At the core of every scientific breakthrough is unwavering confidence in your data. For the cell and gene therapy field, this means having the utmost confidence in your next-generation sequencing (NGS) data to best understand potential genotoxic effects. However, sequencing the entire genome to high depth is neither computationally nor financially feasible. GeneGoCell’s Genome Editing Verification (GEV℠) G-Amp℠ platform is a proprietary sample-to-report solution that utilizes targeted amplicon sequencing to assay regions of interest. The platform includes assay design, library preparation, sequencing, and custom data analysis. G-Amp℠ is built for accuracy, customizability, efficiency, and quality, delivering cost-effective scalability and tailored support from a GxP/CLIAcompliant, ISO/IEC 17025:2017 accredited lab, all within a guaranteed two-week turnaround time.
Issues with traditional Targeted Amplicon Sequencing
Targeted amplicon sequencing begins with polymerase chain reaction (PCR) that targets specific genomic regions (both on- and off-target loci). Through repeated thermal cycling, DNA templates are exponentially amplified, generating a sequencing-ready library. Ideally, this library reflects the true diversity of DNA within the original cell sample. However, amplification efficiency can vary depending on several factors: private SNPs, editing variants, GC content, each introducing PCR bias, potentially distorting variant frequencies. Moreover, traditional amplicon sequencing lacks the ability to uniquely quantify individual copies of genomic DNA (gDNA), making it impossible to trace and account for these biases and false positives. The gold-standard base calling error rate on most sequencing platforms is approximately 1 in 1,000 (Q30). In other words, low-frequency sequencing errors can be mistaken as true variants and can complicate data interpretation. Therefore, high quality library preparation is imperative to genome editing verification, especially in applications requiring high sensitivity.
G-Amp℠ Solution I: Unique Molecular IDs
As a solution to these inherent challenges posed by traditional targeted amplicon sequencing, G-Amp℠ incorporates unique molecular IDs (UMIs) during PCR such that each genomic copy of DNA found in a sample is barcoded, allowing for accurate quantification and tracking during data analysis. UMIs minimize PCR bias, reduce false positive variant calls, and enable accurate quantification to ensure sufficient coverage of the target site. The G-Amp℠ UMI approach allows us to validate your custom amplicon panel to an limit of detection (LOD) and limit of quantification (LOQ) of 0.01% allele frequency (AF).
G-Amp℠ Solution II: Dual Amplicons (customizable)
In addition to UMIs, by default G-Amp℠ incorporates two unique amplicons per target (G-Amp℠ Dual), while other service providers only design one amplicon. This allows for heightened sensitivity (avoiding allelic dropout from private SNPs) and specificity (only report variants occurring on both amplicons vs either amplicon).
Additionally, our G-Amp℠ analysis pipeline is highly customizable. Whether it be custom reference sequences for alignment (in addition to or in lieu of standard references, e.g. hg38), read-based variant calling (e.g. only using Read1 or Read2), read depth or variant frequency, our pipeline can be tailored to your specific analysis and reporting needs. In addition, the optional off-target calling module can be tailored to your specific criteria for reporting bona fide off-target sites.
Together, the G-Amp℠ platform delivers UMI-enabled molecule-level resolution for variant detection, giving you the confidence to evaluate your gene editing outcomes with unmatched precision and accuracy.
G-Amp℠ Solution III: Multi-target Panel Development
G-Amp℠ Multiplex makes genome editing verification economical by combining multi-target amplicon sequencing (400+ targets) into a single assay. In as little as four weeks, our expert team ensures proper balancing and representation of every target in your panel, achieving > 30,000x UMI coverage for all targets to reach panel-wise 0.01% AF LOQ.
Expert Project Support from Start to Finish
At GeneGoCell, we understand the unique needs from our clients when it comes to their proprietary technologies and platforms. That’s why we customize every project to meet your unique goals – from experimental design to data analysis and reporting. Our dedicated team of experienced project managers, scientists, and PhD-level bioinformaticians collaborate to provide seamless, end-to-end support for each individual project.
About GeneGoCell, Inc.
As a GxP/CLIA, GxP-compliant, ISO/IEC 17025:2017-accredited laboratory based in San Diego, we are deeply committed to the highest standards of data integrity and regulatory readiness. With a proven track record of quality and scientific rigor, we’ve supported over 100+ clients across the globe. Our testing and results have been used in 30+ successful IND filing packages. Our team is currently providing GxP-compliant lot-release testing for 10+ clinical trial programs. Our experienced project managers work closely with you providing end-to-end support, ensuring every step is aligned with your program’s specific goals and compliance needs. Wherever you are in your development journey, we’re here to provide reliable, high-quality NGS support.
GEV doesn’t have to be complicated. We’ve simplified the process from start to finish, with quick onboarding, minimal hands-on time for your team, and results delivered in as little as 3 days. Our experts handle the details so you can stay focused on your research and development goals. Contact our team for a complimentary consultation with our SME for G-Amp Panel feasibility review, discuss your G-Amp Panel, get a customized testing plan or request a quote. We are happy to share the technical White Paper about our G-Amp℠ upon request.
Learn more about G-Amp℠ and find out how GeneGoCell’s Genome-Editing Verification (GEV)℠ platform can be tailored to meet your specific goals and help advance life-changing therapies.
Disclaimer: All Rights Reserved. All content (text, images, code) described by GeneGoCell is copyright of GeneGoCell, Inc unless specifically stated. GeneGoCell is a GxP/CLIA-compliant, ISO/IEC 17025:2017 accredited, (CFR Title 21 Part 58) testing company.