Application of a High Throughput Method of Biomarker Discovery to Improvement of the EarlyCDT®-Lung Test
Publication Date
December 13, 2012
Journal
PLOS ONE
Authors
Isabel K. Macdonald, Andrea Murray, Graham F. Healey, Celine B. Parsy Kowalska, et al
Volume
7
Issue
12
Pages
e51002
DOI
https://dx.plos.org/10.1371/journal.pone.0051002
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0051002
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/23272083
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3521770
Europe PMC
http://europepmc.org/abstract/MED/23272083
Web of Science
000312386600016
Scopus
84871310263
Mendeley
http://www.mendeley.com/research/application-high-throughput-method-biomarker-discovery-improvement-earlycdtlung-test
Events
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Mendeley | Further Information

{"title"=>"Application of a High Throughput Method of Biomarker Discovery to Improvement of the EarlyCDT®-Lung Test", "type"=>"journal", "authors"=>[{"first_name"=>"Isabel K.", "last_name"=>"Macdonald", "scopus_author_id"=>"14060647000"}, {"first_name"=>"Andrea", "last_name"=>"Murray", "scopus_author_id"=>"7401933000"}, {"first_name"=>"Graham F.", "last_name"=>"Healey", "scopus_author_id"=>"36463509300"}, {"first_name"=>"Celine B.", "last_name"=>"Parsy-Kowalska", "scopus_author_id"=>"37032958000"}, {"first_name"=>"Jared", "last_name"=>"Allen", "scopus_author_id"=>"57196688556"}, {"first_name"=>"Jane", "last_name"=>"McElveen", "scopus_author_id"=>"57165921800"}, {"first_name"=>"Chris", "last_name"=>"Robertson", "scopus_author_id"=>"7401656177"}, {"first_name"=>"Herbert F.", "last_name"=>"Sewell", "scopus_author_id"=>"7007108445"}, {"first_name"=>"Caroline J.", "last_name"=>"Chapman", "scopus_author_id"=>"55424856500"}, {"first_name"=>"John F.R.", "last_name"=>"Robertson", "scopus_author_id"=>"23398489300"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"366296310", "sgr"=>"84871310263", "issn"=>"19326203", "pmid"=>"23272083", "scopus"=>"2-s2.0-84871310263", "doi"=>"10.1371/journal.pone.0051002"}, "id"=>"8a9ff433-afaa-3a93-8208-fc587022c5ce", "abstract"=>"BACKGROUND: The National Lung Screening Trial showed that CT screening for lung cancer led to a 20% reduction in mortality. However, CT screening has a number of disadvantages including low specificity. A validated autoantibody assay is available commercially (EarlyCDT®-Lung) to aid in the early detection of lung cancer and risk stratification in patients with pulmonary nodules detected by CT. Recent advances in high throughput (HTP) cloning and expression methods have been developed into a discovery pipeline to identify biomarkers that detect autoantibodies. The aim of this study was to demonstrate the successful clinical application of this strategy to add to the EarlyCDT-Lung panel in order to improve its sensitivity and specificity (and hence positive predictive value, (PPV)).\\n\\nMETHODS AND FINDINGS: Serum from two matched independent cohorts of lung cancer patients were used (n = 100 and n = 165). Sixty nine proteins were initially screened on an abridged HTP version of the autoantibody ELISA using protein prepared on small scale by a HTP expression and purification screen. Promising leads were produced in shake flask culture and tested on the full assay. These results were analyzed in combination with those from the EarlyCDT-Lung panel in order to provide a set of re-optimized cut-offs. Five proteins that still displayed cancer/normal differentiation were tested for reproducibility and validation on a second batch of protein and a separate patient cohort. Addition of these proteins resulted in an improvement in the sensitivity and specificity of the test from 38% and 86% to 49% and 93% respectively (PPV improvement from 1 in 16 to 1 in 7).\\n\\nCONCLUSION: This is a practical example of the value of investing resources to develop a HTP technology. Such technology may lead to improvement in the clinical utility of the EarlyCDT--Lung test, and so further aid the early detection of lung cancer.", "link"=>"http://www.mendeley.com/research/application-high-throughput-method-biomarker-discovery-improvement-earlycdtlung-test", "reader_count"=>10, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Researcher"=>2, "Student > Ph. D. Student"=>4, "Other"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Researcher"=>2, "Student > Ph. D. Student"=>4, "Other"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>3, "Agricultural and Biological Sciences"=>4, "Medicine and Dentistry"=>1, "Chemistry"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Chemistry"=>{"Chemistry"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>4}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}, "Unspecified"=>{"Unspecified"=>1}}, "group_count"=>0}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/525394"], "description"=>"<p>Scatter plots showing level of signal from autoantibody binding to fusion proteins coated at 100 nM in 165 cancer patients (black) and 165 individuals with no evidence of malignancy (grey). NY-ESO-1 BirA = the cancer antigen control.</p>", "links"=>[], "tags"=>["differentiation"], "article_id"=>195885, "categories"=>["Cancer", "Biotechnology", "Biochemistry", "Immunology"], "users"=>["Isabel K. Macdonald", "Andrea Murray", "Graham F. Healey", "Celine B. Parsy-Kowalska", "Jared Allen", "Jane McElveen", "Chris Robertson", "Herbert F. Sewell", "Caroline J. Chapman", "John F. R. Robertson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0051002.g002", "stats"=>{"downloads"=>1, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Cancer_normal_differentiation_in_HTPA_/195885", "title"=>"Cancer : normal differentiation in HTPA.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-12-13 01:38:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/525628"], "description"=>"<p>Fusion proteins shown by HTPA to be potential leads were expressed in shake flask culture, purified and used as capture antigens for measurement of AAb by 5 point R&D assay. Cut-offs were optimized to give maximal cancer normal differentiation. Samples that were positive for the <i>e</i>CDT-Lung R&D panel antigens are shown as light blue lines with <i>e</i>CDT-Lung R&D panel positivity shown as dark blue lines. Positivity of lead antigens is shown as red lines if that sample was already positive for one of the antigens in the <i>e</i>CDT-Lung R&D panel (non-additive) and green lines if the lead identified a positive not found using <i>e</i>CDT-Lung R&D panel (additive). Positivity of the total panel of 15 antigens is shown as yellow lines.</p>", "links"=>[], "tags"=>["positivity", "scaled", "cancer"], "article_id"=>196109, "categories"=>["Cancer", "Biotechnology", "Biochemistry", "Immunology"], "users"=>["Isabel K. Macdonald", "Andrea Murray", "Graham F. Healey", "Celine B. Parsy-Kowalska", "Jared Allen", "Jane McElveen", "Chris Robertson", "Herbert F. Sewell", "Caroline J. Chapman", "John F. R. Robertson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0051002.g004", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Panel_positivity_of_scaled_up_lung_cancer_leads_/196109", "title"=>"Panel positivity of scaled up lung cancer leads.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-12-13 01:41:49"}
  • {"files"=>["https://ndownloader.figshare.com/files/525822"], "description"=>"<p>Cut-offs that had been optimised on the cohort 2 sample set using R&D batches of protein were applied to the results of assays of the cohort 1 samples to validate sensitivity (sens) and specificity (spec) for each confirmed lead alone (bold) and in combination with the <i>e</i>CDT-Lung R&D panel (italic). Sensitivity and specificity values are also given for every combination of two or three confirmed leads in when added to the <i>e</i>CDT-Lung R&D panel.</p>", "links"=>[], "tags"=>["specificity", "confirmed"], "article_id"=>196309, "categories"=>["Cancer", "Biotechnology", "Biochemistry", "Immunology"], "users"=>["Isabel K. Macdonald", "Andrea Murray", "Graham F. Healey", "Celine B. Parsy-Kowalska", "Jared Allen", "Jane McElveen", "Chris Robertson", "Herbert F. Sewell", "Caroline J. Chapman", "John F. R. Robertson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0051002.t002", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sensitivity_and_specificity_of_confirmed_leads_/196309", "title"=>"Sensitivity and specificity of confirmed leads.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-12-13 01:45:09"}
  • {"files"=>["https://ndownloader.figshare.com/files/525780"], "description"=>"<p>Cut-offs were optimized to give the maximum number of positive cancers and negative control samples for both the leads and the <i>e</i>CDT-Lung R&D panel antigens. Overall positivity in cancers and controls is given for each lead as well as the additive positivity over the <i>e</i>CDT-Lung R&D panel. Antigens defined as confirmed leads and taken forward for validation on a separate sample cohort are shown in bold italic font.</p>", "links"=>[], "tags"=>["scaled", "cancer", "leads", "compared"], "article_id"=>196262, "categories"=>["Cancer", "Biotechnology", "Biochemistry", "Immunology"], "users"=>["Isabel K. Macdonald", "Andrea Murray", "Graham F. Healey", "Celine B. Parsy-Kowalska", "Jared Allen", "Jane McElveen", "Chris Robertson", "Herbert F. Sewell", "Caroline J. Chapman", "John F. R. Robertson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0051002.t001", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Positivity_of_scaled_up_lung_cancer_leads_compared_with_the_Early_CDT_Lung_panel_/196262", "title"=>"Positivity of scaled up lung cancer leads compared with the <i>Early</i>CDT-Lung panel.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-12-13 01:44:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/525870"], "description"=>"<p>Data derived from application of the commercial panel cut-offs to the <i>Early</i>CDT-Lung panel are shown in bold, italic font. Cut-offs were then optimised on cohort 2 and then applied to the results obtained from cohort 1. The effect of dropping one or more antigens from the panel is shown.</p>", "links"=>[], "tags"=>["cohorts"], "article_id"=>196355, "categories"=>["Cancer", "Biotechnology", "Biochemistry", "Immunology"], "users"=>["Isabel K. Macdonald", "Andrea Murray", "Graham F. Healey", "Celine B. Parsy-Kowalska", "Jared Allen", "Jane McElveen", "Chris Robertson", "Herbert F. Sewell", "Caroline J. Chapman", "John F. R. Robertson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0051002.t003", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_and_Comparison_of_Panel_Performance_for_Cohorts_1_and_2_/196355", "title"=>"Summary and Comparison of Panel Performance for Cohorts 1 and 2.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-12-13 01:45:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/285664", "https://ndownloader.figshare.com/files/285717"], "description"=>"<div><h3>Background</h3><p>The National Lung Screening Trial showed that CT screening for lung cancer led to a 20% reduction in mortality. However, CT screening has a number of disadvantages including low specificity. A validated autoantibody assay is available commercially (<em>Early</em>CDT®-Lung) to aid in the early detection of lung cancer and risk stratification in patients with pulmonary nodules detected by CT.</p> <p>Recent advances in high throughput (HTP) cloning and expression methods have been developed into a discovery pipeline to identify biomarkers that detect autoantibodies. The aim of this study was to demonstrate the successful clinical application of this strategy to add to the <em>Early</em>CDT-Lung panel in order to improve its sensitivity and specificity (and hence positive predictive value, (PPV)).</p> <h3>Methods and Findings</h3><p>Serum from two matched independent cohorts of lung cancer patients were used (n = 100 and n = 165). Sixty nine proteins were initially screened on an abridged HTP version of the autoantibody ELISA using protein prepared on small scale by a HTP expression and purification screen. Promising leads were produced in shake flask culture and tested on the full assay. These results were analyzed in combination with those from the <em>Early</em>CDT-Lung panel in order to provide a set of re-optimized cut-offs. Five proteins that still displayed cancer/normal differentiation were tested for reproducibility and validation on a second batch of protein and a separate patient cohort. Addition of these proteins resulted in an improvement in the sensitivity and specificity of the test from 38% and 86% to 49% and 93% respectively (PPV improvement from 1 in 16 to 1 in 7).</p> <h3>Conclusion</h3><p>This is a practical example of the value of investing resources to develop a HTP technology. Such technology may lead to improvement in the clinical utility of the <em>Early</em>CDT­-Lung test, and so further aid the early detection of lung cancer.</p> </div>", "links"=>[], "tags"=>["throughput", "biomarker", "test"], "article_id"=>116308, "categories"=>["Cancer", "Biotechnology", "Biochemistry", "Immunology"], "users"=>["Isabel K. Macdonald", "Andrea Murray", "Graham F. Healey", "Celine B. Parsy-Kowalska", "Jared Allen", "Jane McElveen", "Chris Robertson", "Herbert F. Sewell", "Caroline J. Chapman", "John F. R. Robertson"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0051002.s001", "https://dx.doi.org/10.1371/journal.pone.0051002.s002"], "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Application_of_a_High_Throughput_Method_of_Biomarker_Discovery_to_Improvement_of_the_Early_CDT_Lung_Test__/116308", "title"=>"Application of a High Throughput Method of Biomarker Discovery to Improvement of the <em>Early</em>CDT<sup>®</sup>-Lung Test", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-12-13 01:45:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/525480"], "description"=>"<p>Fusion proteins shown by HTPA to be potential leads were expressed in shake flask culture, purified and used as capture antigens for measurement of AAb by 5 point R&D assay. Calculations were based on populations of 100 lung cancers and 100 individuals with no evidence of malignant disease (cohort 2). Bars represent fusion protein plated at 160 nM (black) and 50 nM (grey).</p>", "links"=>[], "tags"=>["assay", "scaled", "fusion"], "article_id"=>195964, "categories"=>["Cancer", "Biotechnology", "Biochemistry", "Immunology"], "users"=>["Isabel K. Macdonald", "Andrea Murray", "Graham F. Healey", "Celine B. Parsy-Kowalska", "Jared Allen", "Jane McElveen", "Chris Robertson", "Herbert F. Sewell", "Caroline J. Chapman", "John F. R. Robertson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0051002.g003", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_K_S_Score_for_R_amp_D_assay_analysis_of_scaled_up_fusion_proteins_/195964", "title"=>"K-S Score for R&D assay analysis of scaled up fusion proteins.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-12-13 01:39:24"}
  • {"files"=>["https://ndownloader.figshare.com/files/525285"], "description"=>"<p>Calculations were based on populations of 165 lung cancers and 165 individuals with no evidence of malignant disease (cohort 1). Bars represent fusion protein plated at 100 nM (black) and 50 nM (grey). NY-ESO-1 BirA (comm) = the cancer antigen control.</p>", "links"=>[], "tags"=>["htpa", "69", "fusion"], "article_id"=>195763, "categories"=>["Cancer", "Biotechnology", "Biochemistry", "Immunology"], "users"=>["Isabel K. Macdonald", "Andrea Murray", "Graham F. Healey", "Celine B. Parsy-Kowalska", "Jared Allen", "Jane McElveen", "Chris Robertson", "Herbert F. Sewell", "Caroline J. Chapman", "John F. R. Robertson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0051002.g001", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_K_S_Score_for_HTPA_analysis_of_69_fusion_proteins_/195763", "title"=>"K-S Score for HTPA analysis of 69 fusion proteins.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-12-13 01:36:03"}

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Relative Metric

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