This rotation is four weeks in length. The residents divide their time between Cytogenetics, Histocompatibility & Immunogenetics, and Molecular Oncology, spending one week in each.

Directors: John S. Coon, MD, PhD; and Paul Wong, MD and Wei-Tong Hsu, MD

Histocompatibility & Immunogenetics (one week)
During this rotation the pathology resident observes tissue typing and anti-HLA antibody analysis. They review the HLA system including history, nomenclature, technical procedures, and case files, solid organ and bone marrow transplantation. Residents do not actually generate interpretive. The Laboratory is responsible for a variety of clinical tests related to transplantation, transfusion, and HLA-disease associations. During the past year they provided testing for the 170 renal transplants and 120 bone marrow transplants performed at Rush University Medical Center. The Laboratory testing numbers include 1,000 HLA-A/B/C/DR/DQ typings, 3,800 HLA antibody screens/analyses and 500 cytotoxic and flow cytometric crossmatches.

Molecular Oncology (one week)
Residents observe test procedures in the molecular oncology laboratory that include molecular detection of monoclonal cell populations by DNA and RNA amplification, translocation analysis, mutation detection, DNA sequencing, microsatellite instability testing and molecular monitoring of bone marrow engraftment. They observe results as raw data in context with flow cytometry, cytogenetics and morphological data and participate in clinical interpretation with the Laboratory Director.

Test Name	Method	Tests/Year
Ig Heavy Chain Gene Rearrangement	PCR	300
Ig Light Chain Gene Rearrangement	RT-PCR, Heteroduplex	100
T Cell Receptor Gene Rearrangement	PCR, Heteroduplex	50
Bcl-2 Translocation	qPCR	110
BCRABL Translocation	qRT-PCR	240
PMLRARA Translocation	qRT-PCR	New
JAK2 V617F Mutation Detection	SSP-PCR	110
FLT3 ITD, D835 Mutation Detection	PCR-RFLP	50
Bone Marrow Engraftment / Chimerism	PCR	200
Microsatellite Instability Analysis	PCR	30
KRAS Mutation Analysis	Sequencing	50
BRAF Mutation Analysis	SSP-PCR	New

Cytogenetics

The week-long cytogenetic rotation for pathology residents consists of three components: lectures, bench training and case review. Residents will be given three lectures entitled Introduction of Cytogenetics, Chromosomal Abnormalities in Birth Defects and Cancer Cytogenetics and Its Advances by the director of the cytogenetics laboratory. In the bench-training component, residents will observe important technical procedures, including peripheral blood, bone marrow and tumor specimen processing, practicing chromosome identifications (karyotyping) and participating in FISH analysis. In the latter part of the rotation, they will review cases and sign out along with the director. Upon finishing their rotation, residents should have a working knowledge of the principles and mechanisms of chromosomal abnormalities in constitutional disorders as well as the association between characteristic chromosomal abnormalities (gene rearrangements) and specific types of hematological malignancies. They should be familiar with the utilization of cytogenetic tests and be able to correlate cytogenetic reports and pathology findings. Residents participate in chromosome and FISH analysis as well as the case review and sign out. Graduated responsibility is afforded to those who take additional elective time.