Avance Biosciences NGS Center of Excellence: Comprehensive Sequencing Solutions for Biologics, Gene, and Cell Therapy Development

At Avance Biosciences, our Next-Generation Sequencing (NGS) Center of Excellence provides comprehensive sequencing solutions to support every stage of biologics, gene, and cell therapy development. From short- and long-read DNA sequencing for viral vector and plasmid identity, to RNA sequencing for gene expression and biomarker discovery, and single-cell analyses for immune and engineered cell characterization, our NGS platform delivers precise, high-quality data. Whether confirming genomic fidelity, detecting residual contaminants, or mapping integration sites, Avance combines advanced technology with regulatory-compliant workflows to accelerate therapeutic development with confidence.

Identity Testing by NGS

The sequencing library is prepared using various library preparation methods, followed by paired-end sequencing on either the MiSeq or AVITI instrument. This approach allows for sequence confirmation of plasmid, viral vectors, sgRNA, mRNA, and phage.

RNA-Seq for CHO Clone Selection

RNA-seq is used for CHO (Chinese Hamster Ovary) clone selection, offering several benefits and providing comprehensive insights into the cellular and molecular characteristics of different clones.

Amplicon Sequencing

NGS amplicon sequencing is essential for gene editing, enabling precise on- and off-target analysis and characterization of indels and mutations. It provides high-resolution data on specific DNA regions, ensuring the accuracy and efficiency of tools like CRISPR, prime editing, and zinc-finger nucleases.

On/Off Targets Analysis

GuideSeq, rhAmpSeq, and other custom NGS methods are implemented to assess potential off-targets of gene editing products, including CRISPR-Cas9, Zinc Finger Nucleases, and other gene editing technologies. These advanced techniques ensure precise and comprehensive evaluation of gene editing specificity and safety

Gene Translocation Analysis

Amplicon sequencing results from rhAmpSeq are analyzed to identify potential gene translocation events, providing more in-depth information compared to ddPCR or qPCR-based methods. This advanced analysis offers enhanced sensitivity and specificity, allowing for thorough assessment of genetic alterations and translocations.

Integration Site Analysis

Various methods have been developed to investigate integration sites, including whole-genome sequencing (WGS), linear amplification sequencing, and hybridization-based target sequencing. These techniques are instrumental in elucidating integration sites in CHO clonal cell banks, lentivirus-modified CAR-T cells, and identifying potential integration events in animal and human studies.

Targeted Adventitious Agents Testing

This test is designed to detect a specific, known set of adventitious contaminants. It focuses on a predetermined list of potential pathogen threats and uses targeted sequencing or specific assays to identify these known viruses.

Broad-Spectrum Adventitious Agents Testing

This test aims to detect a wide range of potential viral or bacterial contaminants. It does not rely on prior knowledge of the contaminants and can identify unexpected or novel pathogens by sequencing all genetic material (DNA and RNA) present in the sample.

Gene Editing Preclinical PK Study

NGS amplicon sequencing assays are designed and validated to determine the durability and persistence of gene editing effects in animal biodistribution studies.

Gene Editing Preclinical Progeny Study

NGS amplicon sequencing assays are designed and validated to determine durability and persistence in different generations of animals for progeny study.

Gene Editing Clinical PK Study

NGS amplicon sequencing assays are designed and validated to determine the durability and persistence of gene editing effects in human pharmacokinetics (PK) studies.

Custom Workflows

Custom NGS workflows are developed to meet unique project needs, integrating specialized library prep, sequencing platforms, and bioinformatics pipelines. Ideal for novel assay development, rare variant detection, or unconventional sample types requiring tailored solutions.

Integration Site Analysis

Nanopore sequencing enables precise identification and characterization of gene integration sites, particularly in gene-edited cells of clonal origin, such as CHO cell banks.

Complex DNA Sequence Analysis

Nanopore long-read sequencing excels in traversing repetitive sequences, providing a more comprehensive view of genomic architecture compared to Illumina NGS.

Complex RNA Sequence Analysis

Sequencing synthetic RNA directly on Nanopore platforms eliminates the need for PCR amplification, thereby enhancing the reliability of RNA identity and integrity tests.

Identity Testing

Full-length sequencing of plasmids, viral vectors, viral genomes, mRNA vaccines and therapeutics, and sgRNA+mRNA complexes

Purity Testing (Genetic)

Detection of sequence variants, contaminants, or unintended DNA species in plasmids, viral vectors, mRNA vaccines and therapeutics, and sgRNA+mRNA complexes

Structural Characterization

Verification of the structural integrity of viral vectors, AAV genomes, mRNA vaccines and therapeutics, and circular DNAs (e.g., minicircles) and RNAs (circRNAs)

Integration Site Analysis

Mapping the genomic location(s) and verifying the integrity of transgene integration in engineered cell lines or gene-edited cells

Whole Genome Sequencing

Comprehensive sequencing of engineered cell lines and allogeneic therapeutic cells

Variant Calling

Detection of single nucleotide variants (SNVs), insertions and deletions (indels), structural variants (SVs) such as large insertions, deletions, duplications, inversions, and translocations. Supports phasing (determining which variants are on the same chromosome) and direct detection of DNA methylation (an epigenetic modification affecting gene regulation).

Targeted Sequencing

Deep sequencing of specific genomic regions using gene panels, hybrid capture, or amplicon-based enrichment to analyze plasmids, transgenes, or therapeutic target loci.

Transcriptomics

Comprehensive analysis of full-length mRNA transcripts to resolve isoforms (different mRNA variants produced from the same gene) and single-cell RNA sequencing to study gene expression patterns at the individual cell level.

Epigenetics

Direct measurement of DNA methylation patterns across the genome without requiring bisulfite conversion, enabling analysis of gene regulation, potential biomarkers, and the effect of epigenetic therapies.

Metagenomics / Microbiome

High-resolution profiling of complex microbial communities present in clinical samples, biological materials, or production environments. Also supports detection of adventitious microbial agents (unintended microbial contamination).

Cancer Genomics

Detection of fusion genes (abnormal joining of two separate genes), comprehensive epigenetic profiling, identification of complex structural variants, and cancer-specific circRNA biomarkers frequently involved in cancer development and therapeutic resistance.

Rare Disease and Complex Variant Studies

Phasing of disease-associated variants (determining whether multiple pathogenic variants are inherited on the same or different chromosomes) and detection of repeat expansions (abnormally long repetitive DNA sequences linked to rare diseases).

Single Cell RNA-seq (3’ and 5’)

Single Cell RNA-seq enables profiling of gene expression at single-cell resolution, allowing researchers to identify distinct cell types, states, and responses to drugs. It supports tracking of transgene expression and engineered cell fate, such as CAR-T cells, and contributes to mechanism of action studies, biomarker discovery, and potency assessment.

Single Cell ATAC-seq

Single Cell ATAC-seq maps chromatin accessibility and regulatory element activity, revealing epigenetic changes associated with therapy, differentiation, or cell engineering. This approach also provides insight into transcription factor networks and broader regulatory programs that control cell function.

Single Cell V(D)J Sequencing with 5’ Gene Expression

Single Cell V(D)J sequencing characterizes TCR and BCR repertoires, tracking clonal expansion and diversity, particularly in engineered immune cells like CAR-T or TCR-T. It is used to monitor host immune responses, evaluate immunogenicity, and detect minimal residual disease.

Multiome (RNA + ATAC)

The Multiome approach integrates transcriptomic and epigenomic information from the same cell, enabling elucidation of gene regulatory mechanisms that drive cell identity and therapeutic function. This dual-layer analysis supports optimization of vector design, transgene durability, and overall cell therapy performance.

Spatial Transcriptomics (Visium) and Cell Surface Protein with 3’ or 5’ Gene Expression

Spatial Transcriptomics combined with cell surface protein profiling identifies surface markers, categorizes cell types, and enables exploration of cell signaling and interactions within their tissue context, providing a spatially resolved view of cellular function.

Gene Transfer Analysis

Cell and gene therapies employ viral and nonviral vectors to introduce transgenes into target cells. Accurately assessing transduction/transfection efficiency and vector copy number is essential for characterizing these therapies. The Tapestri Platform facilitates the simultaneous measurement of multiple genotypic and phenotypic attributes across thousands of individual cells.

Gene Editing Analysis

Gene-editing technologies, such as CRISPR, are advancing the development of advanced cell and gene therapies. Genome engineering, however, generates heterogeneous cell populations with diverse edits. Some cells may also contain unwanted or deleterious alterations, including off-target edits and chromosomal aberrations like translocations. The Tapestri Platform enables high-resolution single-cell DNA sequencing to analyze gene-edited cells, covering on-/off-target editing, multiplex edits, zygosity, and chromosomal aberrations.

With an unmatched breadth of sequencing platforms and assays, Avance Biosciences’ NGS Center of Excellence delivers end-to-end solutions for biologics, gene therapy, and cell therapy development. From short- and long-read sequencing to advanced single-cell and multi-omics applications, our capabilities span identity confirmation, integration analysis, safety testing, genomic fidelity, biomarker discovery, and more. By combining cutting-edge technologies with regulatory-compliant workflows and deep scientific expertise, we provide our partners with the high-quality data and actionable insights needed to accelerate innovation and bring safe, effective therapies to patients worldwide.

Avance remains dedicated to expanding our capabilities and investing in advanced technologies that support our clients’ success from early discovery through commercialization.

To learn more about our Next-Generation Sequencing (NGS) Center of Excellence, visit: https://www.avancebio.com/tecchnology/next-generation-sequencing-ngs-center-of-excellence/