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Test ID SMNDX Spinal Muscular Atrophy Diagnostic Assay, Deletion/Duplication Analysis, Varies


Additional Testing Requirements


All prenatal specimens must be accompanied by a maternal blood specimen.

-Order MATCC / Maternal Cell Contamination, Molecular Analysis on the maternal specimen.



Shipping Instructions


Specimen preferred to arrive within 96 hours of collection.

 

Prenatal specimens can be sent Monday through Thursday and must be received by 5 p.m. CST on Friday in order to be processed appropriately.



Specimen Required


Patient Preparation: A previous bone marrow transplant from an allogenic donor will interfere with testing. Call 800-533-1710 for instructions for testing patients who have received a bone marrow transplant.

 

Submit only 1 of the following specimens:

 

Specimen Type: Whole blood

Container/Tube:

Preferred: Lavender top (EDTA) or yellow top (ACD)

Acceptable: Any anticoagulant

Specimen Volume: 3 mL

Collection Instructions:

1. Invert several times to mix blood.

2. Send specimen in original tube.

Additional Information: To ensure a minimum DNA amount and concentration, the preferred blood volume must be submitted. Testing may be canceled if the specimen supplied is inadequate. 

Specimen Stability Information: Ambient (preferred)/Refrigerated

 

Prenatal Specimens

Due to the complexity of prenatal testing, consultation with the laboratory is required for all prenatal testing.

 

Submit only 1 of the following specimens:

 

Specimen Type: Amniotic fluid

Container/Tube:

Preferred: Screw-capped, sterile centrifuge tubes

Acceptable: T-25 flasks of confluent cultured cells

Specimen Volume: 20 mL

Specimen Stability Information: Refrigerated (preferred)/Ambient

 

Specimen Type: Chorionic villi

Container/Tube:

Preferred: 15-mL tube containing 15 mL of transport media

Acceptable: T-25 flasks of confluent cultured cells

Specimen Volume: 20 mg

Specimen Stability Information: Refrigerated

 

Specimen Type: Blood spot

Supplies:

Preferred: Collection card (Whatman Protein Saver 903 Paper)

Acceptable: Ahlstrom 226 filter paper, or Card-Blood Spot Collection Filter paper (T493)

Container/Tube:

Preferred: Collection card (Whatman Protein Saver 903 Paper)

Acceptable: Ahlstrom 226 filter paper, or Blood Spot Collection Card (T493)

Specimen Volume: 5 Blood Spots on collection card (Whatman Protein Saver 903 Paper; Ahlstrom 226 filter paper; or Blood Spot Collection Card)

Collection Instructions:

1. An alternative blood collection option for a patient >1 year of age is finger stick.

2. Let blood dry on the filter paper at ambient temperature in a horizontal position for 3 hours.

3. Do not expose specimen to heat or direct sunlight.

4. Do not stack wet specimens.

5. Keep specimen dry

Specimen Stability Information: Ambient (preferred)/Refrigerated

Additional Information:

1. For collection instructions, see Blood Spot Collection Instructions in Special Instructions.

2. For collection instructions in Spanish, see Blood Spot Collection Card-Spanish Instructions (T777) in Special Instructions.

3. For collection instructions in Chinese, see Blood Spot Collection Card-Chinese Instructions (T800) in Special Instructions.


Forms

1. New York Clients-Informed consent is required. Document on the request form or electronic order that a copy is on file. The following documents are available in Special Instructions:

-Informed Consent for Genetic Testing (T576)

-Informed Consent for Genetic Testing-Spanish (T826)

2. Molecular Genetics: Congenital Inherited Diseases Patient Information (T521) in Special Instructions.

3. If not ordering electronically, complete, print, and send 1 of the following forms with the specimen:

-Neurology Specialty Testing Client Test Request (T732)

-Inborn Errors of Metabolism Test Request (T798)

Useful For

First-tier newborn screening for spinal muscular atrophy (SMA)

 

Prenatal testing for SMA

 

Diagnostic testing to confirm a suspected diagnosis of SMA

Reflex Tests

Test ID Reporting Name Available Separately Always Performed
CULAF Amniotic Fluid Culture/Genetic Test Yes No
CULFB Fibroblast Culture for Genetic Test Yes No
MATCC Maternal Cell Contamination, B Yes No

Testing Algorithm

For prenatal specimens only: If amniotic fluid (nonconfluent cultured cells) is received, amniotic fluid culture/genetic test will be added and charged separately.

 

If chorionic villus specimen (nonconfluent cultured cells) is received, fibroblast culture for genetic test will be added per laboratory protocol and charged separately.

 

For any prenatal specimen that is received, maternal cell contamination testing will be added per laboratory protocol and charged separately.

  

For more information see Newborn Screening Act Sheet Spinal Muscular Atrophy: Zero Functioning Copies of SMN1 in Special Instructions.

 

The following algorithms are available in Special Instructions:

-Inherited Motor Neuron Disease Testing Algorithm

-Newborn Screen Follow-up for Spinal Muscular Atrophy

Method Name

Dosage Analysis by Digital Droplet Polymerase Chain Reaction (ddPCR)

Reporting Name

SMA Diagnostic by Del/Dup

Specimen Type

Varies

Specimen Minimum Volume

Blood: 1 mL
Amniotic Fluid: 10 mL
Chorionic villi: 5 mg

Specimen Stability Information

Specimen Type Temperature Time Special Container
Varies Varies

Clinical Information

Spinal muscular atrophy (SMA) is an autosomal recessive neuromuscular disorder characterized by motor neuron degeneration leading to muscular atrophy with progressive paralysis. It is a genetically complex condition that is traditionally divided into 5 subtypes, depending on the age at which symptoms present and the motor milestones that are achieved. Presentation can range from in utero joint contractures and lack of fetal movement (type 0), to loss of ambulation in adolescence or adulthood (Type IV). All patients with SMA develop symmetrical loss of muscle control, most commonly affecting proximal muscles. The American College of Medical Genetics (ACMG) and The American Congress of Obstetricians and Gynecologists (ACOG) currently recommend offering SMA carrier screening to all couples, regardless of race or ethnicity, before conception or early in pregnancy.

 

The most common form of SMA is associated with the loss of survival motor neuron (SMN) protein, which is encoded by 2 or more genes on chromosome 5. The majority of SMN protein is expressed by the SMN1 gene but a small portion of SMN is also contributed by the SMN2 gene. In fact, SMN1 produces more than 90% of SMN protein, while SMN2 produces less than 10% of residual SMN protein. This occurs because SMN2 differs from SMN1 by 5 nucleotide changes, 1 of which leads to alternative exon 7 splicing, and a reduction of SMN2 expression. Most individuals have 2 copies of SMN1, but individuals with as many as 5 copies of SMN1 have been observed. In addition, individuals may also have 0 to 5 copies of SMN2.

 

SMA is most commonly caused by a homozygous deletion of exon 7 in SMN1. However, some patients with this disorder may be compound heterozygotes, with a deletion of 1 copy of SMN1 and a point mutation in the other allele. The severity of a patient's disease is associated with the number of copies of SMN2 that are present and 3 or more SMN2 copies are associated with a milder SMA phenotype.

 

As the SMA test is a quantitative assay for the number of SMN1 exon 7 deletions, any result showing 2 or more SMN1 copies may, in fact, have 2 copies of SMN1 in cis (on the same chromosome) and a copy of SMN1 with the exon 7 deletion on the other chromosome (in trans). This is called the "2+0" carrier genotype. The frequency of the "2+0" carrier genotype differs by ancestry. Previously, it was not possible to distinguish a "2+0" carrier from an individual with 1 copy of SMN1 on each chromosome. However, following a study performed by Luo et al,(6) it is now possible to provide an adjusted genetic residual carrier risk specific to one’s ancestry, based on the presence or absence of the SMN1 polymorphism g.27134T>G. The presence of this polymorphism is linked to being a "2+0" carrier in the Ashkenazi Jewish and Asian populations and it increases the chances that one is a "2+0" carrier in other populations. Please see the table below for details.

 

SMA carrier residual risk estimates.(6)

Ancestry

Carrier frequency

Detection rate based on copy number alone

Residual risk after detection of 2 copies of SMN1

Detection rate with addition of SMN1 g.27134T>G

Residual risk  of being a 2+0 carrier after absence of SMN1 g.27134T>G

Residual risk of being a 2+0 carrier after presence of SMN1 g.27134T>G

Ashkenazi Jewish

1 in 41.1

90%

1 in 345

94%

1 in 580

2+0 Carrier

Asian

1 in 53

92.6%

1 in 628

93.3%

1 in 701.8

2+0 Carrier

African American

1 in 66

71.1%

1 in 121

N/A

1 in 395.7

1 in 33.5

Hispanic

1 in 117

90.6%

1 in 1,061

N/A

1 in 1,762

1 in 139.6

Caucasian

1 in 35

94.9%

1 in 632

N/A

1 in 769.3

1 in 28.6

Reference Values

An interpretive report will be provided.

Interpretation

An interpretive report will be provided.

Clinical Reference

1. Hendrickson BC, Donohoe C, Akmaev VR, et al: Differences in SMN1 allele frequencies among ethnic groups within North America. J Med Genet 2009;46:641-644

2. Carre A, Empey C: Review of Spinal Muscular Atrophy (SMA) for Prenatal and Pediatric Genetic Counselors. 2016;25:32-43

3. Committee on Genetics: Committee Opinion No. 690: Carrier Screening in the Age of Genomic Medicine. Obstet Gynecol 2017;129:e35-e40

4. Committee on Genetics: Committee Opinion No. 691: Carrier Screening for Genetic Conditions. Obstet Gynecol March 2017;129;e41-e55

5. D'Amico A, Mercuri E, Tiziano FD, Bertini E: Spinal muscular atrophy. Orphanet J Rare Dis 2011;6:71

6. Luo M, Liu L, Peter I, et al: An Ashkenazi Jewish SMN1 haplotype specific to duplication alleles improves pan-ethnic carrier screening for spinal muscular atrophy. Genet Med 2014;16:149-156

7. Prior TW, Nagan N: Spinal muscular atrophy: overview of molecular diagnostic approaches. Curr Protoc Hum Genet 2016;1:88 unit 9.27

8. Prior TW, Nagan N, Sugarman EA, et al: Technical standards and guidelines for spinal muscular atrophy testing. Genet Med 2011;13:686-694

Day(s) and Time(s) Performed

Varies

Analytic Time

5 days

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

81329

88235 (if appropriate)

88240 (if appropriate)

88233 (if appropriate)

88240 (if appropriate)

81265 (if appropriate)

LOINC Code Information

Test ID Test Order Name Order LOINC Value
SMNDX SMA Diagnostic by Del/Dup 49857-6

 

Result ID Test Result Name Result LOINC Value
113452 Result Summary 50397-9
113453 Result 49857-6
113454 Interpretation 69047-9
113455 Additional Information 48767-8
113456 Specimen 31208-2
113457 Source 31208-2
113458 Released By 18771-6
Mayo Clinic Laboratories | Pediatric Catalog Additional Information:

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