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Advances in Genome Biology and Technology (AGBT) General Meeting
Solutions for NGS analysis of ultra-low inputs and degraded samples
This year, the Advances in Genome Biology and Technology (AGBT) General Meeting celebrated 20 years as the preeminent genome science and technology conference, where top researchers, global leaders, and innovators meet to announce new discoveries, share cutting-edge breakthroughs, and forge collaborations.
We enjoyed meeting you at AGBT 2020, and want to thank you for attending our Women's Networking Event. We invite you to review our poster abstracts and materials from AGBT meetings and reach out to us with any questions or requests via the "speak with us" link below.
AGBT 2020: Women's Networking Event
Supporting and promoting the advancement of women in science is important to our company. Takara Bio was proud to host the 2020 Women's Networking Event at AGBT, and we hope you enjoyed an evening of networking and refreshments—and your commemorative tumbler!
Read about some of the women in our company, including several on our NGS team who attended AGBT.
AGBT 2020: posters
ThruPLEX HV: a simplified system for preparation of molecular-tagged NGS libraries from FFPE and cell-free DNA
Creating next-generation sequencing (NGS) libraries from FFPE and cell-free DNA is critical to developing clinical assays. The systems used for generating the libraries must have simple, streamlined workflows that can accommodate clinical samples while not compromising accuracy. To satisfy these requirements, we have developed a complete, fast, and modular NGS library prep system that enables accurate, reproducible sequencing readouts from challenging sample types. For ease of use and automatability, the ThruPLEX HV system features optional, tunable fragmentation of intact genomic samples from blood, tissue, or other sources. The fragmentation approach does not require additional enzymatic steps and results in highly reproducible fragment sizes optimized for Illumina platforms.
Since accurate measurement of low-frequency mutations is critical when looking for rare alleles in heterogeneous samples (e.g., tissue biopsies or plasma), the ThruPLEX HV system includes optional molecular tags to ensure the most accurate data possible. These distinct molecular tags are well-balanced to ensure optimal representation and accuracy, which are critical considerations when looking for rare alleles. By combining the included molecular tags with deeper sequencing, this system can provide a greater degree of accuracy than is otherwise attainable. Additionally, ThruPLEX HV was designed to accommodate a large input volume, which improves mutation detection by increasing the complexity of the input and eliminates the need to concentrate precious DNA samples prior to library preparation. A final important consideration for low-frequency mutations is achieving even coverage throughout the genome in order to ensure optimal read depth at all relevant loci. To facilitate the necessary even coverage, our system has been optimized across a broad range of GC contents.
Here, we illustrate the robust performance of the system with human-derived cell lines, severely degraded FFPE DNA, cell-free DNA samples, and microbial genomic DNA.
Robust and sensitive detection of gene fusions using high-throughput SMART-Seq chemistry on the ICELL8 cx system
Isolating single cells at high-throughput levels and obtaining their full-length transcript information has become critical to the scientific community to generate rich single-cell datasets. We automated SMART-Seq chemistry on the ICELL8 cx Single-Cell System to address this need and show this workflow provides useful information that end-capture technologies cannot. We present performance data showing that capturing junction and spanning reads with this automated, full-length mRNA-seq method enables confident and robust identification of gene fusions in a breast cancer tumor cell line.
Past AGBT meeting activities
AGBT 2019: Women's Networking Event
Takara Bio is proud to have hosted the 2019 Women's Networking Event at AGBT, and we thank our attendees for a wonderful evening!
AGBT 2018: talk and poster
Streamlined single-cell NGS library prep automation
In this talk, Andrew Farmer (CSO/head of R&D, TBUSA) introduced our ICELL8 automation system and discussed several applications, including SMARTer TCR a/b profiling and full-length SMART-Seq chemistry.
High-throughput single-cell T-cell receptor profiling by SMART technology
Single-cell T-cell receptor (scTCR) clonotype analysis permits the determination of the specific TCR alpha-beta (α/β) chain pairing expressed on each cell. This pairing information allows researchers to gain insight into T-cell heterogeneity and plasticity, determine the contribution of the pairing to antigen specificity of the individual TCR, and design therapeutic antibodies. Here we employ a 5'-RACE-like approach and SMART technology, in conjunction with two novel next-generation sequencing (NGS) library preparation kits, using the same primer pairs, to capture full-length variable regions of TCR-α and -β chains.
Method 1, using the SMARTer Human scTCR a/b Profiling Kit, permits NGS library preparation of FACS-sorted cells in 96-well plates. We present data showing α/β pairing from Jurkat, CCRF, PBMCs, and CD4+ T cells. In addition to the sensitivity of this method, the ability to pool the cDNA from 96 wells into 12 sequencing libraries adds to the ease of use. Consistent with immunology reports, unstimulated CCRF-CEM cells examined with this kit expressed a TCR-β but not a TCR-α chain.
Method 2 is an adaptation of the process above that scales to ~1,200 single cells using the ICELL8 Single-Cell System, which enables single-cell isolation and nanoliter PCR in a nanowell chip. For proof-of-principle studies, Jurkat cells and CCRF-CEM cells were processed using an ICELL8 chip preprinted with barcoded oligos. Paired TCR α/β Jurkat clonotypes were detected in 77% and 87% cells in mixed and single cell populations, respectively.
The ability of the core biochemistry and PCR components of these kits to be used with either FACS-sorted cells in 96-well plates or >1,000 cells in novel ICELL8 chips points to the general utility and scalability of this approach in understanding paired scTCR clonotype diversity.
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