Long-Read Sequencing

Comprehensive Analysis of Spinal Muscular Atrophy (CASMA)

Covers the Most SMA Possibilities in One Test

The Challenges of Spinal Muscular Atrophy Testing

Spinal Muscular Atrophy (SMA) is primarily caused by defect in the SMN1 gene. molecular testing for SMA is notoriously difficult due to the high sequence homology between SMN1 and SMN2.

Conventional assays (qPCR and MLPA) typically target the c.840C site in exon 7 as a marker for SMN1 copy. This approach has significant limitations as the marker does not always represent the SMN1 functional copy (e.g. non-exon 7 deletions, SNVs/InDels), and is not applicable to the [2+0] carrier status. Consequently, approximately 9% of SMA carriers—including those with [2+0] status, [1+1D], and [2+1D] genotypes—are missed by current routine testing.¹⁻⁴

Conventional genetic assays fail to detect SMN1 gene defects caused by small variants and cannot identify [2+0] carriers, who

Information derived from reference 1-4

Closing the Gap with LRS

Comprehensive Analysis of Spinal Muscular Atrophy (CASMA) offers a single-assay solution overcoming the limitations of current assays:

Detects mutations in SMN1, including rare SNVs and InDels often missed
Determines both SMN1 and SMN2 copy numbers with >99% accuracy⁵
Capable of identifying [2+0] carriers without the need for a proband

Comparison: CASMA vs. qPCR and MLPA and NGS

Variants

qPCR

MLPA

NGS

CASMA

SMN1/ SMN2 CNVs

✔

SMN1 small variants

✔

[2+0] carrier without proband

✔

When considering our send-out sequencing services:

Contact our team for the most up-to-date test details.
Check sample and shipment requirements before sending out to guarantee result quality. Also verify export requirements and your logistics partner.
Contact Xcelom when placing any order along with a completed Test Request and Consent Form, any required QC data and other required document.

Sample Requirements

Peripheral Blood: 2 mL in EDTA tube

Dried Blood Spot (DBS): 3 spots, ≥ 8mm diameter each

Long-fragment gDNA

Transport Conditions

2-8℃, arrive within 72 hours

Testing Scope

Basic Panel

Detects SMN1 and SMN2 full-length copy number, and 133 Pathogenic (P)/ Likely Pathogenic (LP) SMN1 variants

Comprehensive Panel

Detects SMN1 and SMN2 full-length copy number, and a total of 188 SMN1 variants classified as Pathogenic (P)/ Likely Pathogenic (LP)/ Variants of Uncertain Significance (VUS)

Trio [2+0] Carrier Add-on

Determines whether the individual is a silent [2+0] carrier by analyzing the SMN1 full-length copy number in family relatives and confirming the haplotype through family-based analysis

Turnaround Time (TAT)

15 working days

Xcelom Limited and Berry Genomics provide an end-to-end turnkey solution for labs wishing to conduct this test in-house.

Laboratory Setup: Full consultation
Workflow Integration: SOPs, reagents, and staff training
Bioinformatics: Complete software suite for sample management and automated report generation

Platform

PacBio Sequel IIe, Vega and Revio system

Sample Type

gDNA from dried blood spot, blood, and buccal swab

Test per Batch

Max. 384 Tests per SMRT Cell (Mixed Batching Supported)

Operation Time

~ 80 hours (Hand on time: ~10.5 hours)

Automation

Supported

Coverage

Targets full-length of SMN1 and SMN2 genes

The provided time is based on the PacBio Sequel IIe system and may vary across different labs and systems.

Resources

CASMA Brochure

References:

1. Smith M, Calabro V, Chong B, Gardiner N, Cowie S, du Sart D. Population screening and cascade testing for carriers of SMA. Eur J Hum Genet. 2007;15(7):759-766.

2. Qu YJ, Bai JL, Cao YY, et al. Mutation Spectrum of the Survival of Motor Neuron 1 and Functional Analysis of Variants in Chinese Spinal Muscular Atrophy. J Mol Diagn. 2016;18(5):741-752.

3. Mailman MD, Hemingway T, Darsey RL, et al. Hybrids monosomal for human chromosome 5 reveal the presence of a spinal muscular atrophy (SMA) carrier with two SMN1 copies on one chromosome. Hum Genet. 2001;108(2):109-115.

4. Medical Genetics Branch of Beijing Medical Association, and Beijing Rare Disease Diagnosis and Protection Association. Expert consensus on the genetic diagnosis of spinal muscular atrophy. National Medical Journal of China. 2020, 100(40):3130-31140.

5. Bai J, Qu Y, Huang W, et al. A high-fidelity long-read sequencing-based approach enables accurate and effective genetic diagnosis of spinal muscular atrophy. Clin Chim Acta. 2024;553:117743.