DNAfusion: an R/Bioconductor package for increased sensitivity of detecting gene fusions in liquid biopsies

Background EML4-ALK gene fusions are oncogenic drivers in non-small cell lung cancer (NSCLC), and liquid biopsies containing EML4-ALK fragments can be used to study tumor dynamics using next-generation sequencing (NGS). However, the sensitivity of EML4-ALK detection varies between pipelines and anal...
Ausführliche Beschreibung

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Autor*in:	Maansson, Christoffer Trier [verfasserIn] Andersen, Emma Roger Ulhoi, Maiken Parm Meldgaard, Peter Sorensen, Boe Sandahl

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2023

Schlagwörter:	Gene fusion EML4-ALK R/Bioconductor Non-small cell lung cancer Next-generation sequencing Variant call Biomarker Liquid biopsies

Anmerkung:	© The Author(s) 2023

Übergeordnetes Werk:	Enthalten in: BMC bioinformatics - London : BioMed Central, 2000, 24(2023), 1 vom: 04. Apr.
Übergeordnetes Werk:	volume:24 ; year:2023 ; number:1 ; day:04 ; month:04

Links:	Volltext

DOI / URN:	10.1186/s12859-023-05259-3

Katalog-ID:	SPR049947052

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520			\|a Background EML4-ALK gene fusions are oncogenic drivers in non-small cell lung cancer (NSCLC), and liquid biopsies containing EML4-ALK fragments can be used to study tumor dynamics using next-generation sequencing (NGS). However, the sensitivity of EML4-ALK detection varies between pipelines and analysis tools. Results We developed an R/Bioconductor package, DNAfusion, which can be applied to BAM files generated by commercially available NGS pipelines, such as AVENIO. Forty-eight blood samples from a training cohort consisting of 41 stage IV EML4-ALK-positive NSCLC patients and seven healthy controls were used to develop DNAfusion. DNAfusion detected EML4-ALK in significantly more samples (sensitivity = 61.0%) compared to AVENIO (sensitivity = 36.6%). The newly identified EML4-ALK-positive patients were verified using droplet digital PCR. DNAfusion was subsequently validated in a blinded validation cohort comprising 24 EML4-ALK-positive and 24 EML4-ALK-negative stage IV NSCLC patients. DNAfusion detected significantly more EML4-ALK individuals in the validation cohort (sensitivity = 62.5%) compared to AVENIO (sensitivity = 29.2%). DNAfusion demonstrated a specificity of 100% in both the training and validation cohorts. Conclusion Here we present DNAfusion, which increases the sensitivity of EML4-ALK detection in liquid biopsies and can be implemented downstream of commercially available NGS pipelines. The simplistic method of operating the R package makes it easy to implement in the clinical setting, enabling wider expansion of NGS-based diagnostics.
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allfields	10.1186/s12859-023-05259-3 doi (DE-627)SPR049947052 (SPR)s12859-023-05259-3-e DE-627 ger DE-627 rakwb eng Maansson, Christoffer Trier verfasserin aut DNAfusion: an R/Bioconductor package for increased sensitivity of detecting gene fusions in liquid biopsies 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2023 Background EML4-ALK gene fusions are oncogenic drivers in non-small cell lung cancer (NSCLC), and liquid biopsies containing EML4-ALK fragments can be used to study tumor dynamics using next-generation sequencing (NGS). However, the sensitivity of EML4-ALK detection varies between pipelines and analysis tools. Results We developed an R/Bioconductor package, DNAfusion, which can be applied to BAM files generated by commercially available NGS pipelines, such as AVENIO. Forty-eight blood samples from a training cohort consisting of 41 stage IV EML4-ALK-positive NSCLC patients and seven healthy controls were used to develop DNAfusion. DNAfusion detected EML4-ALK in significantly more samples (sensitivity = 61.0%) compared to AVENIO (sensitivity = 36.6%). The newly identified EML4-ALK-positive patients were verified using droplet digital PCR. DNAfusion was subsequently validated in a blinded validation cohort comprising 24 EML4-ALK-positive and 24 EML4-ALK-negative stage IV NSCLC patients. DNAfusion detected significantly more EML4-ALK individuals in the validation cohort (sensitivity = 62.5%) compared to AVENIO (sensitivity = 29.2%). DNAfusion demonstrated a specificity of 100% in both the training and validation cohorts. Conclusion Here we present DNAfusion, which increases the sensitivity of EML4-ALK detection in liquid biopsies and can be implemented downstream of commercially available NGS pipelines. The simplistic method of operating the R package makes it easy to implement in the clinical setting, enabling wider expansion of NGS-based diagnostics. Gene fusion (dpeaa)DE-He213 EML4-ALK (dpeaa)DE-He213 R/Bioconductor (dpeaa)DE-He213 Non-small cell lung cancer (dpeaa)DE-He213 Next-generation sequencing (dpeaa)DE-He213 Variant call (dpeaa)DE-He213 Biomarker (dpeaa)DE-He213 Liquid biopsies (dpeaa)DE-He213 Andersen, Emma Roger aut Ulhoi, Maiken Parm aut Meldgaard, Peter aut Sorensen, Boe Sandahl aut Enthalten in BMC bioinformatics London : BioMed Central, 2000 24(2023), 1 vom: 04. Apr. (DE-627)326644814 (DE-600)2041484-5 1471-2105 nnns volume:24 year:2023 number:1 day:04 month:04 https://dx.doi.org/10.1186/s12859-023-05259-3 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 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_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 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_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 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_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 24 2023 1 04 04
spelling	10.1186/s12859-023-05259-3 doi (DE-627)SPR049947052 (SPR)s12859-023-05259-3-e DE-627 ger DE-627 rakwb eng Maansson, Christoffer Trier verfasserin aut DNAfusion: an R/Bioconductor package for increased sensitivity of detecting gene fusions in liquid biopsies 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2023 Background EML4-ALK gene fusions are oncogenic drivers in non-small cell lung cancer (NSCLC), and liquid biopsies containing EML4-ALK fragments can be used to study tumor dynamics using next-generation sequencing (NGS). However, the sensitivity of EML4-ALK detection varies between pipelines and analysis tools. Results We developed an R/Bioconductor package, DNAfusion, which can be applied to BAM files generated by commercially available NGS pipelines, such as AVENIO. Forty-eight blood samples from a training cohort consisting of 41 stage IV EML4-ALK-positive NSCLC patients and seven healthy controls were used to develop DNAfusion. DNAfusion detected EML4-ALK in significantly more samples (sensitivity = 61.0%) compared to AVENIO (sensitivity = 36.6%). The newly identified EML4-ALK-positive patients were verified using droplet digital PCR. DNAfusion was subsequently validated in a blinded validation cohort comprising 24 EML4-ALK-positive and 24 EML4-ALK-negative stage IV NSCLC patients. DNAfusion detected significantly more EML4-ALK individuals in the validation cohort (sensitivity = 62.5%) compared to AVENIO (sensitivity = 29.2%). DNAfusion demonstrated a specificity of 100% in both the training and validation cohorts. Conclusion Here we present DNAfusion, which increases the sensitivity of EML4-ALK detection in liquid biopsies and can be implemented downstream of commercially available NGS pipelines. The simplistic method of operating the R package makes it easy to implement in the clinical setting, enabling wider expansion of NGS-based diagnostics. Gene fusion (dpeaa)DE-He213 EML4-ALK (dpeaa)DE-He213 R/Bioconductor (dpeaa)DE-He213 Non-small cell lung cancer (dpeaa)DE-He213 Next-generation sequencing (dpeaa)DE-He213 Variant call (dpeaa)DE-He213 Biomarker (dpeaa)DE-He213 Liquid biopsies (dpeaa)DE-He213 Andersen, Emma Roger aut Ulhoi, Maiken Parm aut Meldgaard, Peter aut Sorensen, Boe Sandahl aut Enthalten in BMC bioinformatics London : BioMed Central, 2000 24(2023), 1 vom: 04. Apr. (DE-627)326644814 (DE-600)2041484-5 1471-2105 nnns volume:24 year:2023 number:1 day:04 month:04 https://dx.doi.org/10.1186/s12859-023-05259-3 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 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_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 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_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 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_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 24 2023 1 04 04
allfields_unstemmed	10.1186/s12859-023-05259-3 doi (DE-627)SPR049947052 (SPR)s12859-023-05259-3-e DE-627 ger DE-627 rakwb eng Maansson, Christoffer Trier verfasserin aut DNAfusion: an R/Bioconductor package for increased sensitivity of detecting gene fusions in liquid biopsies 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2023 Background EML4-ALK gene fusions are oncogenic drivers in non-small cell lung cancer (NSCLC), and liquid biopsies containing EML4-ALK fragments can be used to study tumor dynamics using next-generation sequencing (NGS). However, the sensitivity of EML4-ALK detection varies between pipelines and analysis tools. Results We developed an R/Bioconductor package, DNAfusion, which can be applied to BAM files generated by commercially available NGS pipelines, such as AVENIO. Forty-eight blood samples from a training cohort consisting of 41 stage IV EML4-ALK-positive NSCLC patients and seven healthy controls were used to develop DNAfusion. DNAfusion detected EML4-ALK in significantly more samples (sensitivity = 61.0%) compared to AVENIO (sensitivity = 36.6%). The newly identified EML4-ALK-positive patients were verified using droplet digital PCR. DNAfusion was subsequently validated in a blinded validation cohort comprising 24 EML4-ALK-positive and 24 EML4-ALK-negative stage IV NSCLC patients. DNAfusion detected significantly more EML4-ALK individuals in the validation cohort (sensitivity = 62.5%) compared to AVENIO (sensitivity = 29.2%). DNAfusion demonstrated a specificity of 100% in both the training and validation cohorts. Conclusion Here we present DNAfusion, which increases the sensitivity of EML4-ALK detection in liquid biopsies and can be implemented downstream of commercially available NGS pipelines. The simplistic method of operating the R package makes it easy to implement in the clinical setting, enabling wider expansion of NGS-based diagnostics. Gene fusion (dpeaa)DE-He213 EML4-ALK (dpeaa)DE-He213 R/Bioconductor (dpeaa)DE-He213 Non-small cell lung cancer (dpeaa)DE-He213 Next-generation sequencing (dpeaa)DE-He213 Variant call (dpeaa)DE-He213 Biomarker (dpeaa)DE-He213 Liquid biopsies (dpeaa)DE-He213 Andersen, Emma Roger aut Ulhoi, Maiken Parm aut Meldgaard, Peter aut Sorensen, Boe Sandahl aut Enthalten in BMC bioinformatics London : BioMed Central, 2000 24(2023), 1 vom: 04. Apr. (DE-627)326644814 (DE-600)2041484-5 1471-2105 nnns volume:24 year:2023 number:1 day:04 month:04 https://dx.doi.org/10.1186/s12859-023-05259-3 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 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_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 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_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 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_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 24 2023 1 04 04
allfieldsGer	10.1186/s12859-023-05259-3 doi (DE-627)SPR049947052 (SPR)s12859-023-05259-3-e DE-627 ger DE-627 rakwb eng Maansson, Christoffer Trier verfasserin aut DNAfusion: an R/Bioconductor package for increased sensitivity of detecting gene fusions in liquid biopsies 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2023 Background EML4-ALK gene fusions are oncogenic drivers in non-small cell lung cancer (NSCLC), and liquid biopsies containing EML4-ALK fragments can be used to study tumor dynamics using next-generation sequencing (NGS). However, the sensitivity of EML4-ALK detection varies between pipelines and analysis tools. Results We developed an R/Bioconductor package, DNAfusion, which can be applied to BAM files generated by commercially available NGS pipelines, such as AVENIO. Forty-eight blood samples from a training cohort consisting of 41 stage IV EML4-ALK-positive NSCLC patients and seven healthy controls were used to develop DNAfusion. DNAfusion detected EML4-ALK in significantly more samples (sensitivity = 61.0%) compared to AVENIO (sensitivity = 36.6%). The newly identified EML4-ALK-positive patients were verified using droplet digital PCR. DNAfusion was subsequently validated in a blinded validation cohort comprising 24 EML4-ALK-positive and 24 EML4-ALK-negative stage IV NSCLC patients. DNAfusion detected significantly more EML4-ALK individuals in the validation cohort (sensitivity = 62.5%) compared to AVENIO (sensitivity = 29.2%). DNAfusion demonstrated a specificity of 100% in both the training and validation cohorts. Conclusion Here we present DNAfusion, which increases the sensitivity of EML4-ALK detection in liquid biopsies and can be implemented downstream of commercially available NGS pipelines. The simplistic method of operating the R package makes it easy to implement in the clinical setting, enabling wider expansion of NGS-based diagnostics. Gene fusion (dpeaa)DE-He213 EML4-ALK (dpeaa)DE-He213 R/Bioconductor (dpeaa)DE-He213 Non-small cell lung cancer (dpeaa)DE-He213 Next-generation sequencing (dpeaa)DE-He213 Variant call (dpeaa)DE-He213 Biomarker (dpeaa)DE-He213 Liquid biopsies (dpeaa)DE-He213 Andersen, Emma Roger aut Ulhoi, Maiken Parm aut Meldgaard, Peter aut Sorensen, Boe Sandahl aut Enthalten in BMC bioinformatics London : BioMed Central, 2000 24(2023), 1 vom: 04. Apr. (DE-627)326644814 (DE-600)2041484-5 1471-2105 nnns volume:24 year:2023 number:1 day:04 month:04 https://dx.doi.org/10.1186/s12859-023-05259-3 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 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_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 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_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 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_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 24 2023 1 04 04
allfieldsSound	10.1186/s12859-023-05259-3 doi (DE-627)SPR049947052 (SPR)s12859-023-05259-3-e DE-627 ger DE-627 rakwb eng Maansson, Christoffer Trier verfasserin aut DNAfusion: an R/Bioconductor package for increased sensitivity of detecting gene fusions in liquid biopsies 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2023 Background EML4-ALK gene fusions are oncogenic drivers in non-small cell lung cancer (NSCLC), and liquid biopsies containing EML4-ALK fragments can be used to study tumor dynamics using next-generation sequencing (NGS). However, the sensitivity of EML4-ALK detection varies between pipelines and analysis tools. Results We developed an R/Bioconductor package, DNAfusion, which can be applied to BAM files generated by commercially available NGS pipelines, such as AVENIO. Forty-eight blood samples from a training cohort consisting of 41 stage IV EML4-ALK-positive NSCLC patients and seven healthy controls were used to develop DNAfusion. DNAfusion detected EML4-ALK in significantly more samples (sensitivity = 61.0%) compared to AVENIO (sensitivity = 36.6%). The newly identified EML4-ALK-positive patients were verified using droplet digital PCR. DNAfusion was subsequently validated in a blinded validation cohort comprising 24 EML4-ALK-positive and 24 EML4-ALK-negative stage IV NSCLC patients. DNAfusion detected significantly more EML4-ALK individuals in the validation cohort (sensitivity = 62.5%) compared to AVENIO (sensitivity = 29.2%). DNAfusion demonstrated a specificity of 100% in both the training and validation cohorts. Conclusion Here we present DNAfusion, which increases the sensitivity of EML4-ALK detection in liquid biopsies and can be implemented downstream of commercially available NGS pipelines. The simplistic method of operating the R package makes it easy to implement in the clinical setting, enabling wider expansion of NGS-based diagnostics. Gene fusion (dpeaa)DE-He213 EML4-ALK (dpeaa)DE-He213 R/Bioconductor (dpeaa)DE-He213 Non-small cell lung cancer (dpeaa)DE-He213 Next-generation sequencing (dpeaa)DE-He213 Variant call (dpeaa)DE-He213 Biomarker (dpeaa)DE-He213 Liquid biopsies (dpeaa)DE-He213 Andersen, Emma Roger aut Ulhoi, Maiken Parm aut Meldgaard, Peter aut Sorensen, Boe Sandahl aut Enthalten in BMC bioinformatics London : BioMed Central, 2000 24(2023), 1 vom: 04. Apr. (DE-627)326644814 (DE-600)2041484-5 1471-2105 nnns volume:24 year:2023 number:1 day:04 month:04 https://dx.doi.org/10.1186/s12859-023-05259-3 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 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_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 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_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 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_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 24 2023 1 04 04
language	English
source	Enthalten in BMC bioinformatics 24(2023), 1 vom: 04. Apr. volume:24 year:2023 number:1 day:04 month:04
sourceStr	Enthalten in BMC bioinformatics 24(2023), 1 vom: 04. Apr. volume:24 year:2023 number:1 day:04 month:04
format_phy_str_mv	Article
institution	findex.gbv.de
topic_facet	Gene fusion EML4-ALK R/Bioconductor Non-small cell lung cancer Next-generation sequencing Variant call Biomarker Liquid biopsies
isfreeaccess_bool	true
container_title	BMC bioinformatics
authorswithroles_txt_mv	Maansson, Christoffer Trier @@aut@@ Andersen, Emma Roger @@aut@@ Ulhoi, Maiken Parm @@aut@@ Meldgaard, Peter @@aut@@ Sorensen, Boe Sandahl @@aut@@
publishDateDaySort_date	2023-04-04T00:00:00Z
hierarchy_top_id	326644814
id	SPR049947052
language_de	englisch
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However, the sensitivity of EML4-ALK detection varies between pipelines and analysis tools. Results We developed an R/Bioconductor package, DNAfusion, which can be applied to BAM files generated by commercially available NGS pipelines, such as AVENIO. Forty-eight blood samples from a training cohort consisting of 41 stage IV EML4-ALK-positive NSCLC patients and seven healthy controls were used to develop DNAfusion. DNAfusion detected EML4-ALK in significantly more samples (sensitivity = 61.0%) compared to AVENIO (sensitivity = 36.6%). The newly identified EML4-ALK-positive patients were verified using droplet digital PCR. DNAfusion was subsequently validated in a blinded validation cohort comprising 24 EML4-ALK-positive and 24 EML4-ALK-negative stage IV NSCLC patients. DNAfusion detected significantly more EML4-ALK individuals in the validation cohort (sensitivity = 62.5%) compared to AVENIO (sensitivity = 29.2%). DNAfusion demonstrated a specificity of 100% in both the training and validation cohorts. Conclusion Here we present DNAfusion, which increases the sensitivity of EML4-ALK detection in liquid biopsies and can be implemented downstream of commercially available NGS pipelines. 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author	Maansson, Christoffer Trier
spellingShingle	Maansson, Christoffer Trier misc Gene fusion misc EML4-ALK misc R/Bioconductor misc Non-small cell lung cancer misc Next-generation sequencing misc Variant call misc Biomarker misc Liquid biopsies DNAfusion: an R/Bioconductor package for increased sensitivity of detecting gene fusions in liquid biopsies
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topic_title	DNAfusion: an R/Bioconductor package for increased sensitivity of detecting gene fusions in liquid biopsies Gene fusion (dpeaa)DE-He213 EML4-ALK (dpeaa)DE-He213 R/Bioconductor (dpeaa)DE-He213 Non-small cell lung cancer (dpeaa)DE-He213 Next-generation sequencing (dpeaa)DE-He213 Variant call (dpeaa)DE-He213 Biomarker (dpeaa)DE-He213 Liquid biopsies (dpeaa)DE-He213
topic	misc Gene fusion misc EML4-ALK misc R/Bioconductor misc Non-small cell lung cancer misc Next-generation sequencing misc Variant call misc Biomarker misc Liquid biopsies
topic_unstemmed	misc Gene fusion misc EML4-ALK misc R/Bioconductor misc Non-small cell lung cancer misc Next-generation sequencing misc Variant call misc Biomarker misc Liquid biopsies
topic_browse	misc Gene fusion misc EML4-ALK misc R/Bioconductor misc Non-small cell lung cancer misc Next-generation sequencing misc Variant call misc Biomarker misc Liquid biopsies
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title	DNAfusion: an R/Bioconductor package for increased sensitivity of detecting gene fusions in liquid biopsies
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title_full	DNAfusion: an R/Bioconductor package for increased sensitivity of detecting gene fusions in liquid biopsies
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author_browse	Maansson, Christoffer Trier Andersen, Emma Roger Ulhoi, Maiken Parm Meldgaard, Peter Sorensen, Boe Sandahl
container_volume	24
format_se	Elektronische Aufsätze
author-letter	Maansson, Christoffer Trier
doi_str_mv	10.1186/s12859-023-05259-3
title_sort	dnafusion: an r/bioconductor package for increased sensitivity of detecting gene fusions in liquid biopsies
title_auth	DNAfusion: an R/Bioconductor package for increased sensitivity of detecting gene fusions in liquid biopsies
abstract	Background EML4-ALK gene fusions are oncogenic drivers in non-small cell lung cancer (NSCLC), and liquid biopsies containing EML4-ALK fragments can be used to study tumor dynamics using next-generation sequencing (NGS). However, the sensitivity of EML4-ALK detection varies between pipelines and analysis tools. Results We developed an R/Bioconductor package, DNAfusion, which can be applied to BAM files generated by commercially available NGS pipelines, such as AVENIO. Forty-eight blood samples from a training cohort consisting of 41 stage IV EML4-ALK-positive NSCLC patients and seven healthy controls were used to develop DNAfusion. DNAfusion detected EML4-ALK in significantly more samples (sensitivity = 61.0%) compared to AVENIO (sensitivity = 36.6%). The newly identified EML4-ALK-positive patients were verified using droplet digital PCR. DNAfusion was subsequently validated in a blinded validation cohort comprising 24 EML4-ALK-positive and 24 EML4-ALK-negative stage IV NSCLC patients. DNAfusion detected significantly more EML4-ALK individuals in the validation cohort (sensitivity = 62.5%) compared to AVENIO (sensitivity = 29.2%). DNAfusion demonstrated a specificity of 100% in both the training and validation cohorts. Conclusion Here we present DNAfusion, which increases the sensitivity of EML4-ALK detection in liquid biopsies and can be implemented downstream of commercially available NGS pipelines. The simplistic method of operating the R package makes it easy to implement in the clinical setting, enabling wider expansion of NGS-based diagnostics. © The Author(s) 2023
abstractGer	Background EML4-ALK gene fusions are oncogenic drivers in non-small cell lung cancer (NSCLC), and liquid biopsies containing EML4-ALK fragments can be used to study tumor dynamics using next-generation sequencing (NGS). However, the sensitivity of EML4-ALK detection varies between pipelines and analysis tools. Results We developed an R/Bioconductor package, DNAfusion, which can be applied to BAM files generated by commercially available NGS pipelines, such as AVENIO. Forty-eight blood samples from a training cohort consisting of 41 stage IV EML4-ALK-positive NSCLC patients and seven healthy controls were used to develop DNAfusion. DNAfusion detected EML4-ALK in significantly more samples (sensitivity = 61.0%) compared to AVENIO (sensitivity = 36.6%). The newly identified EML4-ALK-positive patients were verified using droplet digital PCR. DNAfusion was subsequently validated in a blinded validation cohort comprising 24 EML4-ALK-positive and 24 EML4-ALK-negative stage IV NSCLC patients. DNAfusion detected significantly more EML4-ALK individuals in the validation cohort (sensitivity = 62.5%) compared to AVENIO (sensitivity = 29.2%). DNAfusion demonstrated a specificity of 100% in both the training and validation cohorts. Conclusion Here we present DNAfusion, which increases the sensitivity of EML4-ALK detection in liquid biopsies and can be implemented downstream of commercially available NGS pipelines. The simplistic method of operating the R package makes it easy to implement in the clinical setting, enabling wider expansion of NGS-based diagnostics. © The Author(s) 2023
abstract_unstemmed	Background EML4-ALK gene fusions are oncogenic drivers in non-small cell lung cancer (NSCLC), and liquid biopsies containing EML4-ALK fragments can be used to study tumor dynamics using next-generation sequencing (NGS). However, the sensitivity of EML4-ALK detection varies between pipelines and analysis tools. Results We developed an R/Bioconductor package, DNAfusion, which can be applied to BAM files generated by commercially available NGS pipelines, such as AVENIO. Forty-eight blood samples from a training cohort consisting of 41 stage IV EML4-ALK-positive NSCLC patients and seven healthy controls were used to develop DNAfusion. DNAfusion detected EML4-ALK in significantly more samples (sensitivity = 61.0%) compared to AVENIO (sensitivity = 36.6%). The newly identified EML4-ALK-positive patients were verified using droplet digital PCR. DNAfusion was subsequently validated in a blinded validation cohort comprising 24 EML4-ALK-positive and 24 EML4-ALK-negative stage IV NSCLC patients. DNAfusion detected significantly more EML4-ALK individuals in the validation cohort (sensitivity = 62.5%) compared to AVENIO (sensitivity = 29.2%). DNAfusion demonstrated a specificity of 100% in both the training and validation cohorts. Conclusion Here we present DNAfusion, which increases the sensitivity of EML4-ALK detection in liquid biopsies and can be implemented downstream of commercially available NGS pipelines. The simplistic method of operating the R package makes it easy to implement in the clinical setting, enabling wider expansion of NGS-based diagnostics. © The Author(s) 2023
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title_short	DNAfusion: an R/Bioconductor package for increased sensitivity of detecting gene fusions in liquid biopsies
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author2	Andersen, Emma Roger Ulhoi, Maiken Parm Meldgaard, Peter Sorensen, Boe Sandahl
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DNAfusion: an R/Bioconductor package for increased sensitivity of detecting gene fusions in liquid biopsies

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