Next-generation sequencing (NGS) and CRISPR—on the surface, they may not be technologies most would categorize together. One is an industry veteran, ubiquitous in the lab, while the other is an up-and-coming star opening doors for genomic editing. But at Jumpcode Genomics, which is combining NGS and CRISPR editing for new research options, the combination is an obvious next step. DDN spoke with Dr. Stanley Nelson, acting chief scientist at Jumpcode, about the company's technology platform and its implications for industry research.
DDN magazine: To begin with, can you give a quick rundown of Jumpcode Genomics' technology platform?
Dr. Stanley Nelson: CRISPRclean is a proprietary technology that utilizes the CRISPR/CAS system to deplete unwanted nucleic acid molecules from sequencing libraries. The process fits seamlessly within standard NGS workflows and works with most commercially available library preparation solutions.
DDN: What kind of benefits or expanded applicability comes from combining next-generation sequencing with CRISPR?
Nelson: Fragments that are not informative in any next-generation sequencing library type (whole genome, whole transcriptome, etc.) can be specifically depleted of any set of sequences. This allows the removal of uninformative repeats from whole genome libraries, reducing the cost of sequencing. As applied to mRNA sequencing, the removal of highly expressed housekeeping or ribosomal RNAs from gene expression experiments allows better observation of low-level expression genes. Removal of high abundance RNAs from libraries in single cell sequencing with 10X libraries improves the ability to observe lower-level expression genes.
DDN: CRISPRclean offers options for both DNA and RNA sequencing, correct?
Nelson: Yes, the process works by targeting the libraries made from DNA or RNA prior, and can be applied to single libraries or mixed tagged libraries.
DDN: Are there certain indications or types of research for which Jumpcode's CRISPRclean is ideally suited?
Nelson: Jumpcode ribosomal depletion is the most effect ribosomal depletion method to remove uninformative ribosomal RNA from the library to enhance gene expression and alternative splicing experiments. We all spend a vast amount of time sequencing more abundant RNAs, and we can use publicly available data to develop a set of pools to deplete unwanted material from libraries to enhance gene discovery science in any species.
DDN: Where are you excited to see CRISPR editing and next-generation sequencing go in the future—both individually and in terms of being combined in CRISPRclean?
Nelson: Broad removal of RNA from RNA sequencing libraries allows the detection of alternative splicing in lower-level genes; this is a critical capability to enable interpretation of whole genome sequence-detected DNA mutations. I believe that this technology is a key component of making whole genome combined with RNA sequencing a reality in clinical laboratories for the interpretation of individual genomes in a far more powerful fashion.
Stanley F. Nelson, M.D., is a physician scientist specializing in the development and application of genomic tools to facilitate gene discovery and molecular diagnostics for rare diseases, with a special interest in muscular dystrophy. He is Professor of Human Genetics, Pediatrics, Neurology and Pathology and Laboratory Medicine at the David Geffen School of Medicine at UCLA, where he has been faculty since 1993. Nelson established the first genomics core at UCLA in 1996. He also holds the positions of founder and co-director at both the Center for Duchenne Muscular Dystrophy and the Clinical Genomics Center, both of which are at UCLA.