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Author: jhudsl-robot

docs/01-intro.md

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 # Introduction
 
+This course is currently under development. The topics to be covered are outlined below.
+
 ## Motivation
 
 With the advent of massively parallel sequencing, millions of raw sequence reads can no be easily produced for a patient's tumor. Largely automated pipelines now exist to process these raw data, detect various types of molecular alterations (or variants), filter and review to identify high-confidence calls, and annotate these variants for functional significance. However, a major bottleneck remains at the variant interpretation stage. Genome analysts, molecular pathologists, clinical geneticists, laboratory geneticists and others are faced with a deluge of variants of potential relevance [@Good2014]. These variants must be manually reviewed and intersected with a vast ecosystem of knowledgebases and biomedical literature to provide current interpretation of their relevance for clinical application.

docs/index.html

@@ -164,7 +164,7 @@ <h1>
 </div>
 <div id="header">
 <h1 class="title">Introduction to Clinical Interpretation of Somatic Cancer Variants</h1>
-<p class="date"><em>May, 2023</em></p>
+<p class="date"><em>June, 2023</em></p>
 </div>
 <div id="about-this-course" class="section level1 unnumbered">
 <h1>About this Course</h1>

docs/index.md

@@ -1,6 +1,6 @@
 ---
 title: "Introduction to Clinical Interpretation of Somatic Cancer Variants"
-date: "May, 2023"
+date: "June, 2023"
 site: bookdown::bookdown_site
 documentclass: book
 bibliography: [book.bib, packages.bib]

docs/introduction.html

@@ -164,6 +164,7 @@ <h1>
 </div>
 <div id="introduction" class="section level1" number="1">
 <h1><span class="header-section-number">Chapter 1</span> Introduction</h1>
+<p>This course is currently under development. The topics to be covered are outlined below.</p>
 <div id="motivation" class="section level2" number="1.1">
 <h2><span class="header-section-number">1.1</span> Motivation</h2>
 <p>With the advent of massively parallel sequencing, millions of raw sequence reads can no be easily produced for a patient’s tumor. Largely automated pipelines now exist to process these raw data, detect various types of molecular alterations (or variants), filter and review to identify high-confidence calls, and annotate these variants for functional significance. However, a major bottleneck remains at the variant interpretation stage. Genome analysts, molecular pathologists, clinical geneticists, laboratory geneticists and others are faced with a deluge of variants of potential relevance <span class="citation">(<a href="#ref-Good2014" role="doc-biblioref">Good et al. 2014</a>)</span>. These variants must be manually reviewed and intersected with a vast ecosystem of knowledgebases and biomedical literature to provide current interpretation of their relevance for clinical application.</p>

docs/resources/images/01-intro_files/figure-html/1zwvAVLWpN2mKrJLgo5ZcAuSKQrHZ8zunIYHLe-w6bBo_g22509046821_0_0.png

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Largely automated pipelines now exist to process these raw data, detect various types of molecular alterations (or variants), filter and review to identify high-confidence calls, and annotate these variants for functional significance. However, a major bottleneck remains at the variant interpretation stage. Genome analysts, molecular pathologists, clinical geneticists, laboratory geneticists and others are faced with a deluge of variants of potential relevance (Good et al. 2014). These variants must be manually reviewed and intersected with a vast ecosystem of knowledgebases and biomedical literature to provide current interpretation of their relevance for clinical application. 1.2 Target Audience The course is intended for anyone seeking a better understanding of current best practices in somatic cancer variant interpretation. This might include clinical geneticists, laboratory geneticists, molecular pathologists, oncologists, or other cancer care providers or cancer researchers. 1.3 Curriculum This course will teach learners to: Understand key concepts of somatic cancer variant interpretation Introduce ClinGen Somatic Cancer efforts Introduce CIViC as a curation platform for somatic variant interpretation Introduce key SOPs and guidelines for classifying the clinical relevance and oncogenicity of somatic cancer variants References "],["resources-for-the-interpretation-of-somatic-variants.html", "Chapter 2 Resources for the Interpretation of Somatic Variants 2.1 Learning Objectives 2.2 AMP/ASCO/CAP guidelines 2.3 ClinGen/CGC/VICC Oncogenicity SOP 2.4 Knowledgebases", " Chapter 2 Resources for the Interpretation of Somatic Variants 2.1 Learning Objectives This chapter will cover: AMP/ASCO/CAP guidelines ClinGen/CGC/VICC SOP Cancer Variant Knowledgebases and their limitations 2.2 AMP/ASCO/CAP guidelines This section will introduce the AMP/ASCO/CAP guidelines for the Interpretation and Reporting of Sequence Variants in Cancer (Li et al. 2017). 2.2.1 AMP Tiers and Levels This subsection will introduce the concept of AMP Tiers and Levels 2.3 ClinGen/CGC/VICC Oncogenicity SOP This section will introduce the Standards for the classification of pathogenicity of somatic variants in cancer (oncogenicity)(Horak et al. 2022). 2.4 Knowledgebases This section will introduce relevant resources for Somatic Cancer variant interpretation including COSMIC, ClinVar, OncoKB, others. 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These evidence statements are categorized into six types: Predictive (of drug response), Diagnostic, Prognostic, Predisposing, Oncogenic or Functional. Each have different Clinical Significance values (e.g., Sensitivity, Resistance, etc for Predictive).Evidence is further categorized according to Level (A - Validated through E - Inferential) and rating (1-star through 5-star). 3.3 Tour of the CIViC web interface Here is a brief tour of the CIViC v2 interface: References "],["conclusions.html", "Chapter 4 Conclusions 4.1 Learning Objectives 4.2 Key conclusions 4.3 Additional Resources", " Chapter 4 Conclusions 4.1 Learning Objectives This chapter will summarize: Key conclusions of the course Additional learning resources 4.2 Key conclusions 4.3 Additional Resources "],["about-the-authors.html", "About the Authors", " About the Authors These credits are based on course contributors guidelines described here.     Credits Names Pedagogy Lead Content Instructor(s) Obi Griffith, Malachi Griffith Lecturer(s) Arpad Danos Content Author(s) Arpad Danos Content Contributor(s) Kilannin Krysiak Content Editor(s)/Reviewer(s) Malachi Griffith Content Director(s) Content Consultants Acknowledgments Production Content Publisher(s) Content Publishing Reviewer(s) Technical Course Publishing Engineer(s) Template Publishing Engineers Candace Savonen, Carrie Wright, Ava Hoffman Publishing Maintenance Engineer Candace Savonen Technical Publishing Stylists Carrie Wright, Ava Hoffman, Candace Savonen Package Developers (ottrpal) Candace Savonen, John Muschelli, Carrie Wright Art and Design Illustrator(s) Josh McMichael Figure Artist(s) Josh McMichael Videographer(s) Arpad Danos Videography Editor(s) Audiographer(s) Audiography Editor(s) Funding Funder(s) Institution/individual who funded course including grant number Funding Staff National Cancer Institute (NCI) U24CA237719 "],["references.html", "Chapter 5 References", " Chapter 5 References "],["404.html", "Page not found", " Page not found The page you requested cannot be found (perhaps it was moved or renamed). You may want to try searching to find the page's new location, or use the table of contents to find the page you are looking for. "]]
+[["index.html", "Introduction to Clinical Interpretation of Somatic Cancer Variants About this Course", " Introduction to Clinical Interpretation of Somatic Cancer Variants June, 2023 About this Course This course is part of a series of courses for the Informatics Technology for Cancer Research (ITCR) called the Informatics Technology for Cancer Research Education Resource. This material was created by the ITCR funded CIViC resource. This initiative is funded by the following grant: National Cancer Institute (NCI) U24CA237719. "],["introduction.html", "Chapter 1 Introduction 1.1 Motivation 1.2 Target Audience 1.3 Curriculum", " Chapter 1 Introduction This course is currently under development. The topics to be covered are outlined below. 1.1 Motivation With the advent of massively parallel sequencing, millions of raw sequence reads can no be easily produced for a patient’s tumor. Largely automated pipelines now exist to process these raw data, detect various types of molecular alterations (or variants), filter and review to identify high-confidence calls, and annotate these variants for functional significance. However, a major bottleneck remains at the variant interpretation stage. Genome analysts, molecular pathologists, clinical geneticists, laboratory geneticists and others are faced with a deluge of variants of potential relevance (Good et al. 2014). These variants must be manually reviewed and intersected with a vast ecosystem of knowledgebases and biomedical literature to provide current interpretation of their relevance for clinical application. 1.2 Target Audience The course is intended for anyone seeking a better understanding of current best practices in somatic cancer variant interpretation. This might include clinical geneticists, laboratory geneticists, molecular pathologists, oncologists, or other cancer care providers or cancer researchers. 1.3 Curriculum This course will teach learners to: Understand key concepts of somatic cancer variant interpretation Introduce ClinGen Somatic Cancer efforts Introduce CIViC as a curation platform for somatic variant interpretation Introduce key SOPs and guidelines for classifying the clinical relevance and oncogenicity of somatic cancer variants References "],["resources-for-the-interpretation-of-somatic-variants.html", "Chapter 2 Resources for the Interpretation of Somatic Variants 2.1 Learning Objectives 2.2 AMP/ASCO/CAP guidelines 2.3 ClinGen/CGC/VICC Oncogenicity SOP 2.4 Knowledgebases", " Chapter 2 Resources for the Interpretation of Somatic Variants 2.1 Learning Objectives This chapter will cover: AMP/ASCO/CAP guidelines ClinGen/CGC/VICC SOP Cancer Variant Knowledgebases and their limitations 2.2 AMP/ASCO/CAP guidelines This section will introduce the AMP/ASCO/CAP guidelines for the Interpretation and Reporting of Sequence Variants in Cancer (Li et al. 2017). 2.2.1 AMP Tiers and Levels This subsection will introduce the concept of AMP Tiers and Levels 2.3 ClinGen/CGC/VICC Oncogenicity SOP This section will introduce the Standards for the classification of pathogenicity of somatic variants in cancer (oncogenicity)(Horak et al. 2022). 2.4 Knowledgebases This section will introduce relevant resources for Somatic Cancer variant interpretation including COSMIC, ClinVar, OncoKB, others. References "],["introduction-to-the-civic-knowledgebase.html", "Chapter 3 Introduction to the CIViC knowledgebase 3.1 Learning Objectives 3.2 Introduction to the CIViC data model 3.3 Tour of the CIViC web interface", " Chapter 3 Introduction to the CIViC knowledgebase 3.1 Learning Objectives This chapter will cover: Introduction to the CIViC data model Demo of the CIViC web interface 3.2 Introduction to the CIViC data model For background on the CIViC resource and data model please consult the CIViC core papers (Griffith et al. 2017; Krysiak, Danos, Kiwala, et al. 2022; Krysiak, Danos, Saliba, et al. 2022). 3.2.1 CIViC Evidence The core concept of CIViC is an Evidence item linked to a Source (PubMed, ASCO or ASH). CIViC Evidence items include a human-readable evidence statement and supporting structured fields which support (or refute) a specific clinical significance for a specific Gene/Variant in a specific Disease context with optional phenotypes. These evidence statements are categorized into six types: Predictive (of drug response), Diagnostic, Prognostic, Predisposing, Oncogenic or Functional. Each have different Clinical Significance values (e.g., Sensitivity, Resistance, etc for Predictive).Evidence is further categorized according to Level (A - Validated through E - Inferential) and rating (1-star through 5-star). 3.3 Tour of the CIViC web interface Here is a brief tour of the CIViC v2 interface: References "],["conclusions.html", "Chapter 4 Conclusions 4.1 Learning Objectives 4.2 Key conclusions 4.3 Additional Resources", " Chapter 4 Conclusions 4.1 Learning Objectives This chapter will summarize: Key conclusions of the course Additional learning resources 4.2 Key conclusions 4.3 Additional Resources "],["about-the-authors.html", "About the Authors", " About the Authors These credits are based on course contributors guidelines described here.     Credits Names Pedagogy Lead Content Instructor(s) Obi Griffith, Malachi Griffith Lecturer(s) Arpad Danos Content Author(s) Arpad Danos Content Contributor(s) Kilannin Krysiak Content Editor(s)/Reviewer(s) Malachi Griffith Content Director(s) Content Consultants Acknowledgments Production Content Publisher(s) Content Publishing Reviewer(s) Technical Course Publishing Engineer(s) Template Publishing Engineers Candace Savonen, Carrie Wright, Ava Hoffman Publishing Maintenance Engineer Candace Savonen Technical Publishing Stylists Carrie Wright, Ava Hoffman, Candace Savonen Package Developers (ottrpal) Candace Savonen, John Muschelli, Carrie Wright Art and Design Illustrator(s) Josh McMichael Figure Artist(s) Josh McMichael Videographer(s) Arpad Danos Videography Editor(s) Audiographer(s) Audiography Editor(s) Funding Funder(s) Institution/individual who funded course including grant number Funding Staff National Cancer Institute (NCI) U24CA237719 "],["references.html", "Chapter 5 References", " Chapter 5 References "],["404.html", "Page not found", " Page not found The page you requested cannot be found (perhaps it was moved or renamed). 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