Multigene panel sequencing of established and candidate melanoma susceptibility genes in a large cohort of Dutch non‐CDKN2A/CDK4 melanoma families
Germline mutations in the major melanoma susceptibility gene CDKN2A explain genetic predisposition in only 10–40% of melanoma‐prone families. In our study we comprehensively characterized 488 melanoma cases from 451 non‐CDKN2A/CDK4 families for mutations in 30 established and candidate melanoma susc...
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| Veröffentlicht in: | International journal of cancer 2019-05, Vol.144 (10), p.2453-2464 |
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| creator | Potjer, Thomas P. Bollen, Sander Grimbergen, Anneliese J.E.M. Doorn, Remco Gruis, Nelleke A. Asperen, Christi J. Hes, Frederik J. Stoep, Nienke |
| description | Germline mutations in the major melanoma susceptibility gene CDKN2A explain genetic predisposition in only 10–40% of melanoma‐prone families. In our study we comprehensively characterized 488 melanoma cases from 451 non‐CDKN2A/CDK4 families for mutations in 30 established and candidate melanoma susceptibility genes using a custom‐designed targeted gene panel approach. We identified (likely) pathogenic variants in established melanoma susceptibility genes in 18 families (n = 3 BAP1, n = 15 MITF p.E318K; diagnostic yield 4.0%). Among the three identified BAP1‐families, there were no reported diagnoses of uveal melanoma or malignant mesothelioma. We additionally identified two potentially deleterious missense variants in the telomere maintenance genes ACD and TERF2IP, but none in the POT1 gene. MC1R risk variants were strongly enriched in our familial melanoma cohort compared to healthy controls (R variants: OR 3.67, 95% CI 2.88–4.68, p |
| doi_str_mv | 10.1002/ijc.31984 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_pubme</sourceid><recordid>TN_cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_6590189</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>2195293985</sourcerecordid><originalsourceid>FETCH-LOGICAL-c4434-62ebfcfadd49879e71c71553744a8f31a6cfa299160acba478a3fac809165f823</originalsourceid><addsrcrecordid>eNp1kctuEzEUhi0EomlhwQsgS2zoIo1vc_EGqUq5FApsYG2d8ZxJHHnsdDwDyo5HYMET8iQ4pJSLxMaWfD59Puf8hDzi7IwzJhZuY88k17W6Q2ac6WrOBC_uklmusXnFZXlEjlPaMMZ5wdR9ciSZ4kqqcka-vZ386FYYkG4hoKcJrycM1oUVjR3FNELjXVpjSyG01ObDtTAi7dFDiD3QNCWL29E1zrtxR_eqRF2gQD0MK6Q2ruMw7mUX02jXNMTw_cvX5cWbd-J8kS_1W9VBnyWYHpB7HfiED2_uE_LxxfMPy1fzq_cvL5fnV3OrcvfzUmDT2Q7aVum60lhxW_GikJVSUHeSQ5mLQmteMrANqKoG2YGtWX4pulrIE_Ls4N1OTY-txTAO4M12cD0MOxPBmb8rwa3NKn4yZaEZr3UWPL0RDDGvLY2md3kbPs-DcUpGcClEIXSx_-vJP-gmTkPI42UqA1rqusjU6YGyQ0xpwO62Gc7MPmuTszY_s87s4z-7vyV_hZuBxQH47Dzu_m8yl6-XB-UPP-22Hg</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2195293985</pqid></control><display><type>article</type><title>Multigene panel sequencing of established and candidate melanoma susceptibility genes in a large cohort of Dutch non‐CDKN2A/CDK4 melanoma families</title><source>MEDLINE</source><source>Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals</source><source>Access via Wiley Online Library</source><creator>Potjer, Thomas P. ; Bollen, Sander ; Grimbergen, Anneliese J.E.M. ; Doorn, Remco ; Gruis, Nelleke A. ; Asperen, Christi J. ; Hes, Frederik J. ; Stoep, Nienke</creator><creatorcontrib>Potjer, Thomas P. ; Bollen, Sander ; Grimbergen, Anneliese J.E.M. ; Doorn, Remco ; Gruis, Nelleke A. ; Asperen, Christi J. ; Hes, Frederik J. ; Stoep, Nienke ; Dutch Working Group for Clinical Oncogenetics ; on behalf of the Dutch Working Group for Clinical Oncogenetics</creatorcontrib><description>Germline mutations in the major melanoma susceptibility gene CDKN2A explain genetic predisposition in only 10–40% of melanoma‐prone families. In our study we comprehensively characterized 488 melanoma cases from 451 non‐CDKN2A/CDK4 families for mutations in 30 established and candidate melanoma susceptibility genes using a custom‐designed targeted gene panel approach. We identified (likely) pathogenic variants in established melanoma susceptibility genes in 18 families (n = 3 BAP1, n = 15 MITF p.E318K; diagnostic yield 4.0%). Among the three identified BAP1‐families, there were no reported diagnoses of uveal melanoma or malignant mesothelioma. We additionally identified two potentially deleterious missense variants in the telomere maintenance genes ACD and TERF2IP, but none in the POT1 gene. MC1R risk variants were strongly enriched in our familial melanoma cohort compared to healthy controls (R variants: OR 3.67, 95% CI 2.88–4.68, p <0.001). Several variants of interest were also identified in candidate melanoma susceptibility genes, in particular rare (pathogenic) variants in the albinism gene OCA2 were repeatedly found. We conclude that multigene panel testing for familial melanoma is appropriate considering the additional 4% diagnostic yield in non‐CDKN2A/CDK4 families. Our study shows that BAP1 and MITF are important genes to be included in such a diagnostic test.
What's new?
Germline mutations in CDKN2A are major contributors to familial melanoma. These mutations, however, are responsible for only 10 to 40 percent of genetic susceptibility in melanoma‐prone families. In this study, 30 established and candidate melanoma susceptibility genes were investigated for associations with the disease in patients from 451 non‐CDKN2A/CDK4 melanoma families. From the candidate gene panel, (likely) pathogenic variants in BAP1 and MITF were identified in several families, and potentially deleterious variants were identified in the shelterin complex genes ACD and TERF2IP. These genes appear to play a significant role in familial melanoma predisposition and are therefore promising candidates for incorporation into comprehensive genetic tests.</description><identifier>ISSN: 0020-7136</identifier><identifier>EISSN: 1097-0215</identifier><identifier>DOI: 10.1002/ijc.31984</identifier><identifier>PMID: 30414346</identifier><language>eng</language><publisher>Hoboken, USA: John Wiley & Sons, Inc</publisher><subject>Albinism ; BAP1 ; Cancer ; Cancer Genetics and Epigenetics ; candidate susceptibility genes ; Cohort Studies ; Cyclin-dependent kinase 4 ; Cyclin-Dependent Kinase 4 - genetics ; Cyclin-Dependent Kinase Inhibitor p16 - genetics ; familial melanoma ; Female ; gene panel sequencing ; Genes ; Genetic Predisposition to Disease - genetics ; genetic susceptibility ; Germ-Line Mutation - genetics ; Health risk assessment ; high‐penetrance genes ; Humans ; Lung Neoplasms - genetics ; Male ; Medical research ; Melanoma ; Melanoma - genetics ; Mesothelioma ; Mesothelioma - genetics ; Mesothelioma, Malignant ; Microphthalmia-associated transcription factor ; Microphthalmia-Associated Transcription Factor - genetics ; MITF ; Mutation ; OCA2 ; Pot1 gene ; Ubiquitin Thiolesterase - genetics</subject><ispartof>International journal of cancer, 2019-05, Vol.144 (10), p.2453-2464</ispartof><rights>2018 The Authors. published by John Wiley & Sons Ltd on behalf of UICC</rights><rights>2018 The Authors. International Journal of Cancer published by John Wiley & Sons Ltd on behalf of UICC.</rights><rights>2019 UICC</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4434-62ebfcfadd49879e71c71553744a8f31a6cfa299160acba478a3fac809165f823</citedby><cites>FETCH-LOGICAL-c4434-62ebfcfadd49879e71c71553744a8f31a6cfa299160acba478a3fac809165f823</cites><orcidid>0000-0002-3831-6022</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1002%2Fijc.31984$$EPDF$$P50$$Gwiley$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1002%2Fijc.31984$$EHTML$$P50$$Gwiley$$Hfree_for_read</linktohtml><link.rule.ids>230,315,781,785,886,1418,27928,27929,45578,45579</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/30414346$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Potjer, Thomas P.</creatorcontrib><creatorcontrib>Bollen, Sander</creatorcontrib><creatorcontrib>Grimbergen, Anneliese J.E.M.</creatorcontrib><creatorcontrib>Doorn, Remco</creatorcontrib><creatorcontrib>Gruis, Nelleke A.</creatorcontrib><creatorcontrib>Asperen, Christi J.</creatorcontrib><creatorcontrib>Hes, Frederik J.</creatorcontrib><creatorcontrib>Stoep, Nienke</creatorcontrib><creatorcontrib>Dutch Working Group for Clinical Oncogenetics</creatorcontrib><creatorcontrib>on behalf of the Dutch Working Group for Clinical Oncogenetics</creatorcontrib><title>Multigene panel sequencing of established and candidate melanoma susceptibility genes in a large cohort of Dutch non‐CDKN2A/CDK4 melanoma families</title><title>International journal of cancer</title><addtitle>Int J Cancer</addtitle><description>Germline mutations in the major melanoma susceptibility gene CDKN2A explain genetic predisposition in only 10–40% of melanoma‐prone families. In our study we comprehensively characterized 488 melanoma cases from 451 non‐CDKN2A/CDK4 families for mutations in 30 established and candidate melanoma susceptibility genes using a custom‐designed targeted gene panel approach. We identified (likely) pathogenic variants in established melanoma susceptibility genes in 18 families (n = 3 BAP1, n = 15 MITF p.E318K; diagnostic yield 4.0%). Among the three identified BAP1‐families, there were no reported diagnoses of uveal melanoma or malignant mesothelioma. We additionally identified two potentially deleterious missense variants in the telomere maintenance genes ACD and TERF2IP, but none in the POT1 gene. MC1R risk variants were strongly enriched in our familial melanoma cohort compared to healthy controls (R variants: OR 3.67, 95% CI 2.88–4.68, p <0.001). Several variants of interest were also identified in candidate melanoma susceptibility genes, in particular rare (pathogenic) variants in the albinism gene OCA2 were repeatedly found. We conclude that multigene panel testing for familial melanoma is appropriate considering the additional 4% diagnostic yield in non‐CDKN2A/CDK4 families. Our study shows that BAP1 and MITF are important genes to be included in such a diagnostic test.
What's new?
Germline mutations in CDKN2A are major contributors to familial melanoma. These mutations, however, are responsible for only 10 to 40 percent of genetic susceptibility in melanoma‐prone families. In this study, 30 established and candidate melanoma susceptibility genes were investigated for associations with the disease in patients from 451 non‐CDKN2A/CDK4 melanoma families. From the candidate gene panel, (likely) pathogenic variants in BAP1 and MITF were identified in several families, and potentially deleterious variants were identified in the shelterin complex genes ACD and TERF2IP. These genes appear to play a significant role in familial melanoma predisposition and are therefore promising candidates for incorporation into comprehensive genetic tests.</description><subject>Albinism</subject><subject>BAP1</subject><subject>Cancer</subject><subject>Cancer Genetics and Epigenetics</subject><subject>candidate susceptibility genes</subject><subject>Cohort Studies</subject><subject>Cyclin-dependent kinase 4</subject><subject>Cyclin-Dependent Kinase 4 - genetics</subject><subject>Cyclin-Dependent Kinase Inhibitor p16 - genetics</subject><subject>familial melanoma</subject><subject>Female</subject><subject>gene panel sequencing</subject><subject>Genes</subject><subject>Genetic Predisposition to Disease - genetics</subject><subject>genetic susceptibility</subject><subject>Germ-Line Mutation - genetics</subject><subject>Health risk assessment</subject><subject>high‐penetrance genes</subject><subject>Humans</subject><subject>Lung Neoplasms - genetics</subject><subject>Male</subject><subject>Medical research</subject><subject>Melanoma</subject><subject>Melanoma - genetics</subject><subject>Mesothelioma</subject><subject>Mesothelioma - genetics</subject><subject>Mesothelioma, Malignant</subject><subject>Microphthalmia-associated transcription factor</subject><subject>Microphthalmia-Associated Transcription Factor - genetics</subject><subject>MITF</subject><subject>Mutation</subject><subject>OCA2</subject><subject>Pot1 gene</subject><subject>Ubiquitin Thiolesterase - genetics</subject><issn>0020-7136</issn><issn>1097-0215</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2019</creationdate><recordtype>article</recordtype><sourceid>24P</sourceid><sourceid>WIN</sourceid><sourceid>EIF</sourceid><recordid>eNp1kctuEzEUhi0EomlhwQsgS2zoIo1vc_EGqUq5FApsYG2d8ZxJHHnsdDwDyo5HYMET8iQ4pJSLxMaWfD59Puf8hDzi7IwzJhZuY88k17W6Q2ac6WrOBC_uklmusXnFZXlEjlPaMMZ5wdR9ciSZ4kqqcka-vZ386FYYkG4hoKcJrycM1oUVjR3FNELjXVpjSyG01ObDtTAi7dFDiD3QNCWL29E1zrtxR_eqRF2gQD0MK6Q2ruMw7mUX02jXNMTw_cvX5cWbd-J8kS_1W9VBnyWYHpB7HfiED2_uE_LxxfMPy1fzq_cvL5fnV3OrcvfzUmDT2Q7aVum60lhxW_GikJVSUHeSQ5mLQmteMrANqKoG2YGtWX4pulrIE_Ls4N1OTY-txTAO4M12cD0MOxPBmb8rwa3NKn4yZaEZr3UWPL0RDDGvLY2md3kbPs-DcUpGcClEIXSx_-vJP-gmTkPI42UqA1rqusjU6YGyQ0xpwO62Gc7MPmuTszY_s87s4z-7vyV_hZuBxQH47Dzu_m8yl6-XB-UPP-22Hg</recordid><startdate>20190515</startdate><enddate>20190515</enddate><creator>Potjer, Thomas P.</creator><creator>Bollen, Sander</creator><creator>Grimbergen, Anneliese J.E.M.</creator><creator>Doorn, Remco</creator><creator>Gruis, Nelleke A.</creator><creator>Asperen, Christi J.</creator><creator>Hes, Frederik J.</creator><creator>Stoep, Nienke</creator><general>John Wiley & Sons, Inc</general><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>7T5</scope><scope>7TO</scope><scope>7U9</scope><scope>H94</scope><scope>K9.</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0002-3831-6022</orcidid></search><sort><creationdate>20190515</creationdate><title>Multigene panel sequencing of established and candidate melanoma susceptibility genes in a large cohort of Dutch non‐CDKN2A/CDK4 melanoma families</title><author>Potjer, Thomas P. ; Bollen, Sander ; Grimbergen, Anneliese J.E.M. ; Doorn, Remco ; Gruis, Nelleke A. ; Asperen, Christi J. ; Hes, Frederik J. ; Stoep, Nienke</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4434-62ebfcfadd49879e71c71553744a8f31a6cfa299160acba478a3fac809165f823</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2019</creationdate><topic>Albinism</topic><topic>BAP1</topic><topic>Cancer</topic><topic>Cancer Genetics and Epigenetics</topic><topic>candidate susceptibility genes</topic><topic>Cohort Studies</topic><topic>Cyclin-dependent kinase 4</topic><topic>Cyclin-Dependent Kinase 4 - genetics</topic><topic>Cyclin-Dependent Kinase Inhibitor p16 - genetics</topic><topic>familial melanoma</topic><topic>Female</topic><topic>gene panel sequencing</topic><topic>Genes</topic><topic>Genetic Predisposition to Disease - genetics</topic><topic>genetic susceptibility</topic><topic>Germ-Line Mutation - genetics</topic><topic>Health risk assessment</topic><topic>high‐penetrance genes</topic><topic>Humans</topic><topic>Lung Neoplasms - genetics</topic><topic>Male</topic><topic>Medical research</topic><topic>Melanoma</topic><topic>Melanoma - genetics</topic><topic>Mesothelioma</topic><topic>Mesothelioma - genetics</topic><topic>Mesothelioma, Malignant</topic><topic>Microphthalmia-associated transcription factor</topic><topic>Microphthalmia-Associated Transcription Factor - genetics</topic><topic>MITF</topic><topic>Mutation</topic><topic>OCA2</topic><topic>Pot1 gene</topic><topic>Ubiquitin Thiolesterase - genetics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Potjer, Thomas P.</creatorcontrib><creatorcontrib>Bollen, Sander</creatorcontrib><creatorcontrib>Grimbergen, Anneliese J.E.M.</creatorcontrib><creatorcontrib>Doorn, Remco</creatorcontrib><creatorcontrib>Gruis, Nelleke A.</creatorcontrib><creatorcontrib>Asperen, Christi J.</creatorcontrib><creatorcontrib>Hes, Frederik J.</creatorcontrib><creatorcontrib>Stoep, Nienke</creatorcontrib><creatorcontrib>Dutch Working Group for Clinical Oncogenetics</creatorcontrib><creatorcontrib>on behalf of the Dutch Working Group for Clinical Oncogenetics</creatorcontrib><collection>Wiley Online Library (Open Access Collection)</collection><collection>Wiley Online Library (Open Access Collection)</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Immunology Abstracts</collection><collection>Oncogenes and Growth Factors Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>International journal of cancer</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Potjer, Thomas P.</au><au>Bollen, Sander</au><au>Grimbergen, Anneliese J.E.M.</au><au>Doorn, Remco</au><au>Gruis, Nelleke A.</au><au>Asperen, Christi J.</au><au>Hes, Frederik J.</au><au>Stoep, Nienke</au><aucorp>Dutch Working Group for Clinical Oncogenetics</aucorp><aucorp>on behalf of the Dutch Working Group for Clinical Oncogenetics</aucorp><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Multigene panel sequencing of established and candidate melanoma susceptibility genes in a large cohort of Dutch non‐CDKN2A/CDK4 melanoma families</atitle><jtitle>International journal of cancer</jtitle><addtitle>Int J Cancer</addtitle><date>2019-05-15</date><risdate>2019</risdate><volume>144</volume><issue>10</issue><spage>2453</spage><epage>2464</epage><pages>2453-2464</pages><issn>0020-7136</issn><eissn>1097-0215</eissn><abstract>Germline mutations in the major melanoma susceptibility gene CDKN2A explain genetic predisposition in only 10–40% of melanoma‐prone families. In our study we comprehensively characterized 488 melanoma cases from 451 non‐CDKN2A/CDK4 families for mutations in 30 established and candidate melanoma susceptibility genes using a custom‐designed targeted gene panel approach. We identified (likely) pathogenic variants in established melanoma susceptibility genes in 18 families (n = 3 BAP1, n = 15 MITF p.E318K; diagnostic yield 4.0%). Among the three identified BAP1‐families, there were no reported diagnoses of uveal melanoma or malignant mesothelioma. We additionally identified two potentially deleterious missense variants in the telomere maintenance genes ACD and TERF2IP, but none in the POT1 gene. MC1R risk variants were strongly enriched in our familial melanoma cohort compared to healthy controls (R variants: OR 3.67, 95% CI 2.88–4.68, p <0.001). Several variants of interest were also identified in candidate melanoma susceptibility genes, in particular rare (pathogenic) variants in the albinism gene OCA2 were repeatedly found. We conclude that multigene panel testing for familial melanoma is appropriate considering the additional 4% diagnostic yield in non‐CDKN2A/CDK4 families. Our study shows that BAP1 and MITF are important genes to be included in such a diagnostic test.
What's new?
Germline mutations in CDKN2A are major contributors to familial melanoma. These mutations, however, are responsible for only 10 to 40 percent of genetic susceptibility in melanoma‐prone families. In this study, 30 established and candidate melanoma susceptibility genes were investigated for associations with the disease in patients from 451 non‐CDKN2A/CDK4 melanoma families. From the candidate gene panel, (likely) pathogenic variants in BAP1 and MITF were identified in several families, and potentially deleterious variants were identified in the shelterin complex genes ACD and TERF2IP. These genes appear to play a significant role in familial melanoma predisposition and are therefore promising candidates for incorporation into comprehensive genetic tests.</abstract><cop>Hoboken, USA</cop><pub>John Wiley & Sons, Inc</pub><pmid>30414346</pmid><doi>10.1002/ijc.31984</doi><tpages>12</tpages><orcidid>https://orcid.org/0000-0002-3831-6022</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Albinism BAP1 Cancer Cancer Genetics and Epigenetics candidate susceptibility genes Cohort Studies Cyclin-dependent kinase 4 Cyclin-Dependent Kinase 4 - genetics Cyclin-Dependent Kinase Inhibitor p16 - genetics familial melanoma Female gene panel sequencing Genes Genetic Predisposition to Disease - genetics genetic susceptibility Germ-Line Mutation - genetics Health risk assessment high‐penetrance genes Humans Lung Neoplasms - genetics Male Medical research Melanoma Melanoma - genetics Mesothelioma Mesothelioma - genetics Mesothelioma, Malignant Microphthalmia-associated transcription factor Microphthalmia-Associated Transcription Factor - genetics MITF Mutation OCA2 Pot1 gene Ubiquitin Thiolesterase - genetics |
| title | Multigene panel sequencing of established and candidate melanoma susceptibility genes in a large cohort of Dutch non‐CDKN2A/CDK4 melanoma families |
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