Department of
Pathology, Anatomy and Laboratory Medicine

Educational Goals and Objectives

All PGY levels have the similar goals and objectives except where noted throughout the document. However the expectation for the resident’s performance increases as they gain experience.

The following is an outline of expectations of residents during the Molecular Diagnostics rotation (adapted from Smith, et al, 2006).

  • Demonstrate competency in investigating, evaluating, and interpreting molecular diagnostics cases. This includes selecting and recommending the appropriate molecular (or non-molecular) test for a specific indication, as well as trouble-shooting of molecular assays.
  • Demonstrate professional behavior regarding patients, other physicians and all clinical laboratory personnel.
  • Demonstrate commitments to reviewing and improving Molecular Diagnostics practice patterns and to life-long learning.
  • Understand the scientific basis of Molecular Diagnostics, which includes an understanding of basic molecular biology.
  • Recognize the importance of utilizing the medical literature and modern techniques to provide optimal patient care.
  • Communicate effectively in verbal and written form with their clinical colleagues, administrative, technical, and clerical personnel.
  • Discuss the policies and regulations affecting health care (i.e., CAP accreditation, HIPAA, compliance to Medicare and billing regulations, etc.).

Molecular Diagnostics Specific Goals

General Molecular Diagnostics

  • Develop awareness of sample types, preparation, and storage for molecular biology tests.
  • Understand applicability of testing to various sample types including body fluids, lymph node and spleen.
  • Understand the use of whole blood from heel stick and mass screening studies.
  • Understand storage media and conditions for cells, DNA, and RNA.
  • Understand DNA extraction and purification from a variety of biological specimens.
  • Understand quantitation of purified DNA by spectrophotometry/fluorometry and QC of DNA preparations.
  • Understand basic principles of restriction enzyme digestion.
  • Understand electrophoretic separation of DNA fragments (fragment analysis), native DNA gel electrophoresis for verification of DNA quality, photographic documentation of gels, and capillary electrophoresis methods.
  • Have knowledge of total cellular RNA extraction, quantitation, separation of mRNA and reverse transcription to generate complementary DNA.
  • Understand the principles of Southern blotting.
  • Understand the principles of DNA sequencing (Sanger, pyrosequencing) and develop ability to interpret these tests.
  • Gain basic experience with PCR.
  • Understand and be able to apply basic principles of prevention of amplicon contamination.
  • Understand principles of common mutation scanning technologies
  • Understand principles of real-time quantitative PCR.
  • Understand principles of reverse transcriptase PCR.
  • Understand principles of gene expression microarrays.
  • Understand principles of SNP arrays.
  • Understand basic principles of “next generation sequencing” methodology.
  • Develop ability to critically review literature in the field of Molecular Diagnostics, compare various testing platforms, and evaluate the utility of new molecular disease markers.
  • Develop basic experience in the use of web-based genomic databases.
  • Understand the utility of genetic markers based on population-at-risk and disease prevalence.
  • Understand and use pedigrees for familial genetic assessments.
  • Interpret and report molecular results in association with pathological and laboratory findings and clinical history to reach a final diagnosis.
  • Make recommendations for follow-up or confirmatory molecular studies.
  • Assess the sensitivity and specificity of molecular testing for an individual patient’s disease state.

Molecular Genetics

  • Develop understanding of basic molecular biology concepts.
  • Understand and know molecular testing methods for point mutations underlying inherited thrombophilia (factor V Leiden, Prothrombin 20210 mutation, MTHFR, Platelet Glycoprotein IIIa polymorphisms).
  • Understand and be able to interpret cystic fibrosis diagnosis and screening by PCR/fragment analysis, sequencing and MLPA.
  • Understand molecular testing for hereditary hemochromatosis (C282Y, H53D polymorphisms).
  • Understand molecular testing for triplet repeat disorders (Fragile X, Huntington’s chorea).
  • Understand molecular testing for neuromuscular diseases (Duchenne, Becker muscular dystrophies.
  • Understand basic principles of the mitochondrial genome and the molecular genetics of mitochondrial disorders.
  • Understand indications for and the basic techniques used in prenatal and pregestational molecular diagnostic testing.
  • Understand how molecular diagnostics is used in the context of inborn metabolic disorders (PKU, galactosemia, MCAD deficiency).
  • Understanding of basic molecular testing for deafness.
  • Understanding of basic molecular testing for Fibroblast Growth Factor Receptor-related skeletal disorders.
  • Develop basic understanding of the use of Bayesian analysis for risk assessments in molecular genetics.

Pharmacogenetics

  • Understand pharmacogenetic testing for mutations that affect sensitivity to therapeutic agents (cytochrome p450, TPMT ( thiopurine s-methyltransferase), UGT1A1).
  • Discuss application of pharmacogenetic testing for Warfarin sensitivity.

Molecular Identity Testing

  • Understand the technology behind basic identity testing (testing of STR markers) and the way this is used in the context of allogeneic hematopoietic cell. transplantation, paternity testing, twin studies, molar pregnancy, specimen identification and forensics.

Molecular Diagnostics of Solid Tumors

  • Understand molecular testing for inherited cancers (breast, HNCC, FAP, MEN, Li-Fraumeni, von Hippel-Lindau and the neurofibromatoses).
  • Understand molecular testing of other solid tumors (breast, sarcomas, gliomas, colon cancer, head and neck cancer).

Molecular testing in Infections Diseases/Clinical Microbiology

  • Understand molecular diagnostic tests for STD (Chlamydia trachomatis, N gonorrhoeae).
  • Understand molecular diagnostic tests for detection of Herpes and Enteroviruses.
  • Understand molecular testing algorithms for C. difficile.
  • Understand molecular diagnostics tests for detection of high-risk human papillomaviruses.
  • Understand qualitative and quantitative methods used to determine viral load (HIV, CMV, Hep C, EB virus).
  • Understand the role of genotyping of HIV and Hep C in treatment algorithms.
  • Understand basic molecular testing for respiratory pathogens.
  • Understand basic molecular testing for bacterial pathogens.
  • Understand basic molecular testing for mycobacterial infections.

Molecular Hematopathology

  • Develop understanding of basic hematopathology testing for AML, ALL, B and T-cell lymphomas, Myeloproliferative disorders (JAK2), CML (bcr-abl detection and quantitation for therapeutic monitoring; significance of mutations in development of drug resistance).
  • Understand basic molecular aspects of hemoglobinopathies

Ethical and Legal Issues Specific to Molecular Diagnostics

  • Develop awareness of legal and social implications of genetic testing (GINA).
  • Develop awareness of ethical issues related to genetic testing (pregestational testing, prenatal testing, presymptomatic testing, testing of relatives in Huntington Disease, genetic testing of minors).