Heparinized specimens, severely hemolyzed specimens, frozen, clotted or possibly commingled specimens, blood in non-sterile or leaky containers, mislabeled or inappropriately labeled specimens.
Storage/Transport Temperature
For CHOP Phlebotomy: Samples can be collected throughout the week. Samples collected on weekends or holidays are held in Central Labs and sent to the Genomic Diagnostic Lab the following business day.
For External Clients: Refrigerate sample until shipment. Send the sample at room temperature with overnight delivery for receipt Monday through Friday, optimally within 24 hours of collection.
Please contact the lab (267-426-1447) with questions regarding non-blood specimens.
Volume Required
5 mls
Minimum Required
3 mls
Phlebotomy Draw
Yes
Clinical Features
Spinal muscular atrophy (SMA) is a common autosomal recessive disorder affecting ~ 1-2 in 10,000 live births and has a carrier rate of ~1/50. It is a significant cause of infant mortality. The disease is characterized by symmetrical weakness, atrophy of limb muscles, and degeneration of anterior horn cells leading to progressive limb and trunk paralysis. SMA is clinically classified into five types: 0, I, II, III and IV– based on the age that symptoms begin and highest physical milestone achieved. All five types of SMA are caused by mutation of the Survival Motor Neuron 1 (SMN1) gene, also known as the telomeric SMN gene.
A duplicated version of the SMN1 gene lies centromeric on chromosome 5q13.2 and is called SMN2, also known as the centromeric SMN gene. SMN1 and SMN2 have a very high sequence identity and only differ at their 3’ ends by five nucleotides, including a single functional base change in exon 7 (SMN1:c.840C vs SMN2:c.840T) that disrupts a splicing enhancer element in SMN2. Accordingly, only a small amount of full-length transcript is generated by SMN2. Because some functional SMN protein is produced by SMN2, SMA severity is directly influenced by SMN2 copy number, with higher SMN2 dosage predictive of a milder phenotype.
Performing Lab
Division of Genomic Diagnostics
Performed
Monday - Friday 9:00AM - 4.00PM
Methodology
PCR; Fragment Analysis
Genomic DNA is extracted from blood following standard DNA extraction protocols. Exon 7 of the SMN1 and SMN2 genes (NM_000344.3 and NM_017411.4) along with an endogenous control are amplified using the Amplidex PCR/CE SMN1/2 Plus kit (Asuragen Inc). Amplicons are resolved by capillary electrophoresis (ABI 3730). SMN1 and SMN2 copy number are determined by calculating the normalized peak area ratio of the SMN1 and SMN2 amplicons using the AmplideX PCR/CE Reporter and AmplideX PCR/CE SMN analysis module.
Reported
2 days
Detection Rate
The most common SMN1 mutation is a deletion, and about 95% of individuals diagnosed with SMA are homozygous for the SMN1 deletion. An additional 2-5% of individuals with SMA are compound heterozygous for the SMN1 deletion on one allele and a sequence variant in SMN1 on the other allele. Individuals with a heterozygous SMN1 deletion are SMA carriers and have an increased risk of having a child affected by the disorder.
Synonyms
Spinal Muscular Atrophy, SMA, SMN1 & SMN2 Copy Number Analysis
SMN1M
LIS Mnemonic
SMN1M
Available STAT
Yes
Molecular Testing Notes
Homozygous deletion of exon 7 of the SMN1 gene confirms a diagnosis of autosomal recessive spinal muscular atrophy. The AmplideX PCR/CE SMN1/2 Plus assay can be used to detect individuals with SMA (0 copies of SMN1) and SMA carriers (1 copy of SMN1), facilitating therapeutic decisions and determine recurrence risk in families. In addition, this assay can determine SMN2 copy number in individuals with SMA which can provide prognostic information about disease severity and help determine eligibility for these patients to enroll in treatment trials or receive targeted treatment options.
The high level of sequence homology between SMN1 and SMN2 makes the identification of SMN1 deletions by traditional molecular methods challenging. By taking advantage of sequence difference in exon 7 of SMN1 and SMN2, the AmplideX PCR/CE SMN1/2 Plus assay (Asuragen), a rapid PCR-based SMA test, can distinguish between SMN1 and SMN2 and resolve 0 to ≥4 copies of SMN1 and SMN2.
CPT Codes
81400
Collection
Collect
Collect whole blood in a purple-top (EDTA) tube.
Unacceptable Conditions
Heparinized specimens, severely hemolyzed specimens, frozen, clotted or possibly commingled specimens, blood in non-sterile or leaky containers, mislabeled or inappropriately labeled specimens.
Storage/Transport Temperature
For CHOP Phlebotomy: Samples can be collected throughout the week. Samples collected on weekends or holidays are held in Central Labs and sent to the Genomic Diagnostic Lab the following business day.
For External Clients: Refrigerate sample until shipment. Send the sample at room temperature with overnight delivery for receipt Monday through Friday, optimally within 24 hours of collection.
Please contact the lab (267-426-1447) with questions regarding non-blood specimens.
Volume Required
5 mls
Minimum Required
3 mls
Phlebotomy Draw
Yes
Ordering
Clinical Features
Spinal muscular atrophy (SMA) is a common autosomal recessive disorder affecting ~ 1-2 in 10,000 live births and has a carrier rate of ~1/50. It is a significant cause of infant mortality. The disease is characterized by symmetrical weakness, atrophy of limb muscles, and degeneration of anterior horn cells leading to progressive limb and trunk paralysis. SMA is clinically classified into five types: 0, I, II, III and IV– based on the age that symptoms begin and highest physical milestone achieved. All five types of SMA are caused by mutation of the Survival Motor Neuron 1 (SMN1) gene, also known as the telomeric SMN gene.
A duplicated version of the SMN1 gene lies centromeric on chromosome 5q13.2 and is called SMN2, also known as the centromeric SMN gene. SMN1 and SMN2 have a very high sequence identity and only differ at their 3’ ends by five nucleotides, including a single functional base change in exon 7 (SMN1:c.840C vs SMN2:c.840T) that disrupts a splicing enhancer element in SMN2. Accordingly, only a small amount of full-length transcript is generated by SMN2. Because some functional SMN protein is produced by SMN2, SMA severity is directly influenced by SMN2 copy number, with higher SMN2 dosage predictive of a milder phenotype.
Performing Lab
Division of Genomic Diagnostics
Performed
Monday - Friday 9:00AM - 4.00PM
Methodology
PCR; Fragment Analysis
Genomic DNA is extracted from blood following standard DNA extraction protocols. Exon 7 of the SMN1 and SMN2 genes (NM_000344.3 and NM_017411.4) along with an endogenous control are amplified using the Amplidex PCR/CE SMN1/2 Plus kit (Asuragen Inc). Amplicons are resolved by capillary electrophoresis (ABI 3730). SMN1 and SMN2 copy number are determined by calculating the normalized peak area ratio of the SMN1 and SMN2 amplicons using the AmplideX PCR/CE Reporter and AmplideX PCR/CE SMN analysis module.
Reported
2 days
Detection Rate
The most common SMN1 mutation is a deletion, and about 95% of individuals diagnosed with SMA are homozygous for the SMN1 deletion. An additional 2-5% of individuals with SMA are compound heterozygous for the SMN1 deletion on one allele and a sequence variant in SMN1 on the other allele. Individuals with a heterozygous SMN1 deletion are SMA carriers and have an increased risk of having a child affected by the disorder.
Synonyms
Spinal Muscular Atrophy, SMA, SMN1 & SMN2 Copy Number Analysis
SMN1M
LIS Mnemonic
SMN1M
Available STAT
Yes
Molecular Testing Notes
Homozygous deletion of exon 7 of the SMN1 gene confirms a diagnosis of autosomal recessive spinal muscular atrophy. The AmplideX PCR/CE SMN1/2 Plus assay can be used to detect individuals with SMA (0 copies of SMN1) and SMA carriers (1 copy of SMN1), facilitating therapeutic decisions and determine recurrence risk in families. In addition, this assay can determine SMN2 copy number in individuals with SMA which can provide prognostic information about disease severity and help determine eligibility for these patients to enroll in treatment trials or receive targeted treatment options.
The high level of sequence homology between SMN1 and SMN2 makes the identification of SMN1 deletions by traditional molecular methods challenging. By taking advantage of sequence difference in exon 7 of SMN1 and SMN2, the AmplideX PCR/CE SMN1/2 Plus assay (Asuragen), a rapid PCR-based SMA test, can distinguish between SMN1 and SMN2 and resolve 0 to ≥4 copies of SMN1 and SMN2.
