Theory & Practice of Clinical Genomics

Section 1: Focus On Microscopy (online and in person)

This modular laboratory will provide the learner with a strong skills base and knowledge of how the microscope works and the information to choose the appropriate microscopy technique, including basic and cutting-edge applications. Microscopy applications will include transmitted, phase-contrast, differential interference contrast, darkfield, epifluorescence, confocal, and two- and three-dimensional time-lapse microscopy will also be covered. Sessions will primarily be lecture and assignment-based with hands-on training in transmitted, phase-contrast and basic epifluorescence microscopy.

Section 2: In situ techniques

Application of in situ hybridization techniques to detect and localize sequences on chromosomes or tissue sections for the diagnosis of cytogenetic abnormalities, tumor biology, gene amplification and/or gene mapping. Topics include probe design, principles of hybridization, CGH, PRINS and immunocytochemistry.

Instructor: Judy Brown, PhD, Director, Health Care Genetics Master’s Degree Program

Section 3: Genomics data in the clinical laboratory (online and in person)

An introduction to bioinformatics for the design and/or analysis of diagnostic genetic tests. Topics covered include literature and protocol searches, primer design, probe selection, sequence, variant and data analysis.  Databases examined will include Gene Tests, OMIM, Mitelman, CGAP, PubMed, NCBI, and the UCSC genome browser and others as appropriate.

Instructors: Cara Statz, PhD, Clinical Analyst, Jackson Laboratory for Genomic Medicine and Judy Brown, PhD, Director, Health Care Genetics Master’s Degree Program

Section 4: Chromosome analysis 1 (online)

The study of human chromosomes including banding, chromosome identification, polymorphic variation, structural and numerical abnormalities, determination of band level, and the International System for Human Cytogenetic Nomenclature.

Instructor: Lauren Wilson, MA, CG(ASCP), Allied Health Sciences, UConn Storrs or Judy Brown, PhD, Director, Health Care Genetics Master’s Degree Program

Section 5: Chromosome analysis 2 (online)

Analysis of human, mouse and other model system organism karyotypes.  Pre-requisite:  Chromosome analysis 1.

Section 6:  DNA diagnostics 

Practical experience with molecular techniques for the diagnosis of genetic disease. The student will perform genomic nucleic acid extraction, resolution and detection, analysis and characterization of nucleic acids, and nucleic acid amplification. Laboratory procedures will adhere to clinical laboratory quality control and assurance guidelines. Principles delivered online and in-person (1 credit) with varying format of in-person laboratory delivery (weekend and/or evening, or week-long semester break).

Instructor: Denise Anamani, MA, MG(ASCP), Allied Health Sciences, UConn Storrs or Judy Brown, PhD, Director, Health Care Genetics Master’s Degree Program or TBA

Section 7: Principles of Mammalian Cell Culture (online or hybrid course)

The course introduces students to the history, theory, and techniques of maintaining live cells in suspension and adherent culture. Main topics covered include safety considerations in cell culture, aseptic techniques, identification and eradication of culture infections, culture initiation, tissue dissociation methods, maintenance, subculture, and harvesting.  Cell viability, media design, cryopreservation and resuscitation of cells, as well as metaphase preparation, banding and chromosome analysis will also be highlighted. (2) credits online for principles (3) credits to include one-week of laboratory.

Instructor: Judy Brown, PhD, Director, Health Care Genetics Master’s Degree Program

Section 8: Microarray Cytogenetics  

The use of microarray technology for cytogenetic analysis. Pre-requisite: prior research or clinical lab experience in genetics or AH 5720 Section 4, 5 or 7. (2) credits online for principles (3) credits to include one-week of laboratory.

Instructor: Judy Brown, PhD, Director, Health Care Genetics Master’s Degree Program

Section 9: Teratology

Evidence-based case studies about the causes & biological processes leading to abnormal development & birth defects. Online and (2) in-person classes

Instructor: Sharon Voyer Lavigne, MS, Genetic Counselor, Coordinator, MotherToBaby CT

Section 10: Occupational Health and Safety in Laboratory Management (2 credits)

This course aims to provide students with a practical knowledge of Occupational Safety and Health (OSH) laws in the USA and how they apply to the scientific community, with an emphasis on management of health and safety in laboratories.  Reference will be made to the Occupational Safety and Health Administration (OSHA) website for relevant reading materials throughout the course. Students will be provided with an introduction to safety and health in the workplace, the role of OSHA, risk management principals and general aspects of laboratory safety. This interactive class will provide students with practical experience in identifying hazards, assessing risks and learning how to select appropriate controls based on those risks.

Section 11: Next Generation Sequencing  

The advent of Next Generation Sequencing (NGS) technologies has transformed how genetic research and clinical testing is being performed. Today, a human genome can today be sequenced in very short time for costs lower than ever expected allowing scientists and clinicians unprecedented possibilities for investigating human traits, mutations, and diseases. Similarly, whole bacterial communities and their interplay with the environment or human microbiome can be studied, unravelling novel enzymes and organisms. (1) credit online for principles (3) credits to include one-week of laboratory.

Instructor: Bo Reese, Ph.D., Scientist, Center for Genome Innovation, UConn Storrs


Section 12: Genetic Counseling Methods & Practice

Orientation to the translational side of genetic and genomic information, interpersonal psychosocial skill development, ethical considerations, and the contemporary practice of clinical genetic counseling. Live role play, case scenarios and analyses will be conducted and explored within the context of counseling theories and the facilitation of informed decision making. 14-week in-person format, 2-hours per week  1-credit.

Instructor: Maria Gyure, MS, LCGC, Director, Genetic Counseling Master’s Degree Program UConn, Storrs

Section 13: Cancer Panels and Tumor Profiling

Profiling somatic mutations of genes to inform about tumor evolution, prognostics and treatment as a tool in clinical oncology. In silico analysis of input candidates for panel design, evaluation of utility of commercially available cancer gene panels, and review of questions to consider when determining if genomic tumor testing is an appropriate method. Testing assessment will include sensitivity, sample requirements, limitations, panel types, and targeted versus genome profiling. Federal regulations, clinical actionability, as well as variant and tumor classifications will be reviewed.  Online and in-person weekend module training.

Instructor: Cara Statz, PhD, Clinical Analyst, Jackson Laboratory for Genomic Medicine