Pharmacogenomics Applied: Next Generation Sequencing (NGS) Case Study (SAM eligible)

This is one of ten courses in the Pharmacogenomics program. This activity discusses how Next Generation Sequencing (NGS) can be used to sequence areas of the gene in oncology specimens to identify actionable mutations which are known to be pharmacogenomics targets.

Type Course
CME Available Yes
Cost Paid

Date of Resource

Genomic Competencies

Experts from the disciplines listed below have tagged this resource as fulfulling genomic competencies.


  • Basic Genetic Concepts
    • B1:   To demonstrate an understanding of the basic genetic/genomic concepts and nomenclature
    • B2:   To recognize and appreciate the role of behavioral, social, and environmental factors (lifestyle, socioeconomic factors, pollutants, etc.) to modify or influence genetics in the manifestation of disease
    • B3:   To identify drug and disease associated genetic variations that facilitate development of prevention, diagnostic and treatment strategies and appreciate there are differences in testing methodologies and are aware of the need to explore these differences these differences in drug literature evaluation
  • Genetics and Disease
    • G2:   To assess the difference between clinical diagnosis of disease and identification of genetic predisposition to disease (genetic variation is not strictly correlated with disease manifestation)
  • Pharmacogenetics/Pharmacogenomics
    • P1:   To demonstrate an understanding of how genetic variation in a large number of proteins, including drug transporters, drug metabolizing enzymes, direct protein targets of drugs, and other proteins (e.g. signal transduction proteins) influence pharmacokinetics and pharmacodynamics related to pharmacologic effect and drug response


  • Genomic Testing
    • P-GT2A:   Patient Care
      • 2A1:   Discuss the indications for genomic testing - specifically the benefits, risks, and alternatives
      • 2A2:   Explain the implications of placing genomic test results in the patient’s medical record
      • 2A3:   Discuss the possibility of incidental findings and how they will be handled
      • 2A4:   Discuss risks of having genomic testing done: e.g., psychological implications for the individual as well as the family; the potential for discrimination; and the potential effect on insurance coverage.
      • 2A5:   Explain to the patient issues of costs and financial coverage of genomic testing
      • 2A6:   Order, interpret, and communicate the results of appropriate genomic tests, within the physician’s scope of practice
      • 2A7:   Provide referral to an appropriate specialist for genomic testing of a condition outside the physician’s scope of practice
      • 2A8:   Respond to the results of an abnormal genetic screening test, such as newborn screening, including immediate management and appropriate referral
    • P-GT2B:   Knowledge for Practice
      • 2B1:   Describe the major forms of genomic variability
      • 2B2:   Explain how different genomic changes may result in different phenotypes
      • 2B3:   Recognize that genomic tests require interpretation with respect to the patient’s clinical status (e.g., pathogenic, likely pathogenic, benign)
      • 2B4:   Explain the concepts of analytic validity, clinical validity, clinical utility as they relate to genomic testing
      • 2B5:   Recognize that medically ’non-actionable’ genomic results can be useful to the patient and family (i.e., personal utility)
    • P-GT2C:   Practice-Based Learning and Improvement
      • 2C1:   Incorporate genomic findings into the health record and patient-care plan
      • 2C2:   Have a method for periodic review of ’new’ genomic interpretation for clinical applications.
    • P-GT2D:   Interpersonal and Communication Skills
      • 2D1:   Ensure that undergoing genomic testing is a joint decision of the patient and the physician
      • 2D2:   Explain and document findings from genomic testing to patient, including implications for other family members
      • 2D3:   Facilitate access to resources to enhance patient learning about the results of genomic testing
      • 2D4:   Address the needs of the patient as an individual as well as the needs of family members
    • P-GT2E:   Professionalism
      • 2E1:   Be aware of and comply with local and federal laws and regulations regarding use of genomic tests
      • 2E2:   Be aware of and responsive to patients’ concerns about genetic discrimination
      • 2E3:   Respect patient’s privacy and need to maintain confidentiality of genomic information
  • Patient Treatment Based on Genomic Results
    • P-PM3A:   Patient Care
      • 3A1:   Identify medical conditions and drug responses that have a strong genetic component
      • 3A2:   Recognize that variants affecting drug responses found in a patient may also have implications for other family members
      • 3A3:   Discern the potential clinical impact of genetic variation on risk stratification and individualized treatment
    • P-PM3B:   Knowledge for Practice
      • 3B1:   Appreciate the importance of genetic diversity of humans and the abundance of genetic variants in each individual genome
      • 3B2:   Identify single-gene disorders that may be amenable to targeted pharmacological therapy
      • 3B3:   Recognize that genomic test results may guide choice of therapy for multifactorial disorders
      • 3B4:   Recognize that there is variability in the phenotypic expression of genetic variants and in response to therapy
      • 3B5:   Recognize that the effects of some medications are strongly influenced by inherited or somatically acquired genetic variation
    • P-PM3C:   Practice-Based Learning and Improvement
      • 3C1:   Use evidence-based recommendations of professional organizations and others in implementing knowledge gained from genetic discoveries to improve therapeutics
      • 3C2:   Document and periodically reassess therapeutic decision-making into the medical record of patients
      • 3C3:   Incorporate a realistic assessment of personal genomic knowledge and skill in the selection and use of consultants and improve competencies in the wake of these interactions
    • P-PM3D:   Interpersonal and Communication Skills
      • 3D1:   Discuss benefits, risks, and alternatives of various preventive and therapeutic approaches driven by genomic findings
      • 3D2:   Communicate clearly with other medical professionals involved in the care of the patient about the therapeutic implications of the genetic information garnered about the patient 3D3. Discuss pharmacogenomics implications for future health
      • 3D3:   Discuss pharmacogenomics implications for future health
  • Somatic Genomics
    • P-SG4A:   Patient Care
      • 4A1:   Identify or facilitate identification of patients who may benefit from genomic testing of tissue
      • 4A2:   Explain the benefits and limitations of somatic genomic testing to the patient, including implications regarding treatment of their condition and clarification of his/her prognosis
      • 4A3:   Ensure that tissue biopsy procedures are coordinated to make certain that appropriate and sufficient material is obtained for testing
      • 4A4:   Integrate genomic testing results into the patient-care plan
    • P-SG4B:   Knowledge for Practice
      • 4B1:   Explain the concept of somatic genetic change
      • 4B2:   Describe the role of genomic changes in the pathophysiology and treatment of cancer
      • 4B3:   Explain how genomic testing can be used to guide choice of therapy and adjust drug dosage in patients with cancer
    • P-SG4C:   Practice-Based Learning and Improvement
      • 4C1:   Maintain an awareness of and follow evidence-based guidelines and other professional resources regarding somatic genetic disorders appropriate to the physician’s scope of practice
    • P-SG4D:   Interpersonal and Communication Skills
      • 4D1:   Communicate to the patient the importance of genomic testing of his/her tissue sample, including potential implications for treatment and prognosis, and the limitations of genomic testing
      • 4D2:   Address any concerns the patient may have about test results
      • 4D3:   Ensure that specialists involved in a patients care are communicating with one another and with the patient
      • 4D4:   Communicate to patients potential implications for his/her family

Genetic Counselor

  • Genetics Expertise and Analysis
    • 1:   Demonstrate and utilize a depth and breadth of understanding and knowledge of genetics and genomics core concepts and principles.
      • 1a:   Demonstrate knowledge of principles of human, medical, and public health genetics and genomics and their related sciences.
      • 1b:   Apply knowledge of genetic principles and understand how they contribute to etiology, clinical features and disease expression, natural history, differential diagnoses, genetic testing and test report interpretation, pathophysiology, recurrence risk, management and prevention, and population screening.
    • 4:   Identify, assess, facilitate, and integrate genetic testing options in genetic counseling practice.
      • 4a:   Investigate the availability, analytic validity, clinical validity, and clinical utility of screening, diagnostic and predictive genetic/genomic tests.
      • 4b:   Evaluate and assess laboratories and select the most appropriate laboratory and test based on the clinical situation.
      • 4c:   Identify and discuss the potential benefits, risks, limitations and costs of genetic testing.
      • 4d:   Coordinate and facilitate the ordering of appropriate genetic testing for the client.
      • 4e:   Interpret the clinical implications of genetic test reports.
      • 4f:   Recognize and differentiate specific considerations relevant to genetic versus genomic and clinical versus research testing in terms of the informed consent process, results disclosure, institutional review board (IRB) guidelines, and clinical decision-making.
  • Professional Development & Practice
    • 22:   Accept responsibility for one's physical and emotional health as it impacts on professional performance.
      • 22a:   Distinguish the genetic counseling scope of practice in relation to the roles of other health professionals.
      • 22b:   Develop positive relationships with professionals across different disciplines.
      • 22c:   Demonstrate familiarity with the health care system as it relates to genetic counseling practice including relevant privacy regulations, referral and payment systems.
      • 22d:   Demonstrate effective interaction with other professionals within the healthcare infrastructure to promote appropriate and equitable delivery of genetic services.
      • 22e:   Assist non-genetic healthcare providers in utilizing genetic information to improve patient care in a cost-effective manner.
      • 22f:   Promote responsible use of genetic/genomic technologies and information to enhance the health of individuals, communities, and the public.