Test Catalog

Test ID: CHRAF    
Chromosome Analysis, Amniotic Fluid

Useful For Suggests clinical disorders or settings where the test may be helpful

Prenatal diagnosis of chromosome abnormalities, including aneuploidy (ie, trisomy or monosomy) and balanced rearrangements

Genetics Test Information Provides information that may help with selection of the correct genetic test or proper submission of the test request

Cultures from this specimen will be discarded 10 days after all cytogenetic test results have been reported. If further testing is desired, call the laboratory at 507-284-1668.

Testing Algorithm Delineates situations when tests are added to the initial order. This includes reflex and additional tests.

This test includes a charge for cell culture of fresh specimens and professional interpretation of results. Analysis charges will be incurred for total work performed, and generally include 2 banded karyograms and the analysis of 20 metaphase cells. If no metaphase cells are available for analysis, no analysis charges will be incurred. If additional analysis work is required, additional charges may be incurred.


The following algorithms are available in Special Instructions:

-Prenatal Aneuploidy Screening and Diagnostic Testing Options

-High-Risk Pregnancy Based on Fetal Malformations or Positive Serum Screen: Laboratory Testing Algorithm

Clinical Information Discusses physiology, pathophysiology, and general clinical aspects, as they relate to a laboratory test

Chromosome analysis for prenatal diagnosis is appropriate in pregnancies with abnormal maternal screening, advanced maternal age, and features suggestive of or concerns for aneuploidy syndromes, including Down syndrome, Turner syndrome, Klinefelter syndrome, trisomy 13 syndrome, and trisomy 18 syndrome.


Chromosomal abnormalities are the cause of a wide range of disorders associated with birth defects and congenital diseases. Many of these disorders can be diagnosed prenatally by analysis of amniocytes. This method permits diagnosis of chromosome abnormalities during the second trimester of pregnancy or later.


A chromosomal microarray (CMAP / Chromosomal Microarray, Prenatal, Amniotic Fluid/Chorionic Villus Sampling) is recommended, rather than chromosomal analysis, to detect clinically relevant gains or losses of chromosomal material in pregnancies with 1 or more major structural abnormalities. Chromosomal microarray can also be considered, rather than chromosome analysis, for patients undergoing invasive prenatal diagnostic testing with a structurally normal fetus.

Reference Values Describes reference intervals and additional information for interpretation of test results. May include intervals based on age and sex when appropriate. Intervals are Mayo-derived, unless otherwise designated. If an interpretive report is provided, the reference value field will state this.

An interpretative report will be provided.

Interpretation Provides information to assist in interpretation of the test results

Cytogenetic studies on amniotic fluid are considered nearly 100% accurate for the detection of large fetal chromosome abnormalities. However, subtle or cryptic abnormalities involving microdeletions usually can be detected only with the use of targeted FISH testing.


Approximately 3% of amniotic fluid specimens analyzed are found to have chromosome abnormalities. Some of these chromosome abnormalities are balanced and may not be associated with birth defects.


A normal karyotype does not rule out the possibility of birth defects, such as those caused by submicroscopic cytogenetic abnormalities, molecular mutations, and other environmental factors (ie, teratogen exposure). For these reasons, clinicians should inform their patients of the technical limitations of chromosome analysis prior to performing the amniocentesis.


It is recommended that a qualified professional in Medical Genetics communicate all results to the patient.

Cautions Discusses conditions that may cause diagnostic confusion, including improper specimen collection and handling, inappropriate test selection, and interfering substances

Interfering factors:

-Improper syringes or transport vessels may be unsuitable to amniotic cells. Amniotic fluid should not be exposed to the syringe plunger tip for longer than a few seconds and fluid should be transferred to a transport (centrifuge) tube as soon as possible following collection.

-Transport time should not exceed 2 days.

-A bloody specimen may interfere with attempts to culture cells and contamination by maternal cells may cause interpretive problems.

-Inadequate amount of fluid may not permit adequate analysis.

-Improper packaging may result in broken, leaky, and contaminated specimen during transport.

-Exposure of the specimen to temperature extremes (freezing or >30 degrees C) may kill cells and severely interferes with attempts to culture cells.

Clinical Reference Recommendations for in-depth reading of a clinical nature

1. American College of Obstetricians and Gynecologists Committee on Genetics: Committee Opinion No. 581: the use of chromosomal microarray analysis in prenatal diagnosis. Obstet Gynecol 2013;122:1374-1377

2. Society for Maternal-Fetal Medicine (SMFM): The use of chromosomal microarray for prenatal diagnosis. Am J Obstet Gynecol. 2016;215:B2-B9

3. Committee Opinion, 640: Cell-free DNA screening for fetal aneuploidy. American College of Obstetricians and Gynecologists Committee on Genetics. Obstet Gynecol  2015;123:e31-e37

4. Wilson KL, Czerwinski JL, Hoskovec JM, et al: NSGC practice guideline: prenatal screening and diagnostic testing options for chromosome aneuploidy. J Genet Couns 2013;22:4-15

Special Instructions Library of PDFs including pertinent information and forms related to the test