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Citations Citations for NGS library prep technologies

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Cancer genomics and epigenomics

Genome alterations such as mutations, copy number variations, and structural variations, in parallel with dysregulations within the epigenetic landscape (i.e., DNA methylation status), are hallmarks of cancer. Whole genome sequencing and targeted sequencing approaches, mainly focused on the detection of somatic variants and CNVs, allow cancer researchers to obtain a comprehensive picture of genomic alterations. Targeted approaches such as exome or panel sequencing focus on specific regions or genes of interest and allow deeper sequencing for increased sensitivity in variant detection with respect to whole genome sequencing. Epigenetic approaches, on the other hand, have proven useful in describing cancer-specific DNA binding proteins, histone modifications, and the DNA methylation makeup of cancer cells. Understanding how these epigenetic changes act in concert with genomic alterations in tumor onset and progression, and in tumor resistance to therapy, is extremely important for improving cancer care.

Highlighted products

We provide many innovative technologies to speed up your whole-genome and targeted sequencing workflow for somatic variant and CNV discovery, including our patented SMARTer ThruPLEX technology. All of our SMARTer ThruPLEX kits are designed to reduce user error, sample loss, and contamination with a single-tube, two-hour, three-step workflow (Figure 1). The highly sensitive SMARTer ThruPLEX DNA-Seq Kit allows the construction of NGS libraries from picogram amounts of DNA, including FFPE samples and ChIP DNA. The SMARTer ThruPLEX Plasma-Seq Kit has been specifically designed for use with cell-free DNA (cfDNA) and circulating tumor DNA (ctDNA). Lastly, the SMARTer ThruPLEX Tag-seq kits contain more than 16 million unique sequences that are used to tag individual DNA fragments prior to amplification, allowing the tracking of fragments through the library preparation, target enrichment, and data analysis processes to detect low-frequency alleles or to count individual fragments.

SMARTer ThruPLEX technology is also compatible with and has been validated for use with significant target enrichment platforms such as Agilent SureSelect, Roche Nimblegen SeqCap EZ, and IDT xGen Lockdown probes. Moreover, SMARTer ThruPLEX technology has been successfully utilized and cited for whole genome sequencing, targeted sequencing, CNV analysis, and ChIP-seq studies in various types of cancers.

SMARTer ThruPLEX technology

Figure 1. SMARTer ThruPLEX technology workflow.


References and publications citing the use of SMARTer ThruPLEX technology for whole genome sequencing, targeted sequencing, CNV analysis, and ChIP-seq studies in various types of cancer include the following:

Cato, L. et al. Development of Bag-1L as a therapeutic target in androgen receptor-dependent prostate cancer. eLife 6, e27159 (2017).

Jeselsohn, R. et al. Allele-specific chromatin recruitment and therapeutic vulnerabilities of ESR1 activating mutations. Cancer Cell 33, 173–186 (2018).

Jin, X. et al. Targeting glioma stem cells through combined BMI1 and EZH2 inhibition. Nature Med. 23, 1352–1361 (2017).

Klevebring, D. et al. Evaluation of exome sequencing to estimate tumor burden in plasma. PLoS One 18, e104417 (2014).

Markus, H. et al. Evaluation of pre-analytical factors affecting plasma DNA analysis. Sci. Rep. 8, 7375 (2018).

McNair, C. et al. Differential impact of RB status on E2F1 reprogramming in human cancer. J. Clin. Invest. 128, 341–358 (2018).

Murtaza, M. et al. Non-invasive analysis of acquired resistance to cancer therapy by sequencing of plasma DNA. Nature 497, 108–112 (2013).

Patel, K. M. et al. Association of plasma and urinary mutant DNA with clinical outcomes in muscle-invasive bladder cancer. Sci. Rep. 7, 5554 (2017).

Wang, X. et al. Purine synthesis promotes maintenance of brain tumor-initiating cells in glioma. Nature Neurosci. 20, 661–673 (2017).

Weiss, G. J. et al. Tumor cell-free DNA copy number instability predicts therapeutic response to immunotherapy. Clin. Cancer Res. 23, 5074–5081 (2017).


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Cat. # Product Size License Quantity Details
R400674 ThruPLEX® DNA-Seq Kit 24 Rxns USD $658.00

License Statement

ID Number  
326 This product is protected by U.S. Patents 7,803,550; 8,399,199; 8,728,737, 9,598,727, 10,196,686, 10,208,337, 11,072,823 and corresponding foreign patents. Additional patents are pending. For further license information, please contact a Takara Bio USA licensing representative by email at licensing@takarabio.com.
M54 This product is covered by the claims of U.S. Patent Nos. 7,704,713 and its foreign counterparts. 

The ThruPLEX DNA-Seq Kit builds on the innovative ThruPLEX chemistry to generate high-complexity DNA libraries from as little as 50 pg of DNA. Single index, dual index, and unique dual index kits are available and must be purchased separately. This product contains reagents for 24 reactions.

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Our products are to be used for Research Use Only. They may not be used for any other purpose, including, but not limited to, use in humans, therapeutic or diagnostic use, or commercial use of any kind. Our products may not be transferred to third parties, resold, modified for resale, or used to manufacture commercial products or to provide a service to third parties without our prior written approval.

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R400674: ThruPLEX DNA-Seq Kit

R400674: ThruPLEX DNA-Seq Kit
R400679 ThruPLEX® Plasma-Seq Kit 24 Rxns USD $707.00

License Statement

ID Number  
326 This product is protected by U.S. Patents 7,803,550; 8,399,199; 8,728,737, 9,598,727, 10,196,686, 10,208,337, 11,072,823 and corresponding foreign patents. Additional patents are pending. For further license information, please contact a Takara Bio USA licensing representative by email at licensing@takarabio.com.
M54 This product is covered by the claims of U.S. Patent Nos. 7,704,713 and its foreign counterparts. 

The ThruPLEX Plasma-Seq Kit builds on the innovative ThruPLEX chemistry to generate high-complexity DNA libraries from cell-free DNA isolated from plasma. Single index, dual index, and unique dual index kits are available and must be purchased separately. This product contains reagents for 24 reactions.

Notice to purchaser

Our products are to be used for Research Use Only. They may not be used for any other purpose, including, but not limited to, use in humans, therapeutic or diagnostic use, or commercial use of any kind. Our products may not be transferred to third parties, resold, modified for resale, or used to manufacture commercial products or to provide a service to third parties without our prior written approval.

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R400679: ThruPLEX Plasma-Seq Kit

R400679: ThruPLEX Plasma-Seq Kit
R400584 ThruPLEX® Tag-seq 6S (12) Kit 12 Rxns USD $757.00

License Statement

ID Number  
326 This product is protected by U.S. Patents 7,803,550; 8,399,199; 8,728,737, 9,598,727, 10,196,686, 10,208,337, 11,072,823 and corresponding foreign patents. Additional patents are pending. For further license information, please contact a Takara Bio USA licensing representative by email at licensing@takarabio.com.
384 This product is protected by U.S. Patents 7,803,550, 8,399,199; 9,598,727, 10,196,686, 10,208,337, and 10,155,942 and corresponding foreign patents. Additional patents are pending. For further license information, please contact a Takara Bio USA licensing representative by email at licensing@takarabio.com.

The ThruPLEX Tag-seq Kit includes all necessary reagents for generating and multiplexing DNA-seq libraries with the incorporation of Unique Molecular Indexes (UMIs), and includes 6 unique single index PCR primer sets. Once purified and quantified, the resulting library is ready for Illumina NGS instruments using standard Illumina sequencing reagents and protocols. Only 50 pg to 50 ng of fragmented double-stranded DNA is required for library preparation. The entire three-step workflow takes place in a single tube or well in about two hours. No intermediate purification steps or sample transfers are necessary, preventing handling errors and loss of valuable samples. This kit includes reagents sufficient for 12 reactions with 6 single-index primer sets.

Notice to purchaser

Our products are to be used for Research Use Only. They may not be used for any other purpose, including, but not limited to, use in humans, therapeutic or diagnostic use, or commercial use of any kind. Our products may not be transferred to third parties, resold, modified for resale, or used to manufacture commercial products or to provide a service to third parties without our prior written approval.

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R400584: ThruPLEX Tag-seq 6S (12) Kit

R400584: ThruPLEX Tag-seq 6S (12) Kit

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