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Article ; Online: Clinical Applications of Next-Generation Sequencing in Precision Oncology.

Karlovich, Chris A / Williams, P Mickey

2019 Volume 25, Issue 4, Page(s) 264–271

Abstract: The ability of next-generation sequencing (NGS) to comprehensively assess the molecular profile of a tumor specimen has transformed the clinical testing landscape in oncology. Accordingly, recent years have seen broad uptake of clinical NGS to inform ... ...

Abstract	The ability of next-generation sequencing (NGS) to comprehensively assess the molecular profile of a tumor specimen has transformed the clinical testing landscape in oncology. Accordingly, recent years have seen broad uptake of clinical NGS to inform cancer patient management. However, significant challenges remain. The annotation and clinical interpretation of variants identified by NGS tests often require rigorous review and may vary between laboratories. While a clearer regulatory path has emerged, reimbursement for NGS tests remains a subject of continuing debate. Basket clinical studies such as the National Cancer Institute Molecular Analysis of Therapy Choice are evaluating the degree to which matching of a targeted therapy to tumor molecular profile by NGS can be applied independently of tissue histology. Newer applications of NGS such as for circulating tumor DNA testing and to identify novel RNA fusion driver events continue to expand its clinical utility.
MeSH term(s)	Biomarkers, Tumor ; Computational Biology/methods ; Genomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Medical Oncology/methods ; Medical Oncology/standards ; Precision Medicine/methods ; Precision Medicine/standards
Chemical Substances	Biomarkers, Tumor
Language	English
Publishing date	2019-07-20
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2018400-1
ISSN	1540-336X ; 1528-9117 ; 1081-4442
ISSN (online)	1540-336X
ISSN	1528-9117 ; 1081-4442
DOI	10.1097/PPO.0000000000000385
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Zs.A 4470: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MO 163: Show issues

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Article ; Online: Clinical Application of Liquid Biopsies.

Williams, P Mickey / Conley, Barbara A

JAMA oncology

2016 Volume 2, Issue 8, Page(s) 1003–1005

MeSH term(s)	Adenocarcinoma/diagnosis ; Adenocarcinoma/genetics ; Clinical Decision-Making ; DNA, Neoplasm/analysis ; DNA, Neoplasm/blood ; High-Throughput Nucleotide Sequencing ; Humans ; Lung Neoplasms/diagnosis ; Lung Neoplasms/genetics ; Mutation ; Polymerase Chain Reaction/methods ; Precision Medicine ; Proto-Oncogene Proteins p21(ras)/genetics ; Receptor, Epidermal Growth Factor/genetics ; Sequence Analysis, DNA
Chemical Substances	DNA, Neoplasm ; KRAS protein, human ; EGFR protein, human (EC 2.7.10.1) ; Receptor, Epidermal Growth Factor (EC 2.7.10.1) ; Proto-Oncogene Proteins p21(ras) (EC 3.6.5.2)
Language	English
Publishing date	2016-08-01
Publishing country	United States
Document type	Editorial
ISSN	2374-2445
ISSN (online)	2374-2445
DOI	10.1001/jamaoncol.2016.0240
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Article ; Online: The beginnings of real-time PCR.

Williams, P Mickey

Clinical chemistry

2009 Volume 55, Issue 4, Page(s) 833–834

MeSH term(s)	History, 20th Century ; Polymerase Chain Reaction/history
Language	English
Publishing date	2009-03-04
Publishing country	England
Document type	Historical Article ; Journal Article
ZDB-ID	80102-1
ISSN	1530-8561 ; 0009-9147
ISSN (online)	1530-8561
ISSN	0009-9147
DOI	10.1373/clinchem.2008.122226
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Ud II Zs.171: Show issues

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Article ; Online: Trastuzumab and Pertuzumab in Patients with Non-Breast/Gastroesophageal HER2-Amplified Tumors: Results from the NCI-MATCH ECOG-ACRIN Trial (EAY131) Subprotocol J.

Clinical cancer research : an official journal of the American Association for Cancer Research

2024 Volume 30, Issue 7, Page(s) 1273–1280

Abstract: Purpose: NCI-MATCH assigned patients with advanced cancer and progression on prior treatment, based on genomic alterations in pretreatment tumor tissue. Arm J (EAY131-J) evaluated the combination of trastuzumab/pertuzumab (HP) across HER2-amplified ... ...

Abstract	Purpose: NCI-MATCH assigned patients with advanced cancer and progression on prior treatment, based on genomic alterations in pretreatment tumor tissue. Arm J (EAY131-J) evaluated the combination of trastuzumab/pertuzumab (HP) across HER2-amplified tumors. Patients and methods: Eligible patients had high levels of HER2 amplification [copy number (CN) ≥7] detected by central next-generation sequencing (NGS) or through NCI-designated laboratories. Patients with breast/gastroesophageal adenocarcinoma and those who received prior HER2-directed therapy were excluded. Enrollment of patients with colorectal cancer was capped at 4 based on emerging data. Patients received HP IV Q3 weeks until progression or unacceptable toxicity. Primary endpoint was objective response rate (ORR); secondary endpoints included progression-free survival (PFS) and overall survival (OS). Results: Thirty-five patients were enrolled, with 25 included in the primary efficacy analysis (CN ≥7 confirmed by a central lab, median CN = 28). Median age was 66 (range, 31-80), and half of all patients had ≥3 prior therapies (range, 1-11). The confirmed ORR was 12% [3/25 partial responses (colorectal, cholangiocarcinoma, urothelial cancers), 90% confidence interval (CI) 3.4%-28.2%]. There was one additional partial response (urothelial cancer) in a patient with an unconfirmed ERBB2 copy number. Median PFS was 3.3 months (90% CI 2.0-4.1), and median OS 9.4 months (90% CI 5.0-18.9). Treatment-emergent adverse events were consistent with prior studies. There was no association between HER2 CN and response. Conclusions: HP was active in a selection of HER2-amplified tumors (non-breast/gastroesophageal) but did not meet the predefined efficacy benchmark. Additional strategies targeting HER2 and potential resistance pathways are warranted, especially in rare tumors.
MeSH term(s)	Adult ; Aged ; Aged, 80 and over ; Female ; Humans ; Male ; Middle Aged ; Antibodies, Monoclonal, Humanized/adverse effects ; Antibodies, Monoclonal, Humanized/therapeutic use ; Antineoplastic Combined Chemotherapy Protocols/adverse effects ; Breast Neoplasms/pathology ; Progression-Free Survival ; Receptor, ErbB-2/metabolism ; Trastuzumab/adverse effects ; Trastuzumab/therapeutic use
Chemical Substances	Antibodies, Monoclonal, Humanized ; pertuzumab (K16AIQ8CTM) ; Receptor, ErbB-2 (EC 2.7.10.1) ; Trastuzumab (P188ANX8CK)
Language	English
Publishing date	2024-03-04
Publishing country	United States
Document type	Randomized Controlled Trial ; Journal Article
ZDB-ID	1225457-5
ISSN	1557-3265 ; 1078-0432
ISSN (online)	1557-3265
ISSN	1078-0432
DOI	10.1158/1078-0432.CCR-23-0633
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Zs.A 4223: Show issues

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Article ; Online: Phase II Study of Osimertinib in Patients With Epidermal Growth Factor Receptor Mutations: Results From the NCI-MATCH ECOG-ACRIN (EAY131) Trial Subprotocol E.

JCO precision oncology

2024 Volume 8, Page(s) e2300454

Abstract: Purpose: The National Cancer Institute Molecular Analysis for Therapy Choice trial is a signal-finding genomically driven platform trial that assigns patients with any advanced refractory solid tumor, lymphoma, or myeloma to targeted therapies on the ... ...

Abstract	Purpose: The National Cancer Institute Molecular Analysis for Therapy Choice trial is a signal-finding genomically driven platform trial that assigns patients with any advanced refractory solid tumor, lymphoma, or myeloma to targeted therapies on the basis of next-generation sequencing results. Subprotocol E evaluated osimertinib, an epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor, in patients with Methods: Eligible patients had Results: A total of 19 patients were enrolled: 17 were evaluable for toxicity and 13 for efficacy. The median age of the 13 included in the efficacy analysis was 63 years, 62% had Eastern Cooperative Oncology Group performance status 1, and 31% received >three previous systemic therapies. The most common tumor type was brain cancers (54%). The ORR was 15.4% (n = 2 of 13; 90% CI, 2.8 to 41.0) and 6-month PFS was 16.7% (90% CI, 0 to 34.4). The two confirmed RECIST responses were observed in a patient with neuroendocrine carcinoma not otherwise specified ( Conclusion: In this pretreated cohort, osimertinib did not meet the prespecified end point threshold for efficacy, but responses were seen in a neuroendocrine carcinoma with an
MeSH term(s)	United States ; Humans ; Middle Aged ; Lung Neoplasms/drug therapy ; Lung Neoplasms/genetics ; Lung Neoplasms/pathology ; Carcinoma, Non-Small-Cell Lung/genetics ; ErbB Receptors/genetics ; National Cancer Institute (U.S.) ; Antineoplastic Agents/adverse effects ; Protein Kinase Inhibitors/adverse effects ; Mutation ; Carcinoma, Neuroendocrine/drug therapy ; Acrylamides ; Aniline Compounds ; Indoles ; Pyrimidines
Chemical Substances	osimertinib (3C06JJ0Z2O) ; ErbB Receptors (EC 2.7.10.1) ; Antineoplastic Agents ; Protein Kinase Inhibitors ; Acrylamides ; Aniline Compounds ; Indoles ; Pyrimidines
Language	English
Publishing date	2024-04-09
Publishing country	United States
Document type	Clinical Trial, Phase II ; Journal Article
ISSN	2473-4284
ISSN (online)	2473-4284
DOI	10.1200/PO.23.00454
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Article ; Online: Phase II Study of Erdafitinib in Patients With Tumors With

JCO precision oncology

2024 Volume 8, Page(s) e2300406

Abstract: Purpose: Despite fibroblast growth factor receptor (: Methods: EAY131-K1 was an open-label, single-arm, phase II study with central confirmation of presence of : Results: Thirty-five patients were enrolled into this study with 18 included in the ... ...

Abstract	Purpose: Despite fibroblast growth factor receptor ( Methods: EAY131-K1 was an open-label, single-arm, phase II study with central confirmation of presence of Results: Thirty-five patients were enrolled into this study with 18 included in the prespecified primary efficacy analysis. The median age of the 18 patients was 60 years, and 78% had received ≥3 previous lines of therapy. There were no confirmed responses to erdafitinib; however, five patients experienced stable disease (SD) as best response. One patient with an Conclusion: Erdafitinib did not meet its primary end point of efficacy as determined by ORR in treatment-refractory solid tumors harboring
MeSH term(s)	Humans ; Middle Aged ; Neoplasms/drug therapy ; Neoplasms/genetics ; Pyrazoles/therapeutic use ; Quinoxalines ; United States ; Urinary Bladder Neoplasms ; Receptors, Fibroblast Growth Factor/genetics
Chemical Substances	erdafitinib (890E37NHMV) ; Pyrazoles ; Quinoxalines ; Receptors, Fibroblast Growth Factor
Language	English
Publishing date	2024-04-11
Publishing country	United States
Document type	Clinical Trial, Phase II ; Journal Article
ISSN	2473-4284
ISSN (online)	2473-4284
DOI	10.1200/PO.23.00406
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Article ; Online: Phase II Study of Erdafitinib in Patients With Tumors With Fibroblast Growth Factor Receptor Mutations or Fusions: Results From the NCI-MATCH ECOG-ACRIN Trial (EAY131) Subprotocol K2.

JCO precision oncology

2024 Volume 8, Page(s) e2300407

Abstract: Purpose: Subprotocol K2 (EAY131-K2) of the NCI-MATCH platform trial was an open-label, single-arm, phase II study designed to evaluate the antitumor efficacy of the oral FGFR1-4 inhibitor, erdafitinib, in patients with tumors harboring FGFR1-4 mutations ...

Abstract	Purpose: Subprotocol K2 (EAY131-K2) of the NCI-MATCH platform trial was an open-label, single-arm, phase II study designed to evaluate the antitumor efficacy of the oral FGFR1-4 inhibitor, erdafitinib, in patients with tumors harboring FGFR1-4 mutations or fusions. Methods: Central confirmation of tumor FGFR1-4 mutations or fusions was required for outcome analysis. Patients with urothelial carcinoma were excluded. Enrolled subjects received oral erdafitinib at a starting dose of 8 mg daily continuously until intolerable toxicity or disease progression. The primary end point was objective response rate (ORR) with key secondary end points of safety, progression-free survival (PFS), and overall survival (OS). Results: Thirty-five patients were enrolled, and 25 patients were included in the primary efficacy analysis as prespecified in the protocol. The median age was 61 years, and 52% of subjects had received ≥3 previous lines of therapy. The confirmed ORR was 16% (4 of 25 [90% CI, 5.7 to 33.0], Conclusion: This study met its primary end point in patients with several pretreated solid tumor types harboring FGFR1-3 mutations or fusions. These findings support advancement of erdafitinib for patients with fibroblast growth factor receptor-altered tumors outside of currently approved indications in a potentially tumor-agnostic manner.
MeSH term(s)	Humans ; Middle Aged ; Mutation ; Pyrazoles/therapeutic use ; Pyrazoles/adverse effects ; Quinoxalines ; Urinary Bladder Neoplasms ; Neoplasms/drug therapy ; Neoplasms/genetics ; Receptors, Fibroblast Growth Factor/genetics
Chemical Substances	erdafitinib (890E37NHMV) ; Pyrazoles ; Quinoxalines ; Receptors, Fibroblast Growth Factor
Language	English
Publishing date	2024-04-11
Publishing country	United States
Document type	Clinical Trial, Phase II ; Journal Article
ISSN	2473-4284
ISSN (online)	2473-4284
DOI	10.1200/PO.23.00407
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Article: Circulating tumor DNA sequencing provides comprehensive mutation profiling for pediatric central nervous system tumors.

Bonner, Erin R / Harrington, Robin / Eze, Augustine / Bornhorst, Miriam / Kline, Cassie N / Gordish-Dressman, Heather / Dawood, Adam / Das, Biswajit / Chen, Li / Pauly, Rini / Williams, P Mickey / Karlovich, Chris / Peach, Amanda / Howell, D'andra / Doroshow, James / Kilburn, Lindsay / Packer, Roger J / Mueller, Sabine / Nazarian, Javad

NPJ precision oncology

2022 Volume 6, Issue 1, Page(s) 63

Abstract: Molecular profiling of childhood CNS tumors is critical for diagnosis and clinical management, yet tissue access is restricted due to the sensitive tumor location. We developed a targeted deep sequencing platform to detect tumor driver mutations, copy ... ...

Abstract	Molecular profiling of childhood CNS tumors is critical for diagnosis and clinical management, yet tissue access is restricted due to the sensitive tumor location. We developed a targeted deep sequencing platform to detect tumor driver mutations, copy number variations, and heterogeneity in the liquid biome. Here, we present the sensitivity, specificity, and clinical relevance of our minimally invasive platform for tumor mutation profiling in children diagnosed with CNS cancer.
Language	English
Publishing date	2022-09-06
Publishing country	England
Document type	Journal Article
ISSN	2397-768X
ISSN	2397-768X
DOI	10.1038/s41698-022-00306-3
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Article ; Online: TPM, FPKM, or Normalized Counts? A Comparative Study of Quantification Measures for the Analysis of RNA-seq Data from the NCI Patient-Derived Models Repository.

Zhao, Yingdong / Li, Ming-Chung / Konaté, Mariam M / Chen, Li / Das, Biswajit / Karlovich, Chris / Williams, P Mickey / Evrard, Yvonne A / Doroshow, James H / McShane, Lisa M

Journal of translational medicine

2021 Volume 19, Issue 1, Page(s) 269

Abstract: Background: In order to correctly decode phenotypic information from RNA-sequencing (RNA-seq) data, careful selection of the RNA-seq quantification measure is critical for inter-sample comparisons and for downstream analyses, such as differential gene ... ...

Abstract	Background: In order to correctly decode phenotypic information from RNA-sequencing (RNA-seq) data, careful selection of the RNA-seq quantification measure is critical for inter-sample comparisons and for downstream analyses, such as differential gene expression between two or more conditions. Several methods have been proposed and continue to be used. However, a consensus has not been reached regarding the best gene expression quantification method for RNA-seq data analysis. Methods: In the present study, we used replicate samples from each of 20 patient-derived xenograft (PDX) models spanning 15 tumor types, for a total of 61 human tumor xenograft samples available through the NCI patient-derived model repository (PDMR). We compared the reproducibility across replicate samples based on TPM (transcripts per million), FPKM (fragments per kilobase of transcript per million fragments mapped), and normalized counts using coefficient of variation, intraclass correlation coefficient, and cluster analysis. Results: Our results revealed that hierarchical clustering on normalized count data tended to group replicate samples from the same PDX model together more accurately than TPM and FPKM data. Furthermore, normalized count data were observed to have the lowest median coefficient of variation (CV), and highest intraclass correlation (ICC) values across all replicate samples from the same model and for the same gene across all PDX models compared to TPM and FPKM data. Conclusion: We provided compelling evidence for a preferred quantification measure to conduct downstream analyses of PDX RNA-seq data. To our knowledge, this is the first comparative study of RNA-seq data quantification measures conducted on PDX models, which are known to be inherently more variable than cell line models. Our findings are consistent with what others have shown for human tumors and cell lines and add further support to the thesis that normalized counts are the best choice for the analysis of RNA-seq data across samples.
MeSH term(s)	Gene Expression Profiling ; High-Throughput Nucleotide Sequencing ; Humans ; RNA ; RNA-Seq ; Reproducibility of Results ; Sequence Analysis, RNA
Chemical Substances	RNA (63231-63-0)
Language	English
Publishing date	2021-06-22
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ISSN	1479-5876
ISSN (online)	1479-5876
DOI	10.1186/s12967-021-02936-w
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Article ; Online: Tazemetostat for tumors harboring SMARCB1/SMARCA4 or EZH2 alterations: results from NCI-COG pediatric MATCH APEC1621C.

Journal of the National Cancer Institute

2023 Volume 115, Issue 11, Page(s) 1355–1363

Abstract: Background: National Cancer Institute-Children's Oncology Group Pediatric Molecular Analysis for Therapy Choice assigns patients aged 1-21 years with refractory solid tumors, brain tumors, lymphomas, and histiocytic disorders to phase II trials of ... ...

Abstract	Background: National Cancer Institute-Children's Oncology Group Pediatric Molecular Analysis for Therapy Choice assigns patients aged 1-21 years with refractory solid tumors, brain tumors, lymphomas, and histiocytic disorders to phase II trials of molecularly targeted therapies based on detection of predefined genetic alterations. Patients whose tumors harbored EZH2 mutations or loss of SMARCB1 or SMARCA4 by immunohistochemistry were treated with EZH2 inhibitor tazemetostat. Methods: Patients received tazemetostat for 28-day cycles until disease progression or intolerable toxicity (max 26 cycles). The primary endpoint was objective response rate; secondary endpoints included progression-free survival and tolerability of tazemetostat. Results: Twenty patients (median age = 5 years) enrolled, all evaluable for response and toxicities. The most frequent diagnoses were atypical teratoid rhabdoid tumor (n = 8) and malignant rhabdoid tumor (n = 4). Actionable alterations consisted of SMARCB1 loss (n = 16), EZH2 mutation (n = 3), and SMARCA4 loss (n = 1). One objective response was observed in a patient with non-Langerhans cell histiocytosis with SMARCA4 loss (26 cycles, 1200 mg/m2/dose twice daily). Four patients with SMARCB1 loss had a best response of stable disease: epithelioid sarcoma (n = 2), atypical teratoid rhabdoid tumor (n = 1), and renal medullary carcinoma (n = 1). Six-month progression-free survival was 35% (95% confidence interval [CI] = 15.7% to 55.2%) and 6-month overall survival was 45% (95% CI = 23.1% to 64.7%). Treatment-related adverse events were consistent with prior tazemetostat reports. Conclusions: Although tazemetostat did not meet its primary efficacy endpoint in this population of refractory pediatric tumors (objective response rate = 5%, 90% CI = 1% to 20%), 25% of patients with multiple histologic diagnoses experienced prolonged stable disease of 6 months and over (range = 9-26 cycles), suggesting a potential effect of tazemetostat on disease stabilization.
MeSH term(s)	United States/epidemiology ; Humans ; Child ; Child, Preschool ; National Cancer Institute (U.S.) ; Rhabdoid Tumor/drug therapy ; Rhabdoid Tumor/genetics ; Rhabdoid Tumor/diagnosis ; SMARCB1 Protein/genetics ; Benzamides/adverse effects ; DNA Helicases ; Nuclear Proteins ; Transcription Factors/genetics ; Enhancer of Zeste Homolog 2 Protein/genetics
Chemical Substances	tazemetostat (Q40W93WPE1) ; SMARCB1 Protein ; Benzamides ; SMARCA4 protein, human (EC 3.6.1.-) ; DNA Helicases (EC 3.6.4.-) ; Nuclear Proteins ; Transcription Factors ; SMARCB1 protein, human ; EZH2 protein, human (EC 2.1.1.43) ; Enhancer of Zeste Homolog 2 Protein (EC 2.1.1.43)
Language	English
Publishing date	2023-05-25
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2992-0
ISSN	1460-2105 ; 0027-8874 ; 0198-0157
ISSN (online)	1460-2105
ISSN	0027-8874 ; 0198-0157
DOI	10.1093/jnci/djad085
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