How to Choose the Right CRO for Your RNA-Seq Experiment

Published on September 18th, 2023
 9 min read

Exploring Transcriptomics Data Generation

As researchers push the boundaries of our understanding of biological systems, they need to generate ever larger volumes of omics data in order to gain deeper insights. Although some academic labs and biotech and pharmaceutical companies have in-house sequencing units, a large number of them still rely on external service providers for sequencing.

This guide aims to assist scientists seeking to generate RNA-Seq data and find suitable service providers for their research.

The Role of CROs in RNA-seq Data Generation

Some biotech and pharma companies as well as academic institutions have core facilities with specialized equipment to perform sophisticated measurement tasks economically and to make expertise accessible to a larger group of researchers. These core facilities are not always able to deliver services quickly enough though, or they face other constraints. This is where clinical research organizations (CROs) come to the rescue.

Outsourcing sequencing services to CROs offers numerous advantages. First is access to expertise, as keeping up with the latest developments can be a challenge. Since sequencing requires expensive equipment as well as ongoing maintenance, upgrade and personnel costs, it can be cost-effective to outsource it. To obtain the highest quality data and reduce the risk of error, it is important to choose a partner that uses the latest equipment, standardized protocols, and strict quality control measures. Outsourcing to CRO can also result in large time savings. Sequencing can be very time-consuming, with each step taking days or even weeks. Finally, the capacity of CROs gives you the flexibility to ensure your scalability. 

There are CROs for the full spectrum of clinical research and study conduct, ranging from small businesses to multi-billion dollar corporations. As a scientist, it’s not easy to choose the right partner for your requirements.

Which CRO Is Right for You?

CROs are often global genomics services companies and trusted providers of Sanger sequencing, next generation sequencing (NGS), gene synthesis, molecular biology, bioinformatics and GLP regulatory services. They serve research communities across the world and partner with academic, pharmaceutical, biotechnology, agricultural, government, and clinical institutions. 

Most CROs offer a wide range of services with certain specializations. Which of the CROs you should choose depends on several factors. Does the CRO specialize in your unique research questions? Will you receive industry-leading turnaround times, competitive pricing and local support. What are the logistics like? For example, due to time constraints, it may make sense to work with a partner that is located in your region.

Let’s look at some prominent players in the industry that offer sequencing and data acquisition services in transcriptomics.

GENEWIZ from Azenta Life Sciences is based in Leipzig, Germany, and aims to make research more productive and cost-effective through scalable services. Genewiz offers a wide range of services, such as bulk RNA-seq, single cell RNA-seq, whole genome sequencing, protein biomarker detection and exome sequencing. The company also has a growing network of genomics laboratories around the world, including in the U.S., U.K. and China. [1]

With nonclinical and clinical trial laboratories around the world, this CRO can scale quickly and efficiently, conducting more than 15,000 research studies and processing more than 4.4 million clinical trial test kits annually. Labcorp offers integrated genomic testing services through an extensive network of global capabilities and laboratories: core genomic services, NGS, biomarker translation and computational biology. [2] 

Eurofins Genomics
Founded in 1990, Eurofins Genomics is part of the Eurofins Scientific Group, a life science company with laboratories in over 50 countries and more than 55,000 employees focused on delivering high-quality results to its customers on time. [3] In 2017, Eurofins acquired GATC Biotech, a European sequencing services provider with more than 10.000 customers from academia, industry, and healthcare. GATC offers genomics such as transcriptome, epigenome, exome or whole genome analysis, and bioinformatics.

Lexogen focuses on RNA and complete transcriptome studies using NGS technologies. Lexogen provides a fully integrated workflow for sequencing known and unknown RNAs in any species, accurately quantifying gene expression, and detecting novel transcripts and isoforms. The service portfolio includes applications such as gene expression profiling, gene expression screening, mRNA sequencing, whole transcriptome sequencing, small RNA sequencing, single cell, and ultra-low input RNA sequencing. [4]

Psomagen, Inc. formerly Macrogen Corp, provides multiomics services to the clinical, academic and consumer markets. The company operates CLIA- and CAP-certified laboratories in four locations across the United States and is accredited to perform the highest quality Sanger sequencing, NGS, and microarray gene analysis, making multi-omics solutions and genomics technologies accessible and scalable for research and drug discovery. 

LGC Genomics
LGC Genomics is a business unit of LGC Group and was founded in April 2010 as part of a strategic realignment. The company combines the strengths of LGC Group’s former AGOWA Genomics business, based in Berlin, Germany, with the goal of growing in the fast-growing international genomics market. As an international science-based company, it is the market leader in analytical, forensic and diagnostic services and reference standards. 

Sygnature Discovery
Sygnature Discovery is an integrated drug discovery and non-clinical solutions provider. The company provides a wide array of capabilities to support gene expression studies, providing analysis of both single gene changes, as well as, analysis of the expression levels of the entire transcriptome.

In addition to these providers, there are of course many other leading CROs that offer similar services for transcriptomics data generation for research, drug development and clinical applications, e.g. Charles River Laboratories, WuXi App Tec, Q2 Solutions, Illumina Clinical Services, Novogene, and Macrogen.

The Next Challenge: Data Analysis

Data scientist looking at data

After generating omics data, the next challenge is to analyze and understand your data and gain insights into the underlying biology. 

Omics data analysis includes three main stages: Primary analysis involves data acquisition storage and management, secondary analysis focuses on data preprocessing and pipeline analysis, and tertiary analysis encompasses comprehensive data visualization, in-depth exploration and interpretation to derive actionable insights.

It is important to note that most CROs only perform primary and secondary analyses, but do not offer a complete set of tertiary analyses. Usually, customers need to perform tertiary analysis in-house or find another partner to outsource the analysis. In addition, the final results of the analysis by CROs are usually delivered in static PDF files and spreadsheets. Instead, interactive data and result sharing could offer significantly more flexibility and speed in the analysis process. 

Standardization and reproducibility are essential in scientific research, especially for large-scale transcriptomics studies. Implementing standardized tertiary analysis workflows that consistently deliver reliable results gives researchers confidence in the accuracy and consistency of data analysis, which helps them make the right decisions about their research projects.

Can Data Generation and Analysis Be Combined for an End-to-End Solution Service?

From the customer’s experience perspective, the combination of data generation and analysis and getting an end-to-end solution can quickly advance their scientific projects by making the whole process fast and efficient.

We outline some of the benefits of an end-to-end solution below:

A big advantage of end-to-end solutions is convenience. You don’t need to find another provider for data analysis. The more different vendors needed, the longer the process of data generation and analysis. Selecting a vendor requires time for research, qualification, contracting, etc., and then making sure everything works together smoothly. If all services come from a single source, this creates additional costs.

Faster Process and Improved Efficiency
End-to-end solutions result in faster analysis and turnaround times by eliminating unnecessary handoffs between different service providers. This is especially valuable in time-sensitive work, e.g. when quick decisions are required in clinical settings.

Better Information Handling and Analysis
By keeping the same service provider, fewer questions arise about the experiment and data generation during the analysis phase. Second, information transfer and processing is improved, potentially leading to fewer misunderstandings about data analysis requirements and thus better analysis.

Interactive Visualization Software for Better Flexibility, Customization, and Sharing
Another benefit of end-to-end solutions is the ability to integrate advanced visualization software. Traditional static reports by CROs present data in a fixed format, limiting the researchers’ ability to explore and interact with the results effectively, while interactive data visualization tools enable researchers to dive deeper into the data, play with it and gain more insights. Researchers can customize visualizations, perform real-time queries, and uncover patterns that might not be apparent in static reports. Interactive platforms offer researchers greater flexibility and customization options: they can tailor the analysis process to specific questions and explore different data subsets and variables interactively. This allows for more comprehensive exploration of the data.

For these reasons, no matter which CRO you choose, be sure to inquire if they can provide an end-to-end solution.

Importance of an End-to-End Solution for CROs

In the rapidly evolving landscape of omics data generation, providing an end-to-end solution is becoming increasingly important and a strategic imperative that can boost the business of CROs and sequencing units. Embracing this comprehensive approach enables them to offer a transformative value proposition to their customers, setting them apart from competitors and solidifying their position as industry leaders. 

The integration of data visualization into their service offerings enriches the client experience by presenting complex omics data in interactive formats, fostering a deeper understanding of the underlying biological phenomena. 

Moreover, by providing an end-to-end solution, CROs and sequencing units establish enduring partnerships with their clients, as they become a one-stop-shop for all their omics needs. This comprehensive service offering fosters long-term loyalty and strengthens client retention rates, effectively increasing the lifetime value of each customer. 

Furthermore, embracing an end-to-end solution unlocks untapped revenue streams. By adding value through data analysis and visualization services, CROs can command premium pricing, maximizing the return on investment for both parties. As the omics research space becomes increasingly competitive, staying ahead necessitates the provision of comprehensive solutions that cater to the evolving needs of researchers. This positioning as a technology-driven, forward-thinking partner enables CROs and sequencing units to attract new customers and secure larger projects.

A well-selected CRO offering end-to-end solutions can rapidly advance science projects by generating the transcriptomics data and also analyzing it quickly and efficiently. By working with partners and using visualization software to share data with end users, CROs can provide standardized and reproducible analyses, not just static reports. The benefits for the end user are faster analysis and more flexibility in interacting with the data.

At BigOmics, our mission is to simplify and accelerate the visualization and analysis of omics data. Omics Playground, our data analysis platform, provides a comprehensive workflow specifically tailored for the analysis of RNA-Seq and proteomics data. Intelligent tools enable individuals to immerse themselves in advanced omics analysis, streamline dataset integration and reveal key genes and proteins. 

Want to try out Omics Playground for yourself and learn how it can help you as a bioinformatician solve your data challenges and bottlenecks in transcriptome and proteome analysis? 

Free up your time today by letting Omics Playground handle your routine visualizations, allowing you to concentrate on more customized tasks.