Size-indexed PACE (sipace) for SNP genotyping

Overview

The size-indexed Partitioned Amplification with Capillary Electrophoresis (siPACE) technique presents an innovative solution for cost-effective, high-throughput genotyping of single nucleotide polymorphisms (SNPs) associated with micronutrient deficiencies. This method enables PCR-based SNP genotyping at scale by leveraging multiplexing and sample pooling, significantly reducing the cost-per-sample. siPACE is accurate, rapid, and compatible with non-invasive samples such as saliva or cheek swabs, capable of analyzing up to 9,000 samples per capillary electrophoresis (CE) run.

Technical specifications

• Size-indexed PCR: Utilizes 96 primer sets per SNP, with each amplicon having a defined size in ~4 bp increments for effective size-based barcoding.
• Multiplexing and pooling: Samples are pooled post-PCR, allowing for a single CE injection per 96-well plate, optimizing efficiency.
• Equipment compatibility: Designed to work with standard thermocyclers and commercial CE machines, and uses droplet-digital PCR to resist inhibitors.
• Scalable workflow: Compatible with both manual and automated workflows without the need for microfluidic droplet generation.
• Efficiency: Reduces traditional turnaround times by over 40x and processing costs by more than 1,000x.

Technology readiness level

The siPACE technology is currently at Technology Readiness Level 5, having demonstrated its core capabilities in a controlled environment. Future validation involves benchmarking against existing methods and testing on characterized human samples to further establish its efficacy and reliability.