Rotation in Molecular Diagnostics

Learning Objectives

General

1. Familiarize yourself with spatial separation requirements for sample processing, pre-PCR, and post-PCR areas and familiarize yourself with contamination prevention measures.
2. Learn test methodologies, typical problems, and interferences.
3. Learn Quality Control Procedures as they apply to each instrument and methodology.
4. Review levels of assay approval and complexity.
5. Review theory and background of all tests currently offered.
6. Learn the principles and operation of the automated equipment in the laboratory.
7. Familiarize yourself with report recommendations in molecular pathology.
8. Discuss with lab director how to make the website better for future residents.


Week 1 - Clonality Testing

1. Familiarize yourself with the tests run in the lab, read the SOPs and package inserts, and watch how the tests are run.
2. Become familiar with the specimen rejection criteria.
3. What different RNA/DNA extraction methods are used in the laboratory? What are their advantages and disadvantages?
4. Obtain answers to syllabus questions and go over them with the lab director.
5. Discuss case 1
6. More specifically


Week 2 - Thrombophilias, Fragile X, PWS/AS

1. Prepare an in-service presentation for the technicians/supervisors (they can help you pick a topic of interest, but make sure to discuss topic with the lab director).
2. Familiarize yourself with the tests run in the lab, read the SOPs and package inserts, and watch how the tests are run.
3. Become familiar with the specimen rejection criteria.
4. Obtain answers to syllabus questions and go over them with the lab director.
5. Review and interpret current and/or previous assays for Factor V and prothrombin mutations.
6. Review and interpret current and/or previous southern blot results for Fragile X syndrome, Prader-Willi, and Angelman-syndromes.
7. For more detail see:
Thrombophilias
Southern Blot Assay for Fragile X Syndrome
Southern Blot Assay for Prader-Willi/Angelman Syndromes



Week 3 - Gene Sequencing, Mutation Analysis, and CF Screening

1. Familiarize yourself with the tests run in the lab, read the SOPs and package inserts, and watch how the tests are run.
2. Review consent requirements and legal regulations for genetic testing in New York State (Can you “add-on” a test? How long do specimen need to be stored?).
3. Familiarize yourself with genetic testing of chorionic villous tissue.
4. Become familiar with the specimen rejection criteria.
5. Obtain answers to syllabus questions and go over them with the lab director.
6. Discuss case 2
7. Familiarize yourself with the following tests
1. Direct Sequencing of BMPR-II
2. Array-based Primer Extension (“APEX”) test for ABCA4
3. Direct Sequencing of K-ras, Exon 1
4. Direct Sequencing of LGI1
5. TaqMan Allele Specific Probe Assay to Detect the Activating JAK2 Mutation (V617F)
6. Cystic Fibrosis Screening


Week 4 - HPV Testing, Prenatal Screening, Chimerism testing, and MSI Testing

1. Familiarize yourself with the tests run in the lab, read the SOPs and package inserts, and watch how the tests are run.
2. Become familiar with the specimen rejection criteria.
3. Review testing for HPV, including purpose, importance of positive and negative predictive values. What do you do if you don’t have 4 ml of of X left?
4. Obtain answers to syllabus questions and go over them with the lab director.
5. Assist with confirming specimen set-up for high-risk HPV testing.
6. Discuss case 3
7. For more detail see:
   High risk HPV testing
   Prenatal diagnosis
   Chimerism Testing
   Microsatellite instability