CMRI - 2024 Genomic Medicine Short Course - NSGC

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Agreement

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Objective 1: Examine a broad range of topics in human genomics and the use of NGS next generation sequencing technologies through active learning methods

By meeting the above objective my professional competence will increase because I have acquired new strategies to use in my practice.

By meeting the above objective my professional performance will improve because I should be able to implement the new strategies.

By meeting the above objective my patient outcomes should improve due to the implementation of newly-learned strategies.

The teaching methods used were appropriate to the objectives

Objective 2: Summarize the special ethical, legal, and social implications ELSI of genomic research and the differences from clinical genomics

By meeting the above objective my professional competence will increase because I have acquired new strategies to use in my practice.

By meeting the above objective my professional performance will improve because I should be able to implement the new strategies.

By meeting the above objective my patient outcomes should improve due to the implementation of newly-learned strategies.

The teaching methods used were appropriate to the objectives

Objective 3: Identify mechanisms to promote translational genomic research between research and clinical genomic investigators by building opportunities for consultation and collaboration

By meeting the above objective my professional competence will increase because I have acquired new strategies to use in my practice.

By meeting the above objective my professional performance will improve because I should be able to implement the new strategies.

By meeting the above objective my patient outcomes should improve due to the implementation of newly-learned strategies.

The teaching methods used were appropriate to the objectives

Identify various categories of human genomic variatio

Differentiate pathogenic from nonpathogenic variants

Describe the role of next generation sequencing in monogenic disease discovery and diagnosis

Identify components of a genomic bioinformatic pipeline

Discuss the role of the reference genome in variant calling and characterization

Describe the collection of resources used in variant annotation

Identify one or more factors that can affect variant detection accuracy.

Describe sample preparation for short and long read NGS

Discuss library prep, enrichment, and quality control

List types of variants that might be detected by genome sequencing but missed by exome sequencing

Describe how genomic and transcriptomic studies complement one another

Identify methods for comparing transcriptomic data sets 

Identify common flaws in transcriptomic study design

Apply the ACMG variant classification system

Illustrate variant interpretation using cases.

Examine factors in variant call quality, such as depth of coverage, using a publically available genome viewer

State the criteria for evaluating a disease- gene relationship.

Summarize gene specific variant interpretation criteria.

Operate analysis software; selecting cases and beginning next generation sequencing analysis.

Implement changes to software settings to adjust variants and associated data shown.

Construct the parameters and settings of variant analysis tools to detect diagnoses consistent with all common inheritance patterns.

Identify at least five disease causing variants using TruSight Tertiary Analysis software

Examine factors in variant call quality, such as depth of coverage, using a publically available genome viewer

Evaluate the impact of using analysis tool filters for genetic variant analysis.

Explain the difference between variant classification and clinical utility

Recognize the complexity of the patient with multiple diagnoses

Identify key aspects of Secondary Findings, from informed consent to results disclosure and support

Recognize how the revised Common Rule policy affects genomic research

Examine the requirements for informed consent

Discuss the European Commission’s General Data Protection Regulation and how it can affect genomic studies in other countries.

Identify massively parallel genomic assays for profiling the molecular impact of genetic variants

Summarize high-throughput screening technologies for profiling the functional impact of genetic variants

Identify genomic datasets on the Browser that are useful to visualize known variation in the context of benign vs pathogenic, both large CNV and small SNV

Use the Saved Sessions feature to preserve the state of the Browser for specific scenarios

Load Custom Track data to annotate genome

Utilize of the Table Browser to perform intersections between datasets and export genomic coordinates for genes

Import gene coordinates to Multi-region view

Differentiate expectations between clinical and research testing and the associated legal ramifications

Assess the importance of informed consent in clinical research studies in managing patient expectations 

Define population descriptors and why they are so relevant to human genetics and genomics research

Identify whether race and ethnicity are appropriate population descriptors in contemporary genetics research

Describe conclusions and recommendations of the 2023 NASEM report on population descriptors

Identify the ethical principle(s) that apply to genomic sequencing in research.

Examine differences in research and clinical settings in return of results.

Evaluate the impacts of diversity in genomics research on translation to clinical care.

Summarize key characteristics of non-coding DNA variation in the genome

Identify methods to assign function to non-coding DNA variation including new technologies, e.g. scRNA-seq.

Examine implications of non-coding variation today and in the future

Summarize how genetic variation impacts drug metabolism and response

Define variability in pharmacogenes across individuals and populations

Identify challenges unique to pharmacogenetics in pediatric pharmacology

Explain the role of genomic variation in cancer treatment and prognosis

Evaluate the differences in cancer genomic testing analysis compared to analysis for Mendelian Disorders

Examine bioinformation limitations in somatic variant calling and approaches to improve sensitivity.

Compare and contrast the similarities and differences between somatic and germline variant interpretation.

Describe the relationship of genetic variation, gene expression and other cellular traits to disease risk differentiation of tissues

Discuss how environmental exposures can alter methylation and the potential relationship to disease

Appraise the scope of variation in healthy adults

Analyze a variant file and perform curation for variant classification

Evaluate the clinical significance of variants within one’s own or a de-identified variant file.

Describe the impact of variants of unknown significance and incidental findings on an unaffected individual.

Identify classic signs and symptoms of mitochondrial disease

Differentiate between nuclear and mitochondrial genomes in mitochondrial disease

State challenges in sequencing Mitochondria

Describe the principles of parent of origin effects

Describe GGC’s experience with EpiSign Episignature testing

Discuss successes and temporary setbacks associated with Methylation Signatures

Summarize future opportunities and other unfinished work related to Episignatures

Identify potentially diagnostic variants in a trio exome  

Illustrate variant prioritization schemes

Operate public databases to assist in characterizing genomic variants 

Evaluate the inheritance of variants through the use of parental variant files

Interpret variants using parent variant files to rule-in or out as potentially pathogenic

Classify variants as pathogenic, likely or VUS using allele frequency information found in public databases

Identify inheritance patterns from family history and apply to variant analysis.

Apply gene curation criteria analyzing gene-disease evidence

Describe current methods for associating common variants to rare disease phenotypes

Explain how common variant associations in rare diseases can be used to identify novel disease genes and understanding modified penetrance of candidate pathogenic rare variants

Why or why not?

What questions are you having in your practice that you would like to see addressed in an educational activity?

What barriers might you have that would interfere with implementation of new information learned from this training?

How can this training (the overall meeting) be improved to better impact knowledge, strategies/skills, performance and/or patient outcomes?

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