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Illumina Streamlines Nucleic Acid Quality Analysis

Illumina Partners with Advanced Analytical Technologies to Deliver Scalable Quality Assessment Solutions

Illumina Streamlines Nucleic Acid Quality Analysis

Advanced Analytical Technologies, Inc. (AATI) and Illumina recently entered into an agreement to support collaborations and co-marketing activities involving AATI’s Fragment Analyzer™ Automated CE Systems for quality control (QC) analysis of nucleic acids in Illumina next-generation sequencing (NGS) workflows. The Fragment Analyzer accelerates NGS library preparation with simultaneous qualification and quantification of DNA and RNA. AATI’s systems provide a scalable method, tested by Illumina, for accurate analysis of a broad range of sample types in Illumina NGS library prep workflows, including genomic DNA, RNA, cell-free liquid biopsy, single-cell isolates, and prepared libraries before sequencing.

Assessing nucleic acid quality is essential for the success of NGS applications. The identification of DNA and RNA samples likely to produce suboptimal libraries that yield poor sequencing performance due to degradation, fragmentation, or low purity can be achieved by verifying the integrity of samples before library preparation. Similarly, accurate quality and quantity analysis of prepared DNA libraries can be used to optimize cluster generation during sequencing, resulting in cost and time savings while maximizing both sequencing data quality and output. 

“The Fragment Analyzer systems give our customers new options to streamline the analysis of nucleic acid isolates and prepared libraries,” says Kevin Meldrum, Senior Director of Product Marketing at Illumina. “We look forward to working with AATI to provide robust QC solutions, especially as NGS sample numbers grow and multiplexing techniques are empowered by our high-capacity NGS platforms.”

The dynamic field of single-cell genomics is one force driving the expansion of NGS sample numbers.  Steve Quake, Ph.D., is Professor of Bioengineering and Applied Physics at Stanford University, Co-President of the Chan Zuckerberg (CZ) Biohub, and an early adopter of AATI’s Fragment Analyzer technology.  Quake’s teams employ Fragment Analyzers for high-throughput analysis of reverse transcribed single-cell transcriptomes, and low-throughput analysis of their pooled Illumina Nextera® libraries before sequencing.  Norma Neff, Ph.D. implemented AATI systems with Dr. Quake at Stanford before joining the CZ Biohub as Director of Genomics. “The Fragment Analyzers are essential tools for our single-cell RNA-Seq pipeline,” says Dr. Neff.  “The sensitive qualitative analysis and accurate quantification data enable precise normalization of cell inputs before Nextera library construction.  Fragment Analyzer QC of the finished libraries ensures all Illumina sequencing platforms produce optimal data with high efficiency.”

Illumina has published an Application Note that provides an overview of Fragment Analyzer QC solutions for a variety of Illumina’s NGS library preparation workflows such as whole genome, exome, RNA expression, methylation, amplicon and targeted panels.  The Fragment Analyzer solutions include novel quality assessment metrics for FFPE RNA and FFPE DNA samples commonly investigated by cancer researchers.

“We are excited to partner with Illumina as their transformative NGS technologies shape the modern era of personalized medicine and genomic discovery,” says Jonathan Hagopian, Ph.D., Vice President of Business Development at AATI.  “Our collaborations with Illumina are delivering innovative QC solutions that accelerate workflows, optimize NGS data production, and provide critical sample integrity benchmarks.”

The Fragment Analyzer differentiates from alternative QC systems with automated gel priming, improved low molecular weight sensitivity, accurate high molecular weight sizing, the ability to support both low- and high-throughput sequencing operations with scalable parallel analysis of up to 12, 48, or 96 samples, and hands-free automation for as many as 288 samples.  The Fragment Analyzer INFINITY®  system integrates with robotic arms for continuous operation, capable of running over 2,400 samples daily without user intervention.

To learn more about Advanced Analytical Technologies and the Fragment Analyzer, please visit:

To learn more about Fragment Analyzer QC of Illumina applications, please visit:

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