Qualification of tumour mutational burden by targeted next‐generation sequencing as a biomarker in hepatocellular carcinoma
Background & Aims Tumour mutational burden (TMB) predicts improved response and survival to immunotherapy. In this pilot study, we optimized targeted next‐generation sequencing (tNGS) to estimate TMB in hepatocellular carcinoma (HCC). Methods We sequenced 48 non‐paired samples (21 fresh‐frozen [...
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| Veröffentlicht in: | Liver international 2021-01, Vol.41 (1), p.192-203 |
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| creator | Wong, Ching Ngar Fessas, Petros Dominy, Kathy Mauri, Francesco A. Kaneko, Takahiro Parcq, Persephone Du Khorashad, Jamshid Toniutto, Pierluigi Goldin, Robert D. Avellini, Claudio Pinato, David J. |
| description | Background & Aims
Tumour mutational burden (TMB) predicts improved response and survival to immunotherapy. In this pilot study, we optimized targeted next‐generation sequencing (tNGS) to estimate TMB in hepatocellular carcinoma (HCC).
Methods
We sequenced 48 non‐paired samples (21 fresh‐frozen [FF] and 27 paraffin‐embedded [FFPE]), among which 11 FFPE samples were pretreated with uracil‐DNA glycosylase (UDG). Thirty samples satisfied post‐sequencing quality control. High/low TMB was defined by median number of mutations/Mb (Mut/Mb), across different minimum allele frequency (MAF) thresholds (≥0.05, ≥0.1 and ≥0.2).
Results
Eligible patients (n = 29) were cirrhotic (84%) with TNM stage I‐II HCC (75%). FFPE samples had higher TMB (median 958.39 vs 2.51 Mut/Mb, P |
| doi_str_mv | 10.1111/liv.14706 |
| format | Article |
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Tumour mutational burden (TMB) predicts improved response and survival to immunotherapy. In this pilot study, we optimized targeted next‐generation sequencing (tNGS) to estimate TMB in hepatocellular carcinoma (HCC).
Methods
We sequenced 48 non‐paired samples (21 fresh‐frozen [FF] and 27 paraffin‐embedded [FFPE]), among which 11 FFPE samples were pretreated with uracil‐DNA glycosylase (UDG). Thirty samples satisfied post‐sequencing quality control. High/low TMB was defined by median number of mutations/Mb (Mut/Mb), across different minimum allele frequency (MAF) thresholds (≥0.05, ≥0.1 and ≥0.2).
Results
Eligible patients (n = 29) were cirrhotic (84%) with TNM stage I‐II HCC (75%). FFPE samples had higher TMB (median 958.39 vs 2.51 Mut/Mb, P < .0001), estimated deamination counts (median 1335.50 vs 0, P < .0001) and C > T transitions at CpG sites (median 60.3% vs 9.1%, P = .002) compared to FF. UDG‐treated samples had lower TMB (median 4019.92 vs 353 Mut/Mb, P = .041) and deamination counts (median 6393.5 vs 328.5, P = .041) vs untreated FFPE. At 0.2 MAF threshold with UDG treatment, median TMB was 5.48 (range 1.68‐16.07) and did not correlate with salient pathologic features of HCC, including survival.
Conclusion
While tNGS on fresh HCC samples appears to be the optimal source of tumour DNA, the low median TMB values observed may limit the role of TMB as a predictor of response to immunotherapy in HCC.</description><identifier>ISSN: 1478-3223</identifier><identifier>EISSN: 1478-3231</identifier><identifier>DOI: 10.1111/liv.14706</identifier><identifier>PMID: 33098208</identifier><language>eng</language><publisher>United States: Wiley Subscription Services, Inc</publisher><subject>Biomarkers ; Biomarkers, Tumor - genetics ; Carcinoma, Hepatocellular - genetics ; CpG islands ; Deamination ; Deoxyribonucleic acid ; DNA ; DNA glycosylase ; DNA sequencing ; Gene frequency ; Hepatocellular carcinoma ; High-Throughput Nucleotide Sequencing ; Humans ; Immunotherapy ; Liver cancer ; Liver Neoplasms - genetics ; Mutation ; Paraffin ; Paraffins ; Pilot Projects ; Quality control ; Survival ; Tumors ; tumour mutational burden ; Uracil</subject><ispartof>Liver international, 2021-01, Vol.41 (1), p.192-203</ispartof><rights>2020 The Authors. published by John Wiley & Sons Ltd</rights><rights>2020 The Authors. Liver International published by John Wiley & Sons Ltd.</rights><rights>2020. This article is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c3886-b1db21ce193b6f94f196289928fe74444ac6124fc16778f5be1831e86254ab013</citedby><cites>FETCH-LOGICAL-c3886-b1db21ce193b6f94f196289928fe74444ac6124fc16778f5be1831e86254ab013</cites><orcidid>0000-0002-3529-0103 ; 0000-0002-2566-3041</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1111%2Fliv.14706$$EPDF$$P50$$Gwiley$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1111%2Fliv.14706$$EHTML$$P50$$Gwiley$$Hfree_for_read</linktohtml><link.rule.ids>314,780,784,1417,27924,27925,45574,45575</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/33098208$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Wong, Ching Ngar</creatorcontrib><creatorcontrib>Fessas, Petros</creatorcontrib><creatorcontrib>Dominy, Kathy</creatorcontrib><creatorcontrib>Mauri, Francesco A.</creatorcontrib><creatorcontrib>Kaneko, Takahiro</creatorcontrib><creatorcontrib>Parcq, Persephone Du</creatorcontrib><creatorcontrib>Khorashad, Jamshid</creatorcontrib><creatorcontrib>Toniutto, Pierluigi</creatorcontrib><creatorcontrib>Goldin, Robert D.</creatorcontrib><creatorcontrib>Avellini, Claudio</creatorcontrib><creatorcontrib>Pinato, David J.</creatorcontrib><title>Qualification of tumour mutational burden by targeted next‐generation sequencing as a biomarker in hepatocellular carcinoma</title><title>Liver international</title><addtitle>Liver Int</addtitle><description>Background & Aims
Tumour mutational burden (TMB) predicts improved response and survival to immunotherapy. In this pilot study, we optimized targeted next‐generation sequencing (tNGS) to estimate TMB in hepatocellular carcinoma (HCC).
Methods
We sequenced 48 non‐paired samples (21 fresh‐frozen [FF] and 27 paraffin‐embedded [FFPE]), among which 11 FFPE samples were pretreated with uracil‐DNA glycosylase (UDG). Thirty samples satisfied post‐sequencing quality control. High/low TMB was defined by median number of mutations/Mb (Mut/Mb), across different minimum allele frequency (MAF) thresholds (≥0.05, ≥0.1 and ≥0.2).
Results
Eligible patients (n = 29) were cirrhotic (84%) with TNM stage I‐II HCC (75%). FFPE samples had higher TMB (median 958.39 vs 2.51 Mut/Mb, P < .0001), estimated deamination counts (median 1335.50 vs 0, P < .0001) and C > T transitions at CpG sites (median 60.3% vs 9.1%, P = .002) compared to FF. UDG‐treated samples had lower TMB (median 4019.92 vs 353 Mut/Mb, P = .041) and deamination counts (median 6393.5 vs 328.5, P = .041) vs untreated FFPE. At 0.2 MAF threshold with UDG treatment, median TMB was 5.48 (range 1.68‐16.07) and did not correlate with salient pathologic features of HCC, including survival.
Conclusion
While tNGS on fresh HCC samples appears to be the optimal source of tumour DNA, the low median TMB values observed may limit the role of TMB as a predictor of response to immunotherapy in HCC.</description><subject>Biomarkers</subject><subject>Biomarkers, Tumor - genetics</subject><subject>Carcinoma, Hepatocellular - genetics</subject><subject>CpG islands</subject><subject>Deamination</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA glycosylase</subject><subject>DNA sequencing</subject><subject>Gene frequency</subject><subject>Hepatocellular carcinoma</subject><subject>High-Throughput Nucleotide Sequencing</subject><subject>Humans</subject><subject>Immunotherapy</subject><subject>Liver cancer</subject><subject>Liver Neoplasms - genetics</subject><subject>Mutation</subject><subject>Paraffin</subject><subject>Paraffins</subject><subject>Pilot Projects</subject><subject>Quality control</subject><subject>Survival</subject><subject>Tumors</subject><subject>tumour mutational burden</subject><subject>Uracil</subject><issn>1478-3223</issn><issn>1478-3231</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><sourceid>24P</sourceid><sourceid>WIN</sourceid><sourceid>EIF</sourceid><recordid>eNp1kUtOHDEQhq0IFB7JIheILLEJi4Eu291tLyMUHtJIERLJtmV7yhNDPyZ2O2EWSByBM3KSeGhgEYnaVKn81a9y_YR8guIIchy3_s8RiLqo3pHdnOWMMw5brzXjO2QvxuuiAKVKeE92OC-UZIXcJXeXSbfeeatHP_R0cHRM3ZAC7dL41NItNSkssKdmTUcdljjigvZ4Oz7ePyyxxzBNRvydsLe-X1IdqabGD50ONxio7-kvXOlxsNi2qdWBWh0ymN8_kG2n24gfn_M--XH67erkfDb_fnZx8nU-s1zKamZgYRhYBMVN5ZRwoComlWLSYS1yaFsBE85CVdfSlQZBckBZsVJoUwDfJ18m3VUY8ppxbDofN-voHocUGyZKASAFKzN68B96nc-Rz7Chas6l4lJk6nCibBhiDOiaVfD5v-sGimbjSZM9aZ48yeznZ8VkOly8ki8mZOB4Av76FtdvKzXzi5-T5D_Du5gT</recordid><startdate>202101</startdate><enddate>202101</enddate><creator>Wong, Ching Ngar</creator><creator>Fessas, Petros</creator><creator>Dominy, Kathy</creator><creator>Mauri, Francesco A.</creator><creator>Kaneko, Takahiro</creator><creator>Parcq, Persephone Du</creator><creator>Khorashad, Jamshid</creator><creator>Toniutto, Pierluigi</creator><creator>Goldin, Robert D.</creator><creator>Avellini, Claudio</creator><creator>Pinato, David J.</creator><general>Wiley Subscription Services, Inc</general><scope>24P</scope><scope>WIN</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QO</scope><scope>7T5</scope><scope>7U9</scope><scope>8FD</scope><scope>FR3</scope><scope>H94</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0002-3529-0103</orcidid><orcidid>https://orcid.org/0000-0002-2566-3041</orcidid></search><sort><creationdate>202101</creationdate><title>Qualification of tumour mutational burden by targeted next‐generation sequencing as a biomarker in hepatocellular carcinoma</title><author>Wong, Ching Ngar ; Fessas, Petros ; Dominy, Kathy ; Mauri, Francesco A. ; Kaneko, Takahiro ; Parcq, Persephone Du ; Khorashad, Jamshid ; Toniutto, Pierluigi ; Goldin, Robert D. ; Avellini, Claudio ; Pinato, David J.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c3886-b1db21ce193b6f94f196289928fe74444ac6124fc16778f5be1831e86254ab013</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Biomarkers</topic><topic>Biomarkers, Tumor - genetics</topic><topic>Carcinoma, Hepatocellular - genetics</topic><topic>CpG islands</topic><topic>Deamination</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA glycosylase</topic><topic>DNA sequencing</topic><topic>Gene frequency</topic><topic>Hepatocellular carcinoma</topic><topic>High-Throughput Nucleotide Sequencing</topic><topic>Humans</topic><topic>Immunotherapy</topic><topic>Liver cancer</topic><topic>Liver Neoplasms - genetics</topic><topic>Mutation</topic><topic>Paraffin</topic><topic>Paraffins</topic><topic>Pilot Projects</topic><topic>Quality control</topic><topic>Survival</topic><topic>Tumors</topic><topic>tumour mutational burden</topic><topic>Uracil</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Wong, Ching Ngar</creatorcontrib><creatorcontrib>Fessas, Petros</creatorcontrib><creatorcontrib>Dominy, Kathy</creatorcontrib><creatorcontrib>Mauri, Francesco A.</creatorcontrib><creatorcontrib>Kaneko, Takahiro</creatorcontrib><creatorcontrib>Parcq, Persephone Du</creatorcontrib><creatorcontrib>Khorashad, Jamshid</creatorcontrib><creatorcontrib>Toniutto, Pierluigi</creatorcontrib><creatorcontrib>Goldin, Robert D.</creatorcontrib><creatorcontrib>Avellini, Claudio</creatorcontrib><creatorcontrib>Pinato, David J.</creatorcontrib><collection>Wiley Online Library (Open Access Collection)</collection><collection>Wiley Online Library Free Content</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Biotechnology Research Abstracts</collection><collection>Immunology Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Liver international</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Wong, Ching Ngar</au><au>Fessas, Petros</au><au>Dominy, Kathy</au><au>Mauri, Francesco A.</au><au>Kaneko, Takahiro</au><au>Parcq, Persephone Du</au><au>Khorashad, Jamshid</au><au>Toniutto, Pierluigi</au><au>Goldin, Robert D.</au><au>Avellini, Claudio</au><au>Pinato, David J.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Qualification of tumour mutational burden by targeted next‐generation sequencing as a biomarker in hepatocellular carcinoma</atitle><jtitle>Liver international</jtitle><addtitle>Liver Int</addtitle><date>2021-01</date><risdate>2021</risdate><volume>41</volume><issue>1</issue><spage>192</spage><epage>203</epage><pages>192-203</pages><issn>1478-3223</issn><eissn>1478-3231</eissn><abstract>Background & Aims
Tumour mutational burden (TMB) predicts improved response and survival to immunotherapy. In this pilot study, we optimized targeted next‐generation sequencing (tNGS) to estimate TMB in hepatocellular carcinoma (HCC).
Methods
We sequenced 48 non‐paired samples (21 fresh‐frozen [FF] and 27 paraffin‐embedded [FFPE]), among which 11 FFPE samples were pretreated with uracil‐DNA glycosylase (UDG). Thirty samples satisfied post‐sequencing quality control. High/low TMB was defined by median number of mutations/Mb (Mut/Mb), across different minimum allele frequency (MAF) thresholds (≥0.05, ≥0.1 and ≥0.2).
Results
Eligible patients (n = 29) were cirrhotic (84%) with TNM stage I‐II HCC (75%). FFPE samples had higher TMB (median 958.39 vs 2.51 Mut/Mb, P < .0001), estimated deamination counts (median 1335.50 vs 0, P < .0001) and C > T transitions at CpG sites (median 60.3% vs 9.1%, P = .002) compared to FF. UDG‐treated samples had lower TMB (median 4019.92 vs 353 Mut/Mb, P = .041) and deamination counts (median 6393.5 vs 328.5, P = .041) vs untreated FFPE. At 0.2 MAF threshold with UDG treatment, median TMB was 5.48 (range 1.68‐16.07) and did not correlate with salient pathologic features of HCC, including survival.
Conclusion
While tNGS on fresh HCC samples appears to be the optimal source of tumour DNA, the low median TMB values observed may limit the role of TMB as a predictor of response to immunotherapy in HCC.</abstract><cop>United States</cop><pub>Wiley Subscription Services, Inc</pub><pmid>33098208</pmid><doi>10.1111/liv.14706</doi><tpages>12</tpages><orcidid>https://orcid.org/0000-0002-3529-0103</orcidid><orcidid>https://orcid.org/0000-0002-2566-3041</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Biomarkers Biomarkers, Tumor - genetics Carcinoma, Hepatocellular - genetics CpG islands Deamination Deoxyribonucleic acid DNA DNA glycosylase DNA sequencing Gene frequency Hepatocellular carcinoma High-Throughput Nucleotide Sequencing Humans Immunotherapy Liver cancer Liver Neoplasms - genetics Mutation Paraffin Paraffins Pilot Projects Quality control Survival Tumors tumour mutational burden Uracil |
| title | Qualification of tumour mutational burden by targeted next‐generation sequencing as a biomarker in hepatocellular carcinoma |
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