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Test Code KALF Kallmann Syndrome, Xp22.3 Deletion, FISH

Useful For

Establishing a diagnosis of X-linked Kallmann syndrome

 

Detecting cryptic rearrangements involving Xp22.3 that are not demonstrated by conventional chromosome studies

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 application of 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

Kallmann, Xp22.3, FISH

Specimen Type

Varies


Shipping Instructions


Advise Express Mail or equivalent if not on courier service.



Necessary Information


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.



Specimen Required


Submit only 1 of the following specimens:

 

Supplies: Refrigerate/Ambient Mailer, 5 lb (T329)

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.

3. Place the tubes in a Refrigerate/Ambient Mailer, 5 lb (T329).

4. Fill remaining space with packing material.

Additional Information:

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

2. Bloody specimens are undesirable.

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

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

 

Supplies: Hank's Solution (T132)

Specimen Type: Autopsy

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

Specimen Volume: 1 cm(3) biopsy specimen of muscle/fascia from the thigh

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.

 

Supplies: CVS Media (RPMI) and Small Dish (T095)

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 a Petri dish containing transport medium (Such as CVS Media (RPMI) and Small Dish [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

 

Supplies: Hank's Solution (T132)

Specimen Type: Products of conception or stillbirth

Container/Tube: Sterile container with sterile Hank's solution (T132), Ringer's solution, sterile RPMI transport media, 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.

 

Supplies: Hank's Solution (T132)

Specimen Type: Skin biopsy

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

Specimen Volume: 1-cm(3) biopsy specimen of muscle/fascia from the thigh

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)
  Ambient 

Reject Due To

No specimen should be rejected.

Clinical Information

This test is appropriate for individuals with clinical features suggestive of Kallmann syndrome and carrier testing for women with a family history of X-linked ichthyosis.

 

Kallmann syndrome is associated with a deletion on the short arm of the X chromosome. The syndrome is an X-linked disease and can be suspected in patients with complete absence of smell (anosmia), hypogonadism, and delayed sexual development. The phenotype may include gynecomastia, bimanual synkinesis (1 hand copying the movements of the other hand), shortened fourth metacarpal bone, and absence of a kidney. Kallmann syndrome affects mainly males, but rare cases of affected females have been reported.

 

FISH studies are highly specific and do not exclude other chromosome abnormalities.

Reference Values

An interpretive report will be provided.

Interpretation

Any individual with a normal signal pattern (2 signals in females and 1 signal in males) 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 critical region on an X chromosome will be reported as having a deletion of the regions tested by this probe. This is consistent with a diagnosis of Kallmann syndrome (Xp22.3 deletion).

Cautions

Because this FISH test is not approved by the U.S. Food and Drug Administration, it is important to confirm Kallmann syndrome diagnoses by other established methods, such as clinical history or physical evaluation.

 

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 greater than 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 32 patient peripheral blood specimens and compared to cytogenetic or FISH telomere analyses and the patient's phenotype. Using a probe for the Kallmann syndrome, FISH analysis identified a deletion in 1 patient with an X chromosome deletion identified by karyotype analysis and in 1 patient a rearrangement of the X chromosome was further characterized using this probe set. No deletions of the Kallmann critical region were identified in 28 specimens from phenotypically normal males and females. Two patients with a normal result by the KAL1 probe were found to have Xp telomere deletions.

Clinical Reference

Buck C, Balasubramanian R, Crowley WF Jr: Isolated gonadotropin-releasing hormone (GnRH) deficiency. In GeneReviews. Edited by RA Pagon, MP Adam, HH Ardinger, et al: 2007 May 23 (Updated 2013 Jul 18). University of Washington, Seattle. 1993-2014. Accessed 05/27/2013. Available at http://www.ncbi.nlm.nih.gov/books/NBK1334/

Method Description

The detection of the Kallmann syndrome deletion is based on FISH analysis of the critical region (KAL1) on the short arm of the X chromosome (Xp22.3). Metaphase cells are examined for the presence of the critical region loci at Xp22.3 (orange signal) and the control probe at the X centromere (green signal). In metaphase cells with a deletion, the abnormal (deleted) X will exhibit only a control probe signal, while signals for both the critical region and control probes will be present on the normal X homolog in males and on both X chromosomes in females.(Crifasi PA, Michels VV, Driscoll DJ, et al: DNA fluorescent probes for diagnosis of velocardiofacial and related syndromes. Mayo Clin Proc 1995 Dec;195[70]:1148-1153)

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

88271 x 2, 88291-DNA probe, each (first probe set), Interpretation and report

88271 x 2-DNA probe, each; each additional probe set (if appropriate)

88271 x 1-DNA probe, each; coverage for sets containing 3 probes (if appropriate)

88271 x 2-DNA probe, each; coverage for sets containing 4 probes (if appropriate)

88271 x 3-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
KALF Kallmann, Xp22.3, FISH In Process

 

Result ID Test Result Name Result LOINC Value
51955 Result Summary 50397-9
51957 Interpretation In Process
54556 Result In Process
CG701 Reason for Referral 42349-1
CG702 Specimen 31208-2
51958 Source 31208-2
51959 Method 49549-9
51956 Additional Information 48767-8
53858 Disclaimer 62364-5
51960 Released By No LOINC Needed

Forms

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 form (if fetal specimen is sent) in Special Instructions (Only for products of conception or stillbirth specimen).