New Study Shows Improved Genotyping by Sequencing with in vitro Repeat Depletion
SAN DIEGO, June 20, 2023 — Jumpcode Genomics, a genome technology platform company focused on improving the understanding of human biology, today announced the results of a study demonstrating the ability to improve genotyping through CRISPR-Cas9-based in vitro repeat depletion, a new method for high-throughput genotyping where repetitive fragments are removed prior to genotyping with low-pass sequencing. The study, published in the journal Genome Research, shows how Jumpcode Genomics’ depletion technology can be used to remove repetitive elements from genome sequencing libraries, allowing for more accurate genotyping of coding and regulatory regions.
The project was developed by the Functional Genomics Laboratory directed by Prof. Massimo Delledonne of the University of Verona in collaboration with the group of Prof. Roberto Papa of the Polytechnic University of Marche. The researchers designed a custom set of 566,766 gRNAs targeting 2.9 Gbp of repeats in the 3.76-Gb genome of lentil (Lens culinaris). This novel depletion method removed approximately 40% of reads mapping to uninformative repeats and resulted in nearly a 10-fold increase in the number of genotyped bases compared to non-depleted libraries. The researchers also observed an increased genotyping accuracy by rescuing thousands of heterozygous variants that otherwise would be missed due to low coverage.
According to the study’s co-lead author, University of Verona Associate Professor Marzia Rossato, “This method has the potential to accelerate the genetic analysis of crops and other organisms with genomes where such large repeat content increases the cost and complexity of analysis.”
The implications of this study are far-reaching, as high-throughput genotyping enables the large-scale analysis of genetic diversity in population genomics and genome-wide association studies that combine the genotypic and phenotypic characterization of large collections of accessions.
“As the scale and complexity of genetic analysis increases over time, better tools are needed to cut through the noise and help studies maximize useable data. We are excited to see our depletion technology have another meaningful impact in genomics,” said Yaron Hakak, CEO of Jumpcode.
About Jumpcode Genomics: Jumpcode Genomics is changing genomics with technology that enables critical workflows for research and clinical applications to break through existing barriers. Our CRISPR-based technology removes uninformative sequences allowing for the sensitive detection of biologically relevant molecules. Combining this technology and next-generation sequencing, it’s now possible to search for and find novel signals that were previously undetectable for greater insights and broadening the understanding of human biology. Discover what we can do at www.jumpcodegenomics.com.