CRISPR-based depletion method for resolving pseudogene contamination in Next Generation Sequencing (NGS) based genetic testing

Pseudogenes are non-functional or defective relics that are highly (>90%) homologous to their parental genes. Even with approved guidelines for implementation, clinical tests based on next-generation sequencing (NGS) are challenged because of the presence of these pseudogenes. High frequency of mutations in their DNA sequence and high homology to parent genes prevents short NGS reads from mapping uniquely. Owing to this, recent studies have estimated that one in seven pathogenic variants could not be detected by NGS assays. Jumpcode Genomics proposes a CRISPR-based depletion technology to degrade molecules derived from pseudogenes in NGS libraries. The removal of pseudogenes will both drastically reduce false-positive rates and improve sensitivity and specificity in detecting clinically relevant SNPs. Jumpcode Genomics proposes to apply its CRISPR-based depletion technology to remove pseudogene-derived molecules in library preparation workflows for whole-genome sequencing (WGS) assays, specifically for newborn screening (NBS) clinical tests. The goal is to increase the sensitivity and specificity of detecting disease-causing genetic mutations with high accuracy. In this proposal, Jumpcode aims to extend this technology to a list of 80 genes in the NBS panel and resolve mutations undetected in WGS by increasing the depletion of pseudogenes. Jumpcode performed a pilot study by designing CRISPR-gRNAs (guide RNAs) targeted three genes in NBS panels demonstrated that in a small experiment, the number of false-positive calls can be significantly reduced by carefully designing CRISPR- gRNAs (guide RNAs) that target pseudogene molecules. This demonstrates not only the success of sequence- specific depletion of pseudogenes but also the potential of enhancing variant calling accuracy in NGS panels. This provides a basis for expanding to other genes in NBS lists in this proposal, as well as providing proof of concept for applying DepleteX to other NGS applications in the future. The specific aims of this Phase I proposal include computational design of CRISPR-gRNAs and optimization of protocols to deplete pseudogenes, with the objective of resolving ambiguity in variant calling caused by pseudogenes for a subset of genes in the NBS panel. Functional evaluation of the depletion assay will be conducted, along with comparison with long-range PCR (LR-PCR) for variant calling. The assay will then be independently evaluated in a clinical setting to ensure its accuracy and reliability. The successful demonstration of this pseudogene depletion technology in Phase I will pave the way for future Phase II commercialization efforts, including a clinical utility study to further validate its applicability in clinical settings. This innovative approach holds great promise in improving the accuracy of genetic testing for newborn screening and other clinical applications, ultimately enhancing patient outcomes and advancing precision medicine. Project Number: 1R43HG014080-01 | Fiscal Year: 2025 | NIH Institute/Center: National Human Genome Research Institute (NHGRI) | Principal Investigator: Keith Brown | Institution: JUMPCODE GENOMICS, San Diego, CA | Award Amount: $383,748 | Activity Code: R43 | Study Section: Special Emphasis Panel[ZRG1 MCST-G (15)] View on NIH RePORTER: https://reporter.nih.gov/project-details/11066297