Consensus for SMN2 genetic analysis in SMA patients

Number 270
Date 10 March 2023

270th ENMC International Workshop:

Location: Hoofddorp, The Netherlands

Title: Consensus for SMN2 genetic analysis in SMA patients

Date: 10–12 March 2023

Organisers: Prof. Enrico Bertini (Italy), Prof. F. Danilo Tiziano (Italy), Prof. Eduardo F. Tizzano (Spain)

Translations of this report by:
Spanish by Dr. Mar Costa-Roger
Italian by Dr. Emanuela Abiusi
German by Prof. Brunhilde Wirth
Dutch by Dr. Ewout Groen
Polish by Mr Kacper Rucinski
French by Ms Marie-Christine Ouillade

Participants: Dr. Emanuela Abiusi (Italy), Dr. Giovanni Baranello (UK), Dr. François Boemer (Belgium), Prof. Arthur Burghes (USA), Dr. Marta Codina-Solà (Spain), Dr. Mar Costa-Roger (Spain), Dr. Tamara Dangouloff (Belgium), Dr. Ewout Groen (Netherlands), Dr. Monika Gos (Poland), Dr. Maria Jędrzejowska (Poland), Prof. Jan Kirschner (Germany), Dr. Henny Lemmink (Netherlands), Prof. Wolfgang Müller-Felber (Germany), Ms Marie-Christine Ouillade (France), Dr. Susana Quijano-Roy (France), Mr Kacper Rucinski (Poland/UK), Prof. Brunhilde Wirth (Germany).

The 270th ENMC workshop was held from the 10th to the 12th of March 2023 and brought together 20 representatives of patient advocacy groups and industry as well as neuromuscular and clinical experts from 8 European countries and the United States. The main aim of this workshop was the development of a common procedure to optimise the reliability of SMN2 gene copy number determination and the establishment of SMN2 gene networks for the collaboration between laboratories and clinicians.

In previous years, the determination of SMN2 gene copy number was mainly informative and mostly used to elaborate genotype-phenotype correlations, however, this genomic biomarker is currently one of the main determinants for therapeutic decision, especially for patients identified through newborn screening programmes. While genetic confirmation of SMA is relatively straightforward by detecting the absence of both SMN1 gene copies (maternal and paternal; 95% of the patients can be diagnosed with a simple qualitative test), SMN2 gene copy number assessment requires quantitative methodologies that are not easily implemented in most laboratories. Along these lines, retesting DNA samples between laboratories may show surprising discordance up to 40%. SMN2 gene quantification should be rigorously implemented in any laboratory performing SMA tests regardless of their expertise.

DNA sample quality as well as positive and negative calibration controls are of key relevance for testing any sample; additionally, laboratories should take into account parallel testing in different laboratories to resolve ambiguous cases. The group agreed that reports should include the used technology to determine the exact SMN2 gene copy number and to state the precise number of SMN2 gene copies. For this purpose, a session of the workshop was devoted to the discussion with the specialists of different companies that manufacture laboratory kits for SMN2 gene copy number determination; the group has proposed to draw up a series of recommendations for the companies that will help to minimize the risk of errors, regardless of the expertise of individual laboratories.

Much attention has also been paid to the management of cases displaying a genotype-phenotype discordance (severe symptoms in patients with a higher number of SMN2 gene copies or vice versa) and cases with high number of SMN2 gene copies (> 4): the group has agreed upon the definition of a dedicated protocol and the creation of a European network that can share protocols, exchange samples when necessary and support centres with less experience in the most complex diagnoses. In addition, a European patient registry with cases harbouring four SMN2 gene copies has been proposed to better define the natural history.

Besides the number of copies, SMN2 gene punctual and structural variants were also part of the discussion, highlighting the relevance to better investigate these factors. The participants agreed that the validated SMN2 gene positive modifier variants (c.859G>C and c.835-44A>G) should be tested and reported routinely in any diagnostic context (related or not to newborn screening), although there are not enough data to modify treatment decisions based on these variants. Moreover, it was noted that the clinical consequences of hybrid structures are still unclear and require further studies with NGS techniques as well as a database on clinical evolution.

One of the sessions of the workshop was focused on newborn screening. All participants agreed on the need to establish a clear workflow of diagnosis and management of patients identified by neonatal screening with an optimised process of communication. This should also include the presence of a neuromuscular expert during the first meeting with the family, to provide more comprehensive information and perform an accurate clinical assessment of the child. A specialised reference centre, carrying out the confirmatory test and the evaluation of prognostic markers, is highly encouraged. The need for the timeliest diagnosis and patient care was also emphasised: the working group proposes to draw up a recommendation for the turnaround time of the first consultation with the family, the confirmatory test and the treatment start. Another crucial point is that of pre-symptomatic patients with four SMN2 gene copies, for whom the “wait-and-watch” strategy is sometimes used: the main concern with this strategy is related to the risk of early disease manifestation in these individuals, who may onset during early childhood, worsening the therapeutic outcome. For this reason, it was pointed out that, from the biological/physiopathological point of view, early treatment of individuals with four SMN2 gene copies is advisable and there is the need to collect additional clinical data on these individuals to obtain the treatment approval of the regulatory agencies.

Regarding management and treatment of symptomatic patients, it was noted with concern that SMN2 gene copy number has sometimes been used as a regulatory criterion determining access to SMA therapies in certain geographies and it was agreed that treatment decision should be independent of SMN2 gene copies. Again, it has been proposed to define a recommended turnaround time for confirmation genetic test (configured as a true medical urgency) in order to avoid wasting valuable time to initiate treatment.

Lastly, available biomarkers lack reproducibility and longitudinal data and thus are not suitable to predict and monitor treatment response and prognosis of patients (especially for pre-symptomatic); for this reason, the working group encourages future international collaborative studies that may help to define the validity of the candidate biomarkers now available and to evaluate any new ones.

As specific deliverables of this workshop, the participants agreed to determine a standard operating procedure for SMN2 gene copy number determination and a specific workflow for diagnosis and management of SMA newborns identified in neonatal screening as well as to engage collaborative efforts for the creation of a European network to address discrepancies among expert centres. These endeavours will be pursued in the course of 2023.

A full report will be published in Neuromuscular Disorders.