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Purpose: The National Cancer Institute-Children's Oncology Group (NCI-COG) Pediatric MATCH trial assigns patients age 1-21 years with refractory malignancies to phase II treatment arms of molecularly targeted therapies on the basis of genetic alterations detected in their tumor. Patients with activating alterations in the mitogen-activated protein kinase pathway were treated with ulixertinib, an extracellular signal-regulated kinase (ERK)1/2 inhibitor., Methods: As there were no previous pediatric data, ulixertinib was initially tested in a dose escalation cohort to establish the recommended phase II dose (RP2D) before proceeding to the phase II cohort. Ulixertinib was administered at 260 mg/m 2 /dose orally twice a day (dose level 1 [DL1], n = 15) or 350 mg/m 2 /dose orally twice a day (DL2, n = 5). The primary end point was objective response rate; secondary end points included safety/tolerability and progression-free survival (PFS)., Results: Twenty patients (median 12 years; range, 5-20) were treated, all evaluable for response. CNS tumors comprised 55% (11/20) of diagnoses, with high-grade glioma and low-grade glioma most common (n = 5 each). All CNS tumors except one harbored BRAF fusions or V600E mutations. Rhabdomyosarcoma (n = 5) was the most frequent non-CNS diagnosis. DL1 was declared the RP2D in the dose escalation cohort after dose-limiting toxicities in Cycle 1 occurred in 1/6 patients at DL1 and 2/5 patients at DL2, including fatigue, anorexia, rash, nausea, vomiting, diarrhea, dehydration, hypoalbuminemia, and hypernatremia. No objective responses were observed. Six-month PFS was 37% (95% CI, 17 to 58). Three patients with BRAF -altered CNS tumors achieved stable disease >6 months., Conclusion: Ulixertinib, a novel targeted agent with no previous pediatric data, was successfully evaluated in a national precision medicine basket trial. The pediatric RP2D of ulixertinib is 260 mg/m 2 /dose orally twice a day. Limited single-agent efficacy was observed in a biomarker-selected cohort of refractory pediatric tumors.

Purpose: Osteosarcoma risk stratification, on the basis of the presence of metastatic disease at diagnosis and histologic response to chemotherapy, has remained unchanged for four decades, does not include genomic features, and has not facilitated treatment advances. We report on the genomic features of advanced osteosarcoma and provide evidence that genomic alterations can be used for risk stratification., Materials and Methods: In a primary analytic patient cohort, 113 tumor and 69 normal samples from 92 patients with high-grade osteosarcoma were sequenced with OncoPanel, a targeted next-generation sequencing assay. In this primary cohort, we assessed the genomic landscape of advanced disease and evaluated the correlation between recurrent genomic events and outcome. We assessed whether prognostic associations identified in the primary cohort were maintained in a validation cohort of 86 patients with localized osteosarcoma tested with MSK-IMPACT., Results: In the primary cohort, 3-year overall survival (OS) was 65%. Metastatic disease, present in 33% of patients at diagnosis, was associated with poor OS ( P = .04). The most frequently altered genes in the primary cohort were TP 53, RB1, MYC, CCNE1, CCND3, CDKN2A/B, and ATRX . Mutational signature 3 was present in 28% of samples. MYC amplification was associated with a worse 3-year OS in both the primary cohort ( P = .015) and the validation cohort ( P = .012)., Conclusion: The most frequently occurring genomic events in advanced osteosarcoma were similar to those described in prior reports. MYC amplification, detected with clinical targeted next-generation sequencing panel tests, is associated with poorer outcomes in two independent cohorts.

Purpose: Multiple FGFR inhibitors are currently in clinical trials enrolling adults with different solid tumors, while very few enroll pediatric patients. We determined the types and frequency of FGFR alterations ( FGFR1-4 ) in pediatric cancers to inform future clinical trial design., Methods: Tumors with FGFR alterations were identified from two large cohorts of pediatric solid tumors subjected to targeted DNA sequencing: The Dana-Farber/Boston Children's Profile Study (n = 888) and the multi-institution GAIN/iCAT2 (Genomic Assessment Improves Novel Therapy) Study (n = 571). Data from the combined patient population of 1,395 cases (64 patients were enrolled in both studies) were reviewed and cases in which an FGFR alteration was identified by OncoPanel sequencing were further assessed., Results: We identified 41 patients with tumors harboring an oncogenic FGFR alteration. Median age at diagnosis was 8 years (range, 6 months-26 years). Diagnoses included 11 rhabdomyosarcomas, nine low-grade gliomas, and 17 other tumor types. Alterations included gain-of-function sequence variants (n = 19), amplifications (n = 10), oncogenic fusions ( FGFR3 :: TACC3 [n = 3], FGFR1 :: TACC1 [n = 1], FGFR1 :: EBF2 [n = 1], FGFR1 :: CLIP2 [n = 1], and FGFR2 :: CTNNA3 [n = 1]), pathogenic-leaning variants of uncertain significance (n = 4), and amplification in combination with a pathogenic-leaning variant of uncertain significance (n = 1). Two novel FGFR1 fusions in two different patients were identified in this cohort, one of whom showed a response to an FGFR inhibitor., Conclusion: In summary, activating FGFR alterations were found in approximately 3% (41/1,395) of pediatric solid tumors, identifying a population of children with cancer who may be eligible and good candidates for trials evaluating FGFR-targeted therapy. Importantly, the genomic and clinical data from this study can help inform drug development in accordance with the Research to Accelerate Cures and Equity for Children Act.

Purpose: Molecular tumor profiling is becoming a routine part of clinical cancer care, typically involving tumor-only panel testing without matched germline. We hypothesized that integrated germline sequencing could improve clinical interpretation and enhance the identification of germline variants with significant hereditary risks., Materials and Methods: Tumors from pediatric patients with high-risk, extracranial solid malignancies were sequenced with a targeted panel of cancer-associated genes. Later, germline DNA was analyzed for a subset of these genes. We performed a post hoc analysis to identify how an integrated analysis of tumor and germline data would improve clinical interpretation., Results: One hundred sixty participants with both tumor-only and germline sequencing reports were eligible for this analysis. Germline sequencing identified 38 pathogenic or likely pathogenic variants among 35 (22%) patients. Twenty-five (66%) of these were included in the tumor sequencing report. The remaining germline pathogenic or likely pathogenic variants were single-nucleotide variants filtered out of tumor-only analysis because of population frequency or copy-number variation masked by additional copy-number changes in the tumor. In tumor-only sequencing, 308 of 434 (71%) single-nucleotide variants reported were present in the germline, including 31% with suggested clinical utility. Finally, we provide further evidence that the variant allele fraction from tumor-only sequencing is insufficient to differentiate somatic from germline events., Conclusion: A paired approach to analyzing tumor and germline sequencing data would be expected to improve the efficiency and accuracy of distinguishing somatic mutations and germline variants, thereby facilitating the process of variant curation and therapeutic interpretation for somatic reports, as well as the identification of variants associated with germline cancer predisposition., Competing Interests: Alanna J. Church Honoraria: The Jackson Laboratory Consulting or Advisory Role: AlphaSights, The Jackson Laboratory, Bayer Travel, Accommodations, Expenses: Bayer Laura B. Corson Employment: Sema4 Stock and Other Ownership Interests: Alnylam, Inovio Pharmaceuticals, Agios Consulting or Advisory Role: Biomatics Patents, Royalties, Other Intellectual Property: Patent from work done at H3 Biomedicine before 2016 Brennan Decker Employment: Foundation Medicine Stock and Other Ownership Interests: Avidea Technologies, Roche Consulting or Advisory Role: Foundation Medicine, Avidea Technologies Catherine M. Clinton Employment: Helix OpCo LLC Mark A. Applebaum Consulting or Advisory Role: Fennec Pharma Rochelle Bagatell Uncompensated Relationships: Ymabs Therapeutics Inc Steven G. DuBois Consulting or Advisory Role: Bayer, Amgen Research Funding: Merck (Inst), Roche/Genentech (Inst), Lilly (Inst), Curis (Inst), Loxo (Inst), BMS (Inst), Eisai (Inst), Pfizer (Inst), Turning Point Therapeutics (Inst), Bayer (Inst), Salarius Pharmaceuticals (Inst) Travel, Accommodations, Expenses: Roche/Genentech, Salarius Pharmaceuticals Uncompensated Relationships: Ymabs Therapeutics Inc Julia L. Glade-Bender Research Funding: Eisai (Inst), Lilly (Inst), Loxo (Inst), Roche/Genentech (Inst), Bayer (Inst) Patents, Royalties, Other Intellectual Property: Patent on a T lympboblastic lymphoma cell line, CUTLL1 Travel, Accommodations, Expenses: Amgen (Inst) Uncompensated Relationships: SpringWorks Therapeutics, Bristol Myers Squibb, Merck, Eisai Open Payments Link: https://openpaymentsdata.cms.gov/physician/708514 AeRang Kim Research Funding: Esai (Inst); AstraZeneca (Inst); Oncternal (Inst); Ascentage (Inst); BioAlta (Inst). Theodore W. Laetsch Consulting or Advisory Role: Novartis, Bayer, Cellectis, Aptitude Health, Clinical Education Alliance, Deciphera, Jumo Health, Massive Bio, Med Learning Group, Medscape, Physicans' Education Resource, Y-mAbs Therapeutics Research Funding: Pfizer (Inst), Novartis (Inst), Bayer (Inst), AbbVie (Inst), Amgen (Inst), Atara Biotherapeutics (Inst), Bristol Myers Squibb (Inst), Lilly (Inst), Epizyme (Inst), GlaxoSmithKline (Inst), Janssen (Inst), Jubilant Pharmaceuticals (Inst), Novella Clinical (Inst), Servier (Inst), Foundation Medicine (Inst), Merck Sharp & Dohme (Inst) Margaret E. Macy Stock and Other Ownership Interests: Johnson & Johnson, GE Healthcare, Varian Medical Systems Consulting or Advisory Role: Ymabs Therapeutics Inc Research Funding: Bayer (Inst), Ignyta (Inst), Roche (Inst), Lilly (Inst), Merck (Inst), Oncternal Therapeutics Inc (Inst), AbbVie (Inst), Jubilant DraxImage (Inst), Actuate Therapeutics (Inst) Patents, Royalties, Other Intellectual Property: Patent for non-invasive methods of leukemia cell detection with MRI/MRS—Patent No. 8894975 Luke Maese Honoraria: Jazz Pharmaceuticals Consulting or Advisory Role: Jazz Pharmaceuticals Amit J. Sabnis Consulting or Advisory Role: Cardinal Health Joshua D. Schiffman Employment: PEEL Therapeutics Leadership: PEEL Therapeutics Stock and Other Ownership Interests: ItRunsInMyFamily.com, PEEL Therapeutics Honoraria: Affymetrix Consulting or Advisory Role: N-of-One, Fabric Genomics Samuel L. Volchenboum Stock and Other Ownership Interests: Litmus Health Consulting or Advisory Role: Accordant Travel, Accommodations, Expenses: Sanford Health Daniel A. Weiser Consulting or Advisory Role: Illumina Radiopharmaceuticals Jonathan A. Nowak Research Funding: NanoString Technologies, Illumina Katherine A. Janeway Honoraria: Foundation Medicine, Takeda Consulting or Advisory Role: Bayer, Ipsen Travel, Accommodations, Expenses: Bayer Brian D. Crompton Employment: Acceleron Pharma (I) Stock and Other Ownership Interests: Acceleron Pharma (I) Research Funding: Gradalis Junne Kamihara Stock and Other Ownership Interests: PanTher Therapeutics (I), ROME Therapeutics (I), TellBio (I) Honoraria: Pfizer (I), NanoString Technologies (I), Foundation Medicine (I), Ikena Oncology (I) Consulting or Advisory Role: ROME Therapeutics (I), Third Rock Ventures (I), Tekla Capital Management (I) Research Funding: PureTech (I), Ribon Therapeutics (I), ACD Biotechne (I) Patents, Royalties, Other Intellectual Property: Patent on drug delivery device licensed to PanTher Therapeutics (I), Patents on Repeat RNA biomarkers and therapeutics licensed to Rome Therapeutics (I), Patents on Circulating Tumor Cell Biomarkers Licensed to TellBio Inc (I) No other potential conflicts of interest were reported. Alanna J. Church Honoraria: The Jackson Laboratory Consulting or Advisory Role: AlphaSights, The Jackson Laboratory, Bayer Travel, Accommodations, Expenses: Bayer Laura B. Corson Employment: Sema4 Stock and Other Ownership Interests: Alnylam, Inovio Pharmaceuticals, Agios Consulting or Advisory Role: Biomatics Patents, Royalties, Other Intellectual Property: Patent from work done at H3 Biomedicine before 2016 Brennan Decker Employment: Foundation Medicine Stock and Other Ownership Interests: Avidea Technologies, Roche Consulting or Advisory Role: Foundation Medicine, Avidea Technologies Catherine M. Clinton Employment: Helix OpCo LLC Mark A. Applebaum Consulting or Advisory Role: Fennec Pharma Rochelle Bagatell Uncompensated Relationships: Ymabs Therapeutics Inc Steven G. DuBois Consulting or Advisory Role: Bayer, Amgen Research Funding: Merck (Inst), Roche/Genentech (Inst), Lilly (Inst), Curis (Inst), Loxo (Inst), BMS (Inst), Eisai (Inst), Pfizer (Inst), Turning Point Therapeutics (Inst), Bayer (Inst), Salarius Pharmaceuticals (Inst) Travel, Accommodations, Expenses: Roche/Genentech, Salarius Pharmaceuticals Uncompensated Relationships: Ymabs Therapeutics Inc Julia L. Glade-Bender Research Funding: Eisai (Inst), Lilly (Inst), Loxo (Inst), Roche/Genentech (Inst), Bayer (Inst) Patents, Royalties, Other Intellectual Property: Patent on a T lympboblastic lymphoma cell line, CUTLL1 Travel, Accommodations, Expenses: Amgen (Inst) Uncompensated Relationships: SpringWorks Therapeutics, Bristol Myers Squibb, Merck, Eisai Open Payments Link: https://openpaymentsdata.cms.gov/physician/708514 AeRang Kim Research Funding: Esai (Inst); AstraZeneca (Inst); Oncternal (Inst); Ascentage (Inst); BioAlta (Inst). Theodore W. Laetsch Consulting or Advisory Role: Novartis, Bayer, Cellectis, Aptitude Health, Clinical Education Alliance, Deciphera, Jumo Health, Massive Bio, Med Learning Group, Medscape, Physicans' Education Resource, Y-mAbs Therapeutics Research Funding: Pfizer (Inst), Novartis (Inst), Bayer (Inst), AbbVie (Inst), Amgen (Inst), Atara Biotherapeutics (Inst), Bristol Myers Squibb (Inst), Lilly (Inst), Epizyme (Inst), GlaxoSmithKline (Inst), Janssen (Inst), Jubilant Pharmaceuticals (Inst), Novella Clinical (Inst), Servier (Inst), Foundation Medicine (Inst), Merck Sharp & Dohme (Inst) Margaret E. Macy Stock and Other Ownership Interests: Johnson & Johnson, GE Healthcare, Varian Medical Systems Consulting or Advisory Role: Ymabs Therapeutics Inc Research Funding: Bayer (Inst), Ignyta (Inst), Roche (Inst), Lilly (Inst), Merck (Inst), Oncternal Therapeutics Inc (Inst), AbbVie (Inst), Jubilant DraxImage (Inst), Actuate Therapeutics (Inst) Patents, Royalties, Other Intellectual Property: Patent for non-invasive methods of leukemia cell detection with MRI/MRS—Patent No. 8894975 Luke Maese Honoraria: Jazz Pharmaceuticals Consulting or Advisory Role: Jazz Pharmaceuticals Amit J. Sabnis Consulting or Advisory Role: Cardinal Health Joshua D. Schiffman Employment: PEEL Therapeutics Leadership: PEEL Therapeutics Stock and Other Ownership Interests: ItRunsInMyFamily.com, PEEL Therapeutics Honoraria: Affymetrix Consulting or Advisory Role: N-of-One, Fabric Genomics Samuel L. Volchenboum Stock and Other Ownership Interests: Litmus Health Consulting or Advisory Role: Accordant Travel, Accommodations, Expenses: Sanford Health Daniel A. Weiser Consulting or Advisory Role: Illumina Radiopharmaceuticals Jonathan A. Nowak Research Funding: NanoString Technologies, Illumina Katherine A. Janeway Honoraria: Foundation Medicine, Takeda Consulting or Advisory Role: Bayer, Ipsen Travel, Accommodations, Expenses: Bayer Brian D. Crompton Employment: Acceleron Pharma (I) Stock and Other Ownership Interests: Acceleron Pharma (I) Research Funding: Gradalis Junne Kamihara Stock and Other Ownership Interests: PanTher Therapeutics (I), ROME Therapeutics (I), TellBio (I) Honoraria: Pfizer (I), NanoString Technologies (I), Foundation Medicine (I), Ikena Oncology (I) Consulting or Advisory Role: ROME Therapeutics (I), Third Rock Ventures (I), Tekla Capital Management (I) Research Funding: PureTech (I), Ribon Therapeutics (I), ACD Biotechne (I) Patents, Royalties, Other Intellectual Property: Patent on drug delivery device licensed to PanTher Therapeutics (I), Patents on Repeat RNA biomarkers and therapeutics licensed to Rome Therapeutics (I), Patents on Circulating Tumor Cell Biomarkers Licensed to TellBio Inc (I) No other potential conflicts of interest were reported., (© 2021 by American Society of Clinical Oncology.)