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.


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


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: 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: 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 or Brigette Brown-Kipphut, Agilent Technologies



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: online segment: Dr. Judy Brown
Wet-lab Instructors:
Bo Reese, Ph.D., Scientist, Center for Genome Innovation, UConn Storrs  or
Brigette Brown-Kipphut, Agilent


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.