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Test Code XISTF X-Inactivation (XIST), Xq13.2 Deletion, FISH

Useful For

Evaluation of marker chromosomes derived from chromosome X

Genetics Test Information

Only appropriate to characterize X-derived structurally abnormal chromosomes.

Reflex Tests

Test ID Reporting Name Available Separately Always Performed
_I099 Interphases, 25-99 No, (Bill Only) No
_I300 Interphases, >=100 No, (Bill Only) No
_IL25 Interphases, <25 No, (Bill Only) No
_M30 Metaphases, >=10 No, (Bill Only) No
_ML10 Metaphases, 1-9 No, (Bill Only) No
_PADD Probe, +1 No, (Bill Only) No
_PB02 Probe, +2 No, (Bill Only) No
_PB03 Probe, +3 No, (Bill Only) No
_PBCT Probe, +2 No, (Bill Only) No

Testing Algorithm

This test includes a charge for application of the first probe set (2 FISH probes) and professional interpretation of results. Additional charges will be incurred for all reflex probes performed. Analysis charges will be incurred based on the number of cells analyzed per probe set. If no cells are available for analysis, no analysis charges will be incurred.


Method Name

Fluorescence In Situ Hybridization (FISH)

Reporting Name

XIST, Xq13.2, FISH

Specimen Type


Specimen Required

Provide a reason for referral with each specimen. The laboratory will not reject testing if this information is not provided, but appropriate testing and interpretation may be compromised or delayed.


Advise Express Mail or equivalent if not on courier service.


Submit only 1 of the following specimens:


Specimen Type: Amniotic fluid

Container/Tube: Amniotic fluid container

Specimen Volume: 20-25 mL

Collection Instructions:

1. Optimal timing for specimen collection is during 14 to 18 weeks of gestation, but specimens collected at other weeks of gestation are also accepted. Provide gestational age at the time of amniocentesis.

2. Discard the first 2 mL of amniotic fluid.

Additional Information:

1. Place the tubes in a Styrofoam container (T329).

2. Fill remaining space with packing material.

3. Unavoidably, about 1% to 2% of mailed-in specimens are not viable.

4. Bloody specimens are undesirable.

5. If the specimen does not grow in culture, you will be notified within 7 days of receipt.

6. Results will be reported and also telephoned or faxed, if requested.


Specimen Type: Autopsy

Container/Tube: Sterile container with sterile Hank's balanced salt solution (T132), Ringer's solution, or normal saline

Specimen Volume: 4 mm diameter

Collection Instructions:

1. Wash biopsy site with an antiseptic soap.

2. Thoroughly rinse area with sterile water.

3. Do not use alcohol or iodine preparations.

4. Biopsy specimens are best taken by punch biopsy to include full thickness of dermis.


Specimen Type: Blood

Container/Tube: Green top (sodium heparin)

Specimen Volume: 5 mL

Collection Instructions:

1. Invert several times to mix blood.

2. Other anticoagulants are not recommended and are harmful to the viability of the cells.


Specimen Type: Chorionic villi

Container/Tube: 15-mL tube containing 15 mL of transport media

Specimen Volume: 20-25 mg

Collection Instructions:

1. Collect specimen by the transabdominal or transcervical method.

2. Transfer chorionic villi to Petri dish containing transport medium (T095).

3. Using a stereomicroscope and sterile forceps, assess the quality and quantity of the villi and remove any blood clots and maternal decidua.


Specimen Type: Fixed cell pellet

Container/Tube: Sterile container with a 3:1 fixative (methanol:glacial acetic acid)

Specimen Volume: Entire specimen


Specimen Type: Products of conception or stillbirth

Container/Tube: Sterile container with sterile Hank's balanced salt solution (T132), Ringer's solution, or normal saline

Specimen Volume: 1 cm(3) of placenta (including 20-mg of chorionic villi) and a 1-cm(3) biopsy specimen of muscle/fascia from the thigh

Collection Instructions: If a fetus cannot be specifically identified, collect villus material or tissue that appears to be of fetal origin.

Additional Information: Do not send entire fetus.


Specimen Type: Skin biopsy

Container/Tube: Sterile container with sterile Hank's balanced salt solution (T132), Ringer's solution, or normal saline

Specimen Volume: 4 mm diameter

Collection Instructions:

1. Wash biopsy site with an antiseptic soap.

2. Thoroughly rinse area with sterile water.

3. Do not use alcohol or iodine preparations.

4. A local anesthetic may be used.

5. Biopsy specimens are best taken by punch biopsy to include full thickness of dermis.

Specimen Minimum Volume

Amniotic Fluid: 5 mL/Autopsy, Skin Biopsy: 4 mm/Blood: 2 mL/Chorionic Villi: 5 mg/Fixed Cell Pellet: 1 pellet/Products of Conception: 1 cm(3)

Specimen Stability Information

Specimen Type Temperature Time
Varies Refrigerated (preferred)

Reject Due To

Note: No specimen should be rejected. If specimen not received at appropriate temperature or in wrong anticoagulant, include note to laboratory. Contact the laboratory with questions.

Clinical Information

Turner syndrome is characterized by ovarian hypofunction, short stature, loose skin folds at the back of the neck, and cubitus valgus (elbow deformity) and results from complete or partial monosomy of the X chromosome.


Phenotypic expression of Turner syndrome patients is largely dependent on the patient's karyotype and identification of sex chromosomes mosaicism plays a key role in clinical management. In mosaicism, 2 or more populations of cells with different karyotypes are present (eg, 45,X/46,XX). Additionally, mental retardation is more common in patients with a small ring chromosome derived from an X chromosome with a deletion of the X-inactivation center (XIST) at Xq13.2.


FISH studies are highly specific and do not exclude other chromosome abnormalities, we recommend that patients suspected of having Turner syndrome also have conventional chromosome studies (CHRCB / Chromosomes, Congenital, Blood) performed to rule out other chromosome abnormalities or translocations.

Reference Values

An interpretive report will be provided.


Any individual with a normal signal pattern (signal on each normal X homolog) in each metaphase is considered negative for a deletion in the region tested by this probe.


Any patient with a FISH signal pattern indicating loss of the XIST critical region will be reported as having a deletion of the regions by this probe.


Because this FISH test is not approved by the U.S. Food and Drug Administration, it is important to confirm XIST deletions/duplications by other established methods, such as clinical history or physical evaluation. Chromosomal microarray (CMAC / Chromosomal Microarray, Congenital, Blood or CMAP / Chromosomal Microarray, Prenatal, Amniotic Fluid/Chorionic Villus Sampling) may be the more appropriate test to detect unbalanced translocations, deletions or duplications.


Interfering factors

-Cell lysis caused by forcing the blood quickly through the needle

-Use of an improper anticoagulant or improperly mixing the blood with the anticoagulant

-Excessive transport time

-Inadequate amount of specimen 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° C) may kill cells and interfere with attempts to culture cells.

-In prenatal specimens, a bloody specimen may interfere with attempts to culture cells and contamination by maternal cells may cause interpretive problems.

Supportive Data

FISH analysis was performed on a series of 33 patient specimens (peripheral blood or amniotic fluid) and results were compared to cytogenetic analyses and the patient's phenotype. This FISH analyses was performed on 24 samples that demonstrated a ring chromosome derived from the X chromosome. In 23 cases, XIST was present on the ring chromosome. In 1 case a deletion of XIST was identified. X chromosome rearrangements were identified in an additional 8 patients, demonstrating this probe's ability to define other chromosome X rearrangements that are not consistent with XIST. No deletion of XIST was seen in a patient with a normal karyotype.

Method Description

This test is performed using a laboratory-developed probe set including XIST (Xq13.2) and a commercially available X chromosome control probe (DXZ1). Metaphase cells are examined for the presence of XIST.(Unpublished Mayo Method)

Day(s) and Time(s) Performed

Samples processed Monday through Sunday. Results reported Monday through Friday, 8 a.m.-5 p.m. CST.

Analytic Time

7 days

Specimen Retention Time

Amniotic Fl. (remaining supernatant/whole fluid aliquots): Discarded 14 days after report. Blood: 4 weeks. Products of Conception (identifiable fetal tissue): Cremated quarterly after results reported. All Other Specimens: Discarded when results reported.

Performing Laboratory

Mayo Medical Laboratories in Rochester

Test Classification

This test was developed using an analyte specific reagent. Its performance characteristics were determined by Mayo Clinic in a manner consistent with CLIA requirements. This test has not been cleared or approved by the U.S. Food and Drug Administration.

CPT Code Information

88271x2, 88291 – DNA probe, each (first probe set), Interpretation and report

88271x2 – DNA probe, each; each additional probe set (if appropriate)

88271x1 – DNA probe, each; coverage for sets containing 3 probes (if appropriate)

88271x2 – DNA probe, each; coverage for sets containing 4 probes (if appropriate)

88271x3 – DNA probe, each; coverage for sets containing 5 probes (if appropriate)

88273 w/modifier 52-Chromosomal in situ hybridization, less than 10 cells (if appropriate)

88273-Chromosomal in situ hybridization, 10-30 cells (if appropriate)

88274 w/modifier 52 – Interphase in situ hybridization, <25 cells, each probe set (if appropriate)

88274 – Interphase in situ hybridization, 25 to 99 cells, each probe set (if appropriate)     

88275 – Interphase in situ hybridization, 100 to 300 cells, each probe set (if appropriate)


LOINC Code Information

Test ID Test Order Name Order LOINC Value
XISTF XIST, Xq13.2, FISH In Process


Result ID Test Result Name Result LOINC Value
51997 Result Summary 50397-9
51999 Interpretation 69965-2
54564 Result In Process
CG715 Reason for Referral 42349-1
CG716 Specimen 31208-2
52000 Source 31208-2
52001 Method 49549-9
51998 Additional Information 48767-8
53851 Disclaimer 62364-5
52002 Released By 18771-6


1. New York Clients-Informed consent is required. Please document on the request form or electronic order that a copy is on file. An Informed Consent for Genetic Testing (T576) is available in Special Instructions.

2. Final Disposition of Fetal/Stillborn Remains (if fetal specimen is sent) in Special Instructions