Identification of a Biomarker Associated With Cis-duplication of the SMN1 Gene (BADGES)

University Hospital, Rouen

Status: Terminated

Conditions: Spinal Muscular Atrophy

Treatments: Procedure: blood sampling

Study type: Interventional

Funder types: Other

Identifiers

NCT02550691

2015/092/HP

Details and patient eligibility

About

Spinal Muscular Atrophy (SMA) is a neuromuscular disorder characterized by loss of motor neurons in the anterior horn of the spinal cord and leading to muscle atrophy. SMA has an autosomal recessive inheritance and affects 1 in 6000 infants with a carrier frequency of 1 in 40. In most cases, it is caused by homozygous gene deletion or gene conversion of the SMN1 gene (0+0 genotype) on 5q11-q13. This genomic region has been duplicated and inverted during evolution. Thus the SMN1 gene has a very homologous copy, called SMN2. Genetic counseling aim at detecting carriers with only one copy of the SMN1 gene (0+1 genotype). SMA carrier testing relies on total copy number quantification of the SMN1 copies by quantitative PCR methods. Nevertheless, cis-duplication of the SMN1 gene on one allele and deletion on the second allele (2+0 genotype) can lead to a misinterpretation as molecular methods show 2 copies of the SMN1 gene and cannot detect the carrier status.

The aim of the study is the characterization of a biomarker specific of the cis-duplication of the SMN1 gene in order to allow the detection of this 2+0 genotype which constitutes a trap for genetic counseling. We will use molecular combing to identify a genomic morse code (GMC) composed of a combination of probes specific of a structural motif on the cis-duplication chromosome. The characterization of this GMC is based on the comparison of two sample groups:

• The test group, with a maximum of 137 individuals carrying 3 copies of the SMN1 gene (suggesting a cis-duplication on one allele)
• The control-1 group, with a maximum of 137 individuals carrying 2 copies of the SMN1 gene

A pilot study performed on 24 samples in the two groups is needed to define the exact sample number necessary for statistical analysis of the study. When the GMC will be characterized, its specificity will be evaluated by testing two sample groups:

• The test group, with 37 individuals carrying 3 copies of the SMN1 gene
• The control-2 group, with 37 individuals carrying 3 copies of the SMN2 gene Molecular combing needs long DNA fibers and usual methods for DNA extraction are not appropriate. This project requires new blood samples for specific DNA extraction.

If this project is successful, during a second project, this GMC will be converted into a simple and cheap PCR-based method. We will then evaluate the sensitivity of this method on our sample collection, notably on individuals with the 2+0 genotype defined by familial genotyping.

Enrollment: 48 patients

Sex: All

Ages: 18+ years old

Volunteers: Accepts Healthy Volunteers

Inclusion criteria

• Adult individual
• Individual with either 2 copies of the SMN1 gene (control-1 group), 3 copies of the SMN1 gene (test group), or 3 copies of the SMN2 gene (control-2 group).
• Individual with a social insurance
• Signed consent form

Exclusion criteria

• Pregnant women, nursing women
• Individual without freedom by administrative decision or judicial decision or individual under administrative supervision or legal guardianship

Trial design

Primary purpose: Diagnostic

Allocation: Non-Randomized

Interventional model: Parallel Assignment

Masking: None (Open label)

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48 participants in 3 patient groups

Subject carrying 3 copies of the SMN1 gene

Experimental group

Description:

Using blood sampling, use of molecular combing to identify a genomic morse code (GMC) composed of a combination of probes specific of a structural motif on the cis-duplication chromosome.

Treatment:

Procedure: blood sampling

Subject carrying 2 copies of the SMN1 gene

Other group

Description:

Using blood sampling, use of molecular combing to identify a genomic morse code (GMC) composed of a combination of probes specific of a structural motif on the cis-duplication chromosome.

Treatment:

Procedure: blood sampling

Subject carrying 3 copies of the SMN2 gene

Other group

Description:

Using blood sampling, use of molecular combing to identify a genomic morse code (GMC) composed of a combination of probes specific of a structural motif on the cis-duplication chromosome.

Treatment:

Procedure: blood sampling