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Natalie LaFranzo: Cofactor’s New Director of Scientific Projects and Market Development

Dr. LaFranzo  will be leading Cofactor’s Project Scientist team; the team directly responsible for making sure Cofactor’s newly developed CAP/CLIA RNA tests and RNA sequencing services are addressing the needs of our clients.

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Her leadership comes at an instrumental time in Cofactor’s growth as Cofactor releases multiple RNA-based discovery services aimed at the pre-clinical Pharmaceutical research market- as well as the recently announced rollout of RNA-based oncology clinical tests. In addition to providing a key role in sales leadership, Natalie will be critical in making sure that the efforts from our Biomarkers & Diagnostics teams are addressing customers needs.

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Natalie LaFranzo earned her PhD in Chemistry atWashington University, with an interdisciplinary focus on developing new chemical tools to study neurobiology and development. While at  Washington University, she became an active member of The BALSA Group, which ignited her interest in the commercialization of science, specifically in small businesses. When Natalie was with Cofactor earlier in her career, she served as a Project Scientist and developed customized experimental design solutions for both DNA and RNA sequencing and analysis projects.


Most Screen Shot 2016-06-09 at 4.43.13 PMrecently as a Product Manager in Horizon’s Diagnostic division, Natalie supported the development and marketing of their Next Generation Sequencing products, the launch of new products and product variants, provided guidance on the US regulatory environment, and presented at two FDA workshops on next-generation sequencing.

 

When Natalie is not introducing genomic products and developing markets, she is the head coach of the Washington University Cheerleading Team. She is also active within the American Chemical Society both on a local level in St. Louis, serving as Chair-Elect, and within the National Younger Chemists Committee, serving as Chair in 2016.

Cofactor at ASCO

Cofactor is proud to announce that key members of our Executive and R&D teams will be on the ground at ASCO 2016 in Chicago:

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In addition to seeing the latest advances of our colleagues, we are excited to share some developments and products with you. These include:

* CAP/CLIA RNA-seq

* PicoRNA (Low Input RNA-seq)

* Pinnacle (our RNA-based biomarker panel for cancer)

We look forward to seeing you in Chicago! If you are interested in contacting us, please reach out via [email protected]

 

 

picoRNA and Thinking Outside the Kit

Welcome to my first blog post! In dealing with samples obtained in the clinic, as many researchers frequently do, often only a small amount of tissue is available.  RNA-Seq from low input amounts had been a challenge we always wanted to address with a great solution, but when we start offering a particular service to our customers, we want to make sure that we are able to stand behind the results. For this reason, we carry out internal research projects to test our methodology.   This post highlights the benefits we have obtained through our commitment to continuous testing and process improvement for our low input amount sequencing.

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RNA-seq involving standard input amounts is becoming more routine.  However, many sample types that researchers need access to fall below the amount of RNA required by most protocols.  Examples of such sample sources include: fine needle aspirate, laser capture microdissection, sorted cells, tissue biopsy, and many others.  Reliable, low input quantity RNA sequencing is more challenging due to the increased number of molecular manipulations (such as amplification) required to obtain a library that can be sequenced. Some of these challenges are detailed in our previous post.

Cofactor has developed a solution for low in-put RNA-seq called: picoRNA.

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In order to successfully study low input samples, a scientist needs to create a library with sufficient cDNA for sequencing, to effectively remove the ribosomal RNA in the sample, and to avoid over-amplification which may lead to a lower complexity library. Though library kit manufactures include thorough explanations in the form of manuals and guides, experience is extremely useful for ensuring reliable results.

A fundamental test of a low input approach is preserving the diversity of transcripts in the sample as the amount of total RNA decreases.  The earliest version of our service, picoRNA 1.0, shows consistent expression across input amounts.  We compared 1 ng and 100 pg samples, and found a correlation coefficient greater than 0.99 between the two samples using picoRNA 1.0. Additionally, less than 10% of the total transcripts were unique to each input amount.  As you can see in the plots below, even at a 10 fold sample input difference we are still getting consistent results. Importantly, even in the low abundance transcripts.  

This opens up a large number of sample types from FNA, sorted cells, rare samples, and laser microdissection etc. 

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Our first iteration of picoRNA achieved consistency of transcript expression down to the 100 pg range, but we are always looking to improve our process. We want to provide the best results to our customers, and also maintain our leadership in RNA-Seq. Modifications to picoRNA were completed and further testing was required.

In order to assess our further modifications to picoRNA, I took a look at the results from six of our previous picoRNA sequencing projects (three using version 1.0, one using version 1.5 and two using version 2.0).  After examining the results from all of these projects I found several metrics where our change in methodology yielded an improvement.   Insert size, alignment rate and 3’ bias each showed an improvement as we modified our approach.*

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* Here 3’ bias is defined as the ratio of 3’ to 5’ ends covered of the top 1,000 expressed transcripts in a particular sample

It was great to see how our modifications ended up improving our picoRNA protocol.   A greater alignment rate allows for a project to use a smaller number of raw reads, resulting in potential cost savings as not as much depth of sequencing is required. Both the longer read fragments and the more consistent, less biased coverage improves the data’s performance for isoform detection.

My favorite part of reviewing our results is seeing how Cofactor’s approach to RNA-Seq pays off.   While low input kits are available to any sequencing service provider, these results show how we scrutinize our own procedures, gather data, improve our methods and deliver a superior product (in this case picoRNA). Cofactor is committed to lead the industry in sequencing RNA and improving upon the protocols that manufactures provide is one of the ways that we continue both build and utilize our knowledge.

Cofactor’s picoRNA approach enables researchers to obtain a far more complete scientific/medical picture by providing reliable results from limited material.  We want to allow scientists study any samples that they may be able to obtain.

To find out more

2016 Update: Speed and Price- How Cofactor’s specialization in RNA benefits your project

Three years ago we set out on a mission to transform Cofactor into a company that would lead our industry in pre-clinical discovery services using RNA and clinical tests that would fully leverage the power of RNA.

When we made the commitment to create a different path than other next generation sequencing companies — companies who perform every sequencing application/test known in the industry (i.e. becoming the equivalent of a buffet with 200 items… a lot of variety, but none spectacular) — some really great things happened. We became able to focus our development on building a small number of solutions that represent the very best in the industry, while also providing the best turnaround and pricing available. This is the benefit of specialization in any industry, and this is clearly at work at Cofactor.

For all our valued partners and clients, and for those of you we haven’t yet worked with, we would like to share our 2016:Q2 updated RNA-seq preclinical discovery offerings. They allow you to characterize samples with very limited quantities (our picoRNA offering) and also samples that are very challenging due to low quality (our FFPE99 offering). The prices presented below include full comparative expression analysis and Cofactor’s RNA-seq ActiveSite. In addition, we are excited to offer a 3-week turnaround on all of the products listed below. These products are the result of our R&D and refinements we’ve developed from working with thousands of samples.

Contact us today to take advantage of these offerings and be able to include samples in your study that were previously inaccessible.

2016/Q2 Product Price Sheet

Products:

RNAble-seq – Standards and controls crucial for success lacking from core lab facilities and other service providers.

picoRNA – Gain access to valuable and limiting sources such as; FNA, sorted cells, rare samples, laser capture tissue biopsy.

FFPE-99 – Eliminates variability in low quality RNA samples that have high clinical value.

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Circular RNAs Come to the Forefront

cofactor(76of88) Here at Cofactor, we have long believed in the potential of circular RNA (circRNA) for both diagnostic and therapeutic applications.  While previously thought to be a spurious result of aberrant splicing, the biogenesis of circRNAs has recently been found to be highly conserved and actively regulated.  Moreover, circRNAs  have been shown to be instrumental in several biological processes and to influence the pathology of diseases from Parkinson’s Disease to Cancer.  Perhaps the most exciting characteristics of circRNAs are their resistance to exonuclease degradation and their presence in the bloodstream, making them ideal candidates as translatable biomarkers for the diagnosis and monitoring of a variety of diseases.      

 

An intriguing example of this was published this week by Guarnerio et. al. in Cell.  As the chromosomal translocations that cause fusion proteins share some of the genomic features that lead to circRNAs, the researchers hypothesized that these translocations could also lead to circularized fusion protein transcripts, or “f-circRNAs.”  Tcofactor(33of88)he investigators used a variety of molecular biology techniques to confirm the presence of f-circRNAs in patient samples for  several prominent cancer-associated fusions such as PML-RAR, MLL-AF9, and EML4-ALK.  The authors then went on to show that f-circRNAs could induce cellular transformation in non-cancerous cell lines and that co-expression of f-circRNAs with the linear fusion protein counterpart induced leukemia in a mouse model of AML more intensely than either of the two molecules alone.  Next, the investigators found that the presence of f-circRNA MLL-AF9 conferred resistance to Arsenic trioxide (ATO), an approved standard-of-care drug for the treatment for leukemia.  Finally, knockdown of f-circ-M9 in human leukemia cells resulted in  increased  apoptosis, suggesting that targeting f-circRNAs could be a successful therapeutic strategy.

 

These ground-breaking results further highlight that circRNAs are a prominent and relevant biomarker with potential diagnostic and therapeutic implications.  More broadly, the work highlights the interplay between DNA translocations, coding RNA and non-coding RNA and how each of these molecules works in concert with one another to ultimately lead to cellular transformation.  Restricting one’s search for biomarkers or new drug targets to one class of molecules runs the risk of not seeing the full picture.  However, a more holistic view of biomarker discovery enables one to elucidate robust and complementary biomarkers to effectively cofactor(79of88)segment patient populations or discover relevant drug targets.

 

I’m proud to say that, at Cofactor, we are leading the charge in circRNA biomarker discovery.  Our proprietary circRNA discovery platform combines novel molecular biology and bioinformatics techniques to enable us to discover disease relevant circRNAs with over 100x the sensitivity of other technologies on the market.  Furthermore, our years of collective experience in RNA sequencing and transcriptomics allow us to put these discoveries into context to develop robust and relevant disease biomarkers that can be rapidly translated into the clinic.  We are actively applying these technologies for our own internal biomarker discovery efforts as well as in partnerships with other therapeutic companies.  We are excited to see what the future holds – stay tuned!

Learn more about our offerings.