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Test Code P73F 1p36.3 Microdeletion Syndrome, FISH

Useful For

Establishing a diagnosis of 1p36 deletion syndrome

 

Detecting cryptic rearrangements involving 1p36.3 that are not demonstrated by conventional

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

1p36.3 Del, FISH

Specimen Type

Varies


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

5. 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 the CVS to a 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 1-cm(3) biopsy specimen of muscle/fascia from 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)
  Ambient 

Reject Due To

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

Chromosome 1p microdeletion syndrome is associated with a spectrum of dysmorphic features and mental retardation. The syndrome can be suspected in overweight patients with mental retardation, heart defects, and finger abnormalities. Facial features include microcephaly (small head), short neck, malformed ears, and small deep-set eyes. The phenotype is variable and depends on the size of the deletion.

Reference Values

An interpretive report will be provided.

Interpretation

Any individual with a normal signal pattern (2 signals) 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 will be reported as having a deletion of the region tested by this probe. This is consistent with a diagnosis of 1p microdeletion syndrome.

Cautions

Because this FISH test is not approved by the U.S. Food and Drug Administration, it is important to confirm 1p microdeletion syndrome diagnoses by other established methods such as clinical history or physical evaluation.

 

Chromosomal microarray (CMAC / Chromosomal Microarray, Congenital, Blood or CMAP / Chromosomal Microarray, Prenatal) 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

In a series of 41 patients, this FISH analysis identified a 1p36.3 deletion in 6 patients whose phenotypes were consistent with 1p microdeletion syndrome or a cytogenetic or telomere 1p deletion. Six additional patients with chromosome anomalies involving 1p, but not containing 1p36 deletion, were further characterized to define breakpoints using this probe set. This demonstrated this probe's ability to define other chromosome 1 rearrangements in this region that are not consistent with 1p-. In 29 karyotypically normal patient specimens (peripheral blood, tissue, amniotic fluid, or chorionic villus), no deletions of the region were identified.

Method Description

This test is performed using a laboratory developed TP73 enumeration strategy probe. Metaphase cells are examined for the presence TP73.(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 and its performance characteristics 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
P73F 1p36.3 Del, FISH In Process

 

Result ID Test Result Name Result LOINC Value
51973 Result Summary 50397-9
51975 Interpretation In Process
54560 Result In Process
CG707 Reason for Referral 42349-1
CG708 Specimen 31208-2
51976 Source 31208-2
51977 Method 49549-9
51974 Additional Information 48767-8
53855 Disclaimer 62364-5
51978 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 (if fetal specimen is sent) in Special Instructions.