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Low input whole-exome sequencing to determine the representation of the tumor exome in circulating DNA of non-small cell lung cancer patients
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| Veröffentlicht in: | PLOS ONE 11(2016,8) Artikel-Nummer e0161012, 16 Seiten |
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| Personen und Körperschaften: | , , , , , , |
| Titel: | Low input whole-exome sequencing to determine the representation of the tumor exome in circulating DNA of non-small cell lung cancer patients/ Steffen Dietz, Uwe Schirmer, Clémentine Mercé, Nikolas von Bubnoff, Edgar Dahl, Michael Meister, Thomas Muley, Michael Thomas, Holger Sültmann |
| Format: | E-Book-Kapitel |
| Sprache: | Englisch |
| veröffentlicht: |
16 August 2016
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| Gesamtaufnahme: |
: PLOS ONE, 11(2016,8) Artikel-Nummer e0161012, 16 Seiten
, volume:11 |
| Schlagwörter: | |
| Quelle: | Verbunddaten SWB Lizenzfreie Online-Ressourcen |
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| 520 | |a Circulating cell-free DNA (cfDNA) released from cancerous tissues has been found to harbor tumor-associated alterations and to represent the molecular composition of the tumor. Recent advances in technologies, especially in next-generation sequencing, enable the analysis of low amounts of cfDNA from body fluids. We analyzed the exomes of tumor tissue and matched serum samples to investigate the molecular representation of the tumor exome in cfDNA. To this end, we implemented a workflow for sequencing of cfDNA from low serum volumes (200 μl) and performed whole-exome sequencing (WES) of serum and matched tumor tissue samples from six non-small cell lung cancer (NSCLC) patients and two control sera. Exomes, including untranslated regions (UTRs) of cfDNA were sequenced with an average coverage of 68.5x. Enrichment efficiency, target coverage, and sequencing depth of cfDNA reads were comparable to those from matched tissues. Discovered variants were compared between serum and tissue as well as to the COSMIC database of known mutations. Although not all tissue variants could be confirmed in the matched serum, up to 57% of the tumor variants were reflected in matched cfDNA with mutations in PIK3CA, ALK, and PTEN as well as variants at COSMIC annotated sites in all six patients analyzed. Moreover, cfDNA revealed a mutation in MTOR, which was not detected in the matched tissue, potentially from an untested region of the heterogeneous primary tumor or from a distant metastatic clone. WES of cfDNA may provide additional complementary molecular information about clinically relevant mutations and the clonal heterogeneity of the tumors. | ||
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| contents | Circulating cell-free DNA (cfDNA) released from cancerous tissues has been found to harbor tumor-associated alterations and to represent the molecular composition of the tumor. Recent advances in technologies, especially in next-generation sequencing, enable the analysis of low amounts of cfDNA from body fluids. We analyzed the exomes of tumor tissue and matched serum samples to investigate the molecular representation of the tumor exome in cfDNA. To this end, we implemented a workflow for sequencing of cfDNA from low serum volumes (200 μl) and performed whole-exome sequencing (WES) of serum and matched tumor tissue samples from six non-small cell lung cancer (NSCLC) patients and two control sera. Exomes, including untranslated regions (UTRs) of cfDNA were sequenced with an average coverage of 68.5x. Enrichment efficiency, target coverage, and sequencing depth of cfDNA reads were comparable to those from matched tissues. Discovered variants were compared between serum and tissue as well as to the COSMIC database of known mutations. Although not all tissue variants could be confirmed in the matched serum, up to 57% of the tumor variants were reflected in matched cfDNA with mutations in PIK3CA, ALK, and PTEN as well as variants at COSMIC annotated sites in all six patients analyzed. Moreover, cfDNA revealed a mutation in MTOR, which was not detected in the matched tissue, potentially from an untested region of the heterogeneous primary tumor or from a distant metastatic clone. WES of cfDNA may provide additional complementary molecular information about clinically relevant mutations and the clonal heterogeneity of the tumors. |
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| spelling | Dietz, Steffen 1988- VerfasserIn (DE-588)1148996575 (DE-627)1009298062 (DE-576)496511556 aut, Low input whole-exome sequencing to determine the representation of the tumor exome in circulating DNA of non-small cell lung cancer patients Steffen Dietz, Uwe Schirmer, Clémentine Mercé, Nikolas von Bubnoff, Edgar Dahl, Michael Meister, Thomas Muley, Michael Thomas, Holger Sültmann, 16 August 2016, Text txt rdacontent, Computermedien c rdamedia, Online-Ressource cr rdacarrier, Gesehen am 21.03.2018, Circulating cell-free DNA (cfDNA) released from cancerous tissues has been found to harbor tumor-associated alterations and to represent the molecular composition of the tumor. Recent advances in technologies, especially in next-generation sequencing, enable the analysis of low amounts of cfDNA from body fluids. We analyzed the exomes of tumor tissue and matched serum samples to investigate the molecular representation of the tumor exome in cfDNA. To this end, we implemented a workflow for sequencing of cfDNA from low serum volumes (200 μl) and performed whole-exome sequencing (WES) of serum and matched tumor tissue samples from six non-small cell lung cancer (NSCLC) patients and two control sera. Exomes, including untranslated regions (UTRs) of cfDNA were sequenced with an average coverage of 68.5x. Enrichment efficiency, target coverage, and sequencing depth of cfDNA reads were comparable to those from matched tissues. Discovered variants were compared between serum and tissue as well as to the COSMIC database of known mutations. Although not all tissue variants could be confirmed in the matched serum, up to 57% of the tumor variants were reflected in matched cfDNA with mutations in PIK3CA, ALK, and PTEN as well as variants at COSMIC annotated sites in all six patients analyzed. Moreover, cfDNA revealed a mutation in MTOR, which was not detected in the matched tissue, potentially from an untested region of the heterogeneous primary tumor or from a distant metastatic clone. WES of cfDNA may provide additional complementary molecular information about clinically relevant mutations and the clonal heterogeneity of the tumors., DNA libraries, DNA sequencing, Genomic libraries, Mutation databases, Non-small cell lung cancer, Polymerase chain reaction, Somatic mutation, Squamous cell lung carcinoma, Schirmer, Uwe 1967- VerfasserIn (DE-588)123258995 (DE-627)706230868 (DE-576)293625816 aut, Mercé, Clémentine VerfasserIn (DE-588)1098446852 (DE-627)857632833 (DE-576)469125101 aut, Meister, Michael VerfasserIn (DE-588)1078792046 (DE-627)839461402 (DE-576)451890108 aut, Muley, Thomas VerfasserIn (DE-588)1056885432 (DE-627)794179169 (DE-576)16759284X aut, Thomas, Michael VerfasserIn (DE-588)1054438781 (DE-627)79152213X (DE-576)41027089X aut, Sültmann, Holger 1962- VerfasserIn (DE-588)172777291 (DE-627)697708144 (DE-576)133633926 aut, Enthalten in PLOS ONE San Francisco, California, US : PLOS, 2006 11(2016,8) Artikel-Nummer e0161012, 16 Seiten Online-Ressource (DE-627)523574592 (DE-600)2267670-3 (DE-576)281331979 1932-6203 nnns, volume:11 year:2016 number:8, http://dx.doi.org/10.1371/journal.pone.0161012 Verlag Resolving-System kostenfrei Volltext, http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0161012 Verlag kostenfrei Volltext, http://dx.doi.org/10.1371/journal.pone.0161012 LFER, LFER 2018-04-10T00:00:00Z |
| spellingShingle | Dietz, Steffen, Schirmer, Uwe, Mercé, Clémentine, Meister, Michael, Muley, Thomas, Thomas, Michael, Sültmann, Holger, Low input whole-exome sequencing to determine the representation of the tumor exome in circulating DNA of non-small cell lung cancer patients, Circulating cell-free DNA (cfDNA) released from cancerous tissues has been found to harbor tumor-associated alterations and to represent the molecular composition of the tumor. Recent advances in technologies, especially in next-generation sequencing, enable the analysis of low amounts of cfDNA from body fluids. We analyzed the exomes of tumor tissue and matched serum samples to investigate the molecular representation of the tumor exome in cfDNA. To this end, we implemented a workflow for sequencing of cfDNA from low serum volumes (200 μl) and performed whole-exome sequencing (WES) of serum and matched tumor tissue samples from six non-small cell lung cancer (NSCLC) patients and two control sera. Exomes, including untranslated regions (UTRs) of cfDNA were sequenced with an average coverage of 68.5x. Enrichment efficiency, target coverage, and sequencing depth of cfDNA reads were comparable to those from matched tissues. Discovered variants were compared between serum and tissue as well as to the COSMIC database of known mutations. Although not all tissue variants could be confirmed in the matched serum, up to 57% of the tumor variants were reflected in matched cfDNA with mutations in PIK3CA, ALK, and PTEN as well as variants at COSMIC annotated sites in all six patients analyzed. Moreover, cfDNA revealed a mutation in MTOR, which was not detected in the matched tissue, potentially from an untested region of the heterogeneous primary tumor or from a distant metastatic clone. WES of cfDNA may provide additional complementary molecular information about clinically relevant mutations and the clonal heterogeneity of the tumors., DNA libraries, DNA sequencing, Genomic libraries, Mutation databases, Non-small cell lung cancer, Polymerase chain reaction, Somatic mutation, Squamous cell lung carcinoma |
| swb_id_str | 501284575 |
| title | Low input whole-exome sequencing to determine the representation of the tumor exome in circulating DNA of non-small cell lung cancer patients |
| title_auth | Low input whole-exome sequencing to determine the representation of the tumor exome in circulating DNA of non-small cell lung cancer patients |
| title_full | Low input whole-exome sequencing to determine the representation of the tumor exome in circulating DNA of non-small cell lung cancer patients Steffen Dietz, Uwe Schirmer, Clémentine Mercé, Nikolas von Bubnoff, Edgar Dahl, Michael Meister, Thomas Muley, Michael Thomas, Holger Sültmann |
| title_fullStr | Low input whole-exome sequencing to determine the representation of the tumor exome in circulating DNA of non-small cell lung cancer patients Steffen Dietz, Uwe Schirmer, Clémentine Mercé, Nikolas von Bubnoff, Edgar Dahl, Michael Meister, Thomas Muley, Michael Thomas, Holger Sültmann |
| title_full_unstemmed | Low input whole-exome sequencing to determine the representation of the tumor exome in circulating DNA of non-small cell lung cancer patients Steffen Dietz, Uwe Schirmer, Clémentine Mercé, Nikolas von Bubnoff, Edgar Dahl, Michael Meister, Thomas Muley, Michael Thomas, Holger Sültmann |
| title_in_hierarchy | Low input whole-exome sequencing to determine the representation of the tumor exome in circulating DNA of non-small cell lung cancer patients / Steffen Dietz, Uwe Schirmer, Clémentine Mercé, Nikolas von Bubnoff, Edgar Dahl, Michael Meister, Thomas Muley, Michael Thomas, Holger Sültmann, |
| title_short | Low input whole-exome sequencing to determine the representation of the tumor exome in circulating DNA of non-small cell lung cancer patients |
| title_sort | low input whole exome sequencing to determine the representation of the tumor exome in circulating dna of non small cell lung cancer patients |
| topic | DNA libraries, DNA sequencing, Genomic libraries, Mutation databases, Non-small cell lung cancer, Polymerase chain reaction, Somatic mutation, Squamous cell lung carcinoma |
| topic_facet | DNA libraries, DNA sequencing, Genomic libraries, Mutation databases, Non-small cell lung cancer, Polymerase chain reaction, Somatic mutation, Squamous cell lung carcinoma |
| url | http://dx.doi.org/10.1371/journal.pone.0161012, http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0161012 |