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Kickstart your cancer research with long-read sequencing

SMARTer PCR cDNA Synthesis Kit has advanced breast cancer research through long-read sequencing

Genomic changes are a characteristic feature in breast cancer cells, such as those that alter splicing events and transcriptomes (Turnbull and Rahman 2008). Existing short-read sequencing has helped identify some of these splicing events and their resulting isoforms (Stricker et al. 2017). However, short-read sequencing requires transcript assembly, and existing assembly tools remain limited in their ability to reconstruct the longer transcripts encoded in eukaryotic genomes (Amarasinghe et al. 2020).

Long-read (LR) sequencing circumvents genome assembly tools by sequencing genome segments up to several megabases long (Logsdon et al. 2020).  This allows more genomic structural variants to be discovered, uncovering novel sources of genetic variation (De Coster et al. 2021).  Reference-based transcript reconstruction is not required for LR RNA sequencing, which enables the analysis of full-length transcripts (Sharon et al. 2013). LR RNA sequencing has demonstrated value for the identification of tumor-associated spliced isoforms in at least one cancer research study (Tang et al. 2020). Harnessing the power of LR sequencing, however, requires a robust cDNA synthesis protocol that enriches full-length cDNA sequences with high fidelity and sensitivity.

Highlighted product for breast cancer research

Our SMARTer PCR cDNA Synthesis Kit is an ideal library preparation kit for LR sequencing with the PacBio sequencer. Researchers from the Jackson Laboratory for Genomic Medicine harnessed our kit to produce robust LR sequencing reads to identify novel isoforms in breast cancer specimens (Figure 1)(Veiga et al. 2022). The pipeline classified LR-seq isoforms based on their similarity with GENCODE (Frankish et al. 2019) isoforms and identified novel isoforms within or not classified in the GENCODE database. 

Figure 1. How the SMARTer PCR cDNA Synthesis Kit was used to identify novel isoforms in breast tumors. Normal and tumor tissues were collected before long-read (LR) and short-read sequencing libraries were prepared. From the sequencing data, isoforms were identified from the LR-seq data and categorized. Figure reproduced from a prior publication (Veiga et al. 2022), original available at https://europepmc.org/article/pmc/pmc8769553, used under CC BY 4.0 / Cropped from original.  

Adopting this approach helped them identify thousands of previously uncharacterized isoforms for both normal and tumor tissues with an average length of 2.6 kb (Figure 2). This is longer than the average length of 1 kb achieved by current MAS-seq pipelines. At least a quarter of the novel isoforms in breast cancer tumors were not identified by short-read RNA sequencing (Figure 3). The LR sequencing datasets thus revealed a level of genomic complexity not observed with standard annotation databases such as RefSeq and GENCODE. Many of these isoforms were also observed in genes participating in key breast cancer-associated pathways and overrepresented in oncogenes (Figure 4). For example, genes associated with MTORC1 signaling and metabolic pathways were enriched for novel isoforms. AS events thus provide prognostic value as well, revealing novel disease pathways and potential therapeutic targets against breast cancer.

Figure 2. Long-read sequencing, facilitated by the SMARTer PCR cDNA Synthesis Kit, can detect isoforms in individual breast cancer or normal samples. Each stacked bar graph represents a tissue sample, along with its characteristics. Figure reproduced from a prior publication (Veiga et al. 2022), original available at https://europepmc.org/article/pmc/pmc8769553, used under CC BY 4.0 / Cropped from original.  

Figure 3. Long-read sequencing allows novel isoforms not detected by short-read sequencing to be identified. Left: Distribution of isoforms from both normal and tumor samples by splicing category (Figure 1). Right: The proportion of distinct LR-seq isoforms detected by short-read sequencing. Figure reproduced from a prior publication (Veiga et al. 2022), original available at https://europepmc.org/article/pmc/pmc8769553, used under CC BY 4.0 / Cropped from original.  

Figure 4. Multiple pathways are enriched for genes with novel isoforms detected by long-read sequencing. Left: Gene pathways within the MSigDB enriched for genes with novel isoforms in tumor tissues. Right: Identifying oncogenes and tumor suppressors overrepresented or underrepresented with unannotated isoforms. Figure reproduced from a prior publication (Veiga et al. 2022), original available at https://europepmc.org/article/pmc/pmc8769553, used under CC BY 4.0 / Cropped from original.  

Try the SMARTer PCR cDNA Synthesis Kit today

LR sequencing is fast becoming the future of high-throughput sequencing. Here, you can see how using the most sensitive cDNA synthesis kit can help researchers discover previously unappreciated isoforms and splicing events that contribute to breast cancer. Speak with our experienced team today to see how you can harness the power of LR sequencing.

References

Amarasinghe, S.L., Su, S., Dong, X., Zappia, L., Ritchie, M.E., and Gouil, Q. (2020). Opportunities and challenges in long-read sequencing data analysis. Genome Biology 21, 30. 10.1186/s13059-020-1935-5.

De Coster, W., Weissensteiner, M.H., and Sedlazeck, F.J. (2021). Towards population-scale long-read sequencing. Nat Rev Genet 22, 572–587. 10.1038/s41576-021-00367-3.

Frankish, A., Diekhans, M., Ferreira, A.-M., Johnson, R., Jungreis, I., Loveland, J., Mudge, J.M., Sisu, C., Wright, J., Armstrong, J., et al. (2019). GENCODE reference annotation for the human and mouse genomes. Nucleic Acids Research 47, D766–D773. 10.1093/nar/gky955.

Logsdon, G.A., Vollger, M.R., and Eichler, E.E. (2020). Long-read human genome sequencing and its applications. Nat Rev Genet 21, 597–614. 10.1038/s41576-020-0236-x.

Sharon, D., Tilgner, H., Grubert, F., and Snyder, M. (2013). A single-molecule long-read survey of the human transcriptome. Nature Biotechnol, 31(11), 1009–1014. 10.1038/nbt.2705

Stricker, T.P., Brown, C.D., Bandlamudi, C., McNerney, M., Kittler, R., Montoya, V., Peterson, A., Grossman, R., and White, K.P. (2017). Robust stratification of breast cancer subtypes using differential patterns of transcript isoform expression. PLOS Genetics 13, e1006589. 10.1371/journal.pgen.1006589.

Tang, A.D., Soulette, C.M., van Baren, M.J., Hart, K., Hrabeta-Robinson, E., Wu, C.J., and Brooks, A.N. (2020). Full-length transcript characterization of SF3B1 mutation in chronic lymphocytic leukemia reveals downregulation of retained introns. Nature Commun, 11(1), 1438. 10.1038/s41467-020-15171-6

Turnbull, C., and Rahman, N. (2008). Genetic predisposition to breast cancer: past, present, and future. Annu Rev Genomics Hum Genet 9, 321–345. 10.1146/annurev.genom.9.081307.164339.

Veiga, D.F.T., Nesta, A., Zhao, Y., Deslattes Mays, A., Huynh, R., Rossi, R., Wu, T.-C., Palucka, K., Anczukow, O., Beck, C.R., et al. (2022). A comprehensive long-read isoform analysis platform and sequencing resource for breast cancer. Sci Adv 8, eabg6711. 10.1126/sciadv.abg6711.


Featured products

Cat. # Product Size Price License Quantity Details
634928 SMARTer® Pico PCR cDNA Synthesis Kit 10 Rxns USD $1477.00

License Statement

ID Number  
330 This product is the subject of a technology license agreement for internal research use only. Use of this product other than for research use may require additional licenses. Information on license restrictions or for uses other than research may be obtained by contacting licensing@takarabio.com.

The SMARTer Pico PCR cDNA Synthesis Kit provides a PCR-based method for producing high-quality cDNA from picogram quantities of total RNA. The cornerstone of SMARTer cDNA synthesis is still our unique SMART (Switching Mechanism At the 5' End of RNA Transcript) technology; now with a modified SMARTer II A oligo. This new and improved oligo, combined with SMARTScribe Reverse Transcriptase, provides higher specificity and increased yields. The SMARTer Pico PCR cDNA Synthesis Kit allows you to synthesize high-quality cDNA for array probe generation, cDNA subtraction, "Virtual Northern" blots, or other applications, from as little as 1 ng of total RNA at extremely low concentrations (or in diluted samples). It is especially useful for researchers who have limited starting material, such as RNA derived from laser-capture microscopy samples, cells sorted by flow cytometry, or other extremely small samples.

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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SMART(er) cDNA synthesis compared to conventional cDNA synthesis

SMART(er) cDNA synthesis compared to conventional cDNA synthesis
SMART(er) cDNA synthesis compared to conventional cDNA synthesis. Unlike conventional cDNA synthesis methods, which involve a multiple enzyme/multiple step procedure, the SMART(er) cDNA synthesis protocol is performed by one reverse transcription reaction, in a single tube, with no adaptor ligation or intervening purification steps. Following PCR amplification, SMART(er) cDNA is immediately available for a variety of downstream applications.

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Comparison of SMARTer Protocols

Comparison of SMARTer Protocols
Comparison of SMARTer Protocols.

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634928: SMARTer Pico PCR cDNA Synthesis Kit

634928: SMARTer Pico PCR cDNA Synthesis Kit
634926 SMARTer® PCR cDNA Synthesis Kit 20 Rxns USD $1526.00

License Statement

ID Number  
330 This product is the subject of a technology license agreement for internal research use only. Use of this product other than for research use may require additional licenses. Information on license restrictions or for uses other than research may be obtained by contacting licensing@takarabio.com.

A kit for performing twenty cDNA syntheses from nanogram amounts of total or poly A+ RNA. The kit utilizes our SMART (Switching Mechanism At 5' end of RNA Template) technology coupled with PCR amplification to generate high yields of full-length double-stranded cDNA suitable for various applications, including Clontech PCR-Select cDNA subtraction, nondirectional cloning, and preparation of complex cDNA probes. The SMARTer PCR cDNA Synthesis Kit includes the same components as the original SMART PCR cDNA Synthesis Kit plus an improved SMARTer II A oligo and SMARTScribe Reverse Transcriptase, which provide higher specificity and increased yield.

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.

Documents Components Image Data

Back

SMART(er) cDNA synthesis compared to conventional cDNA synthesis

SMART(er) cDNA synthesis compared to conventional cDNA synthesis
SMART(er) cDNA synthesis compared to conventional cDNA synthesis. Unlike conventional cDNA synthesis methods, which involve a multiple enzyme/multiple step procedure, the SMART(er) cDNA synthesis protocol is performed by one reverse transcription reaction, in a single tube, with no adaptor ligation or intervening purification steps. Following PCR amplification, SMART(er) cDNA is immediately available for a variety of downstream applications.

Back

Comparison of SMARTer Protocols

Comparison of SMARTer Protocols
Comparison of SMARTer Protocols.

Back

SMARTer PCR cDNA Synthesis Kit (Cat. # 634926)

SMARTer PCR cDNA Synthesis Kit (Cat. # 634926)
634925 SMARTer® PCR cDNA Synthesis Kit 10 Rxns USD $956.00

License Statement

ID Number  
330 This product is the subject of a technology license agreement for internal research use only. Use of this product other than for research use may require additional licenses. Information on license restrictions or for uses other than research may be obtained by contacting licensing@takarabio.com.

A kit for performing ten cDNA syntheses from nanogram amounts of total or poly A+ RNA. The kit utilizes our SMART (Switching Mechanism At 5' end of RNA Template) technology coupled with PCR amplification to generate high yields of full-length double-stranded cDNA suitable for various applications, including Clontech PCR-Select cDNA subtraction, nondirectional cloning, and preparation of complex cDNA probes. The SMARTer PCR cDNA Synthesis Kit includes the same components as the original SMART PCR cDNA Synthesis Kit plus an improved SMARTer II A oligo and SMARTScribe Reverse Transcriptase, which provide higher specificity and increased yield.

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.

Documents Components Image Data

Back

634925: SMARTer PCR cDNA Synthesis Kit

634925: SMARTer PCR cDNA Synthesis Kit

Back

SMART(er) cDNA synthesis compared to conventional cDNA synthesis

SMART(er) cDNA synthesis compared to conventional cDNA synthesis
SMART(er) cDNA synthesis compared to conventional cDNA synthesis. Unlike conventional cDNA synthesis methods, which involve a multiple enzyme/multiple step procedure, the SMART(er) cDNA synthesis protocol is performed by one reverse transcription reaction, in a single tube, with no adaptor ligation or intervening purification steps. Following PCR amplification, SMART(er) cDNA is immediately available for a variety of downstream applications.

Back

Comparison of SMARTer Protocols

Comparison of SMARTer Protocols
Comparison of SMARTer Protocols.

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Takara Bio USA, Inc. provides kits, reagents, instruments, and services that help researchers explore questions about gene discovery, regulation, and function. As a member of the Takara Bio Group, Takara Bio USA is part of a company that holds a leadership position in the global market and is committed to improving the human condition through biotechnology. Our mission is to develop high-quality innovative tools and services to accelerate discovery.

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