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The trouble with RNA

Here’s the trouble with RNA: In order to sequence and analyze it, you first have to get it out of your biological samples intact. And, as we all know, this requires some nimble fingers – avoiding RNases, moving quickly, and working to ensure the highest quality RNA possible.

We know that the quality of an RNA sequencing experiment starts with the method of its purification from your sample (See 6 CHANGES THAT’LL MAKE A BIG DIFFERENCE WITH YOUR RNA-SEQ; PART 1). But, the primary focus of our Discovery Services laboratory experts is to develop and deliver the BEST in RNA library preparation, sequencing, and analysis.  

So, how can we help you to provide us with the best quality RNA possible?

Cofactor is pleased to announce that we have partnered with ARQ Genetics and their staff of Ph.D.-level molecular biologists, applying their years of experience to consistently deliver high quality material from your samples.

For routine RNA extractions (such as cell pellets, tissue, non-CLIA FFPE), we’ve made the process as easy as possible:

  • The cost of the extraction can be added directly to your RNA-seq quote, no additional billing required.
  • Transit time is minimized by shipping your samples directly to ARQ. Once extracted, the RNA will be transported to Cofactor for all downstream molecular and analysis.
  • Quality Control data are collected following extraction at ARQ and then once again at Cofactor, ensuring high-quality RNA is feeding into the RNA-seq workflow.

“We’ve seen a high quality of work performed by ARQ — with both client projects and internal projects alike.  I’m pleased that we’ll be offering this service to our customers who are unfamiliar with RNA extractions, or unable to devote internal resources. It’s important for us to make the process of obtaining high-quality RNA-seq data as seamless as possible for our clients.”   -Jon Armstrong, CSO 

If you are interested in including RNA extraction as part of your project, just let us know during our experimental design discussions. Contact a Project Scientist at Cofactor Genomics to get started today!


Data Delivery at Cofactor Genomics

Cofactor’s mission is to provide the best quality data and support to our customers.  To meet this – we’re making some exciting updates!

Electronic Data Delivery: Faster access to your data

Custom LIMS System: Improved customer communications and data tracking

Expanded Project Scientist Team: Expert support planning, executing, and interpreting your project

Electronic Data Delivery:  Every project includes delivery of raw FASTQ files. Effective immediately, Cofactor is pleased to provide our customers electronic data download for all projects. In our high-bandwidth, HIPAA-compliant secure cloud data storage center, your data will be safe and sound, accessible only by you.

We guarantee data backups on our servers for up to 90 days, and if you’ve partnered with us for full analysis, your ActiveSite interface will remain online indefinitely.


Custom LIMS System: Cofactor has outgrown our original custom customer relations management (CRM) and laboratory information management system (LIMS), and we’re excited to move towards a more comprehensive CRM, LIMS, and customer communication system.

Launching in Q4 2016, our customers will benefit from increased internal efficiencies and external communications. You will see more standardized project info via email, including updates as your samples progress through our pipeline.

Project Scientist Team: We are always excited to speak with you in real-time on the phone or by web meeting! Our Project Scientist team, responsible for experimental design and customer support, has grown to include:

Natalie LaFranzo, Director of Scientific Projects and Market Development

Brent Wilson, Project Scientist – East Coast  

Sunny Gilbert, Project Scientist – West Coast

These scientists are available to provide technical support, customer support, and make sure you have access to what you need for the success of your project.  Equipped with advanced degrees and knowledge acquired from shepherding thousands of RNA samples through Cofactor’s pipeline – we’re happy to be your technical resource.

“Our customers tell us we have the best customer service in the business, and these updates demonstrate our commitment to be valued partners for everyone we work with.” — Cofactor COO Dr. David Messina


Let us know how we can help provide the support you need to leverage the power of RNA – from Discovery to Diagnostics.

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.


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:


* 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.*


* 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.

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