Molecular Genetics

Goals and Objectives

Patient Care

• Knowledge of proper methodologies for the analysis of the genetic disorders
• Understand test validation in regards to accuracy, precision, analytic sensitivity, and specificity
• Competent in laboratory safety and laboratory regulatory requirements
• Understand the basics of laboratory developed test (LDT) and FDA approved tests.
• Understand pre-analytic concepts before the specimen arrives in the laboratory so education can be provided to the collecting laboratories or ordering physicians.
• Be able to provide advice to clinicians about appropriate specimens and handling requirements for different types of nucleic acid based diagnostic tests, and to communicate urgency of certain samples to the laboratory staff.
• Describe the clinical settings in which various molecular tests are ordered for hematopathology, infectious disease, and solid tumors.
• Know the test of choice for the identification of specific viral diseases, including viral isolation, detection of viral antigens, detection of genomic nucleic acid, or viral serology.
• Know the fundamentals of testing for human immunodeficiency virus, and to be able to correlate the results with the stage of the patient's disease and treatment.
• Know current protocols and recommendations for testing cervical cytology specimens for human papilloma virus, including interpretation of tests.
• Correlate molecular diagnostic data with morphology and clinical information in diagnosing hematopathology, infectious disease, and solid tumors.

Medical Knowledge

• Understanding of pathologic basis disease with respect to genetics and the correlation of genotype/phenotype associations
• Understands inheritance patterns of genetic disorders and in relation to penetrance and variable expression
• Understand the physical and chemical methods used for the purification, analysis and detection of nucleic acids.
• Know the molecular structures, biological functions and physicochemical properties of nucleic acids that are relevant to modem methods of nucleic acid analysis of clinical specimens
• Know the catalytic activities of enzymes used for the analysis of nucleic acid specimens including amplification of specific nucleic acid sequences.
• Understand the rationale for specimen requirements used in molecular testing
• Be able to outline manual preparative methods for DNA/RNA from various sample types and explain rationale of each step and know safety issues for relevant solvents
• Explain the mechanisms of nucleic acid target amplification and nucleic acid signal amplification. List examples of each technique in the molecular diagnosis of hematopathology, infectious disease, and solid tumor specimens.
• Explain the principles of the polymerase chain reaction (PCR) and diagram the steps in the PCR reaction, and now common inhibitors of downstream applications (especially PCR)
• List and describe applications of PCR (including reverse-transcription PCR, multiplex PCR, qualitative and real-time PCR, allele-specific PCR, single base pair extension) in hematopathology, solid tumor and infectious diseases.
• Describe the following methods for nucleic acid detection and how to evaluate quality of extracted nucleic acid or amplified DNA products: gel electrophoresis, blotting, hybridization, and fragment analysis. List examples of each technique in the molecular diagnosis of hematopathology, infectious disease, and solid tumor.
• Explain how the nucleotide sequence of DNA is determined and list applications of DNA sequencing to molecular diagnosis.
• Understand how human identity testing using highly polymorphic short tandem repeats (STR) in the human genome is applied to the analysis of bone marrow engraftment.
• Understand molecular classifications of leukemia and lymphoma and appropriate method for testing
• Understand qualitative/quantitative methods for CML and JAK2 testing in MPN
• Understands principles and techniques associated with direct mutation detection:
  • Restriction fragment length polymorphism
  • FRET analysis
  • Single base extension
  • Allele specific amplification
  • Repeat primed PCR
  • Methylation specific PCR
  • RT-PCR
  • Pyrosequencing
  • Multiple ligation-dependent probe amplification (MLPA)
  • Quantitative PCR
• Know and understand the principles and techniques of Sanger Sequencing
• Recognize and analyze common chromatograph patterns, such as heterozygous bases and insertions and deletions
• Describe the approximate analytic sensitivity for mutation detection
• Know the pitfalls related to PCR that can lead to false negative results 

Practice Based Learning and Improvement

• Understand the use of quality assurance and control in the molecular laboratory.
• Explain 'unidirectional flow' with regards to contamination prevention and effective strategies for contamination prevention, with respect to the appropriate design and workflow in molecular laboratories to ensure quality and reduce the risk of carry-over contamination
• Quantitate purified nucleic acid samples by UV spectrophotometry and is able to use the parameters to determine the quality of extracted nucleic acids.
• Analyze and interpret molecular diagnostic data for inherited diseases, hematopathology, infectious disease, and solid tumor specimens; including appropriate reporting and medical significance of positive and negative test results.
• Perform a literature search on an assigned clinical test and give presentation to the MG faculty and staff.

Professionalism

• Convey information to laboratory staff in a timely manner
• Reading independently on topics related to patient case material and search primary sources
• Demonstrate self-motivation and organization in pursuit of rotation requirements (reading and clinical service time)
• Demonstrate a commitment to ethical principles pertaining to (1) patient privacy and autonomy, (2) the provision or withholding of test results, (3) confidentiality of patient information, (4) informed consent, (5) conflict of interest, and (6) business practices that are in conflict with stated principles of professionalism.
• Demonstrate courteous and collegial behavior with laboratory staff (laboratory supervisor will evaluate resident based on input from laboratory personnel)

Interpersonal and Communication Skills

• To effectively communicate with clinicians about the test results with appropriate interpretation.
• To effectively communicate with lab staff about appropriate sample identification and selection, issues regarding test result interpretation and troubleshooting

Systems-Based Practice

• Understand concepts of laboratory design and procedure that are specific to nucleic acid testing.
• Understand primary issues of QA/QC in molecular amplification, including common sources of false positive and negative results, and basic trouble-shooting
• Explain the regulatory requirements governing all molecular tests, including laboratory developed tests, and compare the differences and similarities among them.
• Define the test designations RUO, IUO, ASR, IVD, and LDT
• Describe the validation process for a lab developed test and requirements for lot validation for all test types.
• Contrast verification of an IVD with validation of an LDT
• Explain the important legal, ethical, and social implications with regards to larger scale/genomic testing and the ability to 'blind' analytes to prevent unintended data analysis (i.e. NGS for tumor discovering AD condition)
• Integrate molecular diagnostic results into hematopathology, inherited disease, infectious disease, and solid tumors pathology reports
• Act as a consultant to clinicians and other pathologists for the use and selection of molecular diagnostics.  Provide appropriate consultations regarding test results.
• Perform an evaluation of lab quality control and quality assurance program.

Duration

The rotation in molecular genetics is two weeks long and typically occurs during year 2.

Duties and Responsibilities of Residents

• Because the core curriculum is taught at one point in the Resident's training, responsibilities do not change on a yearly basis.
• Review and sign out all results with the Attending Pathologist.
• Review molecular laboratory procedures.
• Participate in division case conference, molecular laboratory regular or QA meeting and clinical pathology QA meeting.
• Present a topic to laboratory faculty and staff.

Teaching Staff

• Thomas Prior, PhD – Rotation Director
• James Metcalf – Supervisor, Molecular Genetics laboratory

Supervision and Evaluation

Residents meet on a regular basis with the Attending Pathologist and with the lead technologists for supervision. Residents are evaluated on a monthly basis with regard to acquisition of the Core Competencies listed in this Program Statement. Evaluations are forwarded to the Residency Program Director, where they are available for review. Direct observation and feedback. In addition, residents will take pre- and post-rotation examination.