Breeze: an integrated quality control and data analysis application for high-throughput drug screening
Abstract Summary High-throughput screening (HTS) enables systematic testing of thousands of chemical compounds for potential use as investigational and therapeutic agents. HTS experiments are often conducted in multi-well plates that inherently bear technical and experimental sources of error. Thus,...
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| Veröffentlicht in: | BIOINFORMATICS 2020-06, Vol.36 (11), p.3602-3604 |
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| creator | Potdar, Swapnil Ianevski, Aleksandr Mpindi, John-Patrick Bychkov, Dmitrii Fiere, Clément Ianevski, Philipp Yadav, Bhagwan Wennerberg, Krister Aittokallio, Tero Kallioniemi, Olli Saarela, Jani Östling, Päivi |
| description | Abstract
Summary
High-throughput screening (HTS) enables systematic testing of thousands of chemical compounds for potential use as investigational and therapeutic agents. HTS experiments are often conducted in multi-well plates that inherently bear technical and experimental sources of error. Thus, HTS data processing requires the use of robust quality control procedures before analysis and interpretation. Here, we have implemented an open-source analysis application, Breeze, an integrated quality control and data analysis application for HTS data. Furthermore, Breeze enables a reliable way to identify individual drug sensitivity and resistance patterns in cell lines or patient-derived samples for functional precision medicine applications. The Breeze application provides a complete solution for data quality assessment, dose–response curve fitting and quantification of the drug responses along with interactive visualization of the results.
Availability and implementation
The Breeze application with video tutorial and technical documentation is accessible at https://breeze.fimm.fi; the R source code is publicly available at https://github.com/potdarswapnil/Breeze under GNU General Public License v3.0.
Contact
swapnil.potdar@helsinki.fi
Supplementary information
Supplementary data are available at Bioinformatics online. |
| doi_str_mv | 10.1093/bioinformatics/btaa138 |
| format | Article |
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Summary
High-throughput screening (HTS) enables systematic testing of thousands of chemical compounds for potential use as investigational and therapeutic agents. HTS experiments are often conducted in multi-well plates that inherently bear technical and experimental sources of error. Thus, HTS data processing requires the use of robust quality control procedures before analysis and interpretation. Here, we have implemented an open-source analysis application, Breeze, an integrated quality control and data analysis application for HTS data. Furthermore, Breeze enables a reliable way to identify individual drug sensitivity and resistance patterns in cell lines or patient-derived samples for functional precision medicine applications. The Breeze application provides a complete solution for data quality assessment, dose–response curve fitting and quantification of the drug responses along with interactive visualization of the results.
Availability and implementation
The Breeze application with video tutorial and technical documentation is accessible at https://breeze.fimm.fi; the R source code is publicly available at https://github.com/potdarswapnil/Breeze under GNU General Public License v3.0.
Contact
swapnil.potdar@helsinki.fi
Supplementary information
Supplementary data are available at Bioinformatics online.</description><identifier>ISSN: 1367-4803</identifier><identifier>ISSN: 1367-4811</identifier><identifier>EISSN: 1460-2059</identifier><identifier>EISSN: 1367-4811</identifier><identifier>DOI: 10.1093/bioinformatics/btaa138</identifier><identifier>PMID: 32119072</identifier><language>eng</language><publisher>OXFORD: Oxford University Press</publisher><subject><![CDATA[Applications Notes ; Biochemical Research Methods ; Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Computer Science ; Computer Science, Interdisciplinary Applications ; Life Sciences & Biomedicine ; Mathematical & Computational Biology ; Mathematics ; Medicin och hälsovetenskap ; Physical Sciences ; Science & Technology ; Statistics & Probability ; Technology]]></subject><ispartof>BIOINFORMATICS, 2020-06, Vol.36 (11), p.3602-3604</ispartof><rights>The Author(s) 2020. Published by Oxford University Press. 2020</rights><rights>The Author(s) 2020. Published by Oxford University Press.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>true</woscitedreferencessubscribed><woscitedreferencescount>60</woscitedreferencescount><woscitedreferencesoriginalsourcerecordid>wos000550117300053</woscitedreferencesoriginalsourcerecordid><citedby>FETCH-LOGICAL-c544t-7510ca5ba82610a3f242d21e4a9df974174cb5d1b04702fcb16c7353144a4f563</citedby><cites>FETCH-LOGICAL-c544t-7510ca5ba82610a3f242d21e4a9df974174cb5d1b04702fcb16c7353144a4f563</cites><orcidid>0000-0002-0886-9769 ; 0000-0002-2778-6918 ; 0000-0002-3502-9335 ; 0000-0002-1352-4220 ; 0000-0003-1579-1127 ; 0000-0002-3231-0332 ; 0000-0002-7780-482X ; 0000-0001-7306-7175 ; 0000-0001-5501-466X</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7267830/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7267830/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,315,554,729,782,786,887,1586,1606,27933,27934,28257,53800,53802</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/32119072$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttp://kipublications.ki.se/Default.aspx?queryparsed=id:144201584$$DView record from Swedish Publication Index$$Hfree_for_read</backlink></links><search><contributor>Valencia, Alfonso</contributor><creatorcontrib>Potdar, Swapnil</creatorcontrib><creatorcontrib>Ianevski, Aleksandr</creatorcontrib><creatorcontrib>Mpindi, John-Patrick</creatorcontrib><creatorcontrib>Bychkov, Dmitrii</creatorcontrib><creatorcontrib>Fiere, Clément</creatorcontrib><creatorcontrib>Ianevski, Philipp</creatorcontrib><creatorcontrib>Yadav, Bhagwan</creatorcontrib><creatorcontrib>Wennerberg, Krister</creatorcontrib><creatorcontrib>Aittokallio, Tero</creatorcontrib><creatorcontrib>Kallioniemi, Olli</creatorcontrib><creatorcontrib>Saarela, Jani</creatorcontrib><creatorcontrib>Östling, Päivi</creatorcontrib><title>Breeze: an integrated quality control and data analysis application for high-throughput drug screening</title><title>BIOINFORMATICS</title><addtitle>BIOINFORMATICS</addtitle><addtitle>Bioinformatics</addtitle><description>Abstract
Summary
High-throughput screening (HTS) enables systematic testing of thousands of chemical compounds for potential use as investigational and therapeutic agents. HTS experiments are often conducted in multi-well plates that inherently bear technical and experimental sources of error. Thus, HTS data processing requires the use of robust quality control procedures before analysis and interpretation. Here, we have implemented an open-source analysis application, Breeze, an integrated quality control and data analysis application for HTS data. Furthermore, Breeze enables a reliable way to identify individual drug sensitivity and resistance patterns in cell lines or patient-derived samples for functional precision medicine applications. The Breeze application provides a complete solution for data quality assessment, dose–response curve fitting and quantification of the drug responses along with interactive visualization of the results.
Availability and implementation
The Breeze application with video tutorial and technical documentation is accessible at https://breeze.fimm.fi; the R source code is publicly available at https://github.com/potdarswapnil/Breeze under GNU General Public License v3.0.
Contact
swapnil.potdar@helsinki.fi
Supplementary information
Supplementary data are available at Bioinformatics online.</description><subject>Applications Notes</subject><subject>Biochemical Research Methods</subject><subject>Biochemistry & Molecular Biology</subject><subject>Biotechnology & Applied Microbiology</subject><subject>Computer Science</subject><subject>Computer Science, Interdisciplinary Applications</subject><subject>Life Sciences & Biomedicine</subject><subject>Mathematical & Computational Biology</subject><subject>Mathematics</subject><subject>Medicin och hälsovetenskap</subject><subject>Physical Sciences</subject><subject>Science & Technology</subject><subject>Statistics & Probability</subject><subject>Technology</subject><issn>1367-4803</issn><issn>1367-4811</issn><issn>1460-2059</issn><issn>1367-4811</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><sourceid>TOX</sourceid><sourceid>AOWDO</sourceid><sourceid>D8T</sourceid><recordid>eNqNkk9v1DAQxSMEoqXwFSofkVBa_40TDkiwooBUiQucLcdxEkPWTm2n1fLpmZLtwh6QevLI83tvxtYrinOCLwhu2GXrgvN9iFudnUmXbdaasPpJcUp4hUuKRfMUalbJkteYnRQvUvqBsSCc8-fFCaOENFjS06L_EK39Zd8i7ZHz2Q5RZ9uhm0VPLu-QCT7HMEG3Q53OGgo97ZJLSM_z5AxMDx7BHmh0w1jmMYZlGOcloy4uA0oG3L3zw8viWa-nZF_tz7Pi-9XHb5vP5fXXT182769LIzjPpRQEGy1aXdOKYM16ymlHieW66fpGciK5aUVHWswlpr1pSWUkEwyepXkvKnZWlKtvurPz0qo5uq2OOxW0U_urn1BZxSXDVQN8819-jqH7K3oQwiiKiag5aN-tWgC2tjMWvkpPxxZHHe9GNYRbJWkla4bB4PXeIIabxaasti4ZO03a27AkRVnV1DXB7P5d1YqaGFKKtj-MIVjdB0IdB0LtAwHC83-XPMgeEgDAmxW4s23ok3HWG3vAMGRGYELgt6BiQNePpzcu_8nHJiw-g5Ss0rDMj93-N0m37fE</recordid><startdate>20200601</startdate><enddate>20200601</enddate><creator>Potdar, Swapnil</creator><creator>Ianevski, Aleksandr</creator><creator>Mpindi, John-Patrick</creator><creator>Bychkov, Dmitrii</creator><creator>Fiere, Clément</creator><creator>Ianevski, Philipp</creator><creator>Yadav, Bhagwan</creator><creator>Wennerberg, Krister</creator><creator>Aittokallio, Tero</creator><creator>Kallioniemi, Olli</creator><creator>Saarela, Jani</creator><creator>Östling, Päivi</creator><general>Oxford University Press</general><general>Oxford Univ Press</general><scope>TOX</scope><scope>AOWDO</scope><scope>BLEPL</scope><scope>DTL</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>5PM</scope><scope>ADTPV</scope><scope>AOWAS</scope><scope>D8T</scope><scope>ZZAVC</scope><orcidid>https://orcid.org/0000-0002-0886-9769</orcidid><orcidid>https://orcid.org/0000-0002-2778-6918</orcidid><orcidid>https://orcid.org/0000-0002-3502-9335</orcidid><orcidid>https://orcid.org/0000-0002-1352-4220</orcidid><orcidid>https://orcid.org/0000-0003-1579-1127</orcidid><orcidid>https://orcid.org/0000-0002-3231-0332</orcidid><orcidid>https://orcid.org/0000-0002-7780-482X</orcidid><orcidid>https://orcid.org/0000-0001-7306-7175</orcidid><orcidid>https://orcid.org/0000-0001-5501-466X</orcidid></search><sort><creationdate>20200601</creationdate><title>Breeze: an integrated quality control and data analysis application for high-throughput drug screening</title><author>Potdar, Swapnil ; Ianevski, Aleksandr ; Mpindi, John-Patrick ; Bychkov, Dmitrii ; Fiere, Clément ; Ianevski, Philipp ; Yadav, Bhagwan ; Wennerberg, Krister ; Aittokallio, Tero ; Kallioniemi, Olli ; Saarela, Jani ; Östling, Päivi</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c544t-7510ca5ba82610a3f242d21e4a9df974174cb5d1b04702fcb16c7353144a4f563</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Applications Notes</topic><topic>Biochemical Research Methods</topic><topic>Biochemistry & Molecular Biology</topic><topic>Biotechnology & Applied Microbiology</topic><topic>Computer Science</topic><topic>Computer Science, Interdisciplinary Applications</topic><topic>Life Sciences & Biomedicine</topic><topic>Mathematical & Computational Biology</topic><topic>Mathematics</topic><topic>Medicin och hälsovetenskap</topic><topic>Physical Sciences</topic><topic>Science & Technology</topic><topic>Statistics & Probability</topic><topic>Technology</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Potdar, Swapnil</creatorcontrib><creatorcontrib>Ianevski, Aleksandr</creatorcontrib><creatorcontrib>Mpindi, John-Patrick</creatorcontrib><creatorcontrib>Bychkov, Dmitrii</creatorcontrib><creatorcontrib>Fiere, Clément</creatorcontrib><creatorcontrib>Ianevski, Philipp</creatorcontrib><creatorcontrib>Yadav, Bhagwan</creatorcontrib><creatorcontrib>Wennerberg, Krister</creatorcontrib><creatorcontrib>Aittokallio, Tero</creatorcontrib><creatorcontrib>Kallioniemi, Olli</creatorcontrib><creatorcontrib>Saarela, Jani</creatorcontrib><creatorcontrib>Östling, Päivi</creatorcontrib><collection>Access via Oxford University Press (Open Access Collection)</collection><collection>Web of Science - Science Citation Index Expanded - 2020</collection><collection>Web of Science Core Collection</collection><collection>Science Citation Index Expanded</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>SwePub</collection><collection>SwePub Articles</collection><collection>SWEPUB Freely available online</collection><collection>SwePub Articles full text</collection><jtitle>BIOINFORMATICS</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Potdar, Swapnil</au><au>Ianevski, Aleksandr</au><au>Mpindi, John-Patrick</au><au>Bychkov, Dmitrii</au><au>Fiere, Clément</au><au>Ianevski, Philipp</au><au>Yadav, Bhagwan</au><au>Wennerberg, Krister</au><au>Aittokallio, Tero</au><au>Kallioniemi, Olli</au><au>Saarela, Jani</au><au>Östling, Päivi</au><au>Valencia, Alfonso</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Breeze: an integrated quality control and data analysis application for high-throughput drug screening</atitle><jtitle>BIOINFORMATICS</jtitle><stitle>BIOINFORMATICS</stitle><addtitle>Bioinformatics</addtitle><date>2020-06-01</date><risdate>2020</risdate><volume>36</volume><issue>11</issue><spage>3602</spage><epage>3604</epage><pages>3602-3604</pages><issn>1367-4803</issn><issn>1367-4811</issn><eissn>1460-2059</eissn><eissn>1367-4811</eissn><abstract>Abstract
Summary
High-throughput screening (HTS) enables systematic testing of thousands of chemical compounds for potential use as investigational and therapeutic agents. HTS experiments are often conducted in multi-well plates that inherently bear technical and experimental sources of error. Thus, HTS data processing requires the use of robust quality control procedures before analysis and interpretation. Here, we have implemented an open-source analysis application, Breeze, an integrated quality control and data analysis application for HTS data. Furthermore, Breeze enables a reliable way to identify individual drug sensitivity and resistance patterns in cell lines or patient-derived samples for functional precision medicine applications. The Breeze application provides a complete solution for data quality assessment, dose–response curve fitting and quantification of the drug responses along with interactive visualization of the results.
Availability and implementation
The Breeze application with video tutorial and technical documentation is accessible at https://breeze.fimm.fi; the R source code is publicly available at https://github.com/potdarswapnil/Breeze under GNU General Public License v3.0.
Contact
swapnil.potdar@helsinki.fi
Supplementary information
Supplementary data are available at Bioinformatics online.</abstract><cop>OXFORD</cop><pub>Oxford University Press</pub><pmid>32119072</pmid><doi>10.1093/bioinformatics/btaa138</doi><tpages>3</tpages><orcidid>https://orcid.org/0000-0002-0886-9769</orcidid><orcidid>https://orcid.org/0000-0002-2778-6918</orcidid><orcidid>https://orcid.org/0000-0002-3502-9335</orcidid><orcidid>https://orcid.org/0000-0002-1352-4220</orcidid><orcidid>https://orcid.org/0000-0003-1579-1127</orcidid><orcidid>https://orcid.org/0000-0002-3231-0332</orcidid><orcidid>https://orcid.org/0000-0002-7780-482X</orcidid><orcidid>https://orcid.org/0000-0001-7306-7175</orcidid><orcidid>https://orcid.org/0000-0001-5501-466X</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Applications Notes Biochemical Research Methods Biochemistry & Molecular Biology Biotechnology & Applied Microbiology Computer Science Computer Science, Interdisciplinary Applications Life Sciences & Biomedicine Mathematical & Computational Biology Mathematics Medicin och hälsovetenskap Physical Sciences Science & Technology Statistics & Probability Technology |
| title | Breeze: an integrated quality control and data analysis application for high-throughput drug screening |
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