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Goals and Objectives: 

The cytogenetics rotation is designed to provide the pathology resident with a basic introduction to the theory and methods of cytogenetic analysis and testing. Upon completion of the cytogenetics rotation and the HLA/molecular rotation, the resident should have thoroughly reviewed the basic biochemistry of nucleic acids, including structure, function, replication, and synthesis. The resident will be instructed in the nature of the disease process at the molecular level and the methods used for detection. These disease categories include but are not limited to solid tumors, hematologic diseases, infectious diseases, immunologic disorders, inherited Mendelian diseases, non-Mendelian, and acquired genetic diseases.

The resident is expected to develop the ability to function as a consultant in the selection and application of methods and to provide interpretative support regarding the diagnosis, prognosis, treatment, and recurrence risks in patient care decisions. The resident is expected to be able to correlate cytogenetic and molecular data with all case work-ups as part of a multi-modality diagnostic approach. The resident rotates in the Cytogenetics Laboratory and Molecular Diagnostic laboratory, under the direction of Dr. Mark Pettenati . The trainee is involved in sample preparation, microscopic analysis, and result reporting together with the attending cytogeneticist and molecular geneticists. The residents participate in, but are not primarily responsible for, interpretation and sign-out of final patient reports.

The rotation emphasizes the more common, recurring chromosomal abnormalities found in hematopoietic neoplasms, and the diagnostic and prognostic implications of these abnormalities. The resident will become familiar with conventional cytogenetics procedures including indications for chromosome analysis, culture methods, harvesting and slide preparation, banding techniques, and karyotyping. Teaching and hands-on experience in advanced techniques of molecular cytogenetics will be available, including FISH analysis and chromosomal painting for particular lymphoma/leukemia diagnoses. Additional instruction will include readings from pertinent textbooks and journals, attendance at the weekly Medical Genetics Clinical Conference, and collaboration/participation in case write-ups and research projects.

The required core rotation is for one month. Additional time may subsequently be arranged as an elective at the approval of the laboratory director (Dr. Pettenati) and with the concurrence of the Residency Committee.

Rotation content and activities: 

On the first day of the rotation, the resident will meet with the laboratory director(s) for orientation and to establish a detailed schedule of activities.

A typical rotation will include the following: 

  1. Blood and bone marrow laboratories (week # 1):
    • indications for chromosome analysis
    • culture methods
    • harvesting and slide preparation
    • banding techniques
    • karyotyping
    • resident will perform karyotype on their own chromosomes
  2. FISH Laboratory (week # 2):
    • indications for FISH evaluation
    • slide preparation
    • probe hybridization
    • microscopic evaluation of FISH slides
    • residents will perform FISH on their own chromosomes
  3. Prenatal Laboratory (week # 3):
    • indications for amniotic fluid analysis
    • performance of amniotic fluid analysis
    • interpretation and reporting of results
  4. Concurrent activities (entire rotation):
    • read assigned materials from resource list; discuss with director
    • access assigned web-based materials; discuss with director
    • schedule meeting each week with director for chart review
    • attend and participate in Medical Genetics Clinical meeting (each Wednesday from 3:00 to 4:00 pm in Genomics Conference Room)
    • present cases at Thursday noon CP Conference and at Friday 9:30 CP Rounds
    • review with director: quality control, accreditation, proficiency tests, billing
    • present cytogenetic reports to hemepath and surgical path services
  5. Optional:
    • develop specific project, including case report, abstract, or paper for publication 


Text Books: 

Helm, S. and Mitelman, F. 1995. Cancer Cytogenetics, 2nd Edition. New York: John Wiley & Sons, Inc.
Sandberg, A. 1990. The Chromosomes in Human Cancer and Leukemia, 2nd Edition. New York: Elsevier.
Mitelman, F. 1988. Catalog of Chromosome Aberrations in Cancer. 3rd Edition. New York: A. R. Liss.
Hodgson, S. V. and Maker, E. R. 1993. A Practical Guide to Human Cancer Genetics. Cambridge.


An updated set of internet links can be accessed on the Pathology Department web page.

Two particularly useful internet sites are:

Atlas of Genetics and Cytogenetics in Oncology and Haematology
Online Mendelian Inheritance in Man


The resident will be evaluated by the rotation directors using the Pathology Department system for the ACGME General and specific competencies. The evaluation will be reviewed by the rotation director with each individual resident and with the Program Director. The Residency Committee will review the residents’ performance on the cytogenetic components of the RISE test each year.

Appendix: Laboratory tests and workload volumes: 

Chromosome Analysis (Karyotype) (3,000 per year)
Amniotic Fluid
Peripheral Blood

Bone Marrow (& core)
Chorionic Villi Sampling
Products of Conception
Solid Tumors
Molecular Cytogenetics (3,000 per year)
Fluorescence in situ hybridization: FISH

Prenatal FISH
LSI 13 - CEP-X
CEP 18 - CEP-Y
LSI 21

Microdeletion syndromes:
Di George - 22q11
Velo-cardio-facial - 22q11
Prader-Willi - 15q12
Angelman - 15q12
Williams - 7q12
Miller-Dieker - 17p13
Smith-Magenis - 17p11.2
Wolf-Hirschorn - 4p16
Cri-du-chat - 5p15.3
Kalman - Xp22.3
STS - Xp22.3
SRY - Yp11.3

Chromosome painting

+4/+10 - ALL
TEL/AML - ALL t(12;21)
trisomy 8 - AML
BCR/ABL - CML/ALL t(9;22)
PMR/RARA - APL t(15;17)
MLL - 11q23 rearrangements
+12 - CLL
13q14 - CLL
p53 - CLL 17p13
20q - polycythemia vera
CBFC - AML M4E0 inv(16)
5q- / 7q- - MDS / AML
CCND1 - Mantle Cell lymphoma
t(8;14) - Burkitt’s lymphoma
ALK - lymphoma t(2;5)
i(12p) - germ cell tumor
Her2Nu - Breast Cancer
X/Y - sex mismatch

Neural Tube / Biochemical Genetics (15,000 per year)
Maternal Serum - AFP/hCG/uE3
Amniotic Fluid - AFP
Cancer AFP

Medical Genetics (1,000 per year)
L/S ratio / phosphatidylglycerolAlpha-1-Antitrypsin
Sweat Chlorides for CF testing
Colon Suction Biopsies for Hirschprung’s
Urine chlorides
Human Complement C3

Molecular Genetics (1,000 per year)
Fragile X
Fetal Rh typing (c, D, E)
Cystic Fibrosis
Uniparental disomy*:

  • Prader-Willi syndrome
  • Angelman syndrome
  • Other chromosome specific

    Chimerism for bone marrow transplantation
    Medium chain acyl CoA dehydrogenase (MCAD) deficiency
    Long chain acyl CoA dehydrogenase (LCAD) deficiency
    PWS/AS Methylation Analysis
    Myotonic Dystrophy 

Faculty and Staff:       

Mark J. Pettenati, Ph.D
Professor, Pathology

Quick Reference

Pathology Residency Training Program
Program Director:
Nancy S. Rosenthal, MD

Tel: 336-716-4311
Fax: 336-716-7595

Wake Forest Baptist Medical Center
Medical Center Boulevard
Winston-Salem, NC 27157
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Last Updated: 03-14-2016
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