JCO Precision Oncology Conversations

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JCO Precision Oncology Conversations is a monthly podcast featuring conversations with authors of clinically relevant and significant articles published in the JCO Precision Oncology journal. JCO Precision Oncology Conversations is hosted by the journal's social media editor, Dr. Abdul Rafeh Naqash.

  1. JCO PO Article Insights: Analytical Validation of Tumor-Informed ctDNA Assays for MRD

    3 DAYS AGO

    JCO PO Article Insights: Analytical Validation of Tumor-Informed ctDNA Assays for MRD

    In this JCO PO Article Insights episode, host Jordan Goldstein summarizes the article, "Generic Protocols for Analytical Validation of Tumor-Informed Circulating Tumor DNA Assays for Molecular Residual Disease: The Blood Profiling Atlas in Cancer's Molecular Residual Disease Analytical Validation Working Group Consensus Recommendation" by Baden et al. TRANSCRIPT JCOPOAI 26E03 Jordan Goldstein: Hello, and welcome to JCO Precision Oncology Article Insights. I'm your host, Jordan Goldstein from Stanford University. Today we're discussing a consensus recommendation published in JCO Precision Oncology titled "Generic Protocols for Analytical Validation of Tumor-Informed Circulating Tumor DNA Assays for Molecular Residual Disease" by lead author Jonathan Baden, senior author Lauren Leiman, and colleagues on behalf of the BLOODPAC Consortium. The liquid biopsy space is one of the most exciting frontiers in oncology right now, with rapid development and many potential uses. However, the field has really lacked a shared framework for how these assays should actually be validated. This paper attempts to solve part of that problem. Before going further, I want to mention that BLOODPAC stands for Blood Profiling Atlas in Cancer Consortium. This was developed in 2016 with the goal of accelerating liquid biopsy development through shared standards. It includes the leading cancer diagnostics companies alongside academics, pharmaceutical companies, not for profits, and regulatory agencies. So, what actually is ctDNA MRD, and why does it matter? ctDNA is short for circulating tumor DNA, which is DNA shed by tumors into the bloodstream and can be detected by genomic profiling of a simple blood draw. Compared to tissue biopsies, it's minimally invasive, easily accessible, and can reflect the genetic diversity of the entire tumor across anatomic sites. This can allow for comprehensive genomic profiling, identifying target mutations, and understanding anatomic heterogeneity prior to treatment. It also allows for repeated sampling during and after treatment to explore evolutionary dynamics and, most promisingly, to detect molecular residual disease or MRD, which is what we focus on in this article. MRD is the presence of tumor-derived DNA in blood following therapy at levels below the threshold of conventional imaging or standard pathologic assessment. Accurate MRD detection can transform therapeutic strategies, enabling more precise risk-adapted approaches. But detecting MRD is not simple. There's often a very small amount of tumor DNA in plasma after treatment, even going below one part per million or 0.0001% of the total circulating DNA, most of which is healthy, normal, cell-free DNA. Detecting a signal that faint, reliably and reproducibly, is quite technically demanding. Tumor-informed ctDNA assays address this by first sequencing the patient's primary tumor to identify somatic variants that are unique to that cancer. A personalized panel is then constructed to track those exact variants in serial blood samples. This allows greater sensitivity. However, the methods and protocols for pre-analytical, analytical, and clinical validation for tumor-informed MRD assays can vary greatly. This presents major challenges for regulatory approval and clinical implementation. With these consensus recommendations in this article, BLOODPAC focuses on developing a standardized framework for the analytical validation of any tumor-informed ctDNA MRD assay. Analytical validation ensures these assays are in fact measuring what they claim to measure with defined performance characteristics. BLOODPAC intentionally set out to keep their protocols as generic as possible with the only requirements being intended uses of the assay for: one, patients with cancer who have undergone curative-intent therapy; and two, for prognosis, treatment efficacy, detection of residual disease or recurrence, or serving as the basis for a novel clinical trial strategy. With the goal of accelerating the clinical development and validation of tumor-informed MRD assays, BLOODPAC worked closely with the FDA throughout this process, holding three separate pre-submission meetings, precisely to ensure that assay developers who follow these protocols are well positioned for regulatory approval. Now, let's delve deeper into this paper and highlight the significant challenges of validating tumor-informed MRD assays. These challenges primarily stem from the low concentration of ctDNA found in the bloodstream. These levels can be further impacted by tumor characteristics such as tumor type, heterogeneity, histology, size, stage, and cell turnover or proliferative rate that can impact ctDNA shedding. One complex problem here is sampling heterogeneity or stochastic variation when looking for a single specific variant. When ctDNA is extremely low, a given variant may be present in one blood draw but may be absent in a replicate taken at the same time point, not because the biology changed, but due to random sampling effects at low levels. Tumor-informed assays handle this by evaluating MRD at the sample level rather than at the variant level. If enough variants from the personalized panel are detected collectively, the sample is called positive, even if no single variant is consistently detected. This is a strength for sensitivity, but it complicates traditional validation designs that assume consistent variant level assessments. Additionally, as we previously discussed, tumor-informed assays use personalized panels of mutations unique to the tumor to their advantage to improve their sensitivity. They filter out normal germline variants and non-tumor-derived somatic variants such as those from clonal hematopoiesis or CHIP. This leads to a smaller but highly specific assay. The smaller panel enables more targeted, deeper sequencing, focused on the most likely tumor-derived variants, and reduces the risk of false positives. However, the personalized nature also makes validation difficult because each patient's panel is different. For this, novel approaches are needed to really validate that key performance measures are acceptable and consistent. A final challenge here is the blood sample volume required for ctDNA detection at low levels. A standard blood draw simply doesn't yield enough ctDNA to support the extensive replication and dilution series that conventional analytical validation requires. To address this, test developers can use contrived samples, synthetic DNA sequences from a known cancer patient spiked at defined allele frequencies into healthy donor plasma. These serve as a surrogate for true clinical material when volumes are constrained. The test developer should then perform a contrived sample functional characterization study to demonstrate to the FDA that the contrived samples actually perform equivalently to real clinical specimens. So now that we've actually covered some of the major challenges here, let's dig into the analytical validation protocols that are recommended for the seven key performance characteristics that are defined in this paper. The first two performance characteristics, limit of blank and limit of detection, focus on establishing the analytical performance of the assay, which is the assay's ability to detect a known signal when present in the sample or vice versa. To be clear, this is distinct from the clinical performance, which is defined by the assay's ability to correctly identify patients who do or do not have residual cancer and ultimately relapse. The first performance metric is limit of blank or LOB. This is the analytical specificity, or the highest signal expected in a sample that does not contain tumor DNA. To establish this, BLOODPAC suggests using a minimum of 60 blank samples from healthy donors, in a minimum of two replicates with two reagent lots and multiple panel designs across a range of DNA inputs. Then, the LOB should be set to zero and 60 blank samples should again be tested to determine the false positive rate on a per-sample basis. Typically, the LOB represents the 95th percentile of signal observed in samples without tumor variants, also known as the background signal. The limit of detection or LOD, on the other hand, is the analytical sensitivity, or the lowest concentration of tumor-derived molecules that can be reliably detected in a sample. To establish the LOD, an appropriate number of low allele fraction contrived positive samples or specimen blend panels should be tested in five different dilution levels with a minimum of 10 replicates per dilution level. Two reagent lots must be used with each testing across these 50 measurements. If developers are to use a probit regression model approach to determine the LOD, they should use at least 100 of these measurements. The LOD is ultimately determined as the tumor concentration corresponding to a 95% hit rate. The next two performance metrics prove the accuracy and precision of the assay. The analytical accuracy is how often the assay correctly identifies positive and negative samples. This should be determined by testing a minimum of 100 specimens, ideally from a clinical trial or procured from clinical care that are known to be negative for ctDNA, as well as 10 to 20 cancer positive samples. From this, the sample level percent positive, percent negative, and overall agreement can be used to determine the accuracy. Precision of the assay is determined in two different ways: repeatability and reproducibility, using true patient samples. Repeatability assesses the intra-assay precision. It is measured by assessing the consistency of the assay under the same operating conditions over a short period. For this, multiple samples are tested in replicates of two, using a single operator and single testing site with a minimum 20-day testing interval for 80 total observations. Reproducibility, on the other hand, measures the inter-assay precision. This evaluat

    11 min
  2. Oncotype DX Breast Recurrence Score® Results from Paired CNB & SE Specimens

    25 FEB

    Oncotype DX Breast Recurrence Score® Results from Paired CNB & SE Specimens

    In this JCO Precision Oncology Article Insights episode, host Dr. Carolyn Lineen summaries the article, "Concordance of Oncotype DX Breast Recurrence Score Assay Results Between Paired Core Needle Biopsy and Surgical Excision Specimens in Hormone Receptor Positive, HER2-Negative Early-Stage Breast Cancer," by Nassar et al. TRANSCRIPT Carolyn Lineen: Hello and welcome to JCO Precision Oncology Article Insights. I'm your host, Carolyn Lineen, from St. James's Hospital, Dublin, and today we will be discussing the JCO Precision Oncology article titled "Concordance of Oncotype DX Breast Recurrence Score Assay Results Between Paired Core Needle Biopsy and Surgical Excision Specimens in Hormone Receptor Positive, HER2-Negative Early-Stage Breast Cancer" by Dr. Aziza Nassar and colleagues. The Oncotype DX Breast Recurrence Score assay is a 21-gene expression test that provides both prognostic information regarding distant recurrence risk and predictive information regarding the benefit of adjuvant chemotherapy in hormone receptor-positive, HER2-negative early-stage breast cancer. The recurrence score ranges from 0 to 100, with higher scores indicating a greater risk of recurrence and a potentially higher likelihood of benefit from chemotherapy. Traditionally, genomic testing is performed on surgical excision specimens following tumor resection. However, this approach can potentially delay access to biological risk stratification, which may be important when early treatment planning or neoadjuvant therapy is being considered. The primary objective of this study was to evaluate the level of concordance between recurrence scores derived from paired core needle biopsy specimens and surgical excision specimens obtained from the same untreated primary breast tumors. Investigators specifically evaluated both continuous recurrence score agreement and categorical risk classification concordance. The study included 134 patients with paired biopsy and surgical specimens. The median patient age was 62 years, with a wide age range from 33 to 99 years. Approximately 17% of patients were aged 50 years or younger, while 83% were older than 50 years. All patients had hormone receptor-positive, HER2-negative early-stage breast cancer and had not received prior systemic treatment before either specimen collection. Each patient contributed two tumor samples: a core needle biopsy specimen obtained at initial diagnosis and a surgical excision specimen obtained during definitive tumor resection. Both samples underwent Oncotype DX testing, allowing direct within-patient comparison. The investigators reported mean recurrence scores of 15.6 for core needle biopsy specimens and 16.6 for surgical excision specimens. Although this absolute mean difference between specimen types did reach statistical significance with a P value of 0.003, the authors note that this numerical difference was small at one recurrence score unit and may not therefore be clinically meaningful. Additionally, categorical recurrence score results did not differ significantly. The primary measure of agreement between recurrence scores was the Lin's concordance correlation coefficient. The study demonstrated a Lin concordance correlation coefficient of 0.86 with a 95% confidence interval ranging from 0.80 to 0.90, indicating strong agreement between biopsy and surgical specimens. Additionally, categorical agreement was assessed using Cohen's kappa statistic. The study reported a kappa value of 0.64 with a 95% confidence interval from 0.44 to 0.83, indicating substantial agreement between specimen types. Comparing this study to previously published evidence, the authors referenced prior smaller studies examining concordance between paired tissue samples. For example, earlier research evaluating 50 patients demonstrated correlation coefficients of approximately 0.8 and categorical concordance rates ranging from 72% to 78%, depending on the classification cut points used. Compared with earlier studies, the present study provides stronger evidence supporting consistency between biopsy and surgical testing. These findings have several important implications for clinical practice. First, early availability of recurrence score results may enhance multidisciplinary care planning. Obtaining genomic risk data at the time of diagnosis allows tumor boards to integrate molecular risk stratification into initial treatment discussions rather than waiting for postoperative results. Second, biopsy-based testing may support decision making regarding treatment sequencing. Earlier genomic information may help guide selection of neoadjuvant therapy or inform early decisions about adjuvant chemotherapy necessity. Third, early testing may reduce delays in treatment initiation. Separate research evaluating presurgical Oncotype DX testing has demonstrated potential reductions in time to initiation of adjuvant therapy by approximately 8 days, suggesting potential improvements in care efficiency. Additionally, biopsy-based testing demonstrates strong technical feasibility. Studies examining real-world implementation have reported test success rates as high as 99.1% when performed on core biopsy specimens. Despite the encouraging results, certain limitations must be considered. Core needle biopsy samples evaluate only a portion of the tumor, and intratumoral heterogeneity could theoretically influence recurrence score results in selected cases. Preanalytical factors, including tissue fixation and sample handling, may also affect RNA integrity and assay performance. Standardization of specimen processing protocols will be essential if biopsy-based testing becomes routine. Furthermore, although analytical concordance is strong, prospective outcome studies demonstrating equivalent long-term clinical outcomes based on biopsy-directed treatment decisions would further strengthen the evidence base. In conclusion, this study demonstrates strong concordance between Oncotype DX Breast Recurrence Scores derived from core needle biopsy specimens and surgical excision specimens in patients with hormone receptor-positive, HER2-negative early-stage breast cancer. With a concordance correlation coefficient of 0.86 and overall categorical agreement exceeding 90%, the findings support the clinical feasibility of performing genomic testing at the time of diagnostic biopsy. If validated through additional prospective studies, this approach may enable earlier risk stratification and improve multidisciplinary treatment planning. Thank you for tuning in to JCO Precision Oncology Article Insights. Don't forget to subscribe and join us next time as we explore more groundbreaking research shaping the future of oncology. The purpose of this podcast is to educate and to inform. This is not a substitute for professional medical care and is not intended for use in the diagnosis or treatment of individual conditions. Guests on this podcast express their own opinions, experience, and conclusions. Guest statements on the podcast do not express the opinions of ASCO. The mention of any product, service, organization, activity, or therapy should not be construed as an ASCO endorsement.

    7 min
  3. ctDNA in Metastatic Invasive Lobular Carcinoma

    18 FEB

    ctDNA in Metastatic Invasive Lobular Carcinoma

    JCO PO author Dr. Foldi at UPMC Hillman Cancer Center and University of Pittsburgh School of Medicine shares insights into the JCO PO article, "Personalized Circulating Tumor DNA Testing for Detection of Progression and Treatment Response Monitoring in Patients With Metastatic Invasive Lobular Carcinoma of the Breast." Host Dr. Rafeh Naqash and Dr. Foldi discuss how serial ctDNA testing in patients with mILC is feasible and may enable personalized surveillance and real-time therapeutic monitoring. TRANSCRIPT Dr. Rafeh Naqash: Hello, and welcome to JCO Precision Oncology Conversations, where we bring you engaging conversations with authors of clinically relevant and highly significant JCO PO articles. I am your host, Dr. Rafeh Naqash, podcast editor for JCO Precision Oncology and Associate Professor at the OU Health Stephenson Cancer Center at the University of Oklahoma. Today, we are thrilled to be joined by Dr. Julia Foldi, Assistant Professor of Medicine in the Division of Hematology-Oncology at University of Pittsburgh School of Medicine and the Magee-Womens Hospital of the UPMC. She is also the lead and corresponding author of the JCO Precision Oncology article entitled "Personalized Circulating Tumor DNA Testing for Detection of Progression and Treatment Response Monitoring in Patients with Metastatic Invasive Lobular Carcinoma of the Breast." At the time of this recording, our guest's disclosures will be linked in the transcript. Julia, welcome to our podcast, and thank you for joining us today. Dr. Julia Foldi: Thank you so much for having me. It is a pleasure. Dr. Rafeh Naqash: Again, your manuscript and project address a few interesting things, so we will start with the basics, since we have a broad audience that comprises trainees, community oncologists, and obviously precision medicine experts as well. So, let us start with invasive lobular breast carcinoma. I have been out of fellowship for several years now, and I do not know much about invasive lobular carcinoma. Could you tell us what it is, what some of the genomic characteristics are, why it is different, and why it is important to have a different way to understand disease biology and track disease status with this type of breast cancer? Dr. Julia Foldi: Yes, thank you for that question. It is really important to frame this study. So, lobular breast cancers, which we shorten to ILC, are the second most common histologic subtype of breast cancer after ductal breast cancers. ILC makes up about 10 to 15 percent of all breast cancers, so it is relatively rare, but in the big scheme of things, because breast cancer is so common, this represents actually over 40,000 new diagnoses a year in the US of lobular breast cancers. What is unique about ILC is it is characterized by loss of an adhesion molecule, E-cadherin. It is encoded by the CDH1 gene. What it does is these tumors tend to form discohesive, single-file patterns and infiltrate into the tumor stroma, as opposed to ductal cancers, which generally form more cohesive masses. As we generally explain to patients, ductal cancers tend to form lumps, while lobular cancers often are not palpable because they infiltrate into the stroma. This creates several challenges, particularly when it comes to imaging. In the diagnostic setting, we know that mammograms and ultrasounds have less sensitivity to detect lobular versus ductal breast cancer. When it comes to the metastatic setting, conventional imaging techniques like CT scans have less sensitivity to detect lobular lesions often. One other unique characteristic of ILC is that these tumors tend to have lower proliferation rates. Because our glucose-based PET scans depend on glucose uptake of proliferating cells, often these tumors also are not avid on conventional FDG-PET scans. It is a challenge for us to monitor these patients as they go through treatment. If you think about the metastatic setting, we start a new treatment, we image people every three to four cycles, about every three months, and we combine the imaging results with clinical assessment and tumor markers to decide if the treatment is working. But if your imaging is not reliable, sometimes even at diagnosis, to really detect these tumors, then really, how are we following these patients? This is really the unique challenge in the metastatic setting in patients with lobular breast cancer: we cannot rely on the imaging to tell if patients are responding to treatment. This is where liquid biopsies are really, really important, and as the field is growing up and we have better and better technologies, lobular breast cancer is going to be a field where they are going to play an important role. Dr. Rafeh Naqash: Thank you for that easy-to-understand background. The second aspect that I would like to have some context on, to help the audience understand why you did what you did, is ctDNA, tumor informed and non-informed. Could you tell us what these subtypes of liquid biopsies are and why you chose a tumor informed assay for your study? Dr. Julia Foldi: Yes, it is really important to understand these differences. As you mentioned, there are two main platforms for liquid biopsy assays, circulating tumor DNA assays. I think what is more commonly used in the metastatic setting are non-tumor informed assays, or agnostic assays. These are generally next-generation sequencing-based assays that a lot of companies offer, like Guardant, Tempus, Caris, and FoundationOne. These do not require tumor tissue; they just require a blood sample, a plasma sample, essentially. The next-generation sequencing is done on cell-free DNA that is extracted from the plasma, and it is looking for any cell-free DNA and essentially, figuring out what part of the cell-free DNA comes from the tumor is done through a bioinformatics approach. Most of these assays are panel tests for cancer-associated mutations that we know either have therapeutic significance or biologic significance. So, the results we receive from these tests generally read out specific mutations in oncogenic genes, or sometimes things like fusions where we have specific targeted drugs. Some of the newer assays can also read out tumor fraction; for example, the newest generation Guardant assay that is methylation-based, they can also quantify tumor fraction. But the disadvantage of the tumor agnostic approach is that it is a little bit less sensitive. Opposed to that, we have our tumor informed tests, and these require tumor tissue. Essentially, the tumor is sequenced; this can either be whole exome or whole genome sequencing. The newer generation assays are now using whole genome sequencing of the tumor tissue, and a personalized, patient-specific panel of alterations is essentially barcoded on that tumor tissue. This can be either structural variants or it can be mutations, but generally, these are not driver mutations, but sort of things that are present in the tumor tissue that tend to stay unchanged over time. For each particular patient, a personalized assay, if you want to call it a fingerprint or barcode, is created, and then that is what then is used to test the plasma sample. Essentially, you are looking for that specific cancer in the blood, that barcode or fingerprint in the blood. Because of this, this is a much more sensitive way of looking for ctDNA, and obviously, this detects only that particular tumor that was sequenced originally. So, it is much more sensitive and specific to that tumor that was sequenced. You can argue for both approaches in different settings. We use them in different settings because they give us different information. The tumor agnostic approach gives us mutations, which can be used to determine what the next best therapy to use is, while the tumor informed assay is more sensitive, but it is not going to give us information on therapeutic targets. However, it is quantified, and we can follow it over time to see how it changes. We think that it is going to tell us how patients respond to treatment because we see our circulating tumor DNA levels rise and fall as the cancer burden increases or decreases. We decided to use the tumor informed approach in this particular study because we were really interested in how to determine if patients are having response to treatment versus if they are going to progress on their treatment, more so than looking for specific mutations. Dr. Rafeh Naqash: When you think about these tumor informed assays and you think about barcoding the mutations on the original tumor that you try to track or follow in subsequent blood samples, plasma samples, in your experience, if you have done it in non-lobular cancers, do you think shedding from the tumor has something to do with what you capture or how much you capture? Dr. Julia Foldi: Absolutely. I think there are multiple factors that go into whether someone has detectable ctDNA or not, and that has to do with the type of cancer, the location, right, where is the metastatic site? This is something that we do not fully understand yet: what are tumors that shed more versus not? There is also clearance of ctDNA, and so how fast that clearance occurs is also something that will affect what you can detect in the blood. ctDNA is very short-lived, only has a half-life of hours, and so you can imagine that if there is little shedding and a lot of excretion, then you are not going to be detecting a lot of it. In general, in the metastatic setting, we see that we can detect ctDNA in a lot of cases, especially when patients are progressing on treatment, because we imagine their tumor burden is higher at that point. Even with the non-tumor informed assays, we detect a lot of ctDNA. Part of this study was to actually assess: what is the proportion of patients where we can have this information? Because if we are only going to be able to detect ctDNA in less than 50 percent of patients, then it is not going to be a

    28 min
  4. JCO PO Article Insights: Circulating Tumor DNA in Germ Cell Tumors

    28 JAN

    JCO PO Article Insights: Circulating Tumor DNA in Germ Cell Tumors

    In this JCO Precision Oncology Article Insights episode, host Dr. Jiasen He summaries the article, "Longitudinal Evaluation of Circulating Tumor DNA as a Prognostic Biomarker to Detect Molecular Residual Disease in Germ Cell Tumors," by Hassoun et al. TRANSCRIPT Jiasen He: Hello, and welcome to the JCO Precision Oncology Article Insights. I'm your host, Jiasen He, and today, we'll be discussing the JCO Precision Oncology article, "Longitudinal Evaluation of Circulating Tumor DNA as a Prognostic Biomarker to Detect Molecular Residual Disease in Germ Cell Tumors," by Dr. Rebecca Hassoun and colleagues. Traditionally, treatment response for solid tumors has relied on imaging, which focuses on visible anatomic changes in the tumor. However, imaging does not always reflect molecular or cellular changes and cannot detect microscopic disease, which is clinically important and often linked to relapse. Liquid biopsy, on the other hand, is minimally invasive and can be used for cancer monitoring by analyzing circulating biomarkers in biofluids such as blood. One type of liquid biopsy is circulating tumor DNA, or ctDNA, which measures small fragments of DNA released by tumor cells into the bloodstream. ctDNA can allow precise monitoring of tumor-specific mutations and be a powerful tool for assessing treatment responses. ctDNA has already been applied in clinical settings for cancers such as non-small cell lung cancer and breast cancer, etcetera. However, there is still limited data on the use of ctDNA for germ cell tumors. Germ cell tumors are the most common malignancy affecting men aged 15 to 35 years. Accurate risk stratification and disease monitoring is key to risk-adapted therapy, maximizing the chance of cure while minimizing side effects. One unique tool we use currently for diagnosis, staging, and monitoring is serum tumor markers, such as AFP, beta-hCG, and LDH. However, these markers have limitations, including false elevation in certain clinical scenarios, and studies have shown that they can be normal in up to 40 percent of patients with germ cell tumor. This creates an unmet need for other sensitive and specific biomarkers to improve patient care. In this paper, the authors investigated the use of ctDNA in a cohort of patients with germ cell tumor at various disease time points. They compared ctDNA results with traditional serum tumor markers to evaluate whether ctDNA can predict relapse and survival outcomes. This multi-institutional retrospective study included patients with stage I, II, and III germ cell tumors, primarily testicular cancer, who had at least one ctDNA test result. ctDNA was evaluated longitudinally at different time points, including pre-orchiectomy, during the molecular residual disease, or MRD, window, defined as 1 to 12 weeks post-orchiectomy but before primary therapy, and during the surveillance window, defined as more than 12 weeks post-orchiectomy or follow retroperitoneal lymph node dissection or post-chemotherapy. ctDNA analysis was performed using a tumor-informed 16 multiplex PCR next-generation sequencing assay. A total of 324 plasma samples were analyzed from 74 patients in this cohort. The majority had stage I disease, around 40 percent, and nonseminomatous histology, around 70 percent. 15 patients were evaluated in the pre-orchiectomy window, and only one patient tested negative for ctDNA. This patient had stage I disease. The authors further assessed ctDNA positivity in both the MRD window and surveillance window, evaluating its association with event-free survival. They found that ctDNA outperformed serum tumor markers in both settings. ctDNA positivity was associated with significantly worse event-free survival compared with ctDNA-negative patients. Among the 14 patients with stage II to III disease who had ctDNA assessed in both the MRD window and surveillance window, nine patients consistently had a negative ctDNA or converted from positive to negative over time. In contrast, five patients demonstrated persistent ctDNA positivity, and all of these patients subsequently relapsed. Among the 38 patients who had both ctDNA and serum tumor marker tests during the MRD window, nine patients showed discordant biomarker results. Of these, 6 patients were ctDNA-negative but serum tumor marker-positive, and one of them experienced recurrence. Three patients were ctDNA-positive but serum tumor marker-negative, and one of these patients also recurred. During the surveillance window, 46 patients had both biomarkers available, and 10 showed discordant results. Three patients were ctDNA-negative but serum tumor marker-positive, and none of them recurred. In contrast, all seven patients who were ctDNA-positive but serum tumor marker-negative experienced recurrence. This intriguing data strongly support the potential role of ctDNA in patients with stage I, II, and III germ cell tumors. However, as the authors noted, the retrospective nature of the study presents limitations, as treatment approaches, imaging schedules, and the timing of testing were not standardized, and ctDNA testing varies among participating institutions. Larger prospective trials with standardized protocols and long-term follow-up will be essential to validate these findings and determine how ctDNA can be reliably integrated into clinical practice. Thank you for tuning in to JCO Precision Oncology Article Insights. Don't forget to subscribe and join us next time as we explore more groundbreaking research shaping the future of oncology. The purpose of this podcast is to educate and to inform. This is not a substitute for professional medical care and is not intended for use in the diagnosis or treatment of individual conditions.  Guests on this podcast express their own opinions, experience, and conclusions. Guest statements on the podcast do not express the opinions of ASCO. The mention of any product, service, organization, activity, or therapy should not be construed as an ASCO endorsement.

    7 min
  5. FGFR2b Prevalence in Advanced GC: FORTITUDE-101 Prescreening

    21 JAN

    FGFR2b Prevalence in Advanced GC: FORTITUDE-101 Prescreening

    JCO PO author Dr. Wainberg at UCLA shares insights into the JCO PO article, "Prevalence of FGFR2b Protein Overexpression in Advanced Gastric Cancers During Prescreening for the Phase III FORTITUDE-101 Trial." Host Dr. Rafeh Naqash and Dr. Wainberg discuss how FGFR2b prevalence was similar across geographic regions and within defined patient and sample variables regardless of the level of expression. TRANSCRIPT TO COME

    20 min
  6. Palbociclib in Tumors with CDKN2A Loss or Mutation

    7 JAN

    Palbociclib in Tumors with CDKN2A Loss or Mutation

    In this JCO Precision Oncology Article Insights episode, host Dr. Harold Nathan Tan summarizes "Palbociclib in Patients With Head and Neck Cancer and Other Tumors With CDKN2A Alterations: Results From the Targeted Agent and Profiling Utilization Registry Study" by Worden et al.  TRANSCRIPT Harold Nathan Tan: Welcome to JCO Precision Oncology Article Insights, where we explore research that is reshaping our understanding of cancer therapeutics. I'm your host, Harold Nathan Tan, and today's episode centers on the TAPUR study, an analysis that confronts a long-standing assumption in molecular oncology: namely, whether CDKN2A alterations create a therapeutic vulnerability that can be exploited by CDK4/6 inhibition with palbociclib. CDKN2A is one of the most frequently altered tumor suppressors across solid tumors. Its importance lies in its production of two proteins, p16 and p14, which serve as guardians of cell cycle progression. p16 directly inhibits CDK4 and CDK6, preventing phosphorylation of the RB protein and therefore blocking entry into S phase, whereas p14 stabilizes p53 by counteracting MDM2, enabling cells to pause or die in response to oncogenic stress. When CDKN2A is lost or mutated, these dual checkpoints collapse. CDK4/6 activity becomes unchecked, RB remains phosphorylated and inactive, and p53-mediated surveillance is blunted from a mechanistic standpoint. This creates a possible dependency on CDK4/6 signaling that could, in principle, be therapeutically reversed by palbociclib. The TAPUR study is a prospective phase 2 basket study designed to evaluate whether FDA-approved targeted agents can meaningfully benefit patients with advanced treatment-refractory cancers harboring specific genomic alterations. In this analysis, patients were eligible for palbociclib if their tumors carried CDKN2A loss or mutation and retained RB activity. Two cohorts were examined: one consisting of head and neck cancers, and another composed of a broad spectrum of tumor types that collectively shared the CDK2 alteration. The results from the head and neck cancer cohort are particularly intriguing. Among the 28 available patients, the study observed a disease control rate of 40%, surpassing the predefined threshold for a positive signal. Although the objective response rate was low at only 4% with one partial response, the durability of disease stabilization was clinically meaningful. However, the most important insight comes from examining which head and neck tumors benefited. The strongest and most durable disease control occurred in non-squamous malignancies, particularly salivary gland tumors such as adenocarcinoma, adenoid cystic carcinoma, and poorly differentiated parotid tumors, as well as in esthesioneuroblastoma. In contrast, classic head and neck squamous cell carcinoma rarely demonstrated sustained benefit. When progression-free survival was analyzed, non-squamous tumors achieved a median PFS of approximately 20 weeks compared to just eight weeks in squamous tumors. This divergence reflects deep biological differences. Many non-squamous head and neck cancers preserve an intact RB axis and rely on CDK4/6-driven cell cycle control as a core proliferative mechanism. By contrast, squamous tumors tend to accumulate a dense array of co-alterations that weaken or circumvent CDK4/6 dependency. Many squamous tumors also harbor disruptive TP53 mutations, removing essential checkpoint control and allowing the cell to bypass the growth-arresting effects of palbociclib. In other words, even though CDKN2A loss is present, CDK4/6 is no longer the dominant node controlling proliferation in these cancers, and the tumor simply finds other ways to drive cell cycle entry. One of the most thought-provoking findings from the TAPUR study involves esthesioneuroblastoma. Three patients with this rare tumor achieved durable disease control despite the lack of standardized systemic treatment options for this malignancy. Genomic analyses have shown that while esthesioneuroblastoma often carries TP53 or IDH2 mutations, a meaningful subset exhibits alterations in CDKN2A or related cell cycle regulators. The consistency of this disease stabilization observed in TAPUR may reflect a lineage-specific reliance on CDK4/6 signaling, opening the door for future exploration of CDK4/6 inhibitors in this orphan disease. In the histology-pooled cohort, which included 40 available patients across 18 tumor types, palbociclib did not achieve the disease control threshold required to declare activity, with only a disease control rate of 13% and an ORR of 5%. While a few isolated responses occurred, for instance in thymic carcinoma and B-cell lymphoma, the overall disease control rate was 13%, which failed to rise above what might be expected from the natural history of advanced refractory cancers. This outcome reinforces the principle that CDKN2A loss is not a universal predictor of CDK4/6 dependency. Many of the tumors represented in this cohort, such as pancreatic cancer, melanoma, and gastrointestinal malignancies, are well known to evolve multiple compensatory mechanisms that circumvent CDK4/6 as a critical proliferative node. The safety profile of palbociclib was consistent with its known hematologic toxicities. High rates of neutropenia, leukopenia, and thrombocytopenia were observed, along with one treatment-related death due to respiratory failure. In a setting where activity is limited to specific subgroups, these toxicities underscore the importance of careful patient selection and raise the bar for demonstrating clinically meaningful benefit, particularly in heavily pretreated populations. So what do these findings tell us about the broader landscape of precision oncology? First, they remind us that a mutation's functional role is dependent on the cellular and lineage context in which it occurs. CDKN2A loss may accelerate proliferation in many tumors, but the mechanism of that acceleration varies widely, and the degree to which a tumor relies on CDK4/6 signaling is anything but uniform. Second, the findings suggest that palbociclib monotherapy may hold meaningful and durable benefit in the subset of non-squamous head and neck cancers, particularly salivary gland malignancies and esthesioneuroblastoma. Third and perhaps most importantly, the results reinforce a growing consensus that the future of CDK4/6 inhibition in solid tumors lies not in monotherapy, but in rational combination strategies. CDK4/6 inhibitors have been shown to synergize with EGFR inhibitors, PIK3CA, and mTOR inhibitors, MEK inhibition, and even immune checkpoint blockade. These combinations aim to dismantle the compensatory pathways that allow tumors to escape CDK4/6 blockade and may unlock therapeutic potential in tumors that show limited sensitivity to monotherapy. Ultimately, the TAPUR findings challenge the notion that CDKN2A is a straightforward predictive biomarker. Instead, the study reveals CDKN2A as a biomarker whose meaning is modulated by tumor lineage, co-mutation status, and the broader regulatory circuit governing proliferation. Precision oncology must therefore move beyond single-gene interpretation towards integrated frameworks that situate genomic alterations within their biologic ecosystems. In some head and neck cancer subtypes, particularly non-squamous malignancies, that ecosystem appears amenable to CDK4/6 inhibition, and that insight, not the simplistic gene-to-drug match, represents the true value of the TAPUR analysis. Thank you for joining me for this episode of JCO Precision Oncology Article Insights. I'm Harold Nathan Tan, and I look forward to exploring more research that continues to refine how we understand and strategically exploit the vulnerabilities of cancer. The purpose of this podcast is to educate and to inform. This is not a substitute for professional medical care and is not intended for use in the diagnosis or treatment of individual conditions. Guests on this podcast express their own opinions, experience, and conclusions. Guest statements on the podcast do not express the opinions of ASCO. The mention of any product, service, organization, activity, or therapy should not be construed as an ASCO endorsement.

    9 min

  7. 17/12/2025

    FGFR3 Alteration Status and Immunotherapy in Urothelial Cancer

    JCO PO author Dr. Shilpa Gupta at Cleveland Clinic Children's Hospital shares insights into her article, "Fibroblast Growth Factor Receptor 3 (FGFR3) Alteration Status and Outcomes on Immune Checkpoint Inhibitors (ICPI) in Patients with Metastatic Urothelial Carcinoma". Host Dr. Rafeh Naqash and Dr. Gupta discuss how FGFR3 combined with TMB emerged as a biomarker that may be predictive for response to ICPI in mUC. TRANSCRIPT Dr. Rafeh Naqash: Hello and welcome to JCO Precision Oncology Conversations, where we bring you engaging conversations with authors of clinically relevant and highly significant JCO PO articles. I'm your host, Dr. Rafeh Naqash, podcast editor for JCO Precision Oncology and Associate Professor at the OU Health Stephenson Cancer Center. Today I am excited to be joined by Dr. Shilpa Gupta, Director of Genitourinary Medical Oncology at the Cancer Institute and co-leader of the GU Oncology Program at the Cleveland Clinic, and also lead author of the JCO PO article titled "Fibroblast Growth Factor Receptor 3 Alteration Status and Outcomes on Immune Checkpoint Inhibitors in Patients With Metastatic Urothelial Carcinoma." At the time of this recording, our guest's disclosures will be linked in the transcript. Shilpa, welcome again to the podcast. Thank you for joining us today. Dr. Shilpa Gupta: Thank you, Rafeh. Honor to be here with you again. Dr. Rafeh Naqash: It is nice to connect with you again after two years, approximately. I think we were in our infancy of our JCO PO podcast when we had you first time, and it has been an interesting journey since then. Dr. Shilpa Gupta: Absolutely. Dr. Rafeh Naqash: Well, excited to talk to you about this article that you published. Wanted to first understand what is the genomic landscape of urothelial cancer in general, and why should we be interested in FGFR3 alterations specifically? Dr. Shilpa Gupta: Bladder cancer or urothelial cancer is a very heterogeneous cancer. And while we find there is a lot of mutations can be there, you know, like BRCA1, 2, in HER2, in FGFR, we never really understood what is driving the cancer. Like a lot of old studies with targeted therapies did not really work. For example, we think VEGF can be upregulated, but VEGF inhibitors have not really shown definite promise so far. Now, FGFR3 receptor is the only therapeutic target so far that has an FDA approved therapy for treating metastatic urothelial cancer patients, and erdafitinib was approved in 2019 for patients whose tumors overexpressed FGFR3 mutations, alterations, or fusions. And in the landscape of bladder cancer, it is important because in patients with non-muscle invasive bladder cancer, about 70 to 80% patients can have this FGFR3. But as patients become metastatic, the alterations are seen in, you know, only about 10% of patients. So the clinical trials that got the erdafitinib approved actually used archival tumor from local cancer. So when in the real world, we don't see a lot of patients if we are trying to do metastatic lesion biopsies. And why it is important to know this is because that is the only targeted therapy available for our patients right now. Dr. Rafeh Naqash: Thank you for giving us that overview. Now, on the clinical side, there is obviously some interesting data for FGFR3 on the mutation side and the fusion side. In your clinical practice, do you tend to approach these patients differently when you have a mutation versus when you have a fusion? Dr. Shilpa Gupta: We can use the treatment regardless of that. Dr. Rafeh Naqash: I recently remember I had a patient with lung cancer, squamous lung cancer, who also had a synchronous bladder mass. And the first thought from multiple colleagues was that this is metastatic lung. And interestingly, the liquid biopsy ended up showing an FGFR3-TACC fusion, which we generally don't see in squamous lung cancers. And then eventually, I was able to convince our GU colleagues, urologists, to get a biopsy. They did a transurethral resection of this tumor, ended up being primary urothelial and synchronous lung, which again, going back to the FGFR3 story, I saw in your paper there is a mention of FGFR3-TACC fusions. Anything interesting that you find with these fusions as far as biology or tumor behavior is concerned? Dr. Shilpa Gupta: We found in our paper of all the patients that were sequenced that 20% had the pathognomonic FGFR3 alteration, and the most common were the S249C, and the FGFR3-TACC3 fusion was in 45 patients. And basically I will say that we didn't want to generate too much as to fusion or the differences in that. The key aspect of this paper was that historically there were these anecdotal reports saying that patients who have FGFR alterations or mutations, they may not respond well to checkpoint inhibitors because they have the luminal subtype. And these were backed by some preclinical data and small anecdotal reports. But since then, we have seen that, and that's why a lot of people would say that if somebody's tumor has FGFR3, don't give them immunotherapy, give them erdafitinib first, right? So then we had this Phase 3 trial called the THOR trial, which actually showed that giving erdafitinib before pembrolizumab was not better. That debunked that myth, and we are actually reiterating that because in our work we found that patients who had FGFR3 alterations or fusions, and if they also have TMB-high, they actually respond very well to single agent immunotherapy. And that is, I think, very important because it tells us that we are not really seeing that so-called potential of resistance to immunotherapy in these patients. So to answer your question, yeah, we did see those differences, but I wouldn't say that any one marker is more prominent. Dr. Rafeh Naqash: The analogy is kind of similar to what we see in lung cancer with these mutations called STK11/KEAP1, which are also present in some other tumors. And one of the questions that I don't think has been answered is when you have in lung cancer, if you extrapolate this, where doublet or single agent immunotherapy doesn't do as well in tumors that are STK11 mutated. But then if you have a high TMB, question is does that TMB supersede or trump the actual mutation? Could that be one reason why you see the TMB-high but FGFR3 altered tumors in your dataset responding or having better outcomes to immunotherapy where potentially there is just more neoantigens and that results in a more durable or perhaps better response to checkpoint therapy? Dr. Shilpa Gupta: It could be. But you know, the patients who have FGFR alterations are not that many, right? So we have already seen that just patients with TMB-high respond very well to immunotherapy. Our last podcast was actually on that, regardless of PD-L1 that was a better predictor of response to immunotherapy. So I think it's not clear if this is adding more chances of response or not, because either way they would respond. But what we didn't see, which was good, that if they had FGFR3, it's not really downplaying the fact that they have TMB-high and that patients are not responding to immunotherapy. So we saw that regardless, and that was very reassuring. Dr. Rafeh Naqash: So if tomorrow in your clinic you had an individual with an FGFR3 alteration but TMB-high, I guess one could be comfortable just going ahead with immunotherapy, which is what the THOR trial as you mentioned. Dr. Shilpa Gupta: Yes, absolutely. And you know, when you look at the toxicity profiles of pembrolizumab and erdafitinib, really patients really struggle with using the FGFR3 inhibitors. And of course, if they have to use it, we have to, and we reserve it for patients. But it's not an easy drug to tolerate. Currently the landscape is such that, you know, frontline therapy has now evolved with an ADC and immunotherapy combinations. So really if patients progress and have FGFR3 alterations, we are using erdafitinib. But let's say if there were a situation where a patient has had chemotherapy, no immunotherapy, and they have FGFR3 upregulation and TMB-high, yes, I would be comfortable with using only pembrolizumab. And that really ties well together what we saw in the THOR trial as well. Dr. Rafeh Naqash: Going to the clinical applications, you mentioned a little bit of this in the manuscript, is combination therapies. You alluded to it a second back. Everything tends to get combined with checkpoint therapy these days, as you've seen with the frontline urothelial, pembrolizumab with an ADC. What is the landscape like as far as some of these FGFR alterations are concerned? Is it reasonable to combine some of those drugs with immune checkpoint therapy? And what are some of the toxicity patterns that you've potentially seen in your experience? Dr. Shilpa Gupta: So there was indeed a trial called the NORSE trial. It was a randomized trial but not a comparative cohort, where they looked at FGFR altered patients. And when they combined erdafitinib plus cetrelimab, that did numerically the response rates were much higher than those who got just erdafitinib. So yeah, the combination is definitely doable. There is no overlapping toxicities. But unfortunately that combination has not really moved forward to a Phase 3 trial because it's so challenging to enroll patients with such kind of rare mutations on large trials, especially to do registration trials. And since then the frontline therapy has evolved to enfortumab vedotin and pembrolizumab. I know there is an early phase trial looking at a next generation FGFR inhibitor. There is a triplet combination looking in Phase 1 setting with a next generation FGFR inhibitor with EV-pembro. However, it's not a randomized trial. So you know, I worry about such kinds of combinations where we don't have a path for registration. And in the four patients that have been treated, four or five patients in the early phase as a part of basket

    19 min

  8. 26/11/2025

    JCO PO Article Insights: Genomic Risk Classifiers in Localized Prostate Cancer

    In this JCO Precision Oncology Article Insights episode, Natalie DelRocco summarizes "Genomic Risk Classifiers in Localized Prostate Cancer: Precise but Not Standardized" by Góes et al. published on September 10, 2025. TRANSCRIPT Natalie DelRocco: Hello and welcome to JCO Precision Oncology Article Insights. I'm your host, Natalie DelRocco, and today we will be discussing the editorial "Genomic Risk Classifiers in Localized Prostate Cancer: Precise but Not Standardized." This editorial by Góes, Li, and Chehrazi-Raffle, and Janopaul-Naylor et al. describes genomic risk classifiers, or GRCs, for patients with localized prostate cancer. Like any risk prediction model, GRCs are intended to help identify groups of patients that may benefit from less intense or more intense anticancer therapy. Risk prediction tools can be difficult to bring into clinical practice; they require a lot of validation. And as the authors describe, GRCs in localized prostate cancer are no exception. The authors of this editorial contextualize an article by Janopaul-Naylor et al., which attempts to retrospectively explore the clinical use of three available GRCs for localized prostate cancer: Decipher, Oncotype DX, and Prolaris. Each of these three GRCs is being used in clinical practice currently. In the original article, all three GRCs were associated with less intense therapy being prescribed in practice. However, the editorial authors note that this is likely selection bias due to the observational nature of the study design. It is conceivable that GRCs were more likely ordered to make decisions for patients who were already thought to be good candidates for less intensive therapy. Another weakness of the retrospective study design is that patient level covariates known to be associated with clinical prognosis in localized prostate cancer, such as staging, Gleason score, prostate specific antigen, were unavailable. The authors note that sampling bias may also be an issue. Uninsured patients are not included in the original article, and therefore may impede the ability to make conclusions about the association of GRC use with income level. The editorial authors highlight important study findings as well as these limitations, such as the heterogeneity of interventions following GRC result return. The Prolaris GRC was found to be associated with more surgical interventions, while the Decipher GRC was associated with more androgen deprivation therapy plus radiation. Additionally, patients with active surveillance were more likely to have a GRC in general ordered. While these conclusions are very interesting, the editorial authors note that further exploration and validation, given the retrospective study design and limitations outlined, are needed to fully understand the impact of GRCs in the practice of treating localized prostate cancer. Thank you for listening to JCO Precision Oncology Article Insights. Don't forget to give us a rating or a review and be sure to subscribe so that you never miss an episode. You can find all ASCO shows atasco.org/podcasts. The purpose of this podcast is to educate and to inform. This is not a substitute for professional medical care and is not intended for use in the diagnosis or treatment of individual conditions.  Guests on this podcast express their own opinions, experience, and conclusions. Guest statements on the podcast do not express the opinions of ASCO. The mention of any product, service, organization, activity, or therapy should not be construed as an ASCO endorsement.

    4 min
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JCO Precision Oncology Conversations is a monthly podcast featuring conversations with authors of clinically relevant and significant articles published in the JCO Precision Oncology journal. JCO Precision Oncology Conversations is hosted by the journal's social media editor, Dr. Abdul Rafeh Naqash.

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