PCR hyper-automation: an example of spinal muscular atrophy and severe combined immunodeficiency screening

Abstract Objectives Most newborn bloodspot screening (NBS) programs use manual or semi-automated systems for severe combined immunodeficiency (SCID) and spinal muscular atrophy (SMA) screening. We aimed to implement a hyper-automated, reliable, and greener system for large-scale SMA and SCID screening. Methods Single 3.2 mm punches from dried bloodspots (DBS) of controls and patients were punched into a 96-well plate. Up to four plates were loaded simultaneously onto an interfaced system comprising a Biomek-i7 for DNA extraction, an Echo-525 liquid handler for preparing a miniaturised master mix using acoustic energy in a 384-well plate, and a Quantstudio7-Flex qPCR instrument. The Eonis SMA-SCID kit was used to determine T-cell receptor excision circles (TRECs) semi-quantitatively and qualitatively detect deletion of exon 7 of the survival motor neuron1 gene ( SMN1 ). The AGREE calculator provided the analytical greenness score and EQA was used for ongoing independent assessment of performance. Results The system provided a turnaround time of less than 3 h for 384 DBS samples. The Echo-525 reduced the primer use by half compared to the manual process. The automated system improved the AGREE score compared to a manual process; 0.8 vs. 0.57 out of 1.0 respectively. Since its introduction in May 2023, and up to May 2026, EQA results have consistently demonstrated satisfactory performance using this automated workflow. Conclusions The study indicates the efficiency of this system as a first-tier NBS assay enabling the early, pre-symptomatic detection of SMA and SCID. This open system can potentially be applied to hyper-automate other large scale qPCR screening tests.