveillance mechanisms that halt progression through the division cycle when DNA is damaged or the mitotic spindle is improperly assembled. The checkpoint category as a whole is assigned to only 1.3 percent of all yeast genes, so its dominance among the strongest mutators is statistically striking. The remaining genes in the set are involved in DNA maintenance and repair, sister chromatid cohesion, and spindle formation, processes whose failure can generate damage so extensive that even intact checkpoints cannot contain it. The message is clear: genomes are most vulnerable to complex, multi-chromosome rearrangements when the checkpoints that police DNA integrity and spindle function fail to stop the cell cycle.

Direct examination of the double mutants themselves confirmed the picture. Flow cytometry of roughly 80 independent mutants from each of 43 highly unstable deletion strains revealed that DNA content was often substantially increased or decreased relative to the diploid ancestors, with the variance in DNA content among mutants significantly exceeding that among ancestral replicates. Whole-genome sequencing of mutants from 20 deletion strains went further. The dominant alteration was whole-chromosome aneuploidy, frequently affecting multiple chromosomes beyond the two targeted by selection, with many chromosomes showing non-integer coverage values that indicated mixed populations of cells carrying different chromosome counts. Averaged across all strains and chromosomes, deviations from diploidy appeared in nearly every mutant examined. Crucially, the chromosomes under direct selection, V and XV, showed no more than the average number of changes, evidence that selection at two sites was merely revealing systemic destabilization rather than focused local mutation. Heterozygous point mutations were rare, and the team found essentially no segmental copy number variants, no non-homologous recombination products and no convincing translocations or inversions in non-telomeric regions, despite deliberately validating that their pipelines could detect all such events.

Genetic tests of four particularly unstable strains, deleted for sem1, chl1, mre11 or rad27, provided independent confirmation. When double mutants from these strains were screened for retention of heterozygosity at two additional marker loci on chromosomes II and XII, the frequencies of additional losses were extraordinarily high. In the sem1 background, for example, 16 of 61 double mutants had also lost heterozygosity on chromosome II and 14 on chromosome XII, with 7 losing both, even though such losses normally occur at a rate of only one to a few per ten thousand cell divisions. Triple and quadruple LOH events appeared at frequencies far beyond anything a sequential model could accommodate, reinforcing the conclusion that short periods of hyper-instability, rather than a string of independent accidents, generate these genomes.

The final experiments addressed what happens to these dramatically rearranged genomes over evolutionary time. The team propagated 63 mutant cultures derived from 21 deletion strains for 200 generations in batch culture and re-measured their DNA content. The result was a nearly uniform contraction toward diploidy: strains that started far from two chromosome sets moved markedly closer, and the most divergent isolates showed the greatest fitness gains, growing faster after evolution than before. Aneuploidy, in other words, is typically a transient state, imposed as a cost of rapid adaptation and then pruned by natural selection as faster-growing re-diploidized variants outcompete their unstable relatives. The authors suggest that this ephemerality is exactly why such bursts are so hard to catch in nature, since selection rapidly erases the evidence of a genomic episode.

The findings carry implications well beyond yeast. In free-living microbes, aneuploidy usually slows growth and is quickly eliminated, but it may pay off under multiple stresses, such as exposure to several toxins at once. In the somatic cells of multicellular organisms, the calculus is different. These cells are programmed not to divide, so there is no immediate growth cost to genome restructuring, and a loosening of the brakes on cell division can incidentally expose recessive alleles, a mechanism central to cancer, where the loss of the remaining wild-type copy of a tumor suppressor gene is the classic second hit. The study suggests that failures of cell cycle control may be a common source of the large-scale chromosomal changes that dismantle multiple adaptation barriers during tumor evolution. Complex genome change, on this view, rarely arrives as a leisurely accumulation of small steps; it tends to arrive as a burst, born of a momentarily failing control system, and natural selection then decides what, if anything, survives.

Subject of Research: Loss of heterozygosity and aneuploidy driven by cell cycle control defects in diploid budding yeast

Article Title: Burst of aneuploidy: a cost of adaptation driven by breakdown of cell cycle control

Article References: Pirog, A., Tutaj, H., Tomala, K., & Korona, R. (2026). Burst of aneuploidy: a cost of adaptation driven by breakdown of cell cycle control. Molecular Systems Biology, 22(8), 1292-1311. https://doi.org/10.1038/s44320-026-00217-6

Image Credits: AI Generated

DOI: 10.1038/s44320-026-00217-6

Keywords: aneuploidy, loss of heterozygosity, cell cycle checkpoints, Saccharomyces cerevisiae, genome instability, mitosis, chromosome segregation, DNA repair, mutation rate, experimental evolution, cancer, genome rearrangements