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Tumor mutational burden

Tumor mutational burden (TMB) is defined as the total number of somatic mutations per megabase of interrogated genomic sequence in a tumor's DNA, reflecting the extent of genomic instability and potential for generating neoantigens that can elicit an immune response.^[1] This quantitative measure serves as a key predictive biomarker for the efficacy of immune checkpoint inhibitors (ICIs), such as anti-PD-1/PD-L1 therapies, particularly in solid tumors where higher TMB levels correlate with improved response rates and survival outcomes.^[1] For instance, the U.S. Food and Drug Administration (FDA) approved pembrolizumab in 2020 for adult and pediatric patients with unresectable or metastatic solid tumors exhibiting a TMB of ≥10 mutations per megabase, based on data from clinical trials like KEYNOTE-158.^[1] TMB is typically assessed through next-generation sequencing (NGS) of tumor tissue, with whole exome sequencing (WES) serving as the gold standard by covering approximately 30 megabases of coding regions, though targeted gene panels (e.g., 0.8–2.4 Mb in size, such as MSK-IMPACT or FoundationOne CDx) are more commonly used in clinical settings for their efficiency and cost-effectiveness.^[1] These panels focus on hundreds of cancer-related genes and calculate TMB by counting non-synonymous somatic variants, often excluding germline mutations, driver alterations, and sometimes synonymous changes to emphasize passenger mutations that drive immunogenicity.^[2] Blood-based TMB (bTMB), derived from circulating tumor DNA, offers a non-invasive alternative, showing concordance with tissue TMB and utility in monitoring treatment response, though it requires validation for broader adoption.^[3] Clinically, TMB varies significantly across tumor types, with higher burdens observed in cancers like melanoma (median ~71% high TMB cases), non-small cell lung cancer (44–50%), and microsatellite instability-high (MSI-H) tumors, while lower levels predominate in pediatric cancers, which have notably low TMB (typically <1 mut/Mb, with an average of ~9.6 total nonsynonymous mutations per tumor), and breast cancer.^[1] Approximately 13.2% of patients in the KEYNOTE-158 trial qualified as TMB-high, highlighting its relevance in stratifying patients for ICI therapy across pan-cancer settings.^[1] Despite these advances, challenges persist, including the lack of universal cutoffs (typically 10–20 mut/Mb but tumor-type dependent), variability in assay performance due to panel size and bioinformatics pipelines, and issues with tumor purity, intratumor heterogeneity, and sample quality that can lead to inconsistent reporting. As of 2025, emerging research continues to refine TMB cutoffs, questioning the one-size-fits-all approach of 10 mut/Mb for optimal immunotherapy prediction.^[4]^[5] Ongoing standardization efforts, such as those by Friends of Cancer Research and the Quality Assurance Initiative Pathology, aim to harmonize TMB assessment by recommending panels of at least 1 Mb and alignment with WES benchmarks to ensure reliable clinical decision-making.^[5]

Definition and Background

Core Concept of TMB

Tumor mutational burden (TMB) quantifies the density of somatic mutations within a tumor's genome, specifically the total number of non-synonymous mutations—such as missense, nonsense, and frameshift variants—per megabase of sequenced exome or genome, while excluding germline variants.^[6]^[7] This metric focuses on coding regions where mutations can alter protein sequences, providing a measure of the tumor's genomic instability and potential for immune recognition.^[8] The biological foundation of TMB lies in its role as a proxy for neoantigen load, where somatic mutations generate novel peptides that are processed and presented on the tumor cell surface via major histocompatibility complex (MHC) molecules. These neoantigens can be recognized by T-cells, thereby enhancing the tumor's immunogenicity and facilitating immune-mediated destruction. High TMB thus correlates with increased likelihood of effective antitumor immune responses, as more mutations diversify the neoantigen repertoire available for T-cell targeting.^[1] TMB is typically expressed in units of mutations per megabase (mut/Mb), allowing for standardized comparisons across samples. Measurements can differ based on the sequencing approach: whole exome sequencing (WES) provides a comprehensive assessment of the ~30-60 Mb coding genome, yielding a direct mut/Mb value, whereas targeted gene panels interrogate smaller subsets of genes and often require algorithmic normalization to estimate equivalent TMB scores.^[1] For instance, in non-small cell lung cancer (NSCLC), median TMB values range from approximately 5-10 mut/Mb among smokers, reflecting tobacco-induced mutagenesis, compared to lower levels around 4 mut/Mb in never-smokers.^[9] High TMB has been linked to enhanced responses in immunotherapy, underscoring its relevance in precision oncology.^[7]

Historical Development

The concept of tumor mutational burden (TMB) emerged in the early 2010s through large-scale genomic initiatives like The Cancer Genome Atlas (TCGA), which began sequencing tumor exomes across multiple cancer types starting in 2006 and published pan-cancer analyses by 2013. These efforts revealed wide variations in somatic mutation loads among cancers, with initial observations linking higher mutation burdens to increased immune cell infiltration, such as CD8+ T cells, suggesting a potential role in antitumor immunity.^[10] By cataloging thousands of tumors, TCGA data laid the groundwork for understanding TMB as a quantitative measure of genomic instability, influencing subsequent research on neoantigen generation and immune recognition. Pivotal clinical studies in the mid-2010s established TMB's association with immunotherapy responses. In 2014, Snyder et al. analyzed exomes from melanoma patients treated with ipilimumab, a CTLA-4 inhibitor, finding that responders had significantly higher somatic mutation burdens compared to non-responders, correlating with neoantigen load and clinical benefit.^[11] This was followed in 2015 by Rizvi et al., who examined non-small cell lung cancer (NSCLC) tumors from patients receiving pembrolizumab, a PD-1 inhibitor, and reported that higher nonsynonymous mutation burdens (median 12.4 in responders vs. 6.7 in non-responders) predicted durable responses, independent of smoking history. These findings shifted TMB from a descriptive genomic metric to a candidate predictive biomarker for immune checkpoint blockade. Regulatory milestones accelerated TMB's clinical adoption. In June 2020, the U.S. Food and Drug Administration (FDA) granted accelerated approval for pembrolizumab as a tumor-agnostic therapy in adult and pediatric patients with unresectable or metastatic solid tumors characterized by TMB-high status (≥10 mutations per megabase), based on data from the KEYNOTE-158 trial showing an objective response rate of 29.3% in this group. Concurrently, efforts by the Friends of Cancer Research TMB Harmonization Project, launched in 2017, addressed variability in TMB measurement across assays through multi-lab collaborations and reference standards, promoting standardization from a research tool to a reproducible clinical assay.^[12] By 2024, ongoing initiatives expanded TMB's utility in combination therapies, with subgroup analyses in trials like KEYNOTE-942 showing benefits across TMB and PD-L1 statuses in melanoma adjuvant therapy. In 2023, a phase 3 trial (KEYNOTE-B15) was initiated to further evaluate mRNA-4157 plus pembrolizumab in high-risk melanoma. As of 2025, research explores acquired high TMB post-targeted therapy to enhance immunotherapy sensitivity.^[13]^[14]

Clinical Significance

Biomarker Role in Immunotherapy

Tumor mutational burden (TMB) serves as a predictive biomarker for response to immune checkpoint inhibitors (ICIs), with the U.S. Food and Drug Administration (FDA) granting accelerated approval in June 2020 for pembrolizumab in adult and pediatric patients with unresectable or metastatic solid tumors exhibiting high TMB (≥10 mutations per megabase, mut/Mb), as determined by an FDA-approved companion diagnostic test.^[15] This tumor-agnostic approval highlights TMB's role independent of programmed death-ligand 1 (PD-L1) expression, enabling broader application across cancer types where ICI efficacy was previously limited by PD-L1 status.^[15] Mechanistically, elevated TMB correlates with a higher neoantigen burden, as somatic mutations generate novel peptides presented on major histocompatibility complex molecules, thereby enhancing T-cell recognition and infiltration into the tumor microenvironment.^[16] This increased immunogenicity promotes tumor-infiltrating lymphocytes (TILs), particularly cytotoxic T cells, which synergize with ICIs such as anti-PD-1 and anti-PD-L1 therapies to reinvigorate exhausted immune responses and improve antitumor activity.^[17] Consequently, tumors with high TMB exhibit greater sensitivity to checkpoint blockade compared to those with low TMB, where neoantigen scarcity limits immune activation.^[16] Meta-analyses of patients treated with ICIs substantiate TMB's predictive value, demonstrating that high TMB cohorts achieve significantly better progression-free survival (PFS) than low TMB groups, with pooled hazard ratios (HRs) ranging from 0.45 to 0.54.^[18]^[19] For instance, one analysis of over 4,500 patients across multiple studies reported an HR of 0.45 (95% CI: 0.36–0.56) for PFS in high versus low TMB, underscoring TMB's association with prolonged ICI benefit.^[18] Another meta-analysis in non-small cell lung cancer confirmed an HR of 0.54 (95% CI: 0.46–0.63), reinforcing TMB's utility in stratifying ICI responders.^[19] TMB's predictive strength varies by cancer type, proving more robust in non-smoker-associated malignancies such as microsatellite instability-high (MSI-H) colorectal cancer, where high TMB aligns closely with enhanced ICI responses due to shared defect-driven hypermutation.^[20] In contrast, its predictive value is attenuated in smoker-linked cancers like lung adenocarcinoma, where environmental mutagens confound TMB's direct correlation with neoantigen immunogenicity and ICI efficacy.^[20] This specificity highlights TMB's contextual limitations as a pan-cancer biomarker, emphasizing the need for integrated assessments in diverse tumor etiologies.^[17]

Predictive Value for Treatment Response

Tumor mutational burden (TMB) serves as a predictive biomarker for response to immunotherapy, particularly immune checkpoint inhibitors, with high TMB levels associated with improved objective response rates (ORR), progression-free survival (PFS), and overall survival (OS) in various clinical trials.^[21] In the phase 2 KEYNOTE-158 trial evaluating pembrolizumab in patients with advanced solid tumors, those with high TMB (≥10 mutations per megabase) demonstrated an ORR of 29% compared to 10% in patients with low TMB, highlighting TMB's utility across tumor types independent of microsatellite instability status.^[21] This trial's results supported the FDA approval of pembrolizumab for TMB-high solid tumors, underscoring the biomarker’s role in identifying responders to PD-1 inhibition.^[15] Recent updates from CheckMate trials in non-small cell lung cancer (NSCLC) further affirm TMB's predictive value. In the phase 3 CheckMate 227 trial, patients with high TMB treated with nivolumab plus ipilimumab showed durable OS benefits, with 5-year OS rates exceeding those in chemotherapy arms, particularly in TMB-high subgroups.^[22] Analyses from the CA209-7AL trial in unresectable stage III NSCLC revealed that high TMB patients receiving consolidative nivolumab after neoadjuvant therapy achieved significantly longer PFS (not reached versus 15.2 months in low TMB; p=0.042).^[23] These findings extend TMB's relevance to perioperative and consolidative settings, where high TMB predicted enhanced treatment efficacy.^[23] High TMB correlates with higher rates of complete and partial responses, as well as extended duration of response (DOR). For instance, in melanoma patients treated with PD-1 inhibitors, high TMB subgroups exhibited ORRs up to 45%, reflecting increased neoantigen load and immune activation.^[24] Across trials like KEYNOTE-158, DOR in TMB-high patients was notably prolonged, often not reached at median follow-up, compared to 12-18 months in low TMB cohorts, representing an extension of 6-12 months or more in responsive cases.^[15] This benefit is most pronounced with PD-1 inhibitors such as pembrolizumab and nivolumab, where high TMB independently predicts superior outcomes, whereas responses to CTLA-4 inhibitors like ipilimumab alone are weaker and less TMB-dependent.^[24] Subgroup analyses emphasize TMB's value beyond microsatellite instability-high tumors. In microsatellite-stable (MSS) tumors with high TMB, immunotherapy yields significant benefits, with ORRs comparable to MSI-high cases and improved PFS in PD-1-treated patients.^[25] For rare cancers like small cell lung cancer (SCLC), a 2025 real-world analysis across multiple cancers including SCLC showed a non-significant trend toward better overall survival with high TMB (HR 0.89, 95% CI 0.44-1.09) on immune checkpoint inhibition, supporting further evaluation of TMB in metastatic SCLC immunotherapy.^[26] These insights support TMB-high/MSS identification for expanded immunotherapy access in underrepresented tumor types.^[26]

Prognostic Implications

Tumor mutational burden (TMB) serves as an intrinsic prognostic biomarker in cancer patients, particularly in cohorts not receiving immunotherapy, where high TMB frequently correlates with poorer overall survival due to underlying tumor aggressiveness. In a systematic pan-cancer evaluation of The Cancer Genome Atlas (TCGA) data encompassing 6,035 patients across 20 cancer types, high TMB was significantly associated with worse overall survival in 8 cancers, including adrenocortical carcinoma (hazard ratio [HR] 2.47, 95% CI 1.02–5.98, P=0.045), cholangiocarcinoma (HR 6.10, 95% CI 1.91–19.46, P=0.002), colorectal adenocarcinoma, esophageal carcinoma, kidney renal clear cell carcinoma, liver hepatocellular carcinoma, mesothelioma, and pancreatic adenocarcinoma.^[27] Conversely, high TMB predicted better survival in 6 cancer types, such as bladder urothelial carcinoma and kidney renal papillary cell carcinoma, while showing no significant impact in the remaining 6. This divergent pattern underscores TMB's context-specific prognostic utility for risk stratification independent of treatment.^[27] In immunotherapy-naïve patients with advanced malignancies, TMB exhibits a nonlinear relationship with survival, where intermediate levels (>5 and <20 mutations/Mb) confer the worst outcomes compared to low (≤5 mutations/Mb) or high (≥20 mutations/Mb) burdens. Among 1,415 such patients, those with intermediate TMB had a median overall survival of 174 weeks (HR 1.29, 95% CI 1.07–1.54, P<0.01) versus 238 weeks for low TMB, while high TMB yielded 195 weeks (HR 0.98, P=0.90), suggesting that moderate mutational loads may reflect suboptimal immune equilibrium without therapeutic intervention.^[28] Although high TMB often signals favorable responses in immunotherapy contexts, its prognostic implications in chemotherapy-only or untreated settings are generally adverse, as evidenced by mixed signals in pan-cancer analyses where elevated TMB aligns with reduced survival in over half of evaluated cohorts.^[29] The adverse prognostic role of high TMB in non-immunotherapy scenarios stems from its reflection of genomic instability, driven by defects in DNA repair pathways such as mismatch repair and nucleotide excision repair, which foster tumor proliferation, chromosomal aberrations, and heightened metastasis risk. This instability correlates with aggressive tumor biology, including increased cell cycle activity and structural variants that promote invasive growth, thereby worsening patient outcomes independent of immune checkpoint modulation. For instance, high TMB also enables neoantigen generation that could enhance immune surveillance, but in untreated settings, the dominant effect is unchecked genomic chaos leading to rapid disease progression.^[29]^[30] Specific examples highlight TMB's variable prognostic weight across histologies. In gliomas, elevated TMB is linked to shorter overall survival, with higher burdens associating with advanced grade, older age, and structural mutations that exacerbate poor outcomes in this immunologically "cold" tumor type.^[31] In contrast, breast cancer demonstrates largely neutral TMB-prognosis associations in non-immunotherapy cohorts, where high TMB does not independently influence survival unless integrated with factors like immune infiltration or specific gene signatures, reflecting the hormone-driven stability of many breast tumors.^[32]

Variation Across Cancer Types

Cancers with High TMB

Tumor mutational burden (TMB) is considered high when exceeding 10 mutations per megabase (mut/Mb), a threshold commonly used for classification in clinical and research settings.^[33] Approximately 13% of solid tumors across various cohorts meet this criterion, highlighting a subset of malignancies with elevated genomic instability that may influence therapeutic strategies.^[34] Among cancers frequently exhibiting high TMB, cutaneous melanoma stands out with median values of 10-14 mut/Mb, primarily driven by ultraviolet (UV) radiation exposure that induces characteristic C>T transitions.^[35] Non-small cell lung cancer (NSCLC) in smokers also shows elevated TMB, with medians around 10-12 mut/Mb attributable to tobacco mutagens causing G>T transversions.^[1] Microsatellite instability-high (MSI-high) colorectal cancers, resulting from DNA mismatch repair deficiency, often display markedly higher TMB levels exceeding 50 mut/Mb, reflecting hypermutation due to unrepaired replication errors.^[36] Endometrial cancers harboring POLE proofreading domain mutations represent another example, where these hereditary alterations lead to ultrahigh TMB often surpassing 100 mut/Mb through polymerase infidelity.^[37] Elevated TMB in these cancers arises from diverse etiologies, including environmental factors like UV light in melanoma and smoking in NSCLC, endogenous processes such as APOBEC cytidine deaminase hyperactivity contributing to clustered mutations in multiple tumor types, and hereditary defects like POLE mutations in endometrial carcinoma.^[1] Virus-negative Merkel cell carcinoma, distinct from polyomavirus-positive cases, exhibits high TMB (often >20 mut/Mb) linked to UV signatures, with 2025 analyses confirming its association with aggressive disease and potential immunotherapy responsiveness.^[38] Clinically, high-TMB cancers demonstrate improved outcomes with immune checkpoint inhibitors (ICIs), with objective response rates of approximately 20-30% in pan-solid tumor cohorts treated with anti-PD-1/PD-L1 therapies, underscoring TMB's role as a predictive biomarker.^[39]

Cancers with Low TMB

Tumor mutational burden (TMB) is generally low in the majority of adult solid tumors, reflecting limited exposure to environmental mutagens and proficient DNA repair mechanisms across these cancer types.^[40]^[1] Pediatric tumors characteristically display very low TMB, often below 1 mut/Mb, as evidenced by pan-cancer analyses reporting medians as low as 0.09 mut/Mb, attributed to their embryonal origins and reduced lifetime accumulation of somatic mutations compared to adult cancers.^[35]^[41] Similarly, IDH-mutant gliomas maintain low TMB levels, typically ranging from 1 to 3 mut/Mb, with the vast majority below 2 mut/Mb, due to intact mismatch repair pathways and limited hypermutator phenotypes in these tumors.^[42] Prostate cancers also feature low TMB, averaging 2 to 4 mut/Mb and driven primarily by androgen signaling rather than mutagenic processes, further supported by high-TMB subsets being rare (approximately 2–5% of cases).^[43]^[44]^[45]^[46] The inherently low TMB in these cancers stems from multiple factors, including minimal exposure to exogenous mutagens such as UV radiation or tobacco smoke, which contrasts with high-TMB tumors like melanomas or lung cancers.^[47] Efficient DNA repair mechanisms, such as wild-type BRCA1/2 status and proficient mismatch repair, prevent mutation accumulation in low-TMB cancers like prostate and IDH-mutant gliomas.^[1] Additionally, suppressive tumor microenvironments in these immunologically "cold" tumors, characterized by low T-cell infiltration, further limit neoantigen presentation and mutational evolution.^[48] Clinically, low-TMB cancers exhibit poorer responses to immune checkpoint inhibitors (ICIs), with objective response rates often below 10%, as demonstrated in pan-tumor cohorts where low-TMB groups showed only 6-9% efficacy compared to higher rates in TMB-elevated subsets.^[49] In low-TMB breast cancer, 2024 analyses have highlighted alternative biomarkers, such as T-cell inflamed gene expression signatures, which correlate with improved prognosis and potential ICI benefit independent of TMB, emphasizing the need for multifaceted immune profiling in therapy selection.^[50] These characteristics underscore the challenges in applying TMB-based immunotherapy to low-TMB cancers, prompting exploration of targeted therapies tailored to their molecular drivers.^[26]

Measurement Methods

Sequencing Approaches

Tumor mutational burden (TMB) assessment relies on genomic sequencing to detect somatic mutations in tumor DNA, with various approaches balancing comprehensiveness, cost, and clinical feasibility.^[1] The primary methods include whole exome sequencing (WES), targeted next-generation sequencing (NGS) panels, and whole genome sequencing (WGS), each leveraging high-throughput platforms to quantify mutations per megabase in coding regions.^[51] These techniques typically require paired tumor-normal samples to distinguish somatic from germline variants, though tumor-only approaches are increasingly used with computational adjustments.^[52] Whole exome sequencing (WES) serves as the gold standard for TMB measurement due to its unbiased capture of protein-coding variants across approximately 2% of the human genome, focusing on the ~20,000 genes and 30-60 megabases of exonic sequence.^[51] To ensure accurate detection of low-frequency subclonal mutations in heterogeneous tumors, WES typically demands high sequencing depth of 100-300x coverage for both tumor and matched normal samples.^[1] This method provides a direct count of somatic mutations without extrapolation, making it ideal for research benchmarks, though its broader genomic scope increases data volume and processing demands compared to targeted alternatives.^[53] In clinical settings, targeted NGS panels have become the standard for TMB evaluation, interrogating 300-500 cancer-relevant genes to assess mutations within a focused genomic space of 1-2 megabases, which is then extrapolated to estimate whole-exome equivalents.^[54] Prominent examples include the MSK-IMPACT panel, which sequences 505 genes at depths exceeding 500x, and FoundationOne CDx, a 324-gene assay approved by the FDA for companion diagnostics, both demonstrating strong concordance (r > 0.9) with WES-derived TMB values in validation studies.^[51] These panels prioritize actionable alterations alongside TMB, enabling efficient integration into routine oncology workflows while minimizing off-target noise from non-coding regions.^[55] Whole genome sequencing (WGS) offers the most comprehensive TMB assessment by capturing all somatic mutations across the entire 3-billion-base-pair genome, including non-coding variants that may influence tumor biology or immune recognition.^[56] However, its resource-intensive nature—requiring terabytes of data storage, extended computational runtimes, and costs 10-100 times higher than WES—limits routine adoption to specialized research cohorts, such as those exploring pan-cancer mutational landscapes.^[1] WGS excels in detecting indels, copy number variations, and structural rearrangements that contribute to overall mutational load but is less practical for high-throughput clinical TMB screening.^[57] Most TMB sequencing employs short-read platforms like Illumina's NovaSeq systems, which generate 100-300 base-pair reads with >99.9% accuracy, supporting the high-depth requirements of WES and targeted panels through massively parallel sequencing.^[58] Emerging long-read technologies, such as PacBio's HiFi sequencing, are gaining traction for resolving complex structural variants and repetitive regions that short-read methods struggle with, potentially enhancing TMB accuracy in structurally heterogeneous tumors by 2025.^[59] Additionally, liquid biopsy approaches using circulating tumor DNA (ctDNA) are seeing increased adoption by late 2025, with NGS-based assays like those from Guardant Health enabling non-invasive TMB monitoring from blood samples, though sensitivity remains lower (detecting down to approximately 0.1–0.5% variant allele frequencies) compared to tissue-based methods.^[60]

Calculation Formulas and Pipelines

Tumor mutational burden (TMB) is fundamentally calculated as the number of somatic non-synonymous mutations per megabase (Mb) of the exome, excluding synonymous mutations, intronic variants, and germline alterations unless otherwise specified in the assay protocol.^[1] For whole-exome sequencing (WES), the exome size is typically standardized at 38 Mb to enable consistent normalization across samples.^[40] The core formula can be expressed as:

\text{TMB} = \frac{\sum \text{somatic non-synonymous mutations}}{38}

where the denominator represents the exome size in Mb, yielding mutations per Mb (mut/Mb).^[61] The computational pipeline for deriving TMB from sequencing data involves several sequential steps to ensure accuracy and reproducibility. Initial read alignment is performed using tools like the Genome Analysis Toolkit (GATK) to map tumor and matched normal sequences to a reference genome, followed by preprocessing to mark duplicates and perform base quality score recalibration.^[62] Variant calling then identifies somatic single-nucleotide variants (SNVs) and insertions/deletions (indels), commonly employing MuTect2, which models tumor-specific noise and compares against the matched normal to distinguish somatic from germline events.^[63] Germline filtering is applied using resources like the Genome Aggregation Database (gnomAD) to remove common polymorphisms, retaining only high-confidence somatic calls.^[64] Annotation of variants occurs next, often with the Variant Effect Predictor (VEP) tool, to classify mutations as non-synonymous (e.g., missense, nonsense) and filter out non-coding or synonymous changes.^[65] Finally, burden normalization computes TMB by dividing the count of qualifying somatic mutations by the effectively covered exome size in Mb, accounting for sequencing depth and panel-specific regions if not using WES.^[66] Adjustments to the standard TMB calculation may incorporate distinctions between passenger and driver mutations, as well as clonal versus subclonal variants, to refine estimates for clinical relevance. While TMB traditionally includes both passenger (neutral) and driver (oncogenic) mutations to reflect overall neoantigen potential, some pipelines exclude known drivers or apply weights to emphasize passengers, which constitute the majority of somatic events.^[67] For clonality, subclonal mutations (present in tumor subpopulations) are often downweighted or excluded relative to clonal ones, as they may dilute predictive signals for immunotherapy response.^[68] Tumor purity adjustments are critical, particularly in heterogeneous samples, using an extended formula such as:

\text{TMB}_{\text{adjusted}} = \frac{\sum \text{somatic mutations}}{\text{covered Mb} \times \text{purity estimate}}

where purity is derived from tools like FACETS or ABSOLUTE to correct for stromal contamination.^[69] Recent standards emphasize pipeline reproducibility, with the 2024 Association for Molecular Pathology (AMP), American Society of Clinical Oncology (ASCO), College of American Pathologists (CAP), and Society for Immunotherapy of Cancer (SITC) consensus recommendations advocating detailed documentation of variant calling thresholds, filtering criteria, and normalization methods to minimize inter-assay variability.^[70] Custom scripts, often integrated with GATK workflows, handle Mb normalization, while open-source tools like TMBcalc provide end-to-end pipelines for pan-cancer TMB computation, ensuring alignment with these guidelines.^[66]

Influencing Factors and Standardization

Biological and Technical Variables

Tumor purity, defined as the proportion of cancer cells within a tumor sample relative to non-cancerous components such as stromal or inflammatory cells, significantly influences tumor mutational burden (TMB) estimation. Low tumor purity dilutes the signal from somatic mutations, leading to underestimation of TMB, as non-tumor cells contribute fewer mutations and reduce the variant allele frequency (VAF) of true tumor variants. Guidelines recommend a minimum tumor purity of 20% for reliable tissue-based panel sequencing assays to ensure sufficient sensitivity in detecting mutations above a typical 5% VAF threshold. Computational tools like ABSOLUTE can estimate tumor purity from sequencing data by integrating copy number alterations and allele frequencies, enabling purity-adjusted TMB calculations that improve accuracy in samples with 15-40% purity. Infiltration by immune or tumor microenvironment (TME) cells further complicates estimates, as lower purity correlates with reduced TMB sensitivity and potential false negatives in immunotherapy response prediction. Tumor heterogeneity, both spatial and temporal, introduces variability in TMB measurements by causing differences in mutation profiles across tumor regions or over time. Spatial heterogeneity arises from subclonal evolution, where distinct tumor areas harbor varying mutation burdens, leading to discordant TMB values between biopsy sites; for instance, in pulmonary adenocarcinoma, intratumor regions can show marked differences in somatic mutations that affect panel-based TMB assessments. Temporal heterogeneity, driven by treatment effects or disease progression, can alter TMB as new mutations emerge or subclones expand, as observed in gastroesophageal adenocarcinoma where baseline and post-treatment samples exhibited heterogeneous TMB and PD-L1 expression. This variability underscores the need for multi-region sampling to capture representative TMB, though single biopsies may underestimate overall burden due to sampling bias. Sequencing coverage, or depth, is a critical technical variable affecting TMB accuracy, as insufficient depth fails to detect low-frequency mutations while uneven coverage biases detection toward mutation hotspots. A minimum coverage of 100x is generally required for reliable variant calling in TMB assays, with 250x or higher recommended for subclonal or low-VAF mutations to minimize false negatives; however, TMB estimates remain sensitive to depth variations, with lower depths leading to inconsistent somatic mutation counts above typical thresholds like 5% VAF. High-depth sequencing, such as >750x in targeted panels, enhances stability but increases costs, particularly for heterogeneous tumors where uniform coverage across the genome is challenging. Preprocessing factors, including sample fixation and DNA quality, can introduce artifacts that skew TMB results. Formalin-fixed paraffin-embedded (FFPE) tissues, commonly used in clinical settings, cause DNA damage via cytosine deamination, resulting in artifactual C>T transitions that inflate TMB by mimicking somatic mutations. Fresh frozen samples are preferred to avoid these artifacts, as they yield higher-quality DNA with fewer false positives; FFPE-derived DNA requires quality metrics like fragment lengths exceeding 150 bp to ensure reliable library preparation and sequencing. Microbial contamination in sequencing reads, often from laboratory reagents or environmental sources, can further bias TMB by introducing non-human variants or diluting tumor signal if not filtered, necessitating computational decontamination pipelines to maintain estimate integrity.

Cutoff Determination and Harmonization

Determining appropriate cutoffs for tumor mutational burden (TMB) is essential for identifying patients likely to benefit from immunotherapy, with the U.S. Food and Drug Administration (FDA) establishing a threshold of ≥10 mutations per megabase (mut/Mb) for high TMB in solid tumors based on the KEYNOTE-158 trial, which supported approval of pembrolizumab for this group.^[71] Cancer-specific cutoffs often vary to account for inherent differences in mutational landscapes; for instance, melanoma studies frequently employ a higher threshold of 20 mut/Mb to classify high TMB, reflecting its elevated baseline mutation rates compared to other cancers.^[72] Additionally, percentile-based approaches, such as designating the top 20% of TMB values within a specific cancer type as high, provide a relative framework that adapts to population-level data and enhances prognostic relevance across diverse cohorts.^[32] Efforts to harmonize TMB measurements address discrepancies arising from assay differences, with the Friends of Cancer Research (FOCR) TMB Harmonization Project, culminating in key findings by 2024, demonstrating that inter-laboratory comparisons exhibit 20-30% variability due to panel size, gene coverage, and bioinformatics pipelines.^[73] Phase II of this initiative developed calibration models to align targeted next-generation sequencing panels with whole-exome sequencing (WES) references, promoting consistent TMB estimation and reducing classification discordance for high versus low TMB.^[74] Validation of TMB assays relies on proficiency testing programs, such as those offered by the College of American Pathologists (CAP), which evaluate laboratory performance using standardized samples to ensure reliable quantification across clinical settings.^[75] Reference materials, including those developed through FOCR collaborations, facilitate calibration by providing benchmarks for somatic mutation detection, minimizing technical biases in TMB reporting.^[76] Recent guidelines from the Association for Molecular Pathology (AMP), CAP, and Society for Immunotherapy of Cancer integrate WES as a gold standard with panel-based assays, demonstrating high correlation (often >0.85) between WES and panel-based TMB measurements when appropriate calibration is applied, thereby supporting broader clinical adoption and comparability.^[77]

Challenges and Limitations

Assay and Interpretation Issues

One major challenge in TMB assays is reproducibility, particularly the discordance between targeted next-generation sequencing (NGS) panels and whole-exome sequencing (WES), which can reach up to 40% due to differences in coverage and variant detection sensitivity.^[78] Batch effects in NGS further compromise reproducibility, as variations in library preparation, sequencing depth, and bioinformatics pipelines can lead to inconsistent TMB estimates across runs or laboratories.^[78] Recent 2024 studies have highlighted that formalin-fixed paraffin-embedded (FFPE) artifacts, such as deamination-induced C>T transitions, contribute to false-high TMB calls, necessitating stringent variant allele frequency (VAF) thresholds to mitigate these errors.^[79] Interpretation of TMB results is prone to pitfalls that can distort clinical relevance. Overcounting mutations in hypermutated regions, often driven by positive selection in cancer genes captured by targeted panels, leads to systematic overestimation of TMB compared to genome-wide assessments.^[80] Ignoring tumor evolution exacerbates this, as spatial and temporal heterogeneity—resulting from clonal dynamics and neoantigen loss—causes TMB variability across tumor sites or over time, potentially misrepresenting immunogenicity.^[81] Liquid biopsy approaches, reliant on circulating tumor DNA (ctDNA), frequently underestimate TMB due to variable shedding rates, with high TMB rarely detectable below 1% ctDNA fraction, limiting their utility in low-shedding tumors.^[82] Validation gaps persist in TMB assays, underscored by the scarcity of prospective trials demonstrating consistent predictive value across diverse cohorts. Inter-assay variability compounds this, arising from variations in panel size, germline filtering, and synonymous mutation inclusion, as seen between platforms like FoundationOne CDx and MSK-IMPACT.^[1] Emerging issues involve AI integration in variant calling, where biases toward high-confidence calls can amplify errors in heterogeneous samples. 2025 reports indicate AI models are susceptible to overfitting in low-coverage data, reducing accuracy in TMB quantification for suboptimal sequencing inputs like those from liquid biopsies.^[83] These challenges highlight the need for harmonized protocols to enhance assay reliability, as explored in ongoing standardization efforts.^[77]

Clinical and Regulatory Hurdles

Despite its promise as a predictive biomarker for immunotherapy response, tumor mutational burden (TMB) exhibits inconsistent pan-cancer performance, limiting its clinical utility in routine practice. For instance, while high TMB correlates with improved outcomes in certain immunogenic tumors like non-small cell lung cancer and melanoma, it fails to reliably predict responses in others, such as those with low TMB but alternative responsiveness mechanisms, including microsatellite instability-high (MSI-H) colorectal cancers where neoantigen load drives efficacy independently of TMB levels.^[84] Moreover, retrospective analyses underpinning key approvals, such as the KEYNOTE-158 trial for pembrolizumab, introduce selection biases that overestimate TMB's predictive value, as post-hoc assessments may not capture real-world variability in patient cohorts.^[71] These limitations highlight evidence gaps, with response rates in high-TMB cohorts (≥20 mutations/Mb) varying across studies, often around 30-60%.^[84] Regulatory hurdles further impede TMB's integration into clinical guidelines. The U.S. Food and Drug Administration (FDA) granted accelerated approval in 2020 for pembrolizumab in adults and pediatric patients with unresectable or metastatic TMB-high (≥10 mutations/Mb) solid tumors that have progressed following prior treatments and lack satisfactory alternatives, based on the KEYNOTE-158 basket trial demonstrating a 29% objective response rate.^[15] However, this remains an accelerated approval pending confirmatory trials, and controversies persist regarding the trial's reliance on a single companion diagnostic assay (FoundationOne CDx), raising concerns over generalizability. In contrast, the European Medicines Agency (EMA) has not approved pembrolizumab or any agent specifically for TMB-high indications, leading to regulatory variations across countries where TMB testing lacks harmonized endorsement and reimbursement pathways differ significantly.^[85] These discrepancies complicate global adoption, as evidenced by ongoing debates in 2024 about TMB's agnostic status versus the need for tumor-specific validations.^[86] Adoption barriers exacerbate these challenges, primarily driven by high testing costs and limited accessibility. Next-generation sequencing-based TMB assessments typically range from $3,000 to $5,000 per test in the U.S. as of 2025, often exceeding $5,000 when bundled with comprehensive genomic profiling, straining healthcare budgets and deterring widespread use.^[87] In low-resource settings, inadequate infrastructure and reimbursement mechanisms further restrict access, with surveys indicating that up to 59% of barriers to advanced sequencing stem from funding issues.^[88] Additionally, the requirement for FDA-approved companion diagnostics like FoundationOne CDx mandates specialized labs, creating logistical hurdles in diverse clinical environments. Ethical concerns around over-testing have intensified in 2024, as inconsistent TMB cutoffs and assay variability may lead to unnecessary immunotherapy in non-responders, raising issues of overtreatment, financial burden, and potential harm without clear prospective evidence.^[86] Debates continue on whether TMB should serve as a sole biomarker or be incorporated into composite scores with PD-L1 expression or tumor-infiltrating lymphocytes to mitigate these risks.^[86]

Future Directions

Integration with Other Biomarkers

Tumor mutational burden (TMB) is increasingly integrated with other biomarkers to enhance its predictive utility for immunotherapy response in precision oncology, addressing limitations such as variability across tumor types and incomplete correlation with clinical outcomes. Combining TMB with programmed death-ligand 1 (PD-L1) expression has shown improved prognostic accuracy; for instance, a composite score incorporating TMB, PD-L1 on immune cells, and CD39 expression achieved area under the curve (AUC) values of 0.649 for 12-month overall survival and 0.674 for 24-month survival in muscle-invasive bladder cancer patients treated with PD-L1 blockade, outperforming individual markers. Similarly, in advanced urothelial carcinoma, high TMB (≥175 mutations per exome) combined with PD-L1 combined positive score (CPS) ≥10 identified subgroups with superior progression-free survival and overall survival benefits from pembrolizumab monotherapy or with chemotherapy compared to chemotherapy alone. TMB also overlaps significantly with microsatellite instability (MSI), with approximately 80-100% of MSI-high cases in colorectal cancer exhibiting high TMB (≥10 mutations per megabase), allowing MSI status to serve as a complementary indicator for immunotherapy eligibility in TMB-assessed tumors. Neoantigen prediction tools further refine TMB's role by estimating immunogenic peptide loads from mutations; tools like pVAC-Seq and NetMHCpan-4.1 use whole-exome sequencing data to prioritize neoantigens based on TMB-derived variants, correlating higher predicted neoantigen burdens with improved responses to immune checkpoint inhibitors in non-small cell lung cancer and melanoma. Composite scores that incorporate TMB with immune-related metrics provide a more holistic assessment of tumor immunogenicity. The Tumor Immune Dysfunction and Exclusion (TIDE) score, derived from transcriptomic signatures of T-cell dysfunction and exclusion, is often combined with TMB to predict immunotherapy resistance; for example, in bladder cancer subtypes, TIDE-integrated analyses with TMB and neoantigen load identified immune evasion patterns, with lower TIDE scores in high-TMB groups associating with better checkpoint inhibitor efficacy. Recent multi-omics panels, such as those leveraging machine learning on genomic and histopathological data, integrate TMB with tumor-infiltrating lymphocyte (TIL) density; in colorectal cancer, a 20-gene TMB estimation model correlated with increased CD8+ TIL density (R=0.891 for neoantigen burden), enabling prognostic stratification independent of traditional TMB cutoffs. These 2025-era approaches, including lasso-based models from TCGA cohorts, emphasize TMB's synergy with TIL metrics to forecast progression-free survival. The primary benefits of these integrations include reduced false negatives among low-TMB patients who may still respond to immunotherapy due to other favorable immune features. Clonal TMB variants, when combined with neoantigen predictions, enhance specificity (0.8-0.9) for identifying true responders while minimizing misclassification in heterogeneous tumors like urothelial cancer. Clinical examples from 2024 meta-analyses in head and neck squamous cell carcinoma demonstrate this, where high TMB predicted superior overall response rates (odds ratio 2.62) and survival (hazard ratio 0.53) to immune checkpoint inhibitors across 1,200 patients, with integrations potentially capturing low-TMB subsets via PD-L1 or MSI overlays to broaden treatment access. As of October 2025, studies presented at ESMO highlighted AI-powered histopathology (e.g., Lunit AI) predicting immunotherapy outcomes in colorectal, kidney, and lung cancers, complementing TMB by analyzing H&E slides for immune features.^[89] Professional frameworks endorse TMB within multi-biomarker panels rather than as a standalone metric. The European Society for Medical Oncology (ESMO) guidelines recommend reporting TMB alongside other genomic biomarkers like MSI and homologous recombination deficiency in solid tumor assays, specifying validated thresholds (e.g., ≥10 mutations per megabase) and graphical visualizations to guide immune checkpoint blockade decisions.^[90] This approach ensures TMB contributes to personalized strategies without over-reliance on isolated thresholds.

Ongoing Research and Innovations

Recent phase III clinical trials in 2025 are investigating tumor mutational burden (TMB)-guided immune checkpoint inhibitors (ICIs) in rare tumors, such as the ongoing evaluation of pembrolizumab in advanced miscellaneous rare solid tumors.^[91] Additionally, studies like the envafolimab monotherapy trial in high-TMB advanced solid tumors highlight TMB's role in selecting patients across diverse histologies, including rarer subtypes.^[92] Longitudinal TMB tracking via liquid biopsy has emerged as a key focus for monitoring immunotherapy resistance, with 2025 research demonstrating that early on-treatment TMB dynamics in circulating tumor DNA predict response and clonal evolution in head and neck squamous cell carcinoma.^[93] Innovations in single-cell sequencing are advancing the understanding of intratumor TMB heterogeneity, enabling detection of low-frequency somatic variants and resistant subclones that bulk sequencing misses. Complementing this, artificial intelligence models are predicting TMB directly from hematoxylin and eosin-stained histopathology slides, achieving area under the curve accuracies of 0.910–0.934 in lung and colorectal cancers, which could streamline non-invasive assessments without genomic sequencing.^[94] Emerging research explores germline-tumor TMB interactions, where germline variants in DNA repair genes like APC, FANCL, and MSH6 significantly elevate somatic TMB levels across pan-cancer cohorts, potentially enhancing neoantigen load and ICI efficacy.^[95] The gut microbiome's influence on mutational burden is also under investigation, with microbial interactions inducing mismatch repair deficiency signatures that increase somatic mutation rates in colorectal tumors.^[96] From 2024 to 2025, efforts to standardize liquid biopsy for TMB have intensified through consortia like Friends of Cancer Research, developing guidelines for assay validation, bioinformatics pipelines, and orthogonal confirmation to enable reliable dynamic monitoring.^[81]^[97] Looking ahead, global consortia, such as the Worldwide Innovative Network (WIN) and Friends of Cancer Research, are prioritizing diverse population data to address ancestry-driven TMB variations, aiming to recalibrate thresholds for equitable precision oncology. As of October 2025, ESMO research linked thymic health to immunotherapy response, suggesting it as a complementary biomarker to TMB for patient selection.^[98]^[99]^[100]

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