Tumor mutational burden assessment in non-small-cell lung cancer samples: results from the TMB 2 harmonization project comparing three NGS panels
Tumor mutational burden (TMB) is a recently proposed predictive biomarker for immunotherapy in solid tumors, including non-small cell lung cancer (NSCLC). Available assays for TMB determination differ in horizontal coverage, gene content and algorithms, leading to discrepancies in results, impacting...
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| Veröffentlicht in: | Journal for immunotherapy of cancer 2021-05, Vol.9 (5), p.e001904 |
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| creator | Ramos-Paradas, Javier Hernández-Prieto, Susana Lora, David Sanchez, Elena Rosado, Aranzazu Caniego-Casas, Tamara Carrizo, Nuria Enguita, Ana Belén Muñoz-Jimenez, María Teresa Rodriguez, Borja Perez-Gonzalez, Urbicio Gómez-Sánchez, David Ferrer, Irene Ponce Aix, Santiago Nuñez Buiza, Ángel Garrido, Pilar Palacios, José Lopez-Rios, Fernando Garrido-Martin, Eva M Paz-Ares, Luis |
| description | Tumor mutational burden (TMB) is a recently proposed predictive biomarker for immunotherapy in solid tumors, including non-small cell lung cancer (NSCLC). Available assays for TMB determination differ in horizontal coverage, gene content and algorithms, leading to discrepancies in results, impacting patient selection. A harmonization study of TMB assessment with available assays in a cohort of patients with NSCLC is urgently needed.
We evaluated the TMB assessment obtained with two marketed next generation sequencing panels: TruSight Oncology 500 (TSO500) and Oncomine Tumor Mutation Load (OTML) versus a reference assay (Foundation One, FO) in 96 NSCLC samples. Additionally, we studied the level of agreement among the three methods with respect to PD-L1 expression in tumors, checked the level of different immune infiltrates versus TMB, and performed an inter-laboratory reproducibility study. Finally, adjusted cut-off values were determined.
Both panels showed strong agreement with FO, with concordance correlation coefficients (CCC) of 0.933 (95% CI 0.908 to 0.959) for TSO500 and 0.881 (95% CI 0.840 to 0.922) for OTML. The corresponding CCCs were 0.951 (TSO500-FO) and 0.919 (OTML-FO) in tumors with |
| doi_str_mv | 10.1136/jitc-2020-001904 |
| format | Article |
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We evaluated the TMB assessment obtained with two marketed next generation sequencing panels: TruSight Oncology 500 (TSO500) and Oncomine Tumor Mutation Load (OTML) versus a reference assay (Foundation One, FO) in 96 NSCLC samples. Additionally, we studied the level of agreement among the three methods with respect to PD-L1 expression in tumors, checked the level of different immune infiltrates versus TMB, and performed an inter-laboratory reproducibility study. Finally, adjusted cut-off values were determined.
Both panels showed strong agreement with FO, with concordance correlation coefficients (CCC) of 0.933 (95% CI 0.908 to 0.959) for TSO500 and 0.881 (95% CI 0.840 to 0.922) for OTML. The corresponding CCCs were 0.951 (TSO500-FO) and 0.919 (OTML-FO) in tumors with <1% of cells expressing PD-L1 (PD-L1<1%; N
55), and 0.861 (TSO500-FO) and 0.722 (OTML-FO) in tumors with PD-L1≥1% (N=41). Inter-laboratory reproducibility analyses showed higher reproducibility with TSO500. No significant differences were found in terms of immune infiltration versus TMB. Adjusted cut-off values corresponding to 10 muts/Mb with FO needed to be lowered to 7.847 muts/Mb (TSO500) and 8.380 muts/Mb (OTML) to ensure a sensitivity >88%. With these cut-offs, the positive predictive value was 78.57% (95% CI 67.82 to 89.32) and the negative predictive value was 87.50% (95% CI 77.25 to 97.75) for TSO500, while for OTML they were 73.33% (95% CI 62.14 to 84.52) and 86.11% (95% CI 74.81 to 97.41), respectively.
Both panels exhibited robust analytical performances for TMB assessment, with stronger concordances in patients with negative PD-L1 expression. TSO500 showed a higher inter-laboratory reproducibility. The cut-offs for each assay were lowered to optimal overlap with FO.</description><identifier>ISSN: 2051-1426</identifier><identifier>EISSN: 2051-1426</identifier><identifier>DOI: 10.1136/jitc-2020-001904</identifier><identifier>PMID: 33963008</identifier><language>eng</language><publisher>England</publisher><subject>Biomarkers, Tumor - genetics ; Carcinoma, Non-Small-Cell Lung - genetics ; Carcinoma, Non-Small-Cell Lung - pathology ; Carcinoma, Non-Small-Cell Lung - surgery ; DNA Mutational Analysis ; Genetic Predisposition to Disease ; High-Throughput Nucleotide Sequencing ; Humans ; Lung Neoplasms - genetics ; Lung Neoplasms - pathology ; Lung Neoplasms - surgery ; Mutation ; Observer Variation ; Phenotype ; Predictive Value of Tests ; Prognosis ; Reproducibility of Results</subject><ispartof>Journal for immunotherapy of cancer, 2021-05, Vol.9 (5), p.e001904</ispartof><rights>Author(s) (or their employer(s)) 2021. Re-use permitted under CC BY. Published by BMJ.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c181t-e42bc5e646dbc20dd1a5de8db1e18df7851d72d020d8b1a6abef440a244e405d3</citedby><cites>FETCH-LOGICAL-c181t-e42bc5e646dbc20dd1a5de8db1e18df7851d72d020d8b1a6abef440a244e405d3</cites><orcidid>0000-0002-8094-2668</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,776,780,860,27901,27902</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/33963008$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Ramos-Paradas, Javier</creatorcontrib><creatorcontrib>Hernández-Prieto, Susana</creatorcontrib><creatorcontrib>Lora, David</creatorcontrib><creatorcontrib>Sanchez, Elena</creatorcontrib><creatorcontrib>Rosado, Aranzazu</creatorcontrib><creatorcontrib>Caniego-Casas, Tamara</creatorcontrib><creatorcontrib>Carrizo, Nuria</creatorcontrib><creatorcontrib>Enguita, Ana Belén</creatorcontrib><creatorcontrib>Muñoz-Jimenez, María Teresa</creatorcontrib><creatorcontrib>Rodriguez, Borja</creatorcontrib><creatorcontrib>Perez-Gonzalez, Urbicio</creatorcontrib><creatorcontrib>Gómez-Sánchez, David</creatorcontrib><creatorcontrib>Ferrer, Irene</creatorcontrib><creatorcontrib>Ponce Aix, Santiago</creatorcontrib><creatorcontrib>Nuñez Buiza, Ángel</creatorcontrib><creatorcontrib>Garrido, Pilar</creatorcontrib><creatorcontrib>Palacios, José</creatorcontrib><creatorcontrib>Lopez-Rios, Fernando</creatorcontrib><creatorcontrib>Garrido-Martin, Eva M</creatorcontrib><creatorcontrib>Paz-Ares, Luis</creatorcontrib><title>Tumor mutational burden assessment in non-small-cell lung cancer samples: results from the TMB 2 harmonization project comparing three NGS panels</title><title>Journal for immunotherapy of cancer</title><addtitle>J Immunother Cancer</addtitle><description>Tumor mutational burden (TMB) is a recently proposed predictive biomarker for immunotherapy in solid tumors, including non-small cell lung cancer (NSCLC). Available assays for TMB determination differ in horizontal coverage, gene content and algorithms, leading to discrepancies in results, impacting patient selection. A harmonization study of TMB assessment with available assays in a cohort of patients with NSCLC is urgently needed.
We evaluated the TMB assessment obtained with two marketed next generation sequencing panels: TruSight Oncology 500 (TSO500) and Oncomine Tumor Mutation Load (OTML) versus a reference assay (Foundation One, FO) in 96 NSCLC samples. Additionally, we studied the level of agreement among the three methods with respect to PD-L1 expression in tumors, checked the level of different immune infiltrates versus TMB, and performed an inter-laboratory reproducibility study. Finally, adjusted cut-off values were determined.
Both panels showed strong agreement with FO, with concordance correlation coefficients (CCC) of 0.933 (95% CI 0.908 to 0.959) for TSO500 and 0.881 (95% CI 0.840 to 0.922) for OTML. The corresponding CCCs were 0.951 (TSO500-FO) and 0.919 (OTML-FO) in tumors with <1% of cells expressing PD-L1 (PD-L1<1%; N
55), and 0.861 (TSO500-FO) and 0.722 (OTML-FO) in tumors with PD-L1≥1% (N=41). Inter-laboratory reproducibility analyses showed higher reproducibility with TSO500. No significant differences were found in terms of immune infiltration versus TMB. Adjusted cut-off values corresponding to 10 muts/Mb with FO needed to be lowered to 7.847 muts/Mb (TSO500) and 8.380 muts/Mb (OTML) to ensure a sensitivity >88%. With these cut-offs, the positive predictive value was 78.57% (95% CI 67.82 to 89.32) and the negative predictive value was 87.50% (95% CI 77.25 to 97.75) for TSO500, while for OTML they were 73.33% (95% CI 62.14 to 84.52) and 86.11% (95% CI 74.81 to 97.41), respectively.
Both panels exhibited robust analytical performances for TMB assessment, with stronger concordances in patients with negative PD-L1 expression. TSO500 showed a higher inter-laboratory reproducibility. The cut-offs for each assay were lowered to optimal overlap with FO.</description><subject>Biomarkers, Tumor - genetics</subject><subject>Carcinoma, Non-Small-Cell Lung - genetics</subject><subject>Carcinoma, Non-Small-Cell Lung - pathology</subject><subject>Carcinoma, Non-Small-Cell Lung - surgery</subject><subject>DNA Mutational Analysis</subject><subject>Genetic Predisposition to Disease</subject><subject>High-Throughput Nucleotide Sequencing</subject><subject>Humans</subject><subject>Lung Neoplasms - genetics</subject><subject>Lung Neoplasms - pathology</subject><subject>Lung Neoplasms - surgery</subject><subject>Mutation</subject><subject>Observer Variation</subject><subject>Phenotype</subject><subject>Predictive Value of Tests</subject><subject>Prognosis</subject><subject>Reproducibility of Results</subject><issn>2051-1426</issn><issn>2051-1426</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNpNkLFOwzAURS0Eoqh0Z0LvBwK246QuG1RQkAoMlDly7BeaynYi2xngL_hjWgqI6d3hnTMcQs4YvWAsLy83bdIZp5xmlLIZFQfkhNOCZUzw8vDfHpFJjBu6faJ5LqU8JqM8n5U5pfKEfK4G1wVwQ1Kp7byyUA_BoAcVI8bo0CdoPfjOZ9EpazON1oId_Bto5TUGiMr1FuMVBIyDTRGa0DlIa4TV4w1wWKvgOt9-fPuhD90GdQLduV6FdqtJ64AIT4sX6JVHG0_JUaNsxMnPHZPXu9vV_D5bPi8e5tfLTDPJUoaC17rAUpSm1pwaw1RhUJqaIZOmmcqCmSk32zxG1kyVqsZGCKq4EChoYfIxoXuvDl2MAZuqD61T4b1itNoFrnaBq13gah94i5zvkX6oHZo_4Ddn_gUs-Hp9</recordid><startdate>202105</startdate><enddate>202105</enddate><creator>Ramos-Paradas, Javier</creator><creator>Hernández-Prieto, Susana</creator><creator>Lora, David</creator><creator>Sanchez, Elena</creator><creator>Rosado, Aranzazu</creator><creator>Caniego-Casas, Tamara</creator><creator>Carrizo, Nuria</creator><creator>Enguita, Ana Belén</creator><creator>Muñoz-Jimenez, María Teresa</creator><creator>Rodriguez, Borja</creator><creator>Perez-Gonzalez, Urbicio</creator><creator>Gómez-Sánchez, David</creator><creator>Ferrer, Irene</creator><creator>Ponce Aix, Santiago</creator><creator>Nuñez Buiza, Ángel</creator><creator>Garrido, Pilar</creator><creator>Palacios, José</creator><creator>Lopez-Rios, Fernando</creator><creator>Garrido-Martin, Eva M</creator><creator>Paz-Ares, Luis</creator><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><orcidid>https://orcid.org/0000-0002-8094-2668</orcidid></search><sort><creationdate>202105</creationdate><title>Tumor mutational burden assessment in non-small-cell lung cancer samples: results from the TMB 2 harmonization project comparing three NGS panels</title><author>Ramos-Paradas, Javier ; Hernández-Prieto, Susana ; Lora, David ; Sanchez, Elena ; Rosado, Aranzazu ; Caniego-Casas, Tamara ; Carrizo, Nuria ; Enguita, Ana Belén ; Muñoz-Jimenez, María Teresa ; Rodriguez, Borja ; Perez-Gonzalez, Urbicio ; Gómez-Sánchez, David ; Ferrer, Irene ; Ponce Aix, Santiago ; Nuñez Buiza, Ángel ; Garrido, Pilar ; Palacios, José ; Lopez-Rios, Fernando ; Garrido-Martin, Eva M ; Paz-Ares, Luis</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c181t-e42bc5e646dbc20dd1a5de8db1e18df7851d72d020d8b1a6abef440a244e405d3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Biomarkers, Tumor - genetics</topic><topic>Carcinoma, Non-Small-Cell Lung - genetics</topic><topic>Carcinoma, Non-Small-Cell Lung - pathology</topic><topic>Carcinoma, Non-Small-Cell Lung - surgery</topic><topic>DNA Mutational Analysis</topic><topic>Genetic Predisposition to Disease</topic><topic>High-Throughput Nucleotide Sequencing</topic><topic>Humans</topic><topic>Lung Neoplasms - genetics</topic><topic>Lung Neoplasms - pathology</topic><topic>Lung Neoplasms - surgery</topic><topic>Mutation</topic><topic>Observer Variation</topic><topic>Phenotype</topic><topic>Predictive Value of Tests</topic><topic>Prognosis</topic><topic>Reproducibility of Results</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Ramos-Paradas, Javier</creatorcontrib><creatorcontrib>Hernández-Prieto, Susana</creatorcontrib><creatorcontrib>Lora, David</creatorcontrib><creatorcontrib>Sanchez, Elena</creatorcontrib><creatorcontrib>Rosado, Aranzazu</creatorcontrib><creatorcontrib>Caniego-Casas, Tamara</creatorcontrib><creatorcontrib>Carrizo, Nuria</creatorcontrib><creatorcontrib>Enguita, Ana Belén</creatorcontrib><creatorcontrib>Muñoz-Jimenez, María Teresa</creatorcontrib><creatorcontrib>Rodriguez, Borja</creatorcontrib><creatorcontrib>Perez-Gonzalez, Urbicio</creatorcontrib><creatorcontrib>Gómez-Sánchez, David</creatorcontrib><creatorcontrib>Ferrer, Irene</creatorcontrib><creatorcontrib>Ponce Aix, Santiago</creatorcontrib><creatorcontrib>Nuñez Buiza, Ángel</creatorcontrib><creatorcontrib>Garrido, Pilar</creatorcontrib><creatorcontrib>Palacios, José</creatorcontrib><creatorcontrib>Lopez-Rios, Fernando</creatorcontrib><creatorcontrib>Garrido-Martin, Eva M</creatorcontrib><creatorcontrib>Paz-Ares, Luis</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><jtitle>Journal for immunotherapy of cancer</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Ramos-Paradas, Javier</au><au>Hernández-Prieto, Susana</au><au>Lora, David</au><au>Sanchez, Elena</au><au>Rosado, Aranzazu</au><au>Caniego-Casas, Tamara</au><au>Carrizo, Nuria</au><au>Enguita, Ana Belén</au><au>Muñoz-Jimenez, María Teresa</au><au>Rodriguez, Borja</au><au>Perez-Gonzalez, Urbicio</au><au>Gómez-Sánchez, David</au><au>Ferrer, Irene</au><au>Ponce Aix, Santiago</au><au>Nuñez Buiza, Ángel</au><au>Garrido, Pilar</au><au>Palacios, José</au><au>Lopez-Rios, Fernando</au><au>Garrido-Martin, Eva M</au><au>Paz-Ares, Luis</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Tumor mutational burden assessment in non-small-cell lung cancer samples: results from the TMB 2 harmonization project comparing three NGS panels</atitle><jtitle>Journal for immunotherapy of cancer</jtitle><addtitle>J Immunother Cancer</addtitle><date>2021-05</date><risdate>2021</risdate><volume>9</volume><issue>5</issue><spage>e001904</spage><pages>e001904-</pages><issn>2051-1426</issn><eissn>2051-1426</eissn><abstract>Tumor mutational burden (TMB) is a recently proposed predictive biomarker for immunotherapy in solid tumors, including non-small cell lung cancer (NSCLC). Available assays for TMB determination differ in horizontal coverage, gene content and algorithms, leading to discrepancies in results, impacting patient selection. A harmonization study of TMB assessment with available assays in a cohort of patients with NSCLC is urgently needed.
We evaluated the TMB assessment obtained with two marketed next generation sequencing panels: TruSight Oncology 500 (TSO500) and Oncomine Tumor Mutation Load (OTML) versus a reference assay (Foundation One, FO) in 96 NSCLC samples. Additionally, we studied the level of agreement among the three methods with respect to PD-L1 expression in tumors, checked the level of different immune infiltrates versus TMB, and performed an inter-laboratory reproducibility study. Finally, adjusted cut-off values were determined.
Both panels showed strong agreement with FO, with concordance correlation coefficients (CCC) of 0.933 (95% CI 0.908 to 0.959) for TSO500 and 0.881 (95% CI 0.840 to 0.922) for OTML. The corresponding CCCs were 0.951 (TSO500-FO) and 0.919 (OTML-FO) in tumors with <1% of cells expressing PD-L1 (PD-L1<1%; N
55), and 0.861 (TSO500-FO) and 0.722 (OTML-FO) in tumors with PD-L1≥1% (N=41). Inter-laboratory reproducibility analyses showed higher reproducibility with TSO500. No significant differences were found in terms of immune infiltration versus TMB. Adjusted cut-off values corresponding to 10 muts/Mb with FO needed to be lowered to 7.847 muts/Mb (TSO500) and 8.380 muts/Mb (OTML) to ensure a sensitivity >88%. With these cut-offs, the positive predictive value was 78.57% (95% CI 67.82 to 89.32) and the negative predictive value was 87.50% (95% CI 77.25 to 97.75) for TSO500, while for OTML they were 73.33% (95% CI 62.14 to 84.52) and 86.11% (95% CI 74.81 to 97.41), respectively.
Both panels exhibited robust analytical performances for TMB assessment, with stronger concordances in patients with negative PD-L1 expression. TSO500 showed a higher inter-laboratory reproducibility. The cut-offs for each assay were lowered to optimal overlap with FO.</abstract><cop>England</cop><pmid>33963008</pmid><doi>10.1136/jitc-2020-001904</doi><orcidid>https://orcid.org/0000-0002-8094-2668</orcidid></addata></record> |
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| source | BMJ Open Access Journals; MEDLINE; DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central |
| subjects | Biomarkers, Tumor - genetics Carcinoma, Non-Small-Cell Lung - genetics Carcinoma, Non-Small-Cell Lung - pathology Carcinoma, Non-Small-Cell Lung - surgery DNA Mutational Analysis Genetic Predisposition to Disease High-Throughput Nucleotide Sequencing Humans Lung Neoplasms - genetics Lung Neoplasms - pathology Lung Neoplasms - surgery Mutation Observer Variation Phenotype Predictive Value of Tests Prognosis Reproducibility of Results |
| title | Tumor mutational burden assessment in non-small-cell lung cancer samples: results from the TMB 2 harmonization project comparing three NGS panels |
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