�ݺ�ߣshows by User: KateBarlow8

�ݺ�ߣshows by User: KateBarlow8 / http://www.slideshare.net/images/logo.gif �ݺ�ߣshows by User: KateBarlow8 / Tue, 05 Jun 2018 13:35:51 GMT �ݺ�ߣShare feed for �ݺ�ߣshows by User: KateBarlow8 CoMEHeRe: Co-operative Models for Evidence-based Healthcare Redistribution /slideshow/comehere-cooperative-models-for-evidencebased-healthcare-redistribution/100667385 johncollomosse-180605133551
CoMEHeRe is a two year UKRI/EPSRC funded project that aims to transform personal healthcare through the design and evaluation of new technologies and business models for commodifying and brokering casually captured personal healthcare data (e.g. from wearable biosensors and the IoT) to state and private healthcare providers. CoMEHeRe is developing a Blockchain based platform to incentivise collection and enable secure brokering of large volumes of longitudinal biometric healthcare data, optimising preventative healthcare, helping to achieve a more efficient healthcare system, and contributing to a healthier nation. This presentation will provide a broad picture of the CoMEHeRe project, and describe a prototype of the platform and campus-based user trial delivered across the project’s initial six months.]]>
CoMEHeRe is a two year UKRI/EPSRC funded project that aims to transform personal healthcare through the design and evaluation of new technologies and business models for commodifying and brokering casually captured personal healthcare data (e.g. from wearable biosensors and the IoT) to state and private healthcare providers. CoMEHeRe is developing a Blockchain based platform to incentivise collection and enable secure brokering of large volumes of longitudinal biometric healthcare data, optimising preventative healthcare, helping to achieve a more efficient healthcare system, and contributing to a healthier nation. This presentation will provide a broad picture of the CoMEHeRe project, and describe a prototype of the platform and campus-based user trial delivered across the project’s initial six months.]]> Tue, 05 Jun 2018 13:35:51 GMT /slideshow/comehere-cooperative-models-for-evidencebased-healthcare-redistribution/100667385 KateBarlow8@slideshare.net(KateBarlow8) CoMEHeRe: Co-operative Models for Evidence-based Healthcare Redistribution KateBarlow8 CoMEHeRe is a two year UKRI/EPSRC funded project that aims to transform personal healthcare through the design and evaluation of new technologies and business models for commodifying and brokering casually captured personal healthcare data (e.g. from wearable biosensors and the IoT) to state and private healthcare providers. CoMEHeRe is developing a Blockchain based platform to incentivise collection and enable secure brokering of large volumes of longitudinal biometric healthcare data, optimising preventative healthcare, helping to achieve a more efficient healthcare system, and contributing to a healthier nation. This presentation will provide a broad picture of the CoMEHeRe project, and describe a prototype of the platform and campus-based user trial delivered across the project’s initial six months. <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/johncollomosse-180605133551-thumbnail.jpg?width=120&height=120&fit=bounds" /> CoMEHeRe is a two year UKRI/EPSRC funded project that aims to transform personal healthcare through the design and evaluation of new technologies and business models for commodifying and brokering casually captured personal healthcare data (e.g. from wearable biosensors and the IoT) to state and private healthcare providers. CoMEHeRe is developing a Blockchain based platform to incentivise collection and enable secure brokering of large volumes of longitudinal biometric healthcare data, optimising preventative healthcare, helping to achieve a more efficient healthcare system, and contributing to a healthier nation. This presentation will provide a broad picture of the CoMEHeRe project, and describe a prototype of the platform and campus-based user trial delivered across the project’s initial six months.

CoMEHeRe: Co-operative Models for Evidence-based Healthcare Redistribution from Kate Barlow

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0 Evaluating How Blockchain Can Transform the Pharmaceutical and Healthcare Industries /slideshow/evaluating-how-blockchain-can-transform-the-pharmaceutical-and-healthcare-industries/100666864 disaleechounajibarot-180605133211
- Collaborating with 17 companies across the industry - Understanding the landscape in the pharma and healthcare settings - Exploring the areas where Blockchain could be used - Presenting two detailed use cases (a. Smart Contract: Vendor and Site - Oversight; b. Distributed Asset Ledger: Patient Data Access/Transparency) to support future development and implementation for proof of concept.]]>
- Collaborating with 17 companies across the industry - Understanding the landscape in the pharma and healthcare settings - Exploring the areas where Blockchain could be used - Presenting two detailed use cases (a. Smart Contract: Vendor and Site - Oversight; b. Distributed Asset Ledger: Patient Data Access/Transparency) to support future development and implementation for proof of concept.]]> Tue, 05 Jun 2018 13:32:11 GMT /slideshow/evaluating-how-blockchain-can-transform-the-pharmaceutical-and-healthcare-industries/100666864 KateBarlow8@slideshare.net(KateBarlow8) Evaluating How Blockchain Can Transform the Pharmaceutical and Healthcare Industries KateBarlow8 - Collaborating with 17 companies across the industry - Understanding the landscape in the pharma and healthcare settings - Exploring the areas where Blockchain could be used - Presenting two detailed use cases (a. Smart Contract: Vendor and Site - Oversight; b. Distributed Asset Ledger: Patient Data Access/Transparency) to support future development and implementation for proof of concept. <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/disaleechounajibarot-180605133211-thumbnail.jpg?width=120&height=120&fit=bounds" /> - Collaborating with 17 companies across the industry - Understanding the landscape in the pharma and healthcare settings - Exploring the areas where Blockchain could be used - Presenting two detailed use cases (a. Smart Contract: Vendor and Site - Oversight; b. Distributed Asset Ledger: Patient Data Access/Transparency) to support future development and implementation for proof of concept.

Evaluating How Blockchain Can Transform the Pharmaceutical and Healthcare Industries from Kate Barlow

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0 NIZO: Hotspot for Microbiome Research /slideshow/nizo-hotspot-for-microbiome-research/94472534 nilshijlkema-180420140827
Helping you create microbiome modulators]]>
Helping you create microbiome modulators]]> Fri, 20 Apr 2018 14:08:27 GMT /slideshow/nizo-hotspot-for-microbiome-research/94472534 KateBarlow8@slideshare.net(KateBarlow8) NIZO: Hotspot for Microbiome Research KateBarlow8 Helping you create microbiome modulators <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/nilshijlkema-180420140827-thumbnail.jpg?width=120&height=120&fit=bounds" /> Helping you create microbiome modulators

NIZO: Hotspot for Microbiome Research from Kate Barlow

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0 Precision in Plant Immune Expression: Not Lost in Translation /slideshow/precision-in-plant-immune-expression-not-lost-in-translation/84454816 xinniandong-public-171219133345
Xinnian Dong, HHMI Investigator, Arts & Sciences Professor of Biology, Duke University • Expression of broad-spectrum disease resistance in plants often results in fitness penalty. • Plant immune responses are normally regulated at both transcriptional and translational levels. • Transcriptional and translational regulatory mechanisms of plant immune genes can be manipulated to engineer broad-spectrum resistance in crops. ]]>
Xinnian Dong, HHMI Investigator, Arts & Sciences Professor of Biology, Duke University • Expression of broad-spectrum disease resistance in plants often results in fitness penalty. • Plant immune responses are normally regulated at both transcriptional and translational levels. • Transcriptional and translational regulatory mechanisms of plant immune genes can be manipulated to engineer broad-spectrum resistance in crops. ]]> Tue, 19 Dec 2017 13:33:45 GMT /slideshow/precision-in-plant-immune-expression-not-lost-in-translation/84454816 KateBarlow8@slideshare.net(KateBarlow8) Precision in Plant Immune Expression: Not Lost in Translation KateBarlow8 Xinnian Dong, HHMI Investigator, Arts & Sciences Professor of Biology, Duke University • Expression of broad-spectrum disease resistance in plants often results in fitness penalty. • Plant immune responses are normally regulated at both transcriptional and translational levels. • Transcriptional and translational regulatory mechanisms of plant immune genes can be manipulated to engineer broad-spectrum resistance in crops. <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/xinniandong-public-171219133345-thumbnail.jpg?width=120&height=120&fit=bounds" /> Xinnian Dong, HHMI Investigator, Arts & Sciences Professor of Biology, Duke University • Expression of broad-spectrum disease resistance in plants often results in fitness penalty. • Plant immune responses are normally regulated at both transcriptional and translational levels. • Transcriptional and translational regulatory mechanisms of plant immune genes can be manipulated to engineer broad-spectrum resistance in crops.

Precision in Plant Immune Expression: Not Lost in Translation from Kate Barlow

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0 Beyond GWAS QTL Identification and Strategies to Increase Yield /slideshow/beyond-gwas-qtl-identification-and-strategies-to-increase-yield/84452811 mohsenmohammadi-public-171219125925
Mohsen Mohammadi, Assistant Professor of Wheat Breeding and Quantitative Genetics, Purdue University Genetic variation in yield and yield-related traits in an elite population of soft red winter wheat was studied using field-based low-throughput phenotyping and genotyping-by-sequencing markers. QTL conditioning grain yield, grain number per unit area, and kernel weight were identified. QTL result was mined to identify prospects of parents’ complementarity. Strategies for further improvements of grain yield of SRWW populations will be discussed. ]]>
Mohsen Mohammadi, Assistant Professor of Wheat Breeding and Quantitative Genetics, Purdue University Genetic variation in yield and yield-related traits in an elite population of soft red winter wheat was studied using field-based low-throughput phenotyping and genotyping-by-sequencing markers. QTL conditioning grain yield, grain number per unit area, and kernel weight were identified. QTL result was mined to identify prospects of parents’ complementarity. Strategies for further improvements of grain yield of SRWW populations will be discussed. ]]> Tue, 19 Dec 2017 12:59:25 GMT /slideshow/beyond-gwas-qtl-identification-and-strategies-to-increase-yield/84452811 KateBarlow8@slideshare.net(KateBarlow8) Beyond GWAS QTL Identification and Strategies to Increase Yield KateBarlow8 Mohsen Mohammadi, Assistant Professor of Wheat Breeding and Quantitative Genetics, Purdue University Genetic variation in yield and yield-related traits in an elite population of soft red winter wheat was studied using field-based low-throughput phenotyping and genotyping-by-sequencing markers. QTL conditioning grain yield, grain number per unit area, and kernel weight were identified. QTL result was mined to identify prospects of parents’ complementarity. Strategies for further improvements of grain yield of SRWW populations will be discussed. <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/mohsenmohammadi-public-171219125925-thumbnail.jpg?width=120&height=120&fit=bounds" /> Mohsen Mohammadi, Assistant Professor of Wheat Breeding and Quantitative Genetics, Purdue University Genetic variation in yield and yield-related traits in an elite population of soft red winter wheat was studied using field-based low-throughput phenotyping and genotyping-by-sequencing markers. QTL conditioning grain yield, grain number per unit area, and kernel weight were identified. QTL result was mined to identify prospects of parents’ complementarity. Strategies for further improvements of grain yield of SRWW populations will be discussed.

Beyond GWAS QTL Identification and Strategies to Increase Yield from Kate Barlow

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0 Information Technology Meets Synthetic Biology for Ag-Tech /slideshow/information-technology-meets-synthetic-biology-for-agtech/84452618 mikefero-public-171219125615
Until recently, modifying plants to improve traits for improved tolerance and resistance has been a slow and somewhat artisanal process. With advances in recombinant methods and DNA synthesis, systems can now be put in place that vastly accelerate development. In this talk, we will review the progress made and show how systems can be implemented that help automated plant modification R&D.]]>
Until recently, modifying plants to improve traits for improved tolerance and resistance has been a slow and somewhat artisanal process. With advances in recombinant methods and DNA synthesis, systems can now be put in place that vastly accelerate development. In this talk, we will review the progress made and show how systems can be implemented that help automated plant modification R&D.]]> Tue, 19 Dec 2017 12:56:15 GMT /slideshow/information-technology-meets-synthetic-biology-for-agtech/84452618 KateBarlow8@slideshare.net(KateBarlow8) Information Technology Meets Synthetic Biology for Ag-Tech KateBarlow8 Until recently, modifying plants to improve traits for improved tolerance and resistance has been a slow and somewhat artisanal process. With advances in recombinant methods and DNA synthesis, systems can now be put in place that vastly accelerate development. In this talk, we will review the progress made and show how systems can be implemented that help automated plant modification R&D. <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/mikefero-public-171219125615-thumbnail.jpg?width=120&height=120&fit=bounds" /> Until recently, modifying plants to improve traits for improved tolerance and resistance has been a slow and somewhat artisanal process. With advances in recombinant methods and DNA synthesis, systems can now be put in place that vastly accelerate development. In this talk, we will review the progress made and show how systems can be implemented that help automated plant modification R&D.

Information Technology Meets Synthetic Biology for Ag-Tech from Kate Barlow

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0 From Simple to Complex – Phytobiomes and the 2050 Vision for Agriculture /slideshow/from-simple-to-complex-phytobiomes-and-the-2050-vision-for-agriculture/84452031 kellyeeversole-public-171219124639
Kellye Eversole, Executive Director, Phytobiomes Alliance & the IWGSC Phytobiomes are plants in a biome (a specific geophysical environment - e.g., soil, weather -- and all macro- and micro-organisms – e.g., microbes, insects, animals associated with the specific site). Phytobiomes research is a holistic, systems-level approach that integrates many disciplines including geophysics, biology, breeding, agronomy, modeling, and engineering. By focusing on the phytobiome, we will be able to elucidate, quantify, model, predict, act, manipulate, prevent, and ultimately prescribe the cropping systems, methods, and management practices most suited for sustainable production on a particular farm, grassland, or forest. The International Alliance for Phytobiomes Research, an industry-academic consortium, was created in 2016 to bring this vision to fruition. The phytobiomes concept and the research and resource priorities of the Phytobiomes Alliance will be presented. ]]>
Kellye Eversole, Executive Director, Phytobiomes Alliance & the IWGSC Phytobiomes are plants in a biome (a specific geophysical environment - e.g., soil, weather -- and all macro- and micro-organisms – e.g., microbes, insects, animals associated with the specific site). Phytobiomes research is a holistic, systems-level approach that integrates many disciplines including geophysics, biology, breeding, agronomy, modeling, and engineering. By focusing on the phytobiome, we will be able to elucidate, quantify, model, predict, act, manipulate, prevent, and ultimately prescribe the cropping systems, methods, and management practices most suited for sustainable production on a particular farm, grassland, or forest. The International Alliance for Phytobiomes Research, an industry-academic consortium, was created in 2016 to bring this vision to fruition. The phytobiomes concept and the research and resource priorities of the Phytobiomes Alliance will be presented. ]]> Tue, 19 Dec 2017 12:46:39 GMT /slideshow/from-simple-to-complex-phytobiomes-and-the-2050-vision-for-agriculture/84452031 KateBarlow8@slideshare.net(KateBarlow8) From Simple to Complex – Phytobiomes and the 2050 Vision for Agriculture KateBarlow8 Kellye Eversole, Executive Director, Phytobiomes Alliance & the IWGSC Phytobiomes are plants in a biome (a specific geophysical environment - e.g., soil, weather -- and all macro- and micro-organisms – e.g., microbes, insects, animals associated with the specific site). Phytobiomes research is a holistic, systems-level approach that integrates many disciplines including geophysics, biology, breeding, agronomy, modeling, and engineering. By focusing on the phytobiome, we will be able to elucidate, quantify, model, predict, act, manipulate, prevent, and ultimately prescribe the cropping systems, methods, and management practices most suited for sustainable production on a particular farm, grassland, or forest. The International Alliance for Phytobiomes Research, an industry-academic consortium, was created in 2016 to bring this vision to fruition. The phytobiomes concept and the research and resource priorities of the Phytobiomes Alliance will be presented. <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/kellyeeversole-public-171219124639-thumbnail.jpg?width=120&height=120&fit=bounds" /> Kellye Eversole, Executive Director, Phytobiomes Alliance & the IWGSC Phytobiomes are plants in a biome (a specific geophysical environment - e.g., soil, weather -- and all macro- and micro-organisms – e.g., microbes, insects, animals associated with the specific site). Phytobiomes research is a holistic, systems-level approach that integrates many disciplines including geophysics, biology, breeding, agronomy, modeling, and engineering. By focusing on the phytobiome, we will be able to elucidate, quantify, model, predict, act, manipulate, prevent, and ultimately prescribe the cropping systems, methods, and management practices most suited for sustainable production on a particular farm, grassland, or forest. The International Alliance for Phytobiomes Research, an industry-academic consortium, was created in 2016 to bring this vision to fruition. The phytobiomes concept and the research and resource priorities of the Phytobiomes Alliance will be presented.

From Simple to Complex – Phytobiomes and the 2050 Vision for Agriculture from Kate Barlow

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0 A Universal Genetic Switch for Increasing Plant Yields, Stress Tolerance and Product Shelf Life /slideshow/a-universal-genetic-switch-for-increasing-plant-yields-stress-tolerance-and-product-shelf-life/84451314 jerryfeitelson-public-171219123629
Jerry Feitelson, Ph.D., Co-Founder & CEO, Agribody Technologies, Inc. ATI applies a proven solution to food-sourcing problems due to growing populations, extreme weather and decreasing farmland by significantly increasing crop yields. Our patented genetic modification (GM) or genome editing (GE) technology also delays plant senescence, while increasing resistance to diseases and sublethal stresses such as drought, heat, cold, salt, low nutrients and crowding in many key crop plants, including 2 years of field trial data in alfalfa. Many licenses and co-development projects are underway.]]>
Jerry Feitelson, Ph.D., Co-Founder & CEO, Agribody Technologies, Inc. ATI applies a proven solution to food-sourcing problems due to growing populations, extreme weather and decreasing farmland by significantly increasing crop yields. Our patented genetic modification (GM) or genome editing (GE) technology also delays plant senescence, while increasing resistance to diseases and sublethal stresses such as drought, heat, cold, salt, low nutrients and crowding in many key crop plants, including 2 years of field trial data in alfalfa. Many licenses and co-development projects are underway.]]> Tue, 19 Dec 2017 12:36:29 GMT /slideshow/a-universal-genetic-switch-for-increasing-plant-yields-stress-tolerance-and-product-shelf-life/84451314 KateBarlow8@slideshare.net(KateBarlow8) A Universal Genetic Switch for Increasing Plant Yields, Stress Tolerance and Product Shelf Life KateBarlow8 Jerry Feitelson, Ph.D., Co-Founder & CEO, Agribody Technologies, Inc. ATI applies a proven solution to food-sourcing problems due to growing populations, extreme weather and decreasing farmland by significantly increasing crop yields. Our patented genetic modification (GM) or genome editing (GE) technology also delays plant senescence, while increasing resistance to diseases and sublethal stresses such as drought, heat, cold, salt, low nutrients and crowding in many key crop plants, including 2 years of field trial data in alfalfa. Many licenses and co-development projects are underway. <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/jerryfeitelson-public-171219123629-thumbnail.jpg?width=120&height=120&fit=bounds" /> Jerry Feitelson, Ph.D., Co-Founder & CEO, Agribody Technologies, Inc. ATI applies a proven solution to food-sourcing problems due to growing populations, extreme weather and decreasing farmland by significantly increasing crop yields. Our patented genetic modification (GM) or genome editing (GE) technology also delays plant senescence, while increasing resistance to diseases and sublethal stresses such as drought, heat, cold, salt, low nutrients and crowding in many key crop plants, including 2 years of field trial data in alfalfa. Many licenses and co-development projects are underway.

A Universal Genetic Switch for Increasing Plant Yields, Stress Tolerance and Product Shelf Life from Kate Barlow

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0 Targeted Breeding Applications of CRISPR-Cas /KateBarlow8/targeted-breeding-applications-of-crisprcas doanechilcoat-public-171219123153
Doane Chilcoat, Director, Applied Technology Systems, DuPont Pioneer CRISPR-Cas as an advanced plant breeding tool is a more efficient way to improve plants and help farmers produce more and better food, with fewer resources. The superior properties of CRISPR-Cas allows DuPont Pioneer scientists to develop innovative and sustainable seed products for growers similar to those realized through conventional plant breeding, but with even greater efficiency, accuracy and quality. Pioneer is leading the application of this tool to develop customized agriculture solutions. In this talk, potential product targets of this promising technology will be discussed. Approaches to fostering social license and developing an open innovation model for CRISPR-Cas will also be reviewed.]]>
Doane Chilcoat, Director, Applied Technology Systems, DuPont Pioneer CRISPR-Cas as an advanced plant breeding tool is a more efficient way to improve plants and help farmers produce more and better food, with fewer resources. The superior properties of CRISPR-Cas allows DuPont Pioneer scientists to develop innovative and sustainable seed products for growers similar to those realized through conventional plant breeding, but with even greater efficiency, accuracy and quality. Pioneer is leading the application of this tool to develop customized agriculture solutions. In this talk, potential product targets of this promising technology will be discussed. Approaches to fostering social license and developing an open innovation model for CRISPR-Cas will also be reviewed.]]> Tue, 19 Dec 2017 12:31:53 GMT /KateBarlow8/targeted-breeding-applications-of-crisprcas KateBarlow8@slideshare.net(KateBarlow8) Targeted Breeding Applications of CRISPR-Cas KateBarlow8 Doane Chilcoat, Director, Applied Technology Systems, DuPont Pioneer CRISPR-Cas as an advanced plant breeding tool is a more efficient way to improve plants and help farmers produce more and better food, with fewer resources. The superior properties of CRISPR-Cas allows DuPont Pioneer scientists to develop innovative and sustainable seed products for growers similar to those realized through conventional plant breeding, but with even greater efficiency, accuracy and quality. Pioneer is leading the application of this tool to develop customized agriculture solutions. In this talk, potential product targets of this promising technology will be discussed. Approaches to fostering social license and developing an open innovation model for CRISPR-Cas will also be reviewed. <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/doanechilcoat-public-171219123153-thumbnail.jpg?width=120&height=120&fit=bounds" /> Doane Chilcoat, Director, Applied Technology Systems, DuPont Pioneer CRISPR-Cas as an advanced plant breeding tool is a more efficient way to improve plants and help farmers produce more and better food, with fewer resources. The superior properties of CRISPR-Cas allows DuPont Pioneer scientists to develop innovative and sustainable seed products for growers similar to those realized through conventional plant breeding, but with even greater efficiency, accuracy and quality. Pioneer is leading the application of this tool to develop customized agriculture solutions. In this talk, potential product targets of this promising technology will be discussed. Approaches to fostering social license and developing an open innovation model for CRISPR-Cas will also be reviewed.

Targeted Breeding Applications of CRISPR-Cas from Kate Barlow

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0 Informatics in Context: Managing Sample-to-Answer Multi-Omics Workflows /slideshow/informatics-in-context-managing-sampletoanswer-multiomics-workflows/84450407 chrismueller-public-171219122117
Christopher Mueller, PhD, President & CTO, Lab7 Systems, Inc. Using a case study from Lab7’s work at the USDA Meat Animal Research Center, we will illustrate how understanding the people, process, and technologies used in a data-intensive mutli-omics laboratory environment is essential to developing comprehensive solutions. Questions that impact the development of a solution include: Who is doing the work? Who is requesting the work? Who needs the results How do samples move through workflows? What types of measurements are needed? What types of data is collected? What analysis is required? What options are available, what options make sense given the people and process? How do the pieces fit together to form a cohesive solution? ]]>
Christopher Mueller, PhD, President & CTO, Lab7 Systems, Inc. Using a case study from Lab7’s work at the USDA Meat Animal Research Center, we will illustrate how understanding the people, process, and technologies used in a data-intensive mutli-omics laboratory environment is essential to developing comprehensive solutions. Questions that impact the development of a solution include: Who is doing the work? Who is requesting the work? Who needs the results How do samples move through workflows? What types of measurements are needed? What types of data is collected? What analysis is required? What options are available, what options make sense given the people and process? How do the pieces fit together to form a cohesive solution? ]]> Tue, 19 Dec 2017 12:21:17 GMT /slideshow/informatics-in-context-managing-sampletoanswer-multiomics-workflows/84450407 KateBarlow8@slideshare.net(KateBarlow8) Informatics in Context: Managing Sample-to-Answer Multi-Omics Workflows KateBarlow8 Christopher Mueller, PhD, President & CTO, Lab7 Systems, Inc. Using a case study from Lab7’s work at the USDA Meat Animal Research Center, we will illustrate how understanding the people, process, and technologies used in a data-intensive mutli-omics laboratory environment is essential to developing comprehensive solutions. Questions that impact the development of a solution include: Who is doing the work? Who is requesting the work? Who needs the results How do samples move through workflows? What types of measurements are needed? What types of data is collected? What analysis is required? What options are available, what options make sense given the people and process? How do the pieces fit together to form a cohesive solution? <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/chrismueller-public-171219122117-thumbnail.jpg?width=120&height=120&fit=bounds" /> Christopher Mueller, PhD, President & CTO, Lab7 Systems, Inc. Using a case study from Lab7’s work at the USDA Meat Animal Research Center, we will illustrate how understanding the people, process, and technologies used in a data-intensive mutli-omics laboratory environment is essential to developing comprehensive solutions. Questions that impact the development of a solution include: Who is doing the work? Who is requesting the work? Who needs the results How do samples move through workflows? What types of measurements are needed? What types of data is collected? What analysis is required? What options are available, what options make sense given the people and process? How do the pieces fit together to form a cohesive solution?

Informatics in Context: Managing Sample-to-Answer Multi-Omics Workflows from Kate Barlow

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0 Prospects for Digital PCR in Absolute Quantification of DNA and RNA /slideshow/prospects-for-digital-pcr-in-absolute-quantification-of-dna-and-rna/84449616 warddespiegelaere-171219120738
Ward De Spiegelaere, Assistant Professor, Ghent University, Belgium • Using examples of virology I will talk about the possibilities and pitfalls of current digital PCR technology for absolute quantification of DNA and RNA • I will expand on a tool we developed for data driven threshold setting in digital PCR • I will discuss a method for normalization of RNA data in digital PCR ]]>
Ward De Spiegelaere, Assistant Professor, Ghent University, Belgium • Using examples of virology I will talk about the possibilities and pitfalls of current digital PCR technology for absolute quantification of DNA and RNA • I will expand on a tool we developed for data driven threshold setting in digital PCR • I will discuss a method for normalization of RNA data in digital PCR ]]> Tue, 19 Dec 2017 12:07:38 GMT /slideshow/prospects-for-digital-pcr-in-absolute-quantification-of-dna-and-rna/84449616 KateBarlow8@slideshare.net(KateBarlow8) Prospects for Digital PCR in Absolute Quantification of DNA and RNA KateBarlow8 Ward De Spiegelaere, Assistant Professor, Ghent University, Belgium • Using examples of virology I will talk about the possibilities and pitfalls of current digital PCR technology for absolute quantification of DNA and RNA • I will expand on a tool we developed for data driven threshold setting in digital PCR • I will discuss a method for normalization of RNA data in digital PCR <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/warddespiegelaere-171219120738-thumbnail.jpg?width=120&height=120&fit=bounds" /> Ward De Spiegelaere, Assistant Professor, Ghent University, Belgium • Using examples of virology I will talk about the possibilities and pitfalls of current digital PCR technology for absolute quantification of DNA and RNA • I will expand on a tool we developed for data driven threshold setting in digital PCR • I will discuss a method for normalization of RNA data in digital PCR

Prospects for Digital PCR in Absolute Quantification of DNA and RNA from Kate Barlow

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0 Challenges and Opportunities for Digital PCR in the CLIA Laboratory of the Moffitt Cancer Experience /slideshow/challenges-and-opportunities-for-digital-pcr-in-the-clia-laboratory-of-the-moffitt-cancer-experience/84449291 tonymagliocco-171219120212
Anthony Magliocco, Chair of Anatomical Pathology, Moffitt Cancer Center, USA The Moffit Cancer Center is one of the largest NCI designated comprehensive free-standing cancer centers in the USA. The center has developed one of the most advanced personalized cancer medicine treatment programs in the world. This program is supported by a comprehensive and advanced CLIA molecular diagnostics. Digital PCR assays are currently being developed for several clinical applications including TKI resistance monitoring in patients with advanced lung cancer. The challenges and opportunities in deploying digital PCR into clinical practice will be discussed. ]]>
Anthony Magliocco, Chair of Anatomical Pathology, Moffitt Cancer Center, USA The Moffit Cancer Center is one of the largest NCI designated comprehensive free-standing cancer centers in the USA. The center has developed one of the most advanced personalized cancer medicine treatment programs in the world. This program is supported by a comprehensive and advanced CLIA molecular diagnostics. Digital PCR assays are currently being developed for several clinical applications including TKI resistance monitoring in patients with advanced lung cancer. The challenges and opportunities in deploying digital PCR into clinical practice will be discussed. ]]> Tue, 19 Dec 2017 12:02:12 GMT /slideshow/challenges-and-opportunities-for-digital-pcr-in-the-clia-laboratory-of-the-moffitt-cancer-experience/84449291 KateBarlow8@slideshare.net(KateBarlow8) Challenges and Opportunities for Digital PCR in the CLIA Laboratory of the Moffitt Cancer Experience KateBarlow8 Anthony Magliocco, Chair of Anatomical Pathology, Moffitt Cancer Center, USA The Moffit Cancer Center is one of the largest NCI designated comprehensive free-standing cancer centers in the USA. The center has developed one of the most advanced personalized cancer medicine treatment programs in the world. This program is supported by a comprehensive and advanced CLIA molecular diagnostics. Digital PCR assays are currently being developed for several clinical applications including TKI resistance monitoring in patients with advanced lung cancer. The challenges and opportunities in deploying digital PCR into clinical practice will be discussed. <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/tonymagliocco-171219120212-thumbnail.jpg?width=120&height=120&fit=bounds" /> Anthony Magliocco, Chair of Anatomical Pathology, Moffitt Cancer Center, USA The Moffit Cancer Center is one of the largest NCI designated comprehensive free-standing cancer centers in the USA. The center has developed one of the most advanced personalized cancer medicine treatment programs in the world. This program is supported by a comprehensive and advanced CLIA molecular diagnostics. Digital PCR assays are currently being developed for several clinical applications including TKI resistance monitoring in patients with advanced lung cancer. The challenges and opportunities in deploying digital PCR into clinical practice will be discussed.

Challenges and Opportunities for Digital PCR in the CLIA Laboratory of the Moffitt Cancer Experience from Kate Barlow

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0 Circulating Tumor DNA Detection from Heparinized Plasma Samples by Droplet Digital PCR /slideshow/circulating-tumor-dna-detection-from-heparinized-plasma-samples-by-droplet-digital-pcr/84448104 nasrinsarafan-vasseur-171219114252
Nasrin Sarafan-Vasseur, Liquid Biopsy Scientific Leader, Research Team on Oncology (IRON), INSERM and University of Rouen, France Heparin is often used as plasma anticoagulant for tumor marker analysis but corresponds also to an inhibitory of PCR not enabling circulating tumor DNA (ctDNA) detection, which has been highlighted as a potential “liquid biopsy”. We evaluated the impact of heparinase addition on heparinized plasma samples to allow ctDNA analysis. Circulating ESR1 and KRAS mutations were quantified by digital PCR, in plasma collected in heparinized tubes (n=194) from hormone receptor-positive metastatic breast cancer (HR+MBC) and pancreatic adenocarcinoma (PA) patients. We improved significantly PCR efficiency in 91/144 HR+MBC and 26/50 PA plasma samples, enabling ctDNA detection in 22/91 and 13/26 patients. This new processing did not alter quantitatively and qualitatively ctDNA detection and could make the samples from heparinized blood-derived collections suitable for ctDNA analysis.]]>
Nasrin Sarafan-Vasseur, Liquid Biopsy Scientific Leader, Research Team on Oncology (IRON), INSERM and University of Rouen, France Heparin is often used as plasma anticoagulant for tumor marker analysis but corresponds also to an inhibitory of PCR not enabling circulating tumor DNA (ctDNA) detection, which has been highlighted as a potential “liquid biopsy”. We evaluated the impact of heparinase addition on heparinized plasma samples to allow ctDNA analysis. Circulating ESR1 and KRAS mutations were quantified by digital PCR, in plasma collected in heparinized tubes (n=194) from hormone receptor-positive metastatic breast cancer (HR+MBC) and pancreatic adenocarcinoma (PA) patients. We improved significantly PCR efficiency in 91/144 HR+MBC and 26/50 PA plasma samples, enabling ctDNA detection in 22/91 and 13/26 patients. This new processing did not alter quantitatively and qualitatively ctDNA detection and could make the samples from heparinized blood-derived collections suitable for ctDNA analysis.]]> Tue, 19 Dec 2017 11:42:52 GMT /slideshow/circulating-tumor-dna-detection-from-heparinized-plasma-samples-by-droplet-digital-pcr/84448104 KateBarlow8@slideshare.net(KateBarlow8) Circulating Tumor DNA Detection from Heparinized Plasma Samples by Droplet Digital PCR KateBarlow8 Nasrin Sarafan-Vasseur, Liquid Biopsy Scientific Leader, Research Team on Oncology (IRON), INSERM and University of Rouen, France Heparin is often used as plasma anticoagulant for tumor marker analysis but corresponds also to an inhibitory of PCR not enabling circulating tumor DNA (ctDNA) detection, which has been highlighted as a potential “liquid biopsy”. We evaluated the impact of heparinase addition on heparinized plasma samples to allow ctDNA analysis. Circulating ESR1 and KRAS mutations were quantified by digital PCR, in plasma collected in heparinized tubes (n=194) from hormone receptor-positive metastatic breast cancer (HR+MBC) and pancreatic adenocarcinoma (PA) patients. We improved significantly PCR efficiency in 91/144 HR+MBC and 26/50 PA plasma samples, enabling ctDNA detection in 22/91 and 13/26 patients. This new processing did not alter quantitatively and qualitatively ctDNA detection and could make the samples from heparinized blood-derived collections suitable for ctDNA analysis. <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/nasrinsarafan-vasseur-171219114252-thumbnail.jpg?width=120&height=120&fit=bounds" /> Nasrin Sarafan-Vasseur, Liquid Biopsy Scientific Leader, Research Team on Oncology (IRON), INSERM and University of Rouen, France Heparin is often used as plasma anticoagulant for tumor marker analysis but corresponds also to an inhibitory of PCR not enabling circulating tumor DNA (ctDNA) detection, which has been highlighted as a potential “liquid biopsy”. We evaluated the impact of heparinase addition on heparinized plasma samples to allow ctDNA analysis. Circulating ESR1 and KRAS mutations were quantified by digital PCR, in plasma collected in heparinized tubes (n=194) from hormone receptor-positive metastatic breast cancer (HR+MBC) and pancreatic adenocarcinoma (PA) patients. We improved significantly PCR efficiency in 91/144 HR+MBC and 26/50 PA plasma samples, enabling ctDNA detection in 22/91 and 13/26 patients. This new processing did not alter quantitatively and qualitatively ctDNA detection and could make the samples from heparinized blood-derived collections suitable for ctDNA analysis.

Circulating Tumor DNA Detection from Heparinized Plasma Samples by Droplet Digital PCR from Kate Barlow

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0 Two-Tailed PCR - New Ultrasensitive and Ultraspecific Technique for the Quantification of MicroRNAs /slideshow/twotailed-pcr-new-ultrasensitive-and-ultraspecific-technique-for-the-quantification-of-micrornas/84447520 mikaelkubista-171219113258
Mikael Kubista, Department of Biotechnology, CAS and TATAA Biocenter We present a highly specific, sensitive and cost-effective system to quantify miRNA expression based on novel chemistry called Two-tailed RT-qPCR. It takes advantage of target-specific primers for reverse transcription composed of two hemiprobes complementary to two different parts of the targeted miRNA, connected by a hairpin structure. The introduction of a second probe ensures high sensitivity and enables discrimination of highly homologous miRNAs irrespectively of the position of the mismatched nucleotide. Two-tailed RT-qPCR has a dynamic range of 7 logs and a sensitivity sufficient to detect less than ten target miRNA molecules. The reverse transcription step can be multiplexed and it allows for rapid testing with a total analysis time of less than 2.5 hours.]]>
Mikael Kubista, Department of Biotechnology, CAS and TATAA Biocenter We present a highly specific, sensitive and cost-effective system to quantify miRNA expression based on novel chemistry called Two-tailed RT-qPCR. It takes advantage of target-specific primers for reverse transcription composed of two hemiprobes complementary to two different parts of the targeted miRNA, connected by a hairpin structure. The introduction of a second probe ensures high sensitivity and enables discrimination of highly homologous miRNAs irrespectively of the position of the mismatched nucleotide. Two-tailed RT-qPCR has a dynamic range of 7 logs and a sensitivity sufficient to detect less than ten target miRNA molecules. The reverse transcription step can be multiplexed and it allows for rapid testing with a total analysis time of less than 2.5 hours.]]> Tue, 19 Dec 2017 11:32:58 GMT /slideshow/twotailed-pcr-new-ultrasensitive-and-ultraspecific-technique-for-the-quantification-of-micrornas/84447520 KateBarlow8@slideshare.net(KateBarlow8) Two-Tailed PCR - New Ultrasensitive and Ultraspecific Technique for the Quantification of MicroRNAs KateBarlow8 Mikael Kubista, Department of Biotechnology, CAS and TATAA Biocenter We present a highly specific, sensitive and cost-effective system to quantify miRNA expression based on novel chemistry called Two-tailed RT-qPCR. It takes advantage of target-specific primers for reverse transcription composed of two hemiprobes complementary to two different parts of the targeted miRNA, connected by a hairpin structure. The introduction of a second probe ensures high sensitivity and enables discrimination of highly homologous miRNAs irrespectively of the position of the mismatched nucleotide. Two-tailed RT-qPCR has a dynamic range of 7 logs and a sensitivity sufficient to detect less than ten target miRNA molecules. The reverse transcription step can be multiplexed and it allows for rapid testing with a total analysis time of less than 2.5 hours. <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/mikaelkubista-171219113258-thumbnail.jpg?width=120&height=120&fit=bounds" /> Mikael Kubista, Department of Biotechnology, CAS and TATAA Biocenter We present a highly specific, sensitive and cost-effective system to quantify miRNA expression based on novel chemistry called Two-tailed RT-qPCR. It takes advantage of target-specific primers for reverse transcription composed of two hemiprobes complementary to two different parts of the targeted miRNA, connected by a hairpin structure. The introduction of a second probe ensures high sensitivity and enables discrimination of highly homologous miRNAs irrespectively of the position of the mismatched nucleotide. Two-tailed RT-qPCR has a dynamic range of 7 logs and a sensitivity sufficient to detect less than ten target miRNA molecules. The reverse transcription step can be multiplexed and it allows for rapid testing with a total analysis time of less than 2.5 hours.

Two-Tailed PCR - New Ultrasensitive and Ultraspecific Technique for the Quantification of MicroRNAs from Kate Barlow

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0 Admix™: Custom lyophilised RT-PCR reagents for point-of-use applications /slideshow/admix-custom-lyophilised-rtpcr-reagents-for-pointofuse-applications/84446253 martinlee-171219111435
Martin A. Lee, CEO Fluorogenics Limited Fluorogenics is an ISO 13485 certified provider of lyophilized molecular reagents. Fluorogenics provides its custom product service “Admix™” to deliver ambient stable products using enzymes from almost any supplier. These products may include custom oligonucleotides and other reagents, available in custom packing, for a variety of analysers and workflows. In this presentation we describe the opportunities, technology and product development processes. The development process is exemplified for a commercially available point-of-use hand-held (sample-to-result) PCR system. This system can deliver rapid testing facilitated by an innovative developer’s kit to accelerate the route to market for your assays.]]>
Martin A. Lee, CEO Fluorogenics Limited Fluorogenics is an ISO 13485 certified provider of lyophilized molecular reagents. Fluorogenics provides its custom product service “Admix™” to deliver ambient stable products using enzymes from almost any supplier. These products may include custom oligonucleotides and other reagents, available in custom packing, for a variety of analysers and workflows. In this presentation we describe the opportunities, technology and product development processes. The development process is exemplified for a commercially available point-of-use hand-held (sample-to-result) PCR system. This system can deliver rapid testing facilitated by an innovative developer’s kit to accelerate the route to market for your assays.]]> Tue, 19 Dec 2017 11:14:35 GMT /slideshow/admix-custom-lyophilised-rtpcr-reagents-for-pointofuse-applications/84446253 KateBarlow8@slideshare.net(KateBarlow8) Admix™: Custom lyophilised RT-PCR reagents for point-of-use applications KateBarlow8 Martin A. Lee, CEO Fluorogenics Limited Fluorogenics is an ISO 13485 certified provider of lyophilized molecular reagents. Fluorogenics provides its custom product service “Admix™” to deliver ambient stable products using enzymes from almost any supplier. These products may include custom oligonucleotides and other reagents, available in custom packing, for a variety of analysers and workflows. In this presentation we describe the opportunities, technology and product development processes. The development process is exemplified for a commercially available point-of-use hand-held (sample-to-result) PCR system. This system can deliver rapid testing facilitated by an innovative developer’s kit to accelerate the route to market for your assays. <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/martinlee-171219111435-thumbnail.jpg?width=120&height=120&fit=bounds" /> Martin A. Lee, CEO Fluorogenics Limited Fluorogenics is an ISO 13485 certified provider of lyophilized molecular reagents. Fluorogenics provides its custom product service “Admix™” to deliver ambient stable products using enzymes from almost any supplier. These products may include custom oligonucleotides and other reagents, available in custom packing, for a variety of analysers and workflows. In this presentation we describe the opportunities, technology and product development processes. The development process is exemplified for a commercially available point-of-use hand-held (sample-to-result) PCR system. This system can deliver rapid testing facilitated by an innovative developer’s kit to accelerate the route to market for your assays.

Admix™: Custom lyophilised RT-PCR reagents for point-of-use applications from Kate Barlow

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0 Explaining Biocide Tolerance of Gram Negative Bacteria /slideshow/explaining-biocide-tolerance-of-gram-negative-bacteria/84445960 lucybock-171219110952
Working on multiple organisms and constantly changing gene-targets requires use of an easily optimisable and cheap qPCR method, which is why we use SyBr Green qPCR. We have investigated chlorhexidine resistance in Klebsiella pneumoniae and are about to publish on biocide resistance in Acinetobacter baumannii and Pseudomonas aeruginosa. I will explain our approach and our optimisation and robustness strategies, as well as an overview of the hypotheses we developed and confirmed using our qPCR approach. Lucy Bock, Senior Scientist/Project Team Leader, Technology Development Group, Public Health England, UK]]>
Working on multiple organisms and constantly changing gene-targets requires use of an easily optimisable and cheap qPCR method, which is why we use SyBr Green qPCR. We have investigated chlorhexidine resistance in Klebsiella pneumoniae and are about to publish on biocide resistance in Acinetobacter baumannii and Pseudomonas aeruginosa. I will explain our approach and our optimisation and robustness strategies, as well as an overview of the hypotheses we developed and confirmed using our qPCR approach. Lucy Bock, Senior Scientist/Project Team Leader, Technology Development Group, Public Health England, UK]]> Tue, 19 Dec 2017 11:09:52 GMT /slideshow/explaining-biocide-tolerance-of-gram-negative-bacteria/84445960 KateBarlow8@slideshare.net(KateBarlow8) Explaining Biocide Tolerance of Gram Negative Bacteria KateBarlow8 Working on multiple organisms and constantly changing gene-targets requires use of an easily optimisable and cheap qPCR method, which is why we use SyBr Green qPCR. We have investigated chlorhexidine resistance in Klebsiella pneumoniae and are about to publish on biocide resistance in Acinetobacter baumannii and Pseudomonas aeruginosa. I will explain our approach and our optimisation and robustness strategies, as well as an overview of the hypotheses we developed and confirmed using our qPCR approach. Lucy Bock, Senior Scientist/Project Team Leader, Technology Development Group, Public Health England, UK <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/lucybock-171219110952-thumbnail.jpg?width=120&height=120&fit=bounds" /> Working on multiple organisms and constantly changing gene-targets requires use of an easily optimisable and cheap qPCR method, which is why we use SyBr Green qPCR. We have investigated chlorhexidine resistance in Klebsiella pneumoniae and are about to publish on biocide resistance in Acinetobacter baumannii and Pseudomonas aeruginosa. I will explain our approach and our optimisation and robustness strategies, as well as an overview of the hypotheses we developed and confirmed using our qPCR approach. Lucy Bock, Senior Scientist/Project Team Leader, Technology Development Group, Public Health England, UK

Explaining Biocide Tolerance of Gram Negative Bacteria from Kate Barlow

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0 Optimized Design of Broadly Detecting qPCR Primers and Probes Using a Conservation and Hybridization Prediction Algorithm /slideshow/optimized-design-of-broadly-detecting-qpcr-primers-and-probes-using-a-conservation-and-hybridization-prediction-algorithm/84445713 jonasblomberg-171219110614
Jonas Blomberg, Emeritus Professor of Clinical Virology, Uppsala University, Sweden Design of broadly detecting qPCRs is a challenge. It requires both an accurate analysis of sequence conservation and of how primers and probes interact with their targets. Hybridization prediction has gone from a simple reliance on GC content to more precise algorithms. Nearest neighbour analysis relies on short distance prediction. We developed an algorithm for longer nucleotide distances, NucZip. It allows design of long primers and probes, using wobble positions and inosine. A computer program which embodies both conservation analysis and hybridization prediction, ConSort, was developed. We used it for development of qPCRs for Orthomyxo-, Corona-, Entero-, Retro- and Noroviruses. Different aspects of the design process will be discussed.]]>
Jonas Blomberg, Emeritus Professor of Clinical Virology, Uppsala University, Sweden Design of broadly detecting qPCRs is a challenge. It requires both an accurate analysis of sequence conservation and of how primers and probes interact with their targets. Hybridization prediction has gone from a simple reliance on GC content to more precise algorithms. Nearest neighbour analysis relies on short distance prediction. We developed an algorithm for longer nucleotide distances, NucZip. It allows design of long primers and probes, using wobble positions and inosine. A computer program which embodies both conservation analysis and hybridization prediction, ConSort, was developed. We used it for development of qPCRs for Orthomyxo-, Corona-, Entero-, Retro- and Noroviruses. Different aspects of the design process will be discussed.]]> Tue, 19 Dec 2017 11:06:14 GMT /slideshow/optimized-design-of-broadly-detecting-qpcr-primers-and-probes-using-a-conservation-and-hybridization-prediction-algorithm/84445713 KateBarlow8@slideshare.net(KateBarlow8) Optimized Design of Broadly Detecting qPCR Primers and Probes Using a Conservation and Hybridization Prediction Algorithm KateBarlow8 Jonas Blomberg, Emeritus Professor of Clinical Virology, Uppsala University, Sweden Design of broadly detecting qPCRs is a challenge. It requires both an accurate analysis of sequence conservation and of how primers and probes interact with their targets. Hybridization prediction has gone from a simple reliance on GC content to more precise algorithms. Nearest neighbour analysis relies on short distance prediction. We developed an algorithm for longer nucleotide distances, NucZip. It allows design of long primers and probes, using wobble positions and inosine. A computer program which embodies both conservation analysis and hybridization prediction, ConSort, was developed. We used it for development of qPCRs for Orthomyxo-, Corona-, Entero-, Retro- and Noroviruses. Different aspects of the design process will be discussed. <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/jonasblomberg-171219110614-thumbnail.jpg?width=120&height=120&fit=bounds" /> Jonas Blomberg, Emeritus Professor of Clinical Virology, Uppsala University, Sweden Design of broadly detecting qPCRs is a challenge. It requires both an accurate analysis of sequence conservation and of how primers and probes interact with their targets. Hybridization prediction has gone from a simple reliance on GC content to more precise algorithms. Nearest neighbour analysis relies on short distance prediction. We developed an algorithm for longer nucleotide distances, NucZip. It allows design of long primers and probes, using wobble positions and inosine. A computer program which embodies both conservation analysis and hybridization prediction, ConSort, was developed. We used it for development of qPCRs for Orthomyxo-, Corona-, Entero-, Retro- and Noroviruses. Different aspects of the design process will be discussed.

Optimized Design of Broadly Detecting qPCR Primers and Probes Using a Conservation and Hybridization Prediction Algorithm from Kate Barlow

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0 MelTree: A Novel Workflow for the Automated Identification of a Large Number of Variants through HRM /slideshow/meltree-a-novel-workflow-for-the-automated-identification-of-a-large-number-of-variants-through-hrm/84445434 jean-christopheavarre-171219110138
Jean-Christophe Avarre, Head of the High Throughput qPCR Platform and Research Group Leader, University of Montpellier, France Nucleic acid characterization by High Resolution Melting (HRM) is a simple, flexible, low-cost and powerful technique for identifying sequence variations, making it attractive for a broad range of diagnostic and research applications. However, current procedures for analyzing HRM curves are not suited for large data sets. For this reason, we have developed an innovative method that enables the simultaneous discrimination of a large number of variants from their HRM profile. This method relies on the establishment of a melting profile library and offers a fully automated analysis workflow. Using this workflow, it was possible to discriminate 19 nontuberculous mycobacterial species from their HRM profile. It was also possible to design a multiplex diagnostic tool targeting five pathogens responsible for abortive diseases in cattle. ]]>
Jean-Christophe Avarre, Head of the High Throughput qPCR Platform and Research Group Leader, University of Montpellier, France Nucleic acid characterization by High Resolution Melting (HRM) is a simple, flexible, low-cost and powerful technique for identifying sequence variations, making it attractive for a broad range of diagnostic and research applications. However, current procedures for analyzing HRM curves are not suited for large data sets. For this reason, we have developed an innovative method that enables the simultaneous discrimination of a large number of variants from their HRM profile. This method relies on the establishment of a melting profile library and offers a fully automated analysis workflow. Using this workflow, it was possible to discriminate 19 nontuberculous mycobacterial species from their HRM profile. It was also possible to design a multiplex diagnostic tool targeting five pathogens responsible for abortive diseases in cattle. ]]> Tue, 19 Dec 2017 11:01:38 GMT /slideshow/meltree-a-novel-workflow-for-the-automated-identification-of-a-large-number-of-variants-through-hrm/84445434 KateBarlow8@slideshare.net(KateBarlow8) MelTree: A Novel Workflow for the Automated Identification of a Large Number of Variants through HRM KateBarlow8 Jean-Christophe Avarre, Head of the High Throughput qPCR Platform and Research Group Leader, University of Montpellier, France Nucleic acid characterization by High Resolution Melting (HRM) is a simple, flexible, low-cost and powerful technique for identifying sequence variations, making it attractive for a broad range of diagnostic and research applications. However, current procedures for analyzing HRM curves are not suited for large data sets. For this reason, we have developed an innovative method that enables the simultaneous discrimination of a large number of variants from their HRM profile. This method relies on the establishment of a melting profile library and offers a fully automated analysis workflow. Using this workflow, it was possible to discriminate 19 nontuberculous mycobacterial species from their HRM profile. It was also possible to design a multiplex diagnostic tool targeting five pathogens responsible for abortive diseases in cattle. <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/jean-christopheavarre-171219110138-thumbnail.jpg?width=120&height=120&fit=bounds" /> Jean-Christophe Avarre, Head of the High Throughput qPCR Platform and Research Group Leader, University of Montpellier, France Nucleic acid characterization by High Resolution Melting (HRM) is a simple, flexible, low-cost and powerful technique for identifying sequence variations, making it attractive for a broad range of diagnostic and research applications. However, current procedures for analyzing HRM curves are not suited for large data sets. For this reason, we have developed an innovative method that enables the simultaneous discrimination of a large number of variants from their HRM profile. This method relies on the establishment of a melting profile library and offers a fully automated analysis workflow. Using this workflow, it was possible to discriminate 19 nontuberculous mycobacterial species from their HRM profile. It was also possible to design a multiplex diagnostic tool targeting five pathogens responsible for abortive diseases in cattle.

MelTree: A Novel Workflow for the Automated Identification of a Large Number of Variants through HRM from Kate Barlow

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0 Discordance Between Replicate qPCR Reactions /slideshow/discordance-between-replicate-qpcr-reactions/84444957 janruijter-171219105321
In the analysis of qPCR data, the Cq values of replicate reactions is required to differ no more than 0.5 cycles. However, the sampling error that occurs when pipetting a low number of target molecules into the PCR plate is governed by the Poisson distribution. For each Cq and PCR efficiency value we calculated this unavoidable range of Cq values. This range increases with higher Cq values (less target). A decision to exclude replicate reactions based on this expected sampling error avoids bias, prevents unwanted loss of data and increases the statistical power. For a dataset with replicate qPCR measurements of 12 miRNA targets in 834 patients (20,016 reactions) the fraction of excluded measurements decreased from 39% to 7%.In the analysis of qPCR data, the Cq values of replicate reactions is required to differ no more than 0.5 cycles. However, the sampling error that occurs when pipetting a low number of target molecules into the PCR plate is governed by the Poisson distribution. For each Cq and PCR efficiency value we calculated this unavoidable range of Cq values. This range increases with higher Cq values (less target). A decision to exclude replicate reactions based on this expected sampling error avoids bias, prevents unwanted loss of data and increases the statistical power. For a dataset with replicate qPCR measurements of 12 miRNA targets in 834 patients (20,016 reactions) the fraction of excluded measurements decreased from 39% to 7%. Jan Ruijter, Assistant Professor, University of Amsterdam, The Netherlands]]>
In the analysis of qPCR data, the Cq values of replicate reactions is required to differ no more than 0.5 cycles. However, the sampling error that occurs when pipetting a low number of target molecules into the PCR plate is governed by the Poisson distribution. For each Cq and PCR efficiency value we calculated this unavoidable range of Cq values. This range increases with higher Cq values (less target). A decision to exclude replicate reactions based on this expected sampling error avoids bias, prevents unwanted loss of data and increases the statistical power. For a dataset with replicate qPCR measurements of 12 miRNA targets in 834 patients (20,016 reactions) the fraction of excluded measurements decreased from 39% to 7%.In the analysis of qPCR data, the Cq values of replicate reactions is required to differ no more than 0.5 cycles. However, the sampling error that occurs when pipetting a low number of target molecules into the PCR plate is governed by the Poisson distribution. For each Cq and PCR efficiency value we calculated this unavoidable range of Cq values. This range increases with higher Cq values (less target). A decision to exclude replicate reactions based on this expected sampling error avoids bias, prevents unwanted loss of data and increases the statistical power. For a dataset with replicate qPCR measurements of 12 miRNA targets in 834 patients (20,016 reactions) the fraction of excluded measurements decreased from 39% to 7%. Jan Ruijter, Assistant Professor, University of Amsterdam, The Netherlands]]> Tue, 19 Dec 2017 10:53:21 GMT /slideshow/discordance-between-replicate-qpcr-reactions/84444957 KateBarlow8@slideshare.net(KateBarlow8) Discordance Between Replicate qPCR Reactions KateBarlow8 In the analysis of qPCR data, the Cq values of replicate reactions is required to differ no more than 0.5 cycles. However, the sampling error that occurs when pipetting a low number of target molecules into the PCR plate is governed by the Poisson distribution. For each Cq and PCR efficiency value we calculated this unavoidable range of Cq values. This range increases with higher Cq values (less target). A decision to exclude replicate reactions based on this expected sampling error avoids bias, prevents unwanted loss of data and increases the statistical power. For a dataset with replicate qPCR measurements of 12 miRNA targets in 834 patients (20,016 reactions) the fraction of excluded measurements decreased from 39% to 7%.In the analysis of qPCR data, the Cq values of replicate reactions is required to differ no more than 0.5 cycles. However, the sampling error that occurs when pipetting a low number of target molecules into the PCR plate is governed by the Poisson distribution. For each Cq and PCR efficiency value we calculated this unavoidable range of Cq values. This range increases with higher Cq values (less target). A decision to exclude replicate reactions based on this expected sampling error avoids bias, prevents unwanted loss of data and increases the statistical power. For a dataset with replicate qPCR measurements of 12 miRNA targets in 834 patients (20,016 reactions) the fraction of excluded measurements decreased from 39% to 7%. Jan Ruijter, Assistant Professor, University of Amsterdam, The Netherlands <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/janruijter-171219105321-thumbnail.jpg?width=120&height=120&fit=bounds" /> In the analysis of qPCR data, the Cq values of replicate reactions is required to differ no more than 0.5 cycles. However, the sampling error that occurs when pipetting a low number of target molecules into the PCR plate is governed by the Poisson distribution. For each Cq and PCR efficiency value we calculated this unavoidable range of Cq values. This range increases with higher Cq values (less target). A decision to exclude replicate reactions based on this expected sampling error avoids bias, prevents unwanted loss of data and increases the statistical power. For a dataset with replicate qPCR measurements of 12 miRNA targets in 834 patients (20,016 reactions) the fraction of excluded measurements decreased from 39% to 7%.In the analysis of qPCR data, the Cq values of replicate reactions is required to differ no more than 0.5 cycles. However, the sampling error that occurs when pipetting a low number of target molecules into the PCR plate is governed by the Poisson distribution. For each Cq and PCR efficiency value we calculated this unavoidable range of Cq values. This range increases with higher Cq values (less target). A decision to exclude replicate reactions based on this expected sampling error avoids bias, prevents unwanted loss of data and increases the statistical power. For a dataset with replicate qPCR measurements of 12 miRNA targets in 834 patients (20,016 reactions) the fraction of excluded measurements decreased from 39% to 7%. Jan Ruijter, Assistant Professor, University of Amsterdam, The Netherlands

Discordance Between Replicate qPCR Reactions from Kate Barlow

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0 Development and Clinical Validation of Liquid ddPCR Tests for Actionable Somatic Mutations in NSCLC /slideshow/development-and-clinical-validation-of-liquid-ddpcr-tests-for-actionable-somatic-mutations-in-nsclc/84444818 garypestano-171219105103
We have developed and validated blood-based variant specific ddPCR tests for EGFR, KRAS, BRAF, EML4-ALK, ROS1 and RET variants. These tests are intended for use in patients diagnosed with Non-Small Cell Lung Cancer (NSCLC). The tests have been on the market as ”the GeneStrat® test” since 2015; and in that time, has been utilized to analyze over 80,000 individual variants. Greater than 90% of tests have been delivered in less than 72 hours from receipt at the testing Laboratory. We will report on factors critical to the development, validation and on-market support of these tests. In this talk we will cover: • Learning how Droplet Digital ™ PCR technology is being used for liquid biopsy testing in the clinical setting • Reviewing development and validation case studies for cfDNA testing using ddPCR • Reviewing performance data and quality metrics from on-market experiences Gary Pestano, Vice President, Development and Operations, Biodesix]]>
We have developed and validated blood-based variant specific ddPCR tests for EGFR, KRAS, BRAF, EML4-ALK, ROS1 and RET variants. These tests are intended for use in patients diagnosed with Non-Small Cell Lung Cancer (NSCLC). The tests have been on the market as ”the GeneStrat® test” since 2015; and in that time, has been utilized to analyze over 80,000 individual variants. Greater than 90% of tests have been delivered in less than 72 hours from receipt at the testing Laboratory. We will report on factors critical to the development, validation and on-market support of these tests. In this talk we will cover: • Learning how Droplet Digital ™ PCR technology is being used for liquid biopsy testing in the clinical setting • Reviewing development and validation case studies for cfDNA testing using ddPCR • Reviewing performance data and quality metrics from on-market experiences Gary Pestano, Vice President, Development and Operations, Biodesix]]> Tue, 19 Dec 2017 10:51:03 GMT /slideshow/development-and-clinical-validation-of-liquid-ddpcr-tests-for-actionable-somatic-mutations-in-nsclc/84444818 KateBarlow8@slideshare.net(KateBarlow8) Development and Clinical Validation of Liquid ddPCR Tests for Actionable Somatic Mutations in NSCLC KateBarlow8 We have developed and validated blood-based variant specific ddPCR tests for EGFR, KRAS, BRAF, EML4-ALK, ROS1 and RET variants. These tests are intended for use in patients diagnosed with Non-Small Cell Lung Cancer (NSCLC). The tests have been on the market as ”the GeneStrat® test” since 2015; and in that time, has been utilized to analyze over 80,000 individual variants. Greater than 90% of tests have been delivered in less than 72 hours from receipt at the testing Laboratory. We will report on factors critical to the development, validation and on-market support of these tests. In this talk we will cover: • Learning how Droplet Digital ™ PCR technology is being used for liquid biopsy testing in the clinical setting • Reviewing development and validation case studies for cfDNA testing using ddPCR • Reviewing performance data and quality metrics from on-market experiences Gary Pestano, Vice President, Development and Operations, Biodesix <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/garypestano-171219105103-thumbnail.jpg?width=120&height=120&fit=bounds" /> We have developed and validated blood-based variant specific ddPCR tests for EGFR, KRAS, BRAF, EML4-ALK, ROS1 and RET variants. These tests are intended for use in patients diagnosed with Non-Small Cell Lung Cancer (NSCLC). The tests have been on the market as ”the GeneStrat® test” since 2015; and in that time, has been utilized to analyze over 80,000 individual variants. Greater than 90% of tests have been delivered in less than 72 hours from receipt at the testing Laboratory. We will report on factors critical to the development, validation and on-market support of these tests. In this talk we will cover: • Learning how Droplet Digital ™ PCR technology is being used for liquid biopsy testing in the clinical setting • Reviewing development and validation case studies for cfDNA testing using ddPCR • Reviewing performance data and quality metrics from on-market experiences Gary Pestano, Vice President, Development and Operations, Biodesix

Development and Clinical Validation of Liquid ddPCR Tests for Actionable Somatic Mutations in NSCLC from Kate Barlow

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