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Genetics

Covaris AFA Technology: Innovation in FFPE Sample Processing for DNA, RNA and Proteins

Covaris’ Adaptive Focused Acoustic Technology (AFA) represents a revolutionary breakthrough in sample preparation for genomic and proteomic analysis. This technology uses high-frequency, high-precision ultrasound to perform mechanical processes such as DNA and RNA fragmentation, protein extraction, and sample homogenisation. Designed to work in clinical and research environments, AFA stands out for its ability to process challenging samples, such as formalin-fixed, paraffin-embedded (FFPE) samples, while maintaining quality and consistency of results.

The benefits of Covaris Adaptive Focused Acoustics (AFA) technology for preparing high-quality DNA and RNA libraries from formalin-fixed paraffin embedded (FFE) samples show the superiority of this technology over enzymatic methods in extraction and shearing, producing higher quality fragments and consistent insert sizes, particularly with highly degraded or limited starting material. Integrating this technology into highly automated workflows improves the throughput and reduces sequencing errors. AFA enables comprehensive proteomic an epigenetic analysis on these types of samples, which is a major advance in the study of diseases such as sarcomas.

Covaris mechanical fragmentation based on ultrasound, shear genetic material in a controlled and reproducible manner. This consistency enables higher quality libraries to be obtained compared to enzymatically generated shears, and specially in FPPE samples in several ways:

Fragment quality at extraction is greatly improved based on DV200 metrics, a measure of DNA integrity that refers to the percentage of DNA fragments larger than 200 base pairs and is indicative of DNA degradation, with samples processed with the Covaris AFA system achieving a DV200 of 20% or higher.

This technology facilitates the extraction of longer RNA inserts from FFPE samples, including those in repositories and archives, improving the utility of the extracted material and generally not evidencing any loss in the quality or quantity of the purified DNA and RNA.

AFA technology shows great adaptability to different DNA sources and extraction materials without requiring protocol adjustments, providing versatility in managing a diverse range of clinical samples.

Easy integration with automated sample handling platforms enables high-throughput processing without manual intervention, increasing workflow efficiency and reducing human error. Furthermore, instruments such as the R230 guarantee sample traceability throughout the process, which is essential for diverse clinical settings.

Another feature worth highlighting is the efficiency in extracting proteins from FFPE samples. The combination of ultrasonication with other technologies such as S-trap proves to be quite efficient in this context. In addition, sonication allows for the direct homogenization of FFPE samples in SDS buffer, which saves additional equipment, steps and time in protein processing.

Obtaining consistent, high-quality fragments is eventually reflected in the reliability of the data through the carious applications of this technology in clinical and research environments.

All these features are also desirable in the library construction steps for NGS, especially for long-read sequencing technologies, ant eh precision in cutting combined with the high quality and consistency of the fragments impacts the rate of discordance, what is crucial in the identification of variants, especially in samples with low concentration such as 10 ng.

To sum up, the high performance obtained with degraded samples controllable and consistent fragmentation, and recent solutions in sample transfer and scalability make of Covaris AFA technology an accurate and reliable solution for result interpretation from FFPE samples in clinical and research environments.

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