Modules
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Genomics Primer
Genomics Primer
Overview/Key Objectives
What are Eukaryotic Cells?
DNA Definition
What are Chromosomes?
What is a Genome?
Regulation of Gene Expression in Eukaryotes
Genetic Alterations
References
Assessment Questions
Course Introduction
Course Introduction
Overview/Key Objectives
What is Precision Medicine?
Precision Medicine in the Clinic
Direct-to-Consumer Genomic Testing
Ongoing Genomic Research and Big Data in Precision Medicine
References
Assessment Questions
Pathology Assessment of Tumor Tissue
Pathology Assessment of Tumor Tissue
Overview/Key Objectives
Introduction to the Pathology Laboratory
Specimen Preparation
Initial Pathology Assessment
Common Pathology Tests Performed in Oncology
References
Assessment Questions
Introduction to Liquid Biopsies
Introduction to Liquid Biopsies
Overview/Key Objectives
What is a Liquid Biopsy?
Approaches to Liquid Biopsy Analysis: CTCs and cfDNA
Technologies for Isolation and Detection of CTCs and cfDNA
Liquid Biopsy Applications
Concordance Between Tumor and Liquid Biopsies for Mutational Analysis
Select Commercially Available Liquid Biopsy Assays
References
Assessment Questions
Lung Cancer: Assessment, Treatment
Lung Cancer: Assessment, Treatment
Introduction
Current Oncogenic Biomarkers in Lung Cancer
EGFR Epidermal Growth Factor
EGFR Exon 20 Insertions
EGFR Exon 18
ALK Anaplastic Lymphoma Kinase
ROS1 ROS Proto oncogene 1
BRAF v raf murine sarcoma viral oncogene homolog B
NTRK: Fusion Neurotrophic Tropomyosin Receptor Kinase
MET: Mesenchymal-to-Epithelial Transition
RET Fusion: Rearranged During Transfection
HER2: Human Epidermal Growth Factor 2
KRAS: Kirsten RAT Sarcoma Viral Oncogenic Homolog
References
NTRK3 Fusion
NTRK3 Fusion
Initial Diagnosis
Clinical Progress and Treatment
Imaging
Pathology Part 1
Pathology Part 2
Discussion and Proposed Potential Therapies
References
Whole-Genome Sequencing
Whole-Genome Sequencing
Overview/Key Objectives
What is Whole-Genome Sequencing?
Sanger Sequencing
Whole-Genome Sequencing Methods
Whole-Genome vs. Whole-Exome Sequencing vs. Targeted Sequencing Panels
Strengths and Limitations of Next-Generation Sequencing
Next-Generation Sequencing in the Research and Clinic Settings
Importance of Bioinformatics
References
Assessment Questions
Genomic Medicine in Clinical Practice: Era of Personalized Medicine
Genomic Medicine in Clinical Practice: Era of Personalized Medicine
Overview/Key Objectives
Clinical Settings for Genomic Testing
Considerations When Choosing a Genomic Testing Approach
Liquid Biopsies
Frequently Discussed Topics
Future of Genomic Medicine
References
Assessment Questions
Quizzes
Tumor Boards
Videos
About
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Modules
Genomics Primer
Overview/Key Objectives
What are Eukaryotic Cells?
DNA Definition
What are Chromosomes?
What is a Genome?
Regulation of Gene Expression in Eukaryotes
Genetic Alterations
References
Assessment Questions
Course Introduction
Overview/Key Objectives
What is Precision Medicine?
Precision Medicine in the Clinic
Direct-to-Consumer Genomic Testing
Ongoing Genomic Research and Big Data in Precision Medicine
References
Assessment Questions
Pathology Assessment of Tumor Tissue
Overview/Key Objectives
Introduction to the Pathology Laboratory
Specimen Preparation
Initial Pathology Assessment
Common Pathology Tests Performed in Oncology
References
Assessment Questions
Introduction to Liquid Biopsies
Overview/Key Objectives
What is a Liquid Biopsy?
Approaches to Liquid Biopsy Analysis: CTCs and cfDNA
Technologies for Isolation and Detection of CTCs and cfDNA
Liquid Biopsy Applications
Concordance Between Tumor and Liquid Biopsies for Mutational Analysis
Select Commercially Available Liquid Biopsy Assays
References
Assessment Questions
Lung Cancer: Assessment, Treatment
Introduction
Current Oncogenic Biomarkers in Lung Cancer
EGFR Epidermal Growth Factor
EGFR Exon 20 Insertions
EGFR Exon 18
ALK Anaplastic Lymphoma Kinase
ROS1 ROS Proto oncogene 1
BRAF v raf murine sarcoma viral oncogene homolog B
NTRK: Fusion Neurotrophic Tropomyosin Receptor Kinase
MET: Mesenchymal-to-Epithelial Transition
RET Fusion: Rearranged During Transfection
HER2: Human Epidermal Growth Factor 2
KRAS: Kirsten RAT Sarcoma Viral Oncogenic Homolog
References
Whole-Genome Sequencing
Overview/Key Objectives
What is Whole-Genome Sequencing?
Sanger Sequencing
Whole-Genome Sequencing Methods
Whole-Genome vs. Whole-Exome Sequencing vs. Targeted Sequencing Panels
Strengths and Limitations of Next-Generation Sequencing
Next-Generation Sequencing in the Research and Clinic Settings
Importance of Bioinformatics
References
Assessment Questions
Genomic Medicine in Clinical Practice: Era of Personalized Medicine
Overview/Key Objectives
Clinical Settings for Genomic Testing
Considerations When Choosing a Genomic Testing Approach
Liquid Biopsies
Frequently Discussed Topics
Future of Genomic Medicine
References
Assessment Questions
Quizzes
Tumor Boards
Videos
About
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Hematology/Oncology
Learn Genomics
Introduction to Liquid Biopsies
Lung Cancer: Assessment, Treatment
Module Content
Introduction
Current Oncogenic Biomarkers in Lung Cancer
EGFR: Epidermal Growth Factor
EGFR Exon 20 Insertions
EGFR Exon 18
ALK: Anaplastic Lymphoma Kinase
ROS1: ROS Proto-oncogene 1
BRAF: v-raf murine sarcoma viral oncogene homolog B
NTRK: Fusion Neurotrophic Tropomyosin Receptor Kinase
MET: Mesenchymal-to-Epithelial Transition
RET Fusion: Rearranged During Transfection
HER2: Human Epidermal Growth Factor 2
KRAS: Kirsten RAT Sarcoma Viral Oncogenic Homolog
References
Introduction
Current Oncogenic Biomarkers in Lung Cancer
EGFR: Epidermal Growth Factor
EGFR Exon 20 Insertions
EGFR Exon 18
ALK: Anaplastic Lymphoma Kinase
ROS1: ROS Proto-oncogene 1
BRAF: v-raf murine sarcoma viral oncogene homolog B
NTRK: Fusion Neurotrophic Tropomyosin Receptor Kinase
MET: Mesenchymal-to-Epithelial Transition
RET Fusion: Rearranged During Transfection
HER2: Human Epidermal Growth Factor 2
KRAS: Kirsten RAT Sarcoma Viral Oncogenic Homolog
References
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Introduction
Lung cancer is the third most common cancer and the leading cause of cancer-related death in the United States.
Two Main Types:
Small cell lung cancer: 5-year overall survival (OS) = 7%
Non-small cell lung cancer (NSCLC): 5-year OS = 25%
Includes: adenocarcinoma, squamous cell carcinoma, large cell carcinoma
Initial Diagnosis:
Staging:
Provides information regarding tumor size and extent the tumor has spread throughout the body
.
Clinical Workup:
Imaging:
X-ray, MRI, CT and/or PET scan
Including the brain, bones and liver
Lung Biopsy:
If diagnostic biopsy is an option, enough tissue should be collected to allow for biomarker assessment.
Tumor Molecular Profiling:
Tissue and/or blood biomarkers help guide and optimize a patient’s treatment decisions and outcomes. It is important for tumor biomarker testing to be performed at diagnosis and repeated at time of progression to assess potential mechanisms of acquired resistance, including additional driver mutations that may have developed due to therapy.
FISH (fluorescent in situ hybridization)
: Rapid technique that provides information about tumor DNA.
Limitations include tissue depletion, being more difficult to interpret clinically, and not providing information related to fusion partners or positions.
IHC (immunohistochemistry)
: Rapid low-cost technique that provides information related to transcribed and translated events (protein information).
Limitations include tissue depletion, being less well-validated, and not providing information related to fusion partners or position.
RT-PCR (reverse-transcriptase polymerase chain reaction):
Rapid technique with high sensitivity and specificity that provides information related to RNA and can detect specific fusion partners.
Limitations include specific primer sets being required for each fusion, inability to detect novel fusion partners, difficulty in extracting high-quality RNA from tumor, and limited multiplexing ability.
NGS (next generation sequencing
—
including RNA and DNA):
Technique allows for multiplexing to maximize information obtained from single tissue sample. NGS provides information about targeted DNA and/or RNA locations and/or the whole genome in a single test. It can provide information about fusion partners and identify position.
Limitations include higher cost and longer wait time for results.
Liquid Biopsy:
Noninvasive method for assessing circulating tumor-derived materials
—
cell-free DNA
—
from plasma in patients at advanced stages where biopsy is not an option.
Limitations include lack of reliability in clinical setting
.
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