10061 Background: Genomics precision medicine, deployed via tumor panel sequencing, now assists in deploying targeted therapies to cancer patients. Numerous clinical trials have investigated the utility and benefit of genomics precision medicine in multiple cancer indications. Current large-scale studies report actionability rates from ~35% to ~60%, although clinical benefit rates have been shown to be closer to 10%. While this has positively impacted patients in need, the gap between actionability and benefit remains a clinical challenge attributed to multiple factors including the complex, multi-factorial relationship between molecular status and response to therapy. These differences go beyond simple disease states and may be reflective of multiple clinically relevant features including age, sex, and race/ethnicity. Methods: We implemented a functional precision medicine (FPM) program where patients with advanced pediatric cancers were prospectively profiled via high-throughput drug sensitivity testing (DST) of FDA-approved agents on patient-derived tumor cells as well as genomics testing. The objective was to investigate the clinical utility and benefit of FPM guidance in the treatment of pediatric cancer and elucidate the relationship between molecular status of patients’ diseases and treatment responses. We generated DST data (n = 21 patients) and genomic profiling data (n = 20 patients) on pediatric cancer patients in Miami, FL, as well as post-hoc whole exome and transcriptome sequencing data (n = 13 patients) and investigated three specific relationships. Results: We analyzed the relationship between racial/ethnic background and functional response to anti-cancer agents, determining potential differences in response to therapeutic classes. Next, we examined relationships between functional response and cancer type, identifying an unanticipated lack of clustering between disease indications in patients with advanced pediatric cancers. Finally, we applied an explainable machine learning (xML) framework to the functional genomic dataset to develop multi-omics biomarker hypotheses for the chemotherapy agent idarubicin, pinpointing a potential multi-cancer relationship between response to idarubicin and known disease mechanisms in acute myeloid leukemia (AML), the sole indication where idarubicin is approved. We further present additional proof-of-concept studies generating biomarker hypotheses via xML, demonstrating a framework for development of multi-omics biomarkers. Conclusions: We are now expanding our pan-pediatric cancer functional genomics dataset through an NIMHD-funded expansion cohort (NCT05857969, n = 65 patients) to further investigate multi-omics relationships between functional and molecular characteristics and understand the role of race/ethnicity in the complex relationship.

The aim of this study was to describe the turnaround time, diagnostic yield, and clinical impact of rapid whole-genomic sequencing (rWGS). We conducted a prospective observational study in acutely ill children (0-21 years) with an undiagnosed, potentially genetic abnormality in a children's hospital. A phenotype-prioritized analysis approach for rWGS was utilized. The turnaround times, diagnostic yield, number of genes detected, inheritance pattern, zygosity, and the clinical impact of positive or negative tests were analyzed. Out of a total of 109 children, 92 abnormal (pathogenic or likely pathogenic) gene variants were detected in 60 (55%) patients. There were 45 neonates, 35 infants, and 29 children. The admission location was 49.5, 34.9, and 15.6% in the pediatric intensive care unit (PICU), neonatal intensive care unit (NICU), and cardiac intensive care unit (CICU), respectively. The median (interquartile range [IQR]) times for the return of preliminary and final results were 3 (2-5) and 10 (6-14) days, respectively. With ultra-rapid processing, the median time to final results was shorter (5 [3-7] vs. 12 [7.75-15] days). Neurologic issues were the most common underlying admission diagnoses. The diagnostic yield for a causative gene was 47.7%. The diagnostic yield was not different based on age group or location of admission but higher in metabolic issues (78.6 vs. 43.2%; odds ratio [OR]: 4.8; 95% confidence interval [CI]: 1.3-18.4). There was a change in clinical management in 39.4%. In acutely ill children with undiagnosed conditions and with clinical suspicion of a genetic disorder, rWGS detected gene variants in 55% with a diagnostic yield of 47.7% and resulted in a change in the management in 39.4%. The diagnostic yield in patients with metabolic conditions was the highest.

Children with rare, relapsed or refractory cancers often face limited treatment options, and few predictive biomarkers are available that can enable personalized treatment recommendations. The implementation of functional precision medicine (FPM), which combines genomic profiling with drug sensitivity testing (DST) of patient-derived tumor cells, has potential to identify treatment options when standard-of-care is exhausted. The goal of this prospective observational study was to generate FPM data for pediatric patients with relapsed or refractory cancer. The primary objective was to determine the feasibility of returning FPM-based treatment recommendations in real time to the FPM tumor board (FPMTB) within a clinically actionable timeframe (<4 weeks). The secondary objective was to assess clinical outcomes from patients enrolled in the study. Twenty-five patients with relapsed or refractory solid and hematological cancers were enrolled; 21 patients underwent DST and 20 also completed genomic profiling. Median turnaround times for DST and genomics were within 10 days and 27 days, respectively. Treatment recommendations were made for 19 patients (76%), of whom 14 received therapeutic interventions. Six patients received subsequent FPM-guided treatments. Among these patients, five (83%) experienced a greater than 1.3-fold improvement in progression-free survival associated with their FPM-guided therapy relative to their previous therapy, and demonstrated a significant increase in progression-free survival and objective response rate compared to those of eight non-guided patients. The findings from our proof-of-principle study illustrate the potential for FPM to positively impact clinical care for pediatric and adolescent patients with relapsed or refractory cancers and warrant further validation in large prospective studies. ClinicalTrials.gov registration: NCT03860376 .

1551 Background: Pediatric and adult patients with rare, relapsed, or refractory cancers often have few treatment options. Precision medicine approaches are often the first strategy used to identify salvage therapy options when standard treatments fail. Despite the significant clinical benefit to advanced cancer patients, multiple genomics precision medicine trials have revealed important constraints for patients that lack treatments matched to mutations or biomarkers and have highlighted challenges in drug accessibility associated with novel targeted therapies identified through genomics precision medicine. Current clinical findings from large-scale studies demonstrate ~10% of cancer patients receive clinical benefit from genomics-guided therapies - in part due to limited insight into the complex relationship between tumor molecular characteristics and patient response. Methods: We implemented a functional precision medicine (FPM) approach combining genomic tumor profiling with high-throughput drug sensitivity testing (DST) of FDA-approved agents on patient-derived tumor cells to identify treatment options when standard-of-care is exhausted. Clinical utility and benefit of this program was investigated via a clinical trial (NCT03860376) at Nicklaus Children’s Hospital in Miami, FL. Results: We were returned DST data on 21 of 24 patients DST (median = 102 agents per sample) and genomic profiling on 20 of 24 patients. DST turnaround time was significantly below the 14 days required for clinical use (median = 10 days, p = 0.0012). FPM recommendations were returned to 19 (76%) patients, of which 14 patients underwent therapeutic intervention. Six patients received FPM-guided treatments, and five (83%) patients experienced a >1.3-fold improved progression-free survival over their previous therapy, significantly above the rate from physician’s choice (p = 0.0104). We subsequently opened pan-cancer FPM clinical studies for adults (n = 36 patients) and children (n = 65 patients). A key objective in these trials is optimizing our DST protocol for tissue samples of various sizes. Here, we report preliminary efforts to optimize our DST approach for tissue samples from resections, core biopsies, and fine-needle biopsies from primary and metastatic lesions. Conclusions: The findings from our feasibility study illustrate the potential for FPM to positively impact clinical care for pediatric/adolescent patients with relapsed/refractory cancers, and have supported initiation of currently enrolling clinical studies. An NIMHD-funded expansion cohort now enrolling at Nicklaus Children’s Hospital (NCT05857969, n = 65 patients), and a rare/relapsed/refractory adult patient cohort at Cleveland Clinic Florida (NCT06024603, n = 36 patients). These studies aim to further investigate the impact on clinical outcomes through the use of FPM to recommend treatment options. Clinical trial information: NCT06024603 , NCT05857969 , NCT04956198 , NCT03860376 .

Abstract Current genomics-driven precision oncology identifies actionable mutations in < 10% of cancer patients. Pediatric cancer is especially challenging due to limited mutations and fewer genomics-guided options. Functional precision medicine (FPM) addresses this by integrating genomic profiling with rapid, high-throughput functional ex vivo drug testing on live patient-derived cells. However, there is lack of FPM prospective data showing clinical utility in pediatric cancers. In this prospective, non-randomized, single-arm study (NCT03860376), we investigated feasibility and impact of FPM in pediatric/adolescent with refractory/relapsed solid and hematologic cancers. Of 25 patients, 19 (76%) had FPM data reviewed by the FPM tumor board within four weeks (FPMTB), meeting the primary outcome of the study. Additionally, six patients received FPM-guided treatment. Among these 6 patients, 83% (5 patients) experienced a greater than 1.3-fold improved progression-free survival compared to their previous therapy, and together demonstrated a significant increase in progression-free survival and objective response rate versus physician’s choice-treated patients (8 patients). Post-hoc analysis showed that patients with the same subtype of cancer do not cluster together, reinforcing the concept of optimizing cancer treatments one patient at a time (n-of-1 approach). Additionally, our study used a novel artificial intelligence/machine learning (AI/ML) platform that leveraged drug responses and sequencing data to identify novel biomarkers of drug efficacy and gain potential mechanistic insights within specific subsets of pediatric cancer patients. The findings from our proof-of-principle study illustrate the impact of FPM for relapsed/refractory pediatric/adolescent cancer patients, highlight future integrations of FPM and AI/ML, and support ongoing patient cohort expansion (NCT05857969).

Personalized medicine often serves as the first salvage therapy strategy when standard oncology treatments fail. However, most precision oncology approaches rely on molecular profiling which, unfortunately, provides therapeutic options for less than 10% of cancer patients. Functional precision medicine (FPM) complements molecular profiling by combining it with rapid, high-throughput drug testing on live patient cells to identify promising treatment options. In this study, we investigated the efficacy of FPM in the management of pediatric patients with recurrent and/or refractory cancers. We enrolled 25 pediatric/young adult patients with refractory solid or liquid cancers in this clinical trial (number NCT03860376). Enrolled patients represented the breadth of cancer indications generally presenting in pediatric patients: acute lymphoblastic leukemia (3 patients), acute myeloid leukemia (3 patients), astrocytoma (1 patient), ependymoma (1 patient), Ewing’s sarcoma (4 patients), glioblastoma (1 patient), malignant rhabdoid tumor (1 patient), medulloblastoma (1 patient), neuroblastoma (1 patient), osteosarcoma (4 patients), rhabdomyosarcoma (4 patients) and Wilms’ tumor (1 patient). We used a functional ex vivo drug sensitivity test (DST) panel encompassing 40 formulary drugs frequently used at Nicklaus Children’s Hospital and 47 non-formulary drugs approved by FDA for cancer treatment, as well as drugs from phase III and IV clinical trials. Drug sensitivity scores (DSS) were calculated for each drug based on cancer cells’ responses. DST results were then combined with results from targeted mutation profiles to match actionable mutations with selective targeted therapies. FPM and molecular data were prospectively generated and treatment recommendations were provided to an FPM Molecular Tumor Board (MTB) of clinicians. In total, 19 of 25 patients (76%) had complete functional and molecular profiling data provided to the MTB to support clinical decision-making. Six patients had their subsequent treatment guided by FPM recommendations, of which 83% (five of six patients) demonstrated greater than 1.3x increased progression-free survival compared to their previous therapy. Interestingly, hierarchical clustering analysis of DST results shows that patients with the same subtype of cancer do not cluster together, and no cancer subtype is differentially represented in either high-level cluster, suggesting the importance of functional profiling to provide deeper insight into individual patient pharmacological response. This FPM study is the first pediatric cancer study to enroll both solid and hematologic cancers regardless of tumor type, and the first FPM study in the United States to generate prospective treatment data on pediatric oncology patients. We illustrate the feasibility and efficacy of FPM to meet the needs of cancer patients with both liquid and solid tumors, especially for high-risk populations such as pediatric cancer patients. Citation Format: Arlet Maria Acanda de la Rocha, Maggie Fader, Ebony R. Coats, Joseph Dunn, Leat Perez, Carolina Velasquez, Jeanette Galano, Cima Saghira, Ileana Sotto, Yana Vorontsova, Ziad Khatib, Haneen Abdella, Cristina M. Andrade-Feraud, Alexa Jacome, Victoria Reis, Lilliam Rimblas, Nicole Tomas, Paula S. Espinal, Noah Berlow, Tomás R. Guilarte, Jennifer McCafferty-Fernandez, Daria Salyakina, Diana J. Azzam. Efficacy of a functional precision medicine approach in relapsed/refractory pediatric cancer patients: results from a prospective clinical study [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB358.

Multisystem inflammatory syndrome in children (MIS-C) is a severe, post-infectious sequela of SARS-CoV-2 infection, yet the pathophysiological mechanism connecting the infection to the broad inflammatory syndrome remains unknown. Here we leveraged a large set of MIS-C patient samples (n=199) to identify a distinct set of host proteins that are differentially targeted by patient autoantibodies relative to matched controls. We identified an autoreactive epitope within SNX8, a protein expressed primarily in immune cells which regulates an antiviral pathway associated with MIS-C pathogenesis. In parallel, we also probed the SARS-CoV-2 proteome-wide MIS-C patient antibody response and found it to be differentially reactive to a distinct domain of the SARS-CoV-2 nucleocapsid (N) protein relative to controls. This viral N region and the mapped SNX8 epitope bear remarkable biochemical similarity. Furthermore, we find that many children with anti-SNX8 autoantibodies also have T-cells cross-reactive to both SNX8 and this distinct domain of the SARS-CoV-2 N protein. Together, these findings suggest that MIS-C patients develop a distinct immune response against the SARS-CoV-2 N protein that is associated with cross reactivity to the self-protein SNX8, demonstrating a link from the infection to the inflammatory syndrome.

There is an increasing demand for supporting the adoption of rapid whole-genome sequencing (rWGS) by demonstrating its real-world value. We aimed to assess the cost-effectiveness of rWGS in critically ill pediatric patients with diseases of unknown cause. Data were collected prospectively of patients admitted to the Nicklaus Children’s Hospital’s intensive care units from March 2018 to September 2020, with rWGS (N = 65). Comparative data were collected in a matched retrospective cohort with standard diagnostic genetic testing. We determined total costs, diagnostic yield (DY), and incremental cost-effectiveness ratio (ICER) adjusted for selection bias and right censoring. Sensitivity analyses explored the robustness of ICER through bootstrapping. rWGS resulted in a diagnosis in 39.8% while standard testing in 13.5% (p = 0.026). rWGS resulted in a mean saving per person of $100,440 (SE = 26,497, p < 0.001) and a total of $6.53 M for 65 patients. rWGS in critically ill pediatric patients is cost-effective, cost-saving, shortens diagnostic odyssey, and triples the DY of traditional approaches.

PURPOSE:This study aimed to estimate the cost-effectiveness of exome sequencing (ES) and genome sequencing (GS) for children.METHODS:We modeled costs, diagnoses, and quality-adjusted life years (QALYs) for diagnostic strategies for critically ill infants (aged <1 year) and children (aged <18 years) with suspected genetic conditions: (1) standard of care (SOC) testing, (2) ES, (3) GS, (4) SOC followed by ES, (5) SOC followed by GS, (6) ES followed by GS, and (7) SOC followed by ES followed by GS. We calculated the 10-year incremental cost per additional diagnosis, and lifetime incremental cost per QALY gained, from a health care perspective.RESULTS:First-line GS costs $15,048 per diagnosis vs SOC for infants and $27,349 per diagnosis for children. If GS is unavailable, ES represents the next most efficient option compared with SOC ($15,543 per diagnosis for infants and $28,822 per diagnosis for children). Other strategies provided the same or fewer diagnoses at a higher incremental cost per diagnosis. Lifetime results depend on the patient's assumed long-term prognosis after diagnosis. For infants, GS ranged from cost-saving (vs all alternatives) to $18,877 per QALY (vs SOC). For children, GS (vs SOC) ranged from $119,705 to $490,047 per QALY.CONCLUSION:First-line GS may be the most cost-effective strategy for diagnosing infants with suspected genetic conditions. For all children, GS may be cost-effective under certain assumptions. ES is nearly as efficient as GS and hence is a viable option when GS is unavailable.

Biopreservation and BiobankingVol. 21, No. 1 Brief ReportsPriorities in Biobanking Research: A Report on the 2021 ISBER Round TableJennifer A. Byrne, Anastazia T. Banaszak, Jane E. Carpenter, Steven L. Carroll, Marta G. Castelhano, Paula S. Espinal, Marianne K. Henderson, Anusha Hettiaratchi, Mantombi Maseme, Wayne Ng, Kirtika Patel, Iuliana Popescu, Sergio I. Prada, William S. Schleif, Miranda Smith, Shirley Wee, Carol J. Weil, and Katherine WoodsJennifer A. ByrneAddress correspondence to: Jennifer A. Byrne, PhD, New South Wales Health Pathology, Camperdown 2050, Australia E-mail Address: jennifer.byrne@health.nsw.gov.auhttps://orcid.org/0000-0002-8923-0587New South Wales Health Pathology, Camperdown, Australia.School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia.Search for more papers by this author, Anastazia T. BanaszakInstitute of Ocean Sciences and Limnology, National Autonomous University of Mexico, Mexico City, Mexico.Search for more papers by this author, Jane E. CarpenterNew South Wales Health Pathology, Camperdown, Australia.Search for more papers by this author, Steven L. CarrollDepartment of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, USA.Search for more papers by this author, Marta G. Castelhanohttps://orcid.org/0000-0003-2497-1939Cornell Veterinary Biobank, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA.Search for more papers by this author, Paula S. EspinalNicklaus Children's Biobank, Research Institute, Nicklaus Children's Hospital, Miami, Florida, USA.Search for more papers by this author, Marianne K. HendersonNational Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA.Search for more papers by this author, Anusha HettiaratchiMark Wainwright Analytical Centre, UNSW, Sydney, Australia.Search for more papers by this author, Mantombi MasemeNational Health Laboratory Service, Biobank, Constitution Hill, Johannesburg, South Africa.Search for more papers by this author, Wayne NgVictorian Cancer Biobank, Melbourne, Australia.Search for more papers by this author, Kirtika PatelMoi University, School of Medicine, College of Health Science, Eldoret, Kenya.Search for more papers by this author, Iuliana PopescuBarnstable Brown Diabetes Center, University of Kentucky, College of Medicine, Lexington, Kentucky, USA.Search for more papers by this author, Sergio I. Pradahttps://orcid.org/0000-0001-7986-0959Fundación Valle del Lili, Centro de Investigaciones Clínicas, Cali, Colombia.Centro PROESA, Universidad Icesi, Cali, Colombia.Search for more papers by this author, William S. SchleifJohns Hopkins All Children's Pediatric Biorepository, Johns Hopkins All Children's Hospital, St. Petersburg, Florida, USA.Pediatric Biospecimen Science Program, Johns Hopkins All Children's Institute for Clinical and Translational Research, St. Petersburg, Florida, USA.Search for more papers by this author, Miranda SmithThe Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.Search for more papers by this author, Shirley WeeMenzies Health Institute Queensland, Griffith University, Southport, Australia.Search for more papers by this author, Carol J. WeilNational Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA.Search for more papers by this author, and Katherine WoodsSt Vincent's Biobank, NRL, St Vincent's Institute of Medical Research, Fitzroy, Australia.Search for more papers by this authorPublished Online:14 Feb 2023https://doi.org/10.1089/bio.2021.0178AboutSectionsView articleView Full TextPDF/EPUB Permissions & CitationsPermissionsDownload CitationsTrack CitationsAdd to favorites Back To Publication ShareShare onFacebookTwitterLinked InRedditEmail View articleFiguresReferencesRelatedDetails Volume 21Issue 1Feb 2023 InformationCopyright 2023, Mary Ann Liebert, Inc., publishersTo cite this article:Jennifer A. Byrne, Anastazia T. Banaszak, Jane E. Carpenter, Steven L. Carroll, Marta G. Castelhano, Paula S. Espinal, Marianne K. Henderson, Anusha Hettiaratchi, Mantombi Maseme, Wayne Ng, Kirtika Patel, Iuliana Popescu, Sergio I. Prada, William S. Schleif, Miranda Smith, Shirley Wee, Carol J. Weil, and Katherine Woods.Priorities in Biobanking Research: A Report on the 2021 ISBER Round Table.Biopreservation and Biobanking.Feb 2023.111-113.http://doi.org/10.1089/bio.2021.0178Published in Volume: 21 Issue 1: February 14, 2023Online Ahead of Print:May 4, 2022PDF download

Pediatric cancers are fundamentally different from those in adults, with lower frequency of genetic mutations and fewer options for targeted therapies. The implementation of functional precision medicine (FPM) - the integration of ex vivo drug screening and mutation profiling- can, therefore, provide better treatment options for pediatric tumor patients. In this study, we investigated the feasibility and clinical utility of FPM in the management of pediatric patients with recurrent and/or refractory cancers. We use a functional ex vivo drug screening test (DST) panel encompassed 40 formulary drugs frequently used at Nicklaus Children’s hospital and 47 non-formulary drugs approved by FDA for cancer treatment, as well as drugs from phase III and IV clinical trials. Drug sensitivity scores (DSS) were calculated for each drug based on cancer cells’ responses. DST results were then combined with results from targeted mutation profiles to match actionable mutations with selective targeted therapies. We have recruited a total of 21 patients into this ongoing clinical trial (number NCT03860376) and were able to perform drug testing and mutation profiling on 17 patients. We optimized and successfully performed DST on at least 13 different tumor types including acute myeloid leukemia, chronic lymphoblastic leukemia, ependymoma, osteosarcoma, Ewing’s sarcoma, rhabdomyosarcoma, glioblastoma, medulloblastoma, astrocytoma, neuroblastoma, rhabdoid, lung, and liver tumors. Our feasibility study, so far, has demonstrated that ex vivo DST can be performed within a clinically actionable time frame (median: 7 days). Ex vivo DST returned between 10 and 30 treatment options for each patient. These patients showed different responses to the 103 FDA-approved compounds used in the screen. More than half of the evaluated compounds were not active in any of the patients. Remarkably, DST provided valuable information to the oncologists on drug dosing and treatments that may not be effective and should be avoided. DSS synergizes with genomic data to further refine treatment recommendations. FPM-guided treatment regimens resulted in encouraging partial and complete responses as compared to progressive disease in prior regimens and physician choice regimens. Thus, our study shows technical feasibility of integrating functional precision medicine approaches for patients with refractory/relapsed pediatric cancers. Routine clinical integration of FPM for treatment selection is technically feasible and has led to improved treatment of pediatric cancer patients with refractory malignancies in an initial patient cohort, warranting further investigation. Citation Format: Arlet Maria Acanda de la Rocha, Maggie Fader, Ebony Coats, Joseph Dunn, Leat Perez, Cima Saghira, Ileana Sotto, Ziad Khatib, Ossama Maher, Haneen Abdella, Cristina M. Andrade-Feraud, Alexa Jacome, Lilliam Rimblas, Paula S. Espinal, Tomás R. Guilarte, Jennifer McCafferty-Fernandez, Daria Salyakina, Diana J. Azzam. Feasibility and efficacy of a functional precision medicine approach in the management of relapsed/refractory childhood cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 4103.

Treatments for rhabdomyosarcoma (RMS) including sclerosing and spindle cell rhabdomyosarcoma (SRMS) remains challenging. Aggressive surgical resection and radiation therapy are generally recommended; however, there is no consensus on secondor third-line salvage chemotherapy. Therefore, developing novel therapeutic options for children with all types of RMS suffering relapse under standard protocols is vital. Here, we present results using our functional precision medicine platform in a heavily refractory pediatric SRMS patient who had exhausted all standard options. Our functional precision medicine platform integrates genomic profiling and ex vivo drug sensitivity testing (DST) to determine optimal individualized therapy for each patient (Fig 1).