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Lab Manual for UCSF Clinical Laboratories

Lab Manual for SFGH

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Molecular Rotation

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  • UCSF Departments of Pathology and Laboratory Medicine
  • 185 Berry Street, Lobby 2, Suite 100
  • Box 0506
  • San Francisco, CA 94143-0506

Residents on the two month Molecular Rotation at the UCSF Clinical Labs at China Basin gain experience in Clinical Cytogenetics, Molecular Diagnostics and Molecular Pathology.

The Clinical Cytogenetics and Molecular Pathology Laboratories provide training in cytogenetic and molecular genetic testing for congenital and acquired diagnoses. Testing samples include amniotic fluid, chorionic villi, products of conception, peripheral blood, and tissue samples, including prenatal and neonatal samples. Cancer studies include bone marrow, bone core biopsies, solid tumors, paraffin embedded slides, effusions, lymph nodes, and peripheral blood samples. These labs currently receive annually approximately 2,500 samples for congenital diagnosis and approximately 200 samples for ERBB2 detection. In the near future the Clinical Cytogenetic Lab will be receiving in house 1,000 samples for hematological cancer studies (currently pending validation). Approximately 500 of the cytogenetic samples include Fluorescence in situ hybridization studies for constitutional studies for microdeletions, trisomy detection, subtelomere rearrangements, and structural rearrangements as well as for acquired abnormalities such as ERBB2 amplification. Residents are responsible for all aspects of these FISH test interpretations, as well as a subset of constitutional test interpretations. Residents observe and assist in the preparation of specimens for analysis and are trained in the science and rationale for these analyses. Independently, they review current cases and their results are discussed with the supervisor and Directors. Reference materials are provided to assist in the interpretation prior to the residents’ final sign out and discussion with the referring physician. This is performed in a coordinated fashion, allowing discussion with supervisors and Directors prior to the final sign out when appropriate.

The Molecular Diagnostics Section performs molecular testing for adult, neonatal and prenatal diagnoses. Specific tests include cystic fibrosis, fragile X syndrome, alpha thalassemia, beta-thalassemia, venous thrombosis, Huntington’s disease, breast cancer, non-syndromic deafness, hemochromatosis, frontotemporal dementia, hemophilia A, Prader-Willi/Angelman syndrome and medium chain of Acyl-coA deficiency. These tests are performed using a combination of PCR and Southern blot methods and a reverse dot blot technology to detect point mutations. Furthermore, the Section is actively involved in the molecular testing of minimal residual disease of chronic myelogenous leukemia (CML) and acute lymphocytic leukemia (ALL) using real-time PCR to quantitate bcr-abl transcripts and a reverse dot blot system to detect the different types of translocations. The resident reviews the reports generated prior to signouts and assembles the relevant clinical background information on interesting cases. At signouts, the cases are reviewed with the Section and Medical Directors and the resident attends the discussion as an active participant. This discussion is a pivotal learning experience for the resident. In addition, the discussion often extends as a one-on-one teaching session with the Section Director.

Molecular techniques similar to the ones in the Molecular Diagnostics section are also used in Microbiology. However, techniques in the Immunology section for b-DNA types of assays are distinct and offer residents additional exposure to molecular testing when they rotate in that section (see separate rotation description).

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