Cytogenetics and Genomics Laboratory

Genetics is a branch of biology that studies the science of genes and heredity. Genes correspond to regions of the genome, which is made up of DNA. DNA is packaged in small organelles called chromosomes for proper segregation of genetic material. Cytogenetics refers to the microscopic analysis of chromosomes in individual cells. Genomics refers to the detailed molecular analysis of the entire genome. Cytogenetics and genomics studies can be performed on fresh blood, bone marrow, prenatal specimens, and solid tissue specimens, and on fixed specimens. A chromosome and/or genome analysis is considered an essential component of the important work-up for individuals with congenital malformations, mental retardation, multiple spontaneous miscarriages, or infertility, and for individuals with hematologic neoplasms and solid tumors. Information about genetic abnormalities in cancer patients can be particularly useful for establishing a diagnosis, for disease classification and monitoring, as well as for treatment decisions. Below are examples of the main types of analyses performed in the laboratory: G-banding karyotype analysis, interphase fluorescence in situ hybridization (IFISH) analysis, and chromosome microarray analysis (CMA).

46,XY

Normal

Trisomy 18

Chromosome 13 deletion

G-banding karyotype analysis
The karyotype from a normal male individual comprises 46 chromosomes with one X and one Y chromosome (46,XY), while females have two X chromosomes (46,XX).
IFISH analysis
Nuclei were hybridized to a red probe for the Y chromosome, a green probe for the X chromosome, and a blue probe for chromosome 18. Nucleus from a normal male, and from a male with trisomy 18.
Chromosome Microarray Analysis
DNA from chronic lymphocytic leukemia cells hybridized to an array. A large deletion of part of chromosome 13 is marked in green and flanked with arrows. Note that a small bi-allelic deletion is also present (open arrow). A schematic of chromosome 13 is shown at the bottom.


Testing Types

  • Prenatal Testing: to detect constitutional cytogenetic and genomic anomalies in prenatal specimens
  • Postnatal Testing: to detect constitutional cytogenetic and genomic anomalies in postnatal specimens
  • Neoplasia Testing: to detect acquired cytogenetic and genomic anomalies in cancer
  • Research Testing: to detect cytogenetic and genomic anomalies in research specimens

News: The Neoplasia Genomic Microarray (CGH/SNP) Test Is Now Available at The Cytogenetics and Genomics Laboratory at UW Medicine Pathology

This test can detect both microscopic and submicroscopic genetic abnormalities genome-wide with immediate knowledge of the genes involved in Neoplastic Disorders, including Hematological Neoplasms and Solid Tumors, using either fresh/frozen specimens or formalin-fixed paraffin-embedded (FFPE) tissue sections/blocks.

Why chromosomal microarray analysis (CMA) for cancer?

  • Detects:
    1. copy number abnormalities including deletions, duplications, or amplifications by surveying the entire genome at very high resolution compared to G-banding chromosome analysis and FISH analysis
    2. copy number neutral loss of heterozygosity (LOH) and segmental or whole chromosome uniparental isodisomy, which commonly occur in cancer and are undetectable by traditional methods
    3. clonal and subclonal abnormalities to evaluate the level of clonal mosaicism
  • Serves as a stand-alone test or as a complement to the chromosome and FISH analyses for an integrated diagnosis and interpretation of abnormalities in neoplastic disorders including hematologic neoplasms and solid tumors
  • Provides a rapid and accurate diagnosis by eliminating the tissue culture step and associated artifacts, which can lead to false negative findings due to normal cell overgrowth.
  • Can be done on FFPE tissue to obtain chromosomal imbalance information without the need for fresh tissue and dividing cells.

Limitation: This assay will not detect low level mosaicism (<20%), balanced alterations (e. g. reciprocal translocations, Robertsonian translocations, inversions, balanced insertions), or point mutations that may be responsible for the clinical phenotype. Microarray analysis is not recommended as a method for post therapy follow-up or for minimal residual disease detection.

 
For more detailed information about the Neoplasia Genomic Microarray CGH/SNP test 
please visit our website or call us:
 
http://www.pathology.washington.edu/clinical/Cytogenetics/
Dr. Yajuan Liu - yajuan@uw.edu
Laboratory Main Number: 206-598-4488
 

How To Submit a CGH/SNP Test Specimen:

  1. Review the Cytogenetics and Genomics Sample Collection Instructions
  2. Completely fill out a Cytogenetics and Genomics Service Request Form
  3. Call the Cytogenetics and Genomics Laboratory PRIOR to any specimen shipping:  206-598-4488
  4. Submit the specimen with the Service Request form as directed on the Sample Collection Instruction form.