Foundational Specialty Training

Foundational Specialty Training Course Description (June 30 - July 1)
The ACMG Foundational Specialty Training Course has been developed as a component of the Alternative Pathway to Board Certification in Laboratory Genetics and Genomics. This course follows the GGRC and is a standalone course. It is not live streamed and has two primary tracks: 1) Molecular and 2) Cytogenetics. To enroll in the "Alternative Pathway to Board Certification in Laboratory Genetics and Genomics - Molecular or Cytogenetics Pathway" please go to www.acmgeducation.net and select your appropriate pathway. Due to space limitations priority registration is given to those in the Alternative Pathway to attend the Foundational Specialty Course. 

Agenda – Foundational Specialty Training

*subject to change

Sunday, June 30, 2019

1:00 pm - 1:20 pm

Welcome and Introductions

1:20 pm - 1:30 pm

Transition to assigned meeting room

 

Molecular Genetics and Genomics (MGG) Pathway Course

Cytogenetics and Genomics (CGG) Pathway Course

1:30 pm - 2:30 pm

Normal Structure/Nomenclature/Types of Variation
Elaine Lyon, PhD, FACMG

 

Mitosis/Meiosis, Nondisjunction/Aneuploidy, Chromosome Structure
Catharine Rehder, PhD, FACMG
 

2:30 pm - 3:30 pm

Common Disorders/Screening (CF, Hemophilia,
Hemoglobin disorders, Venous Thromboembolism)
Gerald Feldman, MD, PhD, FACMG

Chromosome Analysis and Cytogenetic Nomenclature
Julie Gastier-Foster, PhD, FACMG

3:30 pm - 3:45 pm

Break

3:45 pm - 4:45 pm

Neurogenetic Disorders – (DMD, SMA, CMT, NF1)
Elaine Lyon, PhD, FACMG

 

Structural Abnormalities-translocation, Inversion, Del/Dup, Abnormal Segregation
Catharine Rehder, PhD, FACMG
 

4:45 pm - 5:45 pm

Triplet Repeat Disorders (FX, MD, HD)
Cindy Vnencak-Jones, PhD, FACMG

Sex Chromosomes Abnormalities, X-Inactivation
Julie Gastier-Foster, PhD, FACMG

Monday, July 1, 2019

7:30 am – 8:00 am

Continental Breakfast

 

Molecular Genetics and Genomics (MGG) Pathway Course

Cytogenetics and Genomics (CGG) Pathway Course

8:00 am - 9:00 am

 

Non-mendelian and Identity (Imprinting, Mitochondrial,
Identity, MCC)
Gerald Feldman, MD, PhD, FACMG
 

Congenital FISH and Microarray Testing, including UPD
Julie Gastier-Foster, PhD, FACMG

9:00 am - 10:00 am

 

 

 

 

Introduction to Next-Generation Sequencing (NGS)
Elaine Lyon, PhD, FACMG

Somatic (FLT3, JAK2, BCR-ABL1, RAS, EGFR)
Interpretation of Sequence Variants – Part 1
Cindy Vnencak-Jones, PhD, FACMG

 

HEME I: Introduction to Technology
Adrian Dubuc, PhD, FACMG

 

 

10:00 am - 10:15 am

Break

10:15 am - 11:15 am

 

Somatic (FLT3, JAK2, BCR-ABL1, RAS, EGFR)
Cindy Vnencak-Jones, PhD, FACMG
 

Heme II: Myeloid Neoplasms
Adrian Dubuc, PhD, FACMG

11:15 am - 12:15 pm

 

Inherited Cancers and Predisposition Screening (Lynch, FAP, BRCA, MEN2)
Julie Gastier-Foster, PhD, FACMG
 

Heme III: Lymphoid Neoplasms
Catharine Rehder, PhD, FACMG

12:15 pm - 1:15 pm

 

Constitutional NGS (including NIPT),
Interpretation of Sequence Variants
Elaine Lyon, PhD, FACMG

 

Solid Tumors [Breast and HER2 amp; Lung (ALK/ROS/RET)]
Adrian Dubuc, PhD, FACMG

 

Cytogenetics and Genomics Lecture Outline

  1. Mitosis/meiosis, nondisjunction/aneuploidy, chromosome structure (I)
  • Describe the cell cycle, mitosis, and meiosis
  • Describe chromosome structure and banding
  • Describe the consequences of meiotic/mitotic errors
  • Differentiate between polymorphisms and pathogenic structural variants
  1. Mitosis/meiosis, nondisjunction/aneuploidy, chromosome structure (II)
  • Describe the basic principles of cell culture (general and selective, stimulated and unstimulated, in situ and suspension
  • Describe the principles of cell culture harvest, slide preparation and staining/banding
  1. Structural abnormalities-translocation, inversion, del/dup, abnormal segregation
  • Describe structural abnormalities and nomenclature
  • Describe meiotic segregation patterns and risks of miscarriage and abnormal offspring
  • Describe mosaicism, particularly in the context of ring/markers, as well as considerations for testing in such situations (skin etc.)
  1. Sex chromosomes abnormalities, X-inactivation
  • Describe the structure and important regions of the X and Y chromosome, dosage
  • Explain the principles of X-inactivation and functional disomy
  • Recognize the different sex chromosome aneuploidies and variants (Turner Syndrome and variants, etc.)
  1. Congenital testing (FISH, microarray), including UPD
  • Explain the basic fundamentals of FISH and chromosomal microarray
  • Describe the various microdeletion/microduplication syndromes and mechanisms (segmental dup mediated and non-seg dup mediated)
  • Identify uniparental disomy (UPD) and how it can be detected using SNP microarray, as well as consanguinity
  • Discuss the detection of uniparental disomy (UPD) and consanguinity using SNP microarray, as well as consanguinity
  1. HEME I: Intro to technology
  • Explain FISH probe basics and validation
  • Demonstrate competence in FISH probe strategies and nomenclature
  • Explain FISH probe patterns (both normal and abnormal)
  1. Heme II: Myeloid neoplasms
  • Describe the process of myelopoeisis
  • Describe the different myeloid neoplasms (MPN, MDS, AML)
  • Define the common cytogenetic abnormalities and what testing is recommended for various myeloid malignancies
  1. Heme III: Lymphoid neoplasms
  • Describe the process of lymphopoeisis
  • Describe the different lymphoid neoplasms (B leukemia/lymphoma, T leukemia/lymphoma, CLL, myeloma)
  • Define the common cytogenetic abnormalities and what testing is recommended for various lymphoid neoplasms
  1. Solid tumors [Breast and HER2 amp; Lung (ALK/ROS/RET)]; Well-described tumors with classic changes (sarcomas, gliomas, renal tumors, for example)
  • Describe genetic mechanisms of oncogenesis and tumor suppression
  • Explain the relevance of structural, numerical, and ploidy changes
  • Define appropriate assays (and limitations) to detect specific types of aberrations
  • Define pathognomonic cytogenetic/genomic aberrations for key solid tumors

 

Molecular Genetics and Genomics Lecture Outline

  1. Normal structure/nomenclature/types of variation;
  • Describe genetic variation, and define mutation, polymorphism, locus, allele, genotype phenotype and copy number
  • Define the different type of mutation: missense, nonsense, synonymous, null, and frameshift
  • Use nomenclature as standardized by the Human Genome Variation Society
  1. Common disorders/screening (CF, Hemophilia, Hemoglobin disorders, Venous Thromboembolism)
  • Differentiate diagnostic vs. carrier screening
  • Calculate residual risk
  • Describe the pathogenesis of each disorder
  • Explain the methodology used in screening for each disorder
  • Evaluate the test performance
  • Interpret test results
  1. Neurogenetic – (DMD, SMA, CMT, NF1)
  • Explain the methodology used in each disorder; exon-level CNV (del/dup), cis/trans
  • Evaluate the test performance
  • Interpret test results
  • Define germline and somatic mosaicism and testing limitations
  1. Triplet repeat disorders (FX, MD, HD)
  • Describe the specific repeats, inheritance, anticipation, pathogenesis of each disorder
  • Evaluate the test performance
  • Interpret test results
  • Explain parental differences in transmissions
  1. Non-mendelian and Identity (Imprinting, Mitochondrial, Identity, MCC)
  • Describe the pathogenesis of each disorder
  • Explain the methodology used in each disorder
  • Methylation, STR, contamination, UPD Evaluate test performance
  • Interpret the test results
  • Define clinical significance of heteroplasmy
  1. Next-Generation Sequencing (NGS)
  • Review the technical details of next-generation sequencing – limitations and advantages of different methods of library preparation and sequencing.
  • Review the assay design process, including selecting capture for hybridization
  • Explain the refinement steps of assay design to optimize data generation at difficult genomic regions, e.g., at repetitive sequences or GC-rich sequences.
  • Discuss the limitations of sequence depth coverage and implications for diagnostic testing.
  • Use software for NGS read alignment, variant calling and confirmation
  1. Inherited cancers (Lynch, FAP, BRCA, MEN2)
  • Describe the pathogenesis of each disorder
  • Discuss predisposition screening in the NGS setting
  • Interpret test results; microsatellite instability, penetrance, tumor suppressor, oncogene, repair gene, loss of heterozygosity, lifetime cancer risk
  1. Somatic (FLT3, JAK2, BCR-ABL1, RAS, EGFR)
  • Describe the pathogenesis of each disorder
  • Explain the methodology used in each disorder; somatic vs germline interpretation
  • Evaluate the test performance
  • Interpret the test results
  1. NGS case (including NIPT); Interpretation of sequence variants
  • Use software for NGS read alignment, depth of coverage, variant calling and confirmation
  • Explain the analysis of NGS data and the biostatistical components
  • Evaluate the test performance
  • Interpret the test results
  • Recognize secondary findings