Cytogenetics Rotation

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
  • provide interpretative support regarding the diagnosis, prognosis, treatment and recurrence risks in patient care decisions
  • be able to correlate cytogenetic and molecular data with all case work-ups as part of a multi-modality diagnostic approach
  • rotate 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.
  • participate in, but not be 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 



  • 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.


Two particularly useful internet sites are:

  1. Atlas of Genetics and Cytogenetics in Oncology and Haematology
  2. 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.


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
  • Tissues
  • 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
  • M-FISH
  • TelVysion
  • Leukemia
    • +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
  • AchE
  • 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
  • Achondroplasia
  • Prothrobin
  • Myotonic Dystrophy