ClinLabGeneticist: a tool for clinical management of genetic variants from whole exome sequencing in clinical genetic laboratories

Abstract Routine clinical application of whole exome sequencing remains challenging due to difficulties in variant interpretation, large dataset management, and workflow integration. We describe a tool named ClinLabGeneticist to implement a workflow in clinical laboratories for management of variant...
Ausführliche Beschreibung

Gespeichert in:

Autor*in:	Wang, Jinlian [verfasserIn] Liao, Jun Zhang, Jinglan Cheng, Wei-Yi Hakenberg, Jörg Ma, Meng Webb, Bryn D. Ramasamudram-chakravarthi, Rajasekar Karger, Lisa Mehta, Lakshmi Kornreich, Ruth Diaz, George A. Li, Shuyu Edelmann, Lisa Chen, Rong

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2015

Schlagwörter:	Genetic Testing Sanger Sequencing Exome Sequencing Whole Exome Sequencing Variant Assessment

Anmerkung:	© Wang et al. 2015

Übergeordnetes Werk:	Enthalten in: Genome medicine - London : BioMed Central, 2009, 7(2015), 1 vom: 29. Juli
Übergeordnetes Werk:	volume:7 ; year:2015 ; number:1 ; day:29 ; month:07

Links:	Volltext

DOI / URN:	10.1186/s13073-015-0207-6

Katalog-ID:	SPR030629829

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allfields	10.1186/s13073-015-0207-6 doi (DE-627)SPR030629829 (SPR)s13073-015-0207-6-e DE-627 ger DE-627 rakwb eng Wang, Jinlian verfasserin aut ClinLabGeneticist: a tool for clinical management of genetic variants from whole exome sequencing in clinical genetic laboratories 2015 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Wang et al. 2015 Abstract Routine clinical application of whole exome sequencing remains challenging due to difficulties in variant interpretation, large dataset management, and workflow integration. We describe a tool named ClinLabGeneticist to implement a workflow in clinical laboratories for management of variant assessment in genetic testing and disease diagnosis. We established an extensive variant annotation data source for the identification of pathogenic variants. A dashboard was deployed to aid a multi-step, hierarchical review process leading to final clinical decisions on genetic variant assessment. In addition, a central database was built to archive all of the genetic testing data, notes, and comments throughout the review process, variant validation data by Sanger sequencing as well as the final clinical reports for future reference. The entire workflow including data entry, distribution of work assignments, variant evaluation and review, selection of variants for validation, report generation, and communications between various personnel is integrated into a single data management platform. Three case studies are presented to illustrate the utility of ClinLabGeneticist. ClinLabGeneticist is freely available to academia at http://rongchenlab.org/software/clinlabgeneticist. Genetic Testing (dpeaa)DE-He213 Sanger Sequencing (dpeaa)DE-He213 Exome Sequencing (dpeaa)DE-He213 Whole Exome Sequencing (dpeaa)DE-He213 Variant Assessment (dpeaa)DE-He213 Liao, Jun aut Zhang, Jinglan aut Cheng, Wei-Yi aut Hakenberg, Jörg aut Ma, Meng aut Webb, Bryn D. aut Ramasamudram-chakravarthi, Rajasekar aut Karger, Lisa aut Mehta, Lakshmi aut Kornreich, Ruth aut Diaz, George A. aut Li, Shuyu aut Edelmann, Lisa aut Chen, Rong aut Enthalten in Genome medicine London : BioMed Central, 2009 7(2015), 1 vom: 29. Juli (DE-627)594424275 (DE-600)2484394-5 1756-994X nnns volume:7 year:2015 number:1 day:29 month:07 https://dx.doi.org/10.1186/s13073-015-0207-6 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_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 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_602 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 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_4338 GBV_ILN_4367 GBV_ILN_4700 AR 7 2015 1 29 07
spelling	10.1186/s13073-015-0207-6 doi (DE-627)SPR030629829 (SPR)s13073-015-0207-6-e DE-627 ger DE-627 rakwb eng Wang, Jinlian verfasserin aut ClinLabGeneticist: a tool for clinical management of genetic variants from whole exome sequencing in clinical genetic laboratories 2015 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Wang et al. 2015 Abstract Routine clinical application of whole exome sequencing remains challenging due to difficulties in variant interpretation, large dataset management, and workflow integration. We describe a tool named ClinLabGeneticist to implement a workflow in clinical laboratories for management of variant assessment in genetic testing and disease diagnosis. We established an extensive variant annotation data source for the identification of pathogenic variants. A dashboard was deployed to aid a multi-step, hierarchical review process leading to final clinical decisions on genetic variant assessment. In addition, a central database was built to archive all of the genetic testing data, notes, and comments throughout the review process, variant validation data by Sanger sequencing as well as the final clinical reports for future reference. The entire workflow including data entry, distribution of work assignments, variant evaluation and review, selection of variants for validation, report generation, and communications between various personnel is integrated into a single data management platform. Three case studies are presented to illustrate the utility of ClinLabGeneticist. ClinLabGeneticist is freely available to academia at http://rongchenlab.org/software/clinlabgeneticist. Genetic Testing (dpeaa)DE-He213 Sanger Sequencing (dpeaa)DE-He213 Exome Sequencing (dpeaa)DE-He213 Whole Exome Sequencing (dpeaa)DE-He213 Variant Assessment (dpeaa)DE-He213 Liao, Jun aut Zhang, Jinglan aut Cheng, Wei-Yi aut Hakenberg, Jörg aut Ma, Meng aut Webb, Bryn D. aut Ramasamudram-chakravarthi, Rajasekar aut Karger, Lisa aut Mehta, Lakshmi aut Kornreich, Ruth aut Diaz, George A. aut Li, Shuyu aut Edelmann, Lisa aut Chen, Rong aut Enthalten in Genome medicine London : BioMed Central, 2009 7(2015), 1 vom: 29. Juli (DE-627)594424275 (DE-600)2484394-5 1756-994X nnns volume:7 year:2015 number:1 day:29 month:07 https://dx.doi.org/10.1186/s13073-015-0207-6 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_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 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_602 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 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_4338 GBV_ILN_4367 GBV_ILN_4700 AR 7 2015 1 29 07
allfields_unstemmed	10.1186/s13073-015-0207-6 doi (DE-627)SPR030629829 (SPR)s13073-015-0207-6-e DE-627 ger DE-627 rakwb eng Wang, Jinlian verfasserin aut ClinLabGeneticist: a tool for clinical management of genetic variants from whole exome sequencing in clinical genetic laboratories 2015 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Wang et al. 2015 Abstract Routine clinical application of whole exome sequencing remains challenging due to difficulties in variant interpretation, large dataset management, and workflow integration. We describe a tool named ClinLabGeneticist to implement a workflow in clinical laboratories for management of variant assessment in genetic testing and disease diagnosis. We established an extensive variant annotation data source for the identification of pathogenic variants. A dashboard was deployed to aid a multi-step, hierarchical review process leading to final clinical decisions on genetic variant assessment. In addition, a central database was built to archive all of the genetic testing data, notes, and comments throughout the review process, variant validation data by Sanger sequencing as well as the final clinical reports for future reference. The entire workflow including data entry, distribution of work assignments, variant evaluation and review, selection of variants for validation, report generation, and communications between various personnel is integrated into a single data management platform. Three case studies are presented to illustrate the utility of ClinLabGeneticist. ClinLabGeneticist is freely available to academia at http://rongchenlab.org/software/clinlabgeneticist. Genetic Testing (dpeaa)DE-He213 Sanger Sequencing (dpeaa)DE-He213 Exome Sequencing (dpeaa)DE-He213 Whole Exome Sequencing (dpeaa)DE-He213 Variant Assessment (dpeaa)DE-He213 Liao, Jun aut Zhang, Jinglan aut Cheng, Wei-Yi aut Hakenberg, Jörg aut Ma, Meng aut Webb, Bryn D. aut Ramasamudram-chakravarthi, Rajasekar aut Karger, Lisa aut Mehta, Lakshmi aut Kornreich, Ruth aut Diaz, George A. aut Li, Shuyu aut Edelmann, Lisa aut Chen, Rong aut Enthalten in Genome medicine London : BioMed Central, 2009 7(2015), 1 vom: 29. Juli (DE-627)594424275 (DE-600)2484394-5 1756-994X nnns volume:7 year:2015 number:1 day:29 month:07 https://dx.doi.org/10.1186/s13073-015-0207-6 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_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 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_602 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 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_4338 GBV_ILN_4367 GBV_ILN_4700 AR 7 2015 1 29 07
allfieldsGer	10.1186/s13073-015-0207-6 doi (DE-627)SPR030629829 (SPR)s13073-015-0207-6-e DE-627 ger DE-627 rakwb eng Wang, Jinlian verfasserin aut ClinLabGeneticist: a tool for clinical management of genetic variants from whole exome sequencing in clinical genetic laboratories 2015 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Wang et al. 2015 Abstract Routine clinical application of whole exome sequencing remains challenging due to difficulties in variant interpretation, large dataset management, and workflow integration. We describe a tool named ClinLabGeneticist to implement a workflow in clinical laboratories for management of variant assessment in genetic testing and disease diagnosis. We established an extensive variant annotation data source for the identification of pathogenic variants. A dashboard was deployed to aid a multi-step, hierarchical review process leading to final clinical decisions on genetic variant assessment. In addition, a central database was built to archive all of the genetic testing data, notes, and comments throughout the review process, variant validation data by Sanger sequencing as well as the final clinical reports for future reference. The entire workflow including data entry, distribution of work assignments, variant evaluation and review, selection of variants for validation, report generation, and communications between various personnel is integrated into a single data management platform. Three case studies are presented to illustrate the utility of ClinLabGeneticist. ClinLabGeneticist is freely available to academia at http://rongchenlab.org/software/clinlabgeneticist. Genetic Testing (dpeaa)DE-He213 Sanger Sequencing (dpeaa)DE-He213 Exome Sequencing (dpeaa)DE-He213 Whole Exome Sequencing (dpeaa)DE-He213 Variant Assessment (dpeaa)DE-He213 Liao, Jun aut Zhang, Jinglan aut Cheng, Wei-Yi aut Hakenberg, Jörg aut Ma, Meng aut Webb, Bryn D. aut Ramasamudram-chakravarthi, Rajasekar aut Karger, Lisa aut Mehta, Lakshmi aut Kornreich, Ruth aut Diaz, George A. aut Li, Shuyu aut Edelmann, Lisa aut Chen, Rong aut Enthalten in Genome medicine London : BioMed Central, 2009 7(2015), 1 vom: 29. Juli (DE-627)594424275 (DE-600)2484394-5 1756-994X nnns volume:7 year:2015 number:1 day:29 month:07 https://dx.doi.org/10.1186/s13073-015-0207-6 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_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 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_602 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 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_4338 GBV_ILN_4367 GBV_ILN_4700 AR 7 2015 1 29 07
allfieldsSound	10.1186/s13073-015-0207-6 doi (DE-627)SPR030629829 (SPR)s13073-015-0207-6-e DE-627 ger DE-627 rakwb eng Wang, Jinlian verfasserin aut ClinLabGeneticist: a tool for clinical management of genetic variants from whole exome sequencing in clinical genetic laboratories 2015 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Wang et al. 2015 Abstract Routine clinical application of whole exome sequencing remains challenging due to difficulties in variant interpretation, large dataset management, and workflow integration. We describe a tool named ClinLabGeneticist to implement a workflow in clinical laboratories for management of variant assessment in genetic testing and disease diagnosis. We established an extensive variant annotation data source for the identification of pathogenic variants. A dashboard was deployed to aid a multi-step, hierarchical review process leading to final clinical decisions on genetic variant assessment. In addition, a central database was built to archive all of the genetic testing data, notes, and comments throughout the review process, variant validation data by Sanger sequencing as well as the final clinical reports for future reference. The entire workflow including data entry, distribution of work assignments, variant evaluation and review, selection of variants for validation, report generation, and communications between various personnel is integrated into a single data management platform. Three case studies are presented to illustrate the utility of ClinLabGeneticist. ClinLabGeneticist is freely available to academia at http://rongchenlab.org/software/clinlabgeneticist. Genetic Testing (dpeaa)DE-He213 Sanger Sequencing (dpeaa)DE-He213 Exome Sequencing (dpeaa)DE-He213 Whole Exome Sequencing (dpeaa)DE-He213 Variant Assessment (dpeaa)DE-He213 Liao, Jun aut Zhang, Jinglan aut Cheng, Wei-Yi aut Hakenberg, Jörg aut Ma, Meng aut Webb, Bryn D. aut Ramasamudram-chakravarthi, Rajasekar aut Karger, Lisa aut Mehta, Lakshmi aut Kornreich, Ruth aut Diaz, George A. aut Li, Shuyu aut Edelmann, Lisa aut Chen, Rong aut Enthalten in Genome medicine London : BioMed Central, 2009 7(2015), 1 vom: 29. Juli (DE-627)594424275 (DE-600)2484394-5 1756-994X nnns volume:7 year:2015 number:1 day:29 month:07 https://dx.doi.org/10.1186/s13073-015-0207-6 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_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 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_602 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 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_4338 GBV_ILN_4367 GBV_ILN_4700 AR 7 2015 1 29 07
language	English
source	Enthalten in Genome medicine 7(2015), 1 vom: 29. Juli volume:7 year:2015 number:1 day:29 month:07
sourceStr	Enthalten in Genome medicine 7(2015), 1 vom: 29. Juli volume:7 year:2015 number:1 day:29 month:07
format_phy_str_mv	Article
institution	findex.gbv.de
topic_facet	Genetic Testing Sanger Sequencing Exome Sequencing Whole Exome Sequencing Variant Assessment
isfreeaccess_bool	true
container_title	Genome medicine
authorswithroles_txt_mv	Wang, Jinlian @@aut@@ Liao, Jun @@aut@@ Zhang, Jinglan @@aut@@ Cheng, Wei-Yi @@aut@@ Hakenberg, Jörg @@aut@@ Ma, Meng @@aut@@ Webb, Bryn D. @@aut@@ Ramasamudram-chakravarthi, Rajasekar @@aut@@ Karger, Lisa @@aut@@ Mehta, Lakshmi @@aut@@ Kornreich, Ruth @@aut@@ Diaz, George A. @@aut@@ Li, Shuyu @@aut@@ Edelmann, Lisa @@aut@@ Chen, Rong @@aut@@
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author	Wang, Jinlian
spellingShingle	Wang, Jinlian misc Genetic Testing misc Sanger Sequencing misc Exome Sequencing misc Whole Exome Sequencing misc Variant Assessment ClinLabGeneticist: a tool for clinical management of genetic variants from whole exome sequencing in clinical genetic laboratories
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topic_title	ClinLabGeneticist: a tool for clinical management of genetic variants from whole exome sequencing in clinical genetic laboratories Genetic Testing (dpeaa)DE-He213 Sanger Sequencing (dpeaa)DE-He213 Exome Sequencing (dpeaa)DE-He213 Whole Exome Sequencing (dpeaa)DE-He213 Variant Assessment (dpeaa)DE-He213
topic	misc Genetic Testing misc Sanger Sequencing misc Exome Sequencing misc Whole Exome Sequencing misc Variant Assessment
topic_unstemmed	misc Genetic Testing misc Sanger Sequencing misc Exome Sequencing misc Whole Exome Sequencing misc Variant Assessment
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title	ClinLabGeneticist: a tool for clinical management of genetic variants from whole exome sequencing in clinical genetic laboratories
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title_full	ClinLabGeneticist: a tool for clinical management of genetic variants from whole exome sequencing in clinical genetic laboratories
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author_browse	Wang, Jinlian Liao, Jun Zhang, Jinglan Cheng, Wei-Yi Hakenberg, Jörg Ma, Meng Webb, Bryn D. Ramasamudram-chakravarthi, Rajasekar Karger, Lisa Mehta, Lakshmi Kornreich, Ruth Diaz, George A. Li, Shuyu Edelmann, Lisa Chen, Rong
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title_sort	clinlabgeneticist: a tool for clinical management of genetic variants from whole exome sequencing in clinical genetic laboratories
title_auth	ClinLabGeneticist: a tool for clinical management of genetic variants from whole exome sequencing in clinical genetic laboratories
abstract	Abstract Routine clinical application of whole exome sequencing remains challenging due to difficulties in variant interpretation, large dataset management, and workflow integration. We describe a tool named ClinLabGeneticist to implement a workflow in clinical laboratories for management of variant assessment in genetic testing and disease diagnosis. We established an extensive variant annotation data source for the identification of pathogenic variants. A dashboard was deployed to aid a multi-step, hierarchical review process leading to final clinical decisions on genetic variant assessment. In addition, a central database was built to archive all of the genetic testing data, notes, and comments throughout the review process, variant validation data by Sanger sequencing as well as the final clinical reports for future reference. The entire workflow including data entry, distribution of work assignments, variant evaluation and review, selection of variants for validation, report generation, and communications between various personnel is integrated into a single data management platform. Three case studies are presented to illustrate the utility of ClinLabGeneticist. ClinLabGeneticist is freely available to academia at http://rongchenlab.org/software/clinlabgeneticist. © Wang et al. 2015
abstractGer	Abstract Routine clinical application of whole exome sequencing remains challenging due to difficulties in variant interpretation, large dataset management, and workflow integration. We describe a tool named ClinLabGeneticist to implement a workflow in clinical laboratories for management of variant assessment in genetic testing and disease diagnosis. We established an extensive variant annotation data source for the identification of pathogenic variants. A dashboard was deployed to aid a multi-step, hierarchical review process leading to final clinical decisions on genetic variant assessment. In addition, a central database was built to archive all of the genetic testing data, notes, and comments throughout the review process, variant validation data by Sanger sequencing as well as the final clinical reports for future reference. The entire workflow including data entry, distribution of work assignments, variant evaluation and review, selection of variants for validation, report generation, and communications between various personnel is integrated into a single data management platform. Three case studies are presented to illustrate the utility of ClinLabGeneticist. ClinLabGeneticist is freely available to academia at http://rongchenlab.org/software/clinlabgeneticist. © Wang et al. 2015
abstract_unstemmed	Abstract Routine clinical application of whole exome sequencing remains challenging due to difficulties in variant interpretation, large dataset management, and workflow integration. We describe a tool named ClinLabGeneticist to implement a workflow in clinical laboratories for management of variant assessment in genetic testing and disease diagnosis. We established an extensive variant annotation data source for the identification of pathogenic variants. A dashboard was deployed to aid a multi-step, hierarchical review process leading to final clinical decisions on genetic variant assessment. In addition, a central database was built to archive all of the genetic testing data, notes, and comments throughout the review process, variant validation data by Sanger sequencing as well as the final clinical reports for future reference. The entire workflow including data entry, distribution of work assignments, variant evaluation and review, selection of variants for validation, report generation, and communications between various personnel is integrated into a single data management platform. Three case studies are presented to illustrate the utility of ClinLabGeneticist. ClinLabGeneticist is freely available to academia at http://rongchenlab.org/software/clinlabgeneticist. © Wang et al. 2015
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title_short	ClinLabGeneticist: a tool for clinical management of genetic variants from whole exome sequencing in clinical genetic laboratories
url	https://dx.doi.org/10.1186/s13073-015-0207-6
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author2	Liao, Jun Zhang, Jinglan Cheng, Wei-Yi Hakenberg, Jörg Ma, Meng Webb, Bryn D. Ramasamudram-chakravarthi, Rajasekar Karger, Lisa Mehta, Lakshmi Kornreich, Ruth Diaz, George A. Li, Shuyu Edelmann, Lisa Chen, Rong
author2Str	Liao, Jun Zhang, Jinglan Cheng, Wei-Yi Hakenberg, Jörg Ma, Meng Webb, Bryn D. Ramasamudram-chakravarthi, Rajasekar Karger, Lisa Mehta, Lakshmi Kornreich, Ruth Diaz, George A. Li, Shuyu Edelmann, Lisa Chen, Rong
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up_date	2024-07-03T19:12:38.793Z
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We describe a tool named ClinLabGeneticist to implement a workflow in clinical laboratories for management of variant assessment in genetic testing and disease diagnosis. We established an extensive variant annotation data source for the identification of pathogenic variants. A dashboard was deployed to aid a multi-step, hierarchical review process leading to final clinical decisions on genetic variant assessment. In addition, a central database was built to archive all of the genetic testing data, notes, and comments throughout the review process, variant validation data by Sanger sequencing as well as the final clinical reports for future reference. The entire workflow including data entry, distribution of work assignments, variant evaluation and review, selection of variants for validation, report generation, and communications between various personnel is integrated into a single data management platform. Three case studies are presented to illustrate the utility of ClinLabGeneticist. 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ClinLabGeneticist: a tool for clinical management of genetic variants from whole exome sequencing in clinical genetic laboratories

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