Recommendations for the clinical interpretation and reporting of copy number gains using gene panel NGS analysis in routine diagnostics
Abstract Next-generation sequencing (NGS) panel analysis on DNA from formalin-fixed paraffin-embedded (FFPE) tissue is increasingly used to also identify actionable copy number gains (gene amplifications) in addition to sequence variants. While guidelines for the reporting of sequence variants are a...
Ausführliche Beschreibung
Gespeichert in:
| Autor*in: |
Eijkelenboom, Astrid [verfasserIn] Tops, Bastiaan B. J. [verfasserIn] van den Berg, Anke [verfasserIn] van den Brule, Adrianus J. C. [verfasserIn] Dinjens, Winand N. M. [verfasserIn] Dubbink, Hendrikus J. [verfasserIn] ter Elst, Arja [verfasserIn] Geurts-Giele, Willemina R. R. [verfasserIn] Groenen, Patricia J. T. A. [verfasserIn] Groenendijk, Floris H. [verfasserIn] Heideman, Daniëlle A. M. [verfasserIn] Huibers, Manon M. H. [verfasserIn] Huijsmans, Cornelis J. J. [verfasserIn] Jeuken, Judith W. M. [verfasserIn] van Kempen, Léon C. [verfasserIn] Korpershoek, Esther [verfasserIn] Kroeze, Leonie I. [verfasserIn] de Leng, Wendy W. J. [verfasserIn] van Noesel, Carel J. M. [verfasserIn] Speel, Ernst-Jan M. [verfasserIn] Vogel, Maartje J. [verfasserIn] van Wezel, Tom [verfasserIn] Nederlof, Petra M. [verfasserIn] Schuuring, Ed [verfasserIn] Ligtenberg, Marjolijn J. L. [verfasserIn] |
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| Format: |
E-Artikel |
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| Sprache: |
Englisch |
| Erschienen: |
2019 |
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| Schlagwörter: |
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| Übergeordnetes Werk: |
Enthalten in: Virchows Archiv - Berlin : Springer, 1847, 474(2019), 6 vom: 19. März, Seite 673-680 |
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| Übergeordnetes Werk: |
volume:474 ; year:2019 ; number:6 ; day:19 ; month:03 ; pages:673-680 |
| Links: |
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| DOI / URN: |
10.1007/s00428-019-02555-3 |
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| Katalog-ID: |
SPR005826012 |
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| 245 | 1 | 0 | |a Recommendations for the clinical interpretation and reporting of copy number gains using gene panel NGS analysis in routine diagnostics |
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| 520 | |a Abstract Next-generation sequencing (NGS) panel analysis on DNA from formalin-fixed paraffin-embedded (FFPE) tissue is increasingly used to also identify actionable copy number gains (gene amplifications) in addition to sequence variants. While guidelines for the reporting of sequence variants are available, guidance with respect to reporting copy number gains from gene-panel NGS data is limited. Here, we report on Dutch consensus recommendations obtained in the context of the national Predictive Analysis for THerapy (PATH) project, which aims to optimize and harmonize routine diagnostics in molecular pathology. We briefly discuss two common approaches to detect gene copy number gains from NGS data, i.e., the relative coverage and B-allele frequencies. In addition, we provide recommendations for reporting gene copy gains for clinical purposes. In addition to general QC metrics associated with NGS in routine diagnostics, it is recommended to include clinically relevant quantitative parameters of copy number gains in the clinical report, such as (i) relative coverage and estimated copy numbers in neoplastic cells, (ii) statistical scores to show significance (e.g., z-scores), and (iii) the sensitivity of the assay and restrictions of NGS-based detection of copy number gains. Collectively, this information can guide clinical and analytical decisions such as the reliable detection of high-level gene amplifications and the requirement for additional in situ assays in case of borderline results or limited sensitivity. | ||
| 650 | 4 | |a Copy number gain |7 (dpeaa)DE-He213 | |
| 650 | 4 | |a Amplification |7 (dpeaa)DE-He213 | |
| 650 | 4 | |a NGS |7 (dpeaa)DE-He213 | |
| 650 | 4 | |a Targeted therapy |7 (dpeaa)DE-He213 | |
| 650 | 4 | |a Routine diagnostics |7 (dpeaa)DE-He213 | |
| 650 | 4 | |a Molecular pathology |7 (dpeaa)DE-He213 | |
| 700 | 1 | |a Tops, Bastiaan B. J. |e verfasserin |4 aut | |
| 700 | 1 | |a van den Berg, Anke |e verfasserin |4 aut | |
| 700 | 1 | |a van den Brule, Adrianus J. C. |e verfasserin |4 aut | |
| 700 | 1 | |a Dinjens, Winand N. M. |e verfasserin |4 aut | |
| 700 | 1 | |a Dubbink, Hendrikus J. |e verfasserin |4 aut | |
| 700 | 1 | |a ter Elst, Arja |e verfasserin |4 aut | |
| 700 | 1 | |a Geurts-Giele, Willemina R. R. |e verfasserin |4 aut | |
| 700 | 1 | |a Groenen, Patricia J. T. A. |e verfasserin |4 aut | |
| 700 | 1 | |a Groenendijk, Floris H. |e verfasserin |4 aut | |
| 700 | 1 | |a Heideman, Daniëlle A. M. |e verfasserin |4 aut | |
| 700 | 1 | |a Huibers, Manon M. H. |e verfasserin |4 aut | |
| 700 | 1 | |a Huijsmans, Cornelis J. J. |e verfasserin |4 aut | |
| 700 | 1 | |a Jeuken, Judith W. M. |e verfasserin |4 aut | |
| 700 | 1 | |a van Kempen, Léon C. |e verfasserin |4 aut | |
| 700 | 1 | |a Korpershoek, Esther |e verfasserin |4 aut | |
| 700 | 1 | |a Kroeze, Leonie I. |e verfasserin |4 aut | |
| 700 | 1 | |a de Leng, Wendy W. J. |e verfasserin |4 aut | |
| 700 | 1 | |a van Noesel, Carel J. M. |e verfasserin |4 aut | |
| 700 | 1 | |a Speel, Ernst-Jan M. |e verfasserin |4 aut | |
| 700 | 1 | |a Vogel, Maartje J. |e verfasserin |4 aut | |
| 700 | 1 | |a van Wezel, Tom |e verfasserin |4 aut | |
| 700 | 1 | |a Nederlof, Petra M. |e verfasserin |4 aut | |
| 700 | 1 | |a Schuuring, Ed |e verfasserin |4 aut | |
| 700 | 1 | |a Ligtenberg, Marjolijn J. L. |e verfasserin |4 aut | |
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10.1007/s00428-019-02555-3 doi (DE-627)SPR005826012 (SPR)s00428-019-02555-3-e DE-627 ger DE-627 rakwb eng 610 ASE 44.47 bkl Eijkelenboom, Astrid verfasserin aut Recommendations for the clinical interpretation and reporting of copy number gains using gene panel NGS analysis in routine diagnostics 2019 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Next-generation sequencing (NGS) panel analysis on DNA from formalin-fixed paraffin-embedded (FFPE) tissue is increasingly used to also identify actionable copy number gains (gene amplifications) in addition to sequence variants. While guidelines for the reporting of sequence variants are available, guidance with respect to reporting copy number gains from gene-panel NGS data is limited. Here, we report on Dutch consensus recommendations obtained in the context of the national Predictive Analysis for THerapy (PATH) project, which aims to optimize and harmonize routine diagnostics in molecular pathology. We briefly discuss two common approaches to detect gene copy number gains from NGS data, i.e., the relative coverage and B-allele frequencies. In addition, we provide recommendations for reporting gene copy gains for clinical purposes. In addition to general QC metrics associated with NGS in routine diagnostics, it is recommended to include clinically relevant quantitative parameters of copy number gains in the clinical report, such as (i) relative coverage and estimated copy numbers in neoplastic cells, (ii) statistical scores to show significance (e.g., z-scores), and (iii) the sensitivity of the assay and restrictions of NGS-based detection of copy number gains. Collectively, this information can guide clinical and analytical decisions such as the reliable detection of high-level gene amplifications and the requirement for additional in situ assays in case of borderline results or limited sensitivity. Copy number gain (dpeaa)DE-He213 Amplification (dpeaa)DE-He213 NGS (dpeaa)DE-He213 Targeted therapy (dpeaa)DE-He213 Routine diagnostics (dpeaa)DE-He213 Molecular pathology (dpeaa)DE-He213 Tops, Bastiaan B. J. verfasserin aut van den Berg, Anke verfasserin aut van den Brule, Adrianus J. C. verfasserin aut Dinjens, Winand N. M. verfasserin aut Dubbink, Hendrikus J. verfasserin aut ter Elst, Arja verfasserin aut Geurts-Giele, Willemina R. R. verfasserin aut Groenen, Patricia J. T. A. verfasserin aut Groenendijk, Floris H. verfasserin aut Heideman, Daniëlle A. M. verfasserin aut Huibers, Manon M. H. verfasserin aut Huijsmans, Cornelis J. J. verfasserin aut Jeuken, Judith W. M. verfasserin aut van Kempen, Léon C. verfasserin aut Korpershoek, Esther verfasserin aut Kroeze, Leonie I. verfasserin aut de Leng, Wendy W. J. verfasserin aut van Noesel, Carel J. M. verfasserin aut Speel, Ernst-Jan M. verfasserin aut Vogel, Maartje J. verfasserin aut van Wezel, Tom verfasserin aut Nederlof, Petra M. verfasserin aut Schuuring, Ed verfasserin aut Ligtenberg, Marjolijn J. L. verfasserin aut Enthalten in Virchows Archiv Berlin : Springer, 1847 474(2019), 6 vom: 19. März, Seite 673-680 (DE-627)254910645 (DE-600)1463276-7 1432-2307 nnns volume:474 year:2019 number:6 day:19 month:03 pages:673-680 https://dx.doi.org/10.1007/s00428-019-02555-3 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_101 GBV_ILN_105 GBV_ILN_110 GBV_ILN_120 GBV_ILN_138 GBV_ILN_150 GBV_ILN_151 GBV_ILN_152 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_187 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_250 GBV_ILN_267 GBV_ILN_281 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_636 GBV_ILN_702 GBV_ILN_711 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2031 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2039 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 GBV_ILN_2070 GBV_ILN_2086 GBV_ILN_2088 GBV_ILN_2093 GBV_ILN_2106 GBV_ILN_2107 GBV_ILN_2108 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2113 GBV_ILN_2116 GBV_ILN_2118 GBV_ILN_2119 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2144 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2188 GBV_ILN_2190 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2446 GBV_ILN_2470 GBV_ILN_2472 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_2548 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4046 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4242 GBV_ILN_4246 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4393 GBV_ILN_4700 44.47 ASE AR 474 2019 6 19 03 673-680 |
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10.1007/s00428-019-02555-3 doi (DE-627)SPR005826012 (SPR)s00428-019-02555-3-e DE-627 ger DE-627 rakwb eng 610 ASE 44.47 bkl Eijkelenboom, Astrid verfasserin aut Recommendations for the clinical interpretation and reporting of copy number gains using gene panel NGS analysis in routine diagnostics 2019 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Next-generation sequencing (NGS) panel analysis on DNA from formalin-fixed paraffin-embedded (FFPE) tissue is increasingly used to also identify actionable copy number gains (gene amplifications) in addition to sequence variants. While guidelines for the reporting of sequence variants are available, guidance with respect to reporting copy number gains from gene-panel NGS data is limited. Here, we report on Dutch consensus recommendations obtained in the context of the national Predictive Analysis for THerapy (PATH) project, which aims to optimize and harmonize routine diagnostics in molecular pathology. We briefly discuss two common approaches to detect gene copy number gains from NGS data, i.e., the relative coverage and B-allele frequencies. In addition, we provide recommendations for reporting gene copy gains for clinical purposes. In addition to general QC metrics associated with NGS in routine diagnostics, it is recommended to include clinically relevant quantitative parameters of copy number gains in the clinical report, such as (i) relative coverage and estimated copy numbers in neoplastic cells, (ii) statistical scores to show significance (e.g., z-scores), and (iii) the sensitivity of the assay and restrictions of NGS-based detection of copy number gains. Collectively, this information can guide clinical and analytical decisions such as the reliable detection of high-level gene amplifications and the requirement for additional in situ assays in case of borderline results or limited sensitivity. Copy number gain (dpeaa)DE-He213 Amplification (dpeaa)DE-He213 NGS (dpeaa)DE-He213 Targeted therapy (dpeaa)DE-He213 Routine diagnostics (dpeaa)DE-He213 Molecular pathology (dpeaa)DE-He213 Tops, Bastiaan B. J. verfasserin aut van den Berg, Anke verfasserin aut van den Brule, Adrianus J. C. verfasserin aut Dinjens, Winand N. M. verfasserin aut Dubbink, Hendrikus J. verfasserin aut ter Elst, Arja verfasserin aut Geurts-Giele, Willemina R. R. verfasserin aut Groenen, Patricia J. T. A. verfasserin aut Groenendijk, Floris H. verfasserin aut Heideman, Daniëlle A. M. verfasserin aut Huibers, Manon M. H. verfasserin aut Huijsmans, Cornelis J. J. verfasserin aut Jeuken, Judith W. M. verfasserin aut van Kempen, Léon C. verfasserin aut Korpershoek, Esther verfasserin aut Kroeze, Leonie I. verfasserin aut de Leng, Wendy W. J. verfasserin aut van Noesel, Carel J. M. verfasserin aut Speel, Ernst-Jan M. verfasserin aut Vogel, Maartje J. verfasserin aut van Wezel, Tom verfasserin aut Nederlof, Petra M. verfasserin aut Schuuring, Ed verfasserin aut Ligtenberg, Marjolijn J. L. verfasserin aut Enthalten in Virchows Archiv Berlin : Springer, 1847 474(2019), 6 vom: 19. März, Seite 673-680 (DE-627)254910645 (DE-600)1463276-7 1432-2307 nnns volume:474 year:2019 number:6 day:19 month:03 pages:673-680 https://dx.doi.org/10.1007/s00428-019-02555-3 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_101 GBV_ILN_105 GBV_ILN_110 GBV_ILN_120 GBV_ILN_138 GBV_ILN_150 GBV_ILN_151 GBV_ILN_152 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_187 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_250 GBV_ILN_267 GBV_ILN_281 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_636 GBV_ILN_702 GBV_ILN_711 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2031 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2039 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 GBV_ILN_2070 GBV_ILN_2086 GBV_ILN_2088 GBV_ILN_2093 GBV_ILN_2106 GBV_ILN_2107 GBV_ILN_2108 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2113 GBV_ILN_2116 GBV_ILN_2118 GBV_ILN_2119 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2144 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2188 GBV_ILN_2190 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2446 GBV_ILN_2470 GBV_ILN_2472 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_2548 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4046 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4242 GBV_ILN_4246 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4393 GBV_ILN_4700 44.47 ASE AR 474 2019 6 19 03 673-680 |
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10.1007/s00428-019-02555-3 doi (DE-627)SPR005826012 (SPR)s00428-019-02555-3-e DE-627 ger DE-627 rakwb eng 610 ASE 44.47 bkl Eijkelenboom, Astrid verfasserin aut Recommendations for the clinical interpretation and reporting of copy number gains using gene panel NGS analysis in routine diagnostics 2019 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Next-generation sequencing (NGS) panel analysis on DNA from formalin-fixed paraffin-embedded (FFPE) tissue is increasingly used to also identify actionable copy number gains (gene amplifications) in addition to sequence variants. While guidelines for the reporting of sequence variants are available, guidance with respect to reporting copy number gains from gene-panel NGS data is limited. Here, we report on Dutch consensus recommendations obtained in the context of the national Predictive Analysis for THerapy (PATH) project, which aims to optimize and harmonize routine diagnostics in molecular pathology. We briefly discuss two common approaches to detect gene copy number gains from NGS data, i.e., the relative coverage and B-allele frequencies. In addition, we provide recommendations for reporting gene copy gains for clinical purposes. In addition to general QC metrics associated with NGS in routine diagnostics, it is recommended to include clinically relevant quantitative parameters of copy number gains in the clinical report, such as (i) relative coverage and estimated copy numbers in neoplastic cells, (ii) statistical scores to show significance (e.g., z-scores), and (iii) the sensitivity of the assay and restrictions of NGS-based detection of copy number gains. Collectively, this information can guide clinical and analytical decisions such as the reliable detection of high-level gene amplifications and the requirement for additional in situ assays in case of borderline results or limited sensitivity. Copy number gain (dpeaa)DE-He213 Amplification (dpeaa)DE-He213 NGS (dpeaa)DE-He213 Targeted therapy (dpeaa)DE-He213 Routine diagnostics (dpeaa)DE-He213 Molecular pathology (dpeaa)DE-He213 Tops, Bastiaan B. J. verfasserin aut van den Berg, Anke verfasserin aut van den Brule, Adrianus J. C. verfasserin aut Dinjens, Winand N. M. verfasserin aut Dubbink, Hendrikus J. verfasserin aut ter Elst, Arja verfasserin aut Geurts-Giele, Willemina R. R. verfasserin aut Groenen, Patricia J. T. A. verfasserin aut Groenendijk, Floris H. verfasserin aut Heideman, Daniëlle A. M. verfasserin aut Huibers, Manon M. H. verfasserin aut Huijsmans, Cornelis J. J. verfasserin aut Jeuken, Judith W. M. verfasserin aut van Kempen, Léon C. verfasserin aut Korpershoek, Esther verfasserin aut Kroeze, Leonie I. verfasserin aut de Leng, Wendy W. J. verfasserin aut van Noesel, Carel J. M. verfasserin aut Speel, Ernst-Jan M. verfasserin aut Vogel, Maartje J. verfasserin aut van Wezel, Tom verfasserin aut Nederlof, Petra M. verfasserin aut Schuuring, Ed verfasserin aut Ligtenberg, Marjolijn J. L. verfasserin aut Enthalten in Virchows Archiv Berlin : Springer, 1847 474(2019), 6 vom: 19. März, Seite 673-680 (DE-627)254910645 (DE-600)1463276-7 1432-2307 nnns volume:474 year:2019 number:6 day:19 month:03 pages:673-680 https://dx.doi.org/10.1007/s00428-019-02555-3 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_101 GBV_ILN_105 GBV_ILN_110 GBV_ILN_120 GBV_ILN_138 GBV_ILN_150 GBV_ILN_151 GBV_ILN_152 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_187 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_250 GBV_ILN_267 GBV_ILN_281 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_636 GBV_ILN_702 GBV_ILN_711 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2031 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2039 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 GBV_ILN_2070 GBV_ILN_2086 GBV_ILN_2088 GBV_ILN_2093 GBV_ILN_2106 GBV_ILN_2107 GBV_ILN_2108 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2113 GBV_ILN_2116 GBV_ILN_2118 GBV_ILN_2119 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2144 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2188 GBV_ILN_2190 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2446 GBV_ILN_2470 GBV_ILN_2472 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_2548 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4046 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4242 GBV_ILN_4246 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4393 GBV_ILN_4700 44.47 ASE AR 474 2019 6 19 03 673-680 |
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10.1007/s00428-019-02555-3 doi (DE-627)SPR005826012 (SPR)s00428-019-02555-3-e DE-627 ger DE-627 rakwb eng 610 ASE 44.47 bkl Eijkelenboom, Astrid verfasserin aut Recommendations for the clinical interpretation and reporting of copy number gains using gene panel NGS analysis in routine diagnostics 2019 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Next-generation sequencing (NGS) panel analysis on DNA from formalin-fixed paraffin-embedded (FFPE) tissue is increasingly used to also identify actionable copy number gains (gene amplifications) in addition to sequence variants. While guidelines for the reporting of sequence variants are available, guidance with respect to reporting copy number gains from gene-panel NGS data is limited. Here, we report on Dutch consensus recommendations obtained in the context of the national Predictive Analysis for THerapy (PATH) project, which aims to optimize and harmonize routine diagnostics in molecular pathology. We briefly discuss two common approaches to detect gene copy number gains from NGS data, i.e., the relative coverage and B-allele frequencies. In addition, we provide recommendations for reporting gene copy gains for clinical purposes. In addition to general QC metrics associated with NGS in routine diagnostics, it is recommended to include clinically relevant quantitative parameters of copy number gains in the clinical report, such as (i) relative coverage and estimated copy numbers in neoplastic cells, (ii) statistical scores to show significance (e.g., z-scores), and (iii) the sensitivity of the assay and restrictions of NGS-based detection of copy number gains. Collectively, this information can guide clinical and analytical decisions such as the reliable detection of high-level gene amplifications and the requirement for additional in situ assays in case of borderline results or limited sensitivity. Copy number gain (dpeaa)DE-He213 Amplification (dpeaa)DE-He213 NGS (dpeaa)DE-He213 Targeted therapy (dpeaa)DE-He213 Routine diagnostics (dpeaa)DE-He213 Molecular pathology (dpeaa)DE-He213 Tops, Bastiaan B. J. verfasserin aut van den Berg, Anke verfasserin aut van den Brule, Adrianus J. C. verfasserin aut Dinjens, Winand N. M. verfasserin aut Dubbink, Hendrikus J. verfasserin aut ter Elst, Arja verfasserin aut Geurts-Giele, Willemina R. R. verfasserin aut Groenen, Patricia J. T. A. verfasserin aut Groenendijk, Floris H. verfasserin aut Heideman, Daniëlle A. M. verfasserin aut Huibers, Manon M. H. verfasserin aut Huijsmans, Cornelis J. J. verfasserin aut Jeuken, Judith W. M. verfasserin aut van Kempen, Léon C. verfasserin aut Korpershoek, Esther verfasserin aut Kroeze, Leonie I. verfasserin aut de Leng, Wendy W. J. verfasserin aut van Noesel, Carel J. M. verfasserin aut Speel, Ernst-Jan M. verfasserin aut Vogel, Maartje J. verfasserin aut van Wezel, Tom verfasserin aut Nederlof, Petra M. verfasserin aut Schuuring, Ed verfasserin aut Ligtenberg, Marjolijn J. L. verfasserin aut Enthalten in Virchows Archiv Berlin : Springer, 1847 474(2019), 6 vom: 19. März, Seite 673-680 (DE-627)254910645 (DE-600)1463276-7 1432-2307 nnns volume:474 year:2019 number:6 day:19 month:03 pages:673-680 https://dx.doi.org/10.1007/s00428-019-02555-3 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_101 GBV_ILN_105 GBV_ILN_110 GBV_ILN_120 GBV_ILN_138 GBV_ILN_150 GBV_ILN_151 GBV_ILN_152 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_187 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_250 GBV_ILN_267 GBV_ILN_281 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_636 GBV_ILN_702 GBV_ILN_711 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2031 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2039 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 GBV_ILN_2070 GBV_ILN_2086 GBV_ILN_2088 GBV_ILN_2093 GBV_ILN_2106 GBV_ILN_2107 GBV_ILN_2108 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2113 GBV_ILN_2116 GBV_ILN_2118 GBV_ILN_2119 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2144 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2188 GBV_ILN_2190 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2446 GBV_ILN_2470 GBV_ILN_2472 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_2548 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4046 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4242 GBV_ILN_4246 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4393 GBV_ILN_4700 44.47 ASE AR 474 2019 6 19 03 673-680 |
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10.1007/s00428-019-02555-3 doi (DE-627)SPR005826012 (SPR)s00428-019-02555-3-e DE-627 ger DE-627 rakwb eng 610 ASE 44.47 bkl Eijkelenboom, Astrid verfasserin aut Recommendations for the clinical interpretation and reporting of copy number gains using gene panel NGS analysis in routine diagnostics 2019 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Next-generation sequencing (NGS) panel analysis on DNA from formalin-fixed paraffin-embedded (FFPE) tissue is increasingly used to also identify actionable copy number gains (gene amplifications) in addition to sequence variants. While guidelines for the reporting of sequence variants are available, guidance with respect to reporting copy number gains from gene-panel NGS data is limited. Here, we report on Dutch consensus recommendations obtained in the context of the national Predictive Analysis for THerapy (PATH) project, which aims to optimize and harmonize routine diagnostics in molecular pathology. We briefly discuss two common approaches to detect gene copy number gains from NGS data, i.e., the relative coverage and B-allele frequencies. In addition, we provide recommendations for reporting gene copy gains for clinical purposes. In addition to general QC metrics associated with NGS in routine diagnostics, it is recommended to include clinically relevant quantitative parameters of copy number gains in the clinical report, such as (i) relative coverage and estimated copy numbers in neoplastic cells, (ii) statistical scores to show significance (e.g., z-scores), and (iii) the sensitivity of the assay and restrictions of NGS-based detection of copy number gains. Collectively, this information can guide clinical and analytical decisions such as the reliable detection of high-level gene amplifications and the requirement for additional in situ assays in case of borderline results or limited sensitivity. Copy number gain (dpeaa)DE-He213 Amplification (dpeaa)DE-He213 NGS (dpeaa)DE-He213 Targeted therapy (dpeaa)DE-He213 Routine diagnostics (dpeaa)DE-He213 Molecular pathology (dpeaa)DE-He213 Tops, Bastiaan B. J. verfasserin aut van den Berg, Anke verfasserin aut van den Brule, Adrianus J. C. verfasserin aut Dinjens, Winand N. M. verfasserin aut Dubbink, Hendrikus J. verfasserin aut ter Elst, Arja verfasserin aut Geurts-Giele, Willemina R. R. verfasserin aut Groenen, Patricia J. T. A. verfasserin aut Groenendijk, Floris H. verfasserin aut Heideman, Daniëlle A. M. verfasserin aut Huibers, Manon M. H. verfasserin aut Huijsmans, Cornelis J. J. verfasserin aut Jeuken, Judith W. M. verfasserin aut van Kempen, Léon C. verfasserin aut Korpershoek, Esther verfasserin aut Kroeze, Leonie I. verfasserin aut de Leng, Wendy W. J. verfasserin aut van Noesel, Carel J. M. verfasserin aut Speel, Ernst-Jan M. verfasserin aut Vogel, Maartje J. verfasserin aut van Wezel, Tom verfasserin aut Nederlof, Petra M. verfasserin aut Schuuring, Ed verfasserin aut Ligtenberg, Marjolijn J. L. verfasserin aut Enthalten in Virchows Archiv Berlin : Springer, 1847 474(2019), 6 vom: 19. März, Seite 673-680 (DE-627)254910645 (DE-600)1463276-7 1432-2307 nnns volume:474 year:2019 number:6 day:19 month:03 pages:673-680 https://dx.doi.org/10.1007/s00428-019-02555-3 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_101 GBV_ILN_105 GBV_ILN_110 GBV_ILN_120 GBV_ILN_138 GBV_ILN_150 GBV_ILN_151 GBV_ILN_152 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_187 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_250 GBV_ILN_267 GBV_ILN_281 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_636 GBV_ILN_702 GBV_ILN_711 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2031 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2039 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2065 GBV_ILN_2068 GBV_ILN_2070 GBV_ILN_2086 GBV_ILN_2088 GBV_ILN_2093 GBV_ILN_2106 GBV_ILN_2107 GBV_ILN_2108 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2113 GBV_ILN_2116 GBV_ILN_2118 GBV_ILN_2119 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2144 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2188 GBV_ILN_2190 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2446 GBV_ILN_2470 GBV_ILN_2472 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_2548 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4046 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4242 GBV_ILN_4246 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4393 GBV_ILN_4700 44.47 ASE AR 474 2019 6 19 03 673-680 |
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Eijkelenboom, Astrid @@aut@@ Tops, Bastiaan B. J. @@aut@@ van den Berg, Anke @@aut@@ van den Brule, Adrianus J. C. @@aut@@ Dinjens, Winand N. M. @@aut@@ Dubbink, Hendrikus J. @@aut@@ ter Elst, Arja @@aut@@ Geurts-Giele, Willemina R. R. @@aut@@ Groenen, Patricia J. T. A. @@aut@@ Groenendijk, Floris H. @@aut@@ Heideman, Daniëlle A. M. @@aut@@ Huibers, Manon M. H. @@aut@@ Huijsmans, Cornelis J. J. @@aut@@ Jeuken, Judith W. M. @@aut@@ van Kempen, Léon C. @@aut@@ Korpershoek, Esther @@aut@@ Kroeze, Leonie I. @@aut@@ de Leng, Wendy W. J. @@aut@@ van Noesel, Carel J. M. @@aut@@ Speel, Ernst-Jan M. @@aut@@ Vogel, Maartje J. @@aut@@ van Wezel, Tom @@aut@@ Nederlof, Petra M. @@aut@@ Schuuring, Ed @@aut@@ Ligtenberg, Marjolijn J. L. @@aut@@ |
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3610 |
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SPR005826012 |
| language_de |
englisch |
| fullrecord |
<?xml version="1.0" encoding="UTF-8"?><collection xmlns="http://www.loc.gov/MARC21/slim"><record><leader>01000caa a22002652 4500</leader><controlfield tag="001">SPR005826012</controlfield><controlfield tag="003">DE-627</controlfield><controlfield tag="005">20230519070144.0</controlfield><controlfield tag="007">cr uuu---uuuuu</controlfield><controlfield tag="008">201002s2019 xx |||||o 00| ||eng c</controlfield><datafield tag="024" ind1="7" ind2=" "><subfield code="a">10.1007/s00428-019-02555-3</subfield><subfield code="2">doi</subfield></datafield><datafield tag="035" ind1=" " ind2=" "><subfield code="a">(DE-627)SPR005826012</subfield></datafield><datafield tag="035" ind1=" " ind2=" "><subfield code="a">(SPR)s00428-019-02555-3-e</subfield></datafield><datafield tag="040" ind1=" " ind2=" "><subfield code="a">DE-627</subfield><subfield code="b">ger</subfield><subfield code="c">DE-627</subfield><subfield code="e">rakwb</subfield></datafield><datafield tag="041" ind1=" " ind2=" "><subfield code="a">eng</subfield></datafield><datafield tag="082" ind1="0" ind2="4"><subfield code="a">610</subfield><subfield code="q">ASE</subfield></datafield><datafield tag="084" ind1=" " ind2=" "><subfield code="a">44.47</subfield><subfield code="2">bkl</subfield></datafield><datafield tag="100" ind1="1" ind2=" "><subfield code="a">Eijkelenboom, Astrid</subfield><subfield code="e">verfasserin</subfield><subfield code="4">aut</subfield></datafield><datafield tag="245" ind1="1" ind2="0"><subfield code="a">Recommendations for the clinical interpretation and reporting of copy number gains using gene panel NGS analysis in routine diagnostics</subfield></datafield><datafield tag="264" ind1=" " ind2="1"><subfield code="c">2019</subfield></datafield><datafield tag="336" ind1=" " ind2=" "><subfield code="a">Text</subfield><subfield code="b">txt</subfield><subfield code="2">rdacontent</subfield></datafield><datafield tag="337" ind1=" " ind2=" "><subfield code="a">Computermedien</subfield><subfield code="b">c</subfield><subfield code="2">rdamedia</subfield></datafield><datafield tag="338" ind1=" " ind2=" "><subfield code="a">Online-Ressource</subfield><subfield code="b">cr</subfield><subfield code="2">rdacarrier</subfield></datafield><datafield tag="520" ind1=" " ind2=" "><subfield code="a">Abstract Next-generation sequencing (NGS) panel analysis on DNA from formalin-fixed paraffin-embedded (FFPE) tissue is increasingly used to also identify actionable copy number gains (gene amplifications) in addition to sequence variants. While guidelines for the reporting of sequence variants are available, guidance with respect to reporting copy number gains from gene-panel NGS data is limited. Here, we report on Dutch consensus recommendations obtained in the context of the national Predictive Analysis for THerapy (PATH) project, which aims to optimize and harmonize routine diagnostics in molecular pathology. We briefly discuss two common approaches to detect gene copy number gains from NGS data, i.e., the relative coverage and B-allele frequencies. In addition, we provide recommendations for reporting gene copy gains for clinical purposes. In addition to general QC metrics associated with NGS in routine diagnostics, it is recommended to include clinically relevant quantitative parameters of copy number gains in the clinical report, such as (i) relative coverage and estimated copy numbers in neoplastic cells, (ii) statistical scores to show significance (e.g., z-scores), and (iii) the sensitivity of the assay and restrictions of NGS-based detection of copy number gains. Collectively, this information can guide clinical and analytical decisions such as the reliable detection of high-level gene amplifications and the requirement for additional in situ assays in case of borderline results or limited sensitivity.</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">Copy number gain</subfield><subfield code="7">(dpeaa)DE-He213</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">Amplification</subfield><subfield code="7">(dpeaa)DE-He213</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">NGS</subfield><subfield code="7">(dpeaa)DE-He213</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">Targeted therapy</subfield><subfield code="7">(dpeaa)DE-He213</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">Routine diagnostics</subfield><subfield code="7">(dpeaa)DE-He213</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">Molecular pathology</subfield><subfield code="7">(dpeaa)DE-He213</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Tops, Bastiaan B. J.</subfield><subfield code="e">verfasserin</subfield><subfield code="4">aut</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">van den Berg, Anke</subfield><subfield code="e">verfasserin</subfield><subfield code="4">aut</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">van den Brule, Adrianus J. C.</subfield><subfield code="e">verfasserin</subfield><subfield code="4">aut</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Dinjens, Winand N. M.</subfield><subfield code="e">verfasserin</subfield><subfield code="4">aut</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Dubbink, Hendrikus J.</subfield><subfield code="e">verfasserin</subfield><subfield code="4">aut</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">ter Elst, Arja</subfield><subfield code="e">verfasserin</subfield><subfield code="4">aut</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Geurts-Giele, Willemina R. R.</subfield><subfield code="e">verfasserin</subfield><subfield code="4">aut</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Groenen, Patricia J. T. 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Eijkelenboom, Astrid Tops, Bastiaan B. J. van den Berg, Anke van den Brule, Adrianus J. C. Dinjens, Winand N. M. Dubbink, Hendrikus J. ter Elst, Arja Geurts-Giele, Willemina R. R. Groenen, Patricia J. T. A. Groenendijk, Floris H. Heideman, Daniëlle A. M. Huibers, Manon M. H. Huijsmans, Cornelis J. J. Jeuken, Judith W. M. van Kempen, Léon C. Korpershoek, Esther Kroeze, Leonie I. de Leng, Wendy W. J. van Noesel, Carel J. M. Speel, Ernst-Jan M. Vogel, Maartje J. van Wezel, Tom Nederlof, Petra M. Schuuring, Ed Ligtenberg, Marjolijn J. L. |
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recommendations for the clinical interpretation and reporting of copy number gains using gene panel ngs analysis in routine diagnostics |
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Recommendations for the clinical interpretation and reporting of copy number gains using gene panel NGS analysis in routine diagnostics |
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Abstract Next-generation sequencing (NGS) panel analysis on DNA from formalin-fixed paraffin-embedded (FFPE) tissue is increasingly used to also identify actionable copy number gains (gene amplifications) in addition to sequence variants. While guidelines for the reporting of sequence variants are available, guidance with respect to reporting copy number gains from gene-panel NGS data is limited. Here, we report on Dutch consensus recommendations obtained in the context of the national Predictive Analysis for THerapy (PATH) project, which aims to optimize and harmonize routine diagnostics in molecular pathology. We briefly discuss two common approaches to detect gene copy number gains from NGS data, i.e., the relative coverage and B-allele frequencies. In addition, we provide recommendations for reporting gene copy gains for clinical purposes. In addition to general QC metrics associated with NGS in routine diagnostics, it is recommended to include clinically relevant quantitative parameters of copy number gains in the clinical report, such as (i) relative coverage and estimated copy numbers in neoplastic cells, (ii) statistical scores to show significance (e.g., z-scores), and (iii) the sensitivity of the assay and restrictions of NGS-based detection of copy number gains. Collectively, this information can guide clinical and analytical decisions such as the reliable detection of high-level gene amplifications and the requirement for additional in situ assays in case of borderline results or limited sensitivity. |
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Abstract Next-generation sequencing (NGS) panel analysis on DNA from formalin-fixed paraffin-embedded (FFPE) tissue is increasingly used to also identify actionable copy number gains (gene amplifications) in addition to sequence variants. While guidelines for the reporting of sequence variants are available, guidance with respect to reporting copy number gains from gene-panel NGS data is limited. Here, we report on Dutch consensus recommendations obtained in the context of the national Predictive Analysis for THerapy (PATH) project, which aims to optimize and harmonize routine diagnostics in molecular pathology. We briefly discuss two common approaches to detect gene copy number gains from NGS data, i.e., the relative coverage and B-allele frequencies. In addition, we provide recommendations for reporting gene copy gains for clinical purposes. In addition to general QC metrics associated with NGS in routine diagnostics, it is recommended to include clinically relevant quantitative parameters of copy number gains in the clinical report, such as (i) relative coverage and estimated copy numbers in neoplastic cells, (ii) statistical scores to show significance (e.g., z-scores), and (iii) the sensitivity of the assay and restrictions of NGS-based detection of copy number gains. Collectively, this information can guide clinical and analytical decisions such as the reliable detection of high-level gene amplifications and the requirement for additional in situ assays in case of borderline results or limited sensitivity. |
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Abstract Next-generation sequencing (NGS) panel analysis on DNA from formalin-fixed paraffin-embedded (FFPE) tissue is increasingly used to also identify actionable copy number gains (gene amplifications) in addition to sequence variants. While guidelines for the reporting of sequence variants are available, guidance with respect to reporting copy number gains from gene-panel NGS data is limited. Here, we report on Dutch consensus recommendations obtained in the context of the national Predictive Analysis for THerapy (PATH) project, which aims to optimize and harmonize routine diagnostics in molecular pathology. We briefly discuss two common approaches to detect gene copy number gains from NGS data, i.e., the relative coverage and B-allele frequencies. In addition, we provide recommendations for reporting gene copy gains for clinical purposes. In addition to general QC metrics associated with NGS in routine diagnostics, it is recommended to include clinically relevant quantitative parameters of copy number gains in the clinical report, such as (i) relative coverage and estimated copy numbers in neoplastic cells, (ii) statistical scores to show significance (e.g., z-scores), and (iii) the sensitivity of the assay and restrictions of NGS-based detection of copy number gains. Collectively, this information can guide clinical and analytical decisions such as the reliable detection of high-level gene amplifications and the requirement for additional in situ assays in case of borderline results or limited sensitivity. |
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