Automated HMW DNA Extraction
Automated high molecular weight DNA extraction for archiving and long read sequencing
Extraction of High Molecular Weight (HMW) DNA (> 100 kb) is currently often performed with manual, time-consuming, and costly methods. As manual workflows are subject to risk of human error and confirm differences in operator handling or laboratory conditions, more time and effort are often required to confirm experimental findings. In worst case scenarios, integrity of samples may compromised.
The chemagic™ nucleic acid purification systems automate the extraction of HMW DNA, improving consistency of results while ensuring sample integrity at higher throughputs and faster turnaround times. Compared with other automated platforms, the chemagic system provided higher DNA yields of good purity alongside a significantly greater HMW DNA extraction efficiency. The chemagic systems have been used successfully in conjunction with long read sequencing technologies from Oxford Nanopore2,4,5,6 and PacBio1,3. The greater HMW DNA extraction efficiency afforded by chemagic technology also makes it the choice of many biobanks worldwide that require long-term storage stability for archiving and a nucleic acid quality that can be applied to diverse molecular assays2,7,8.
Webinars:
For research use only. Not for use in diagnostic procedures.
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Customer experiences
Automated DNA extraction methods are revolutionizing genetic research, as demonstrated by these two insightful webinars. Karine Auribault from Paris and Emily Farrow from Kansas will share their experiences implementing high-throughput DNA isolation techniques in hospital settings. These presentations underscore the critical importance of efficient (HMW) DNA extraction in enabling a wide range of genetic tests and assays, from MLPA and Sanger sequencing to cutting-edge long read sequencing.
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Webinar review: High quality DNA for genetic testing
In the ever-evolving field of genetic testing, the webinar titled “High Quality DNA with Revvity’s chemagic 360 for Genetic Testing” presented by Dr. Karine Auribault, a seasoned expert in molecular genetics and diagnostics, offered valuable insights.
Dr. Karine Auribault, a laboratory manager at George Pompidou European Hospital, has extensive experience in molecular genetics and diagnostics, including a significant contribution to a patent on a tool for diagnosing and treating prostate cancer.
The chemagic 360 instrument was implemented into Dr. Auribault´s laboratory workflow and validated through rigorous testing. The instrument demonstrated high reproducibility and yielded high-quality DNA suitable for various downstream applications such as Next Generation Sequencing (NGS), Multiplex Ligation-dependent Probe Amplification (MLPA), PCR, and Sanger sequencing.
The webinar highlights several downstream applications of the high integrity DNA extracted using the chemagic 360 instrument. These applications ranged from NGS and MLPA to more recent technologies like long-read sequencing and digital PCR. The high-quality DNA obtained from the chemagic 360 instrument proved to be compatible with all these applications, demonstrating the instrument’s versatility.
This webinar shows the significant role that instruments like the chemagic 360 instrument play in advancing the field of genetic workflows The high integrity DNA opens a plethora of possibilities in downstream analysis, contributing to the ongoing evolution of genetic analysis.
<em>For research use only. Not for use in diagnostic procedures.</em>
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Unleashing the power of genomics: A webinar review
Are you interested in the fascinating world of genomics and its potential to transform medicine? If so, there’s a webinar that you simply cannot miss. Dr. Emily Farrow, an Assistant Laboratory Director at Children’s Mercy Hospital, has presented an enlightening webinar on automated DNA isolation for long-read next-generation sequencing.
<strong>The promise of long read sequencing</strong>
Dr. Farrow discusses the importance of high integrity, high molecular weight DNA for various assays and the challenges faced in pediatric DNA isolation. She emphasizes the need for a single DNA isolation method that supports current and future assays, including long read sequencing.
Long-read sequencing has shown superior metrics in detecting single nucleotide variants, structural variants, and methylation patterns. It has led to improved diagnostic yields for rare diseases and has the potential to redefine our understanding of carrier frequencies for certain genetic conditions.
The hospital’s research program, Genomic Answers for Kids, has sequenced over 1500 HiFi genomes, leading to significant findings and the validation of long read sequencing as a clinical laboratory developed test. The technology has proven beneficial in diagnosing complex cases, such as spinal muscular atrophy caused by single nucleotide variants, which were undetectable by short-read sequencing. In this webinar, Dr. Farrow concludes that long-read sequencing, enabled by high-quality DNA isolation, is transforming genomic medicine by providing comprehensive and accurate genetic analysis in a single assay. The center aims to expand long-read sequencing to the outpatient population and refine de Novo assembly for clinical use.
This webinar is not just about the science; it’s about the real-world impact of these advancements. The presentation by Dr. Farrow highlights the successful implementation of long-read sequencing in an inpatient population at Children’s Mercy, resulting in a diagnostic rate of over 50%. The center has standardized DNA isolation processes and has a large biobank of samples, allowing for efficient genetic testing.
So, if you’re interested in the future of genomics and its potential to revolutionize medicine, check out. Tune in to learn, be inspired, and see how the power of genomics is being harnessed to make a real difference in patients’ lives.
<em>For research use only. Not for use in diagnostic procedures.</em>
Learn more HMW DNA extraction for long read sequencing
Learn more about efficient HMW DNA isolation in our Application Note. We compared extraction performance from blood based on DNA yield, purity, and integrity between two automated nucleic acid extraction systems.
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Comparison of automated nucleic acid purification systems HMW DNA extraction efficiency
With automation being increasingly employed in laboratories performing nucleic acid purification, a more consistent quality of nucleic acids is generally expected. A high quality of should also be obtainable with automation to meet requirements of demanding downstream assays such as NGS, long read sequencing, and MLPA, while ensuring long-term storage stability. However, differences in mechanical processes and kit chemistries between commercial automation platforms may result in varying qualities of nucleic acid which can impact downstream results. Here, we evaluated two systems of magnetic bead-based automated nucleic acid purification using blood samples. High molecular weight DNA acid quality was assessed in terms of yield and purity. Integrity of DNA as seen by the extraction efficiency of HMW DNA was also assessed.
Extraction performance from blood based on DNA yield, purity, and integrity (DNA length) was compared between two automated nucleic acid extraction systems. The chemagic™ 360 instrument extracted pure DNA at higher yields and integrity with chemagic™ DNA Blood 400 Kit H96 (CMG-1091) or chemagic DNA Blood 4k Kit H24 (CMG-1074). A greater HMW DNA extraction efficiency was obtained with the chemagic 360 instrument that can improve performance in long-read sequencing as well as long-term storage stability.
<em>For research use only. Not for use in diagnostic procedures.</em>
Learn more Biobanking
Drawing on extensive expertise in high-throughput extractions across diverse sample types such as blood, buffy coat, swabs, and saliva, we have established a global presence in biobanking. Our chemagic nucleic acid isolation ensures archive-quality specimens, and our ability to automate entire workflows, from primary sample handling to downstream QC and assay setup, has positioned us as a trusted collaborator in various population genetic cohort studies.
Our contributions extend to notable initiatives like the "All of Us Research Programme" from the Mayo Clinic7, the German National Cohort/NAKO Gesundheitsstudie8, and the British Initiative, including the 100,000 Genomes Project, among others.
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Dried blood spots for advanced DNA sequencing
Dried blood spots (DBS) are widely utilized in newborn screening, large population-based surveys, and biobanking due to their minimal blood volume requirements, ease of collection, and convenient transportation and storage. However, extracting high-quality DNA from DBS for next-generation sequencing (NGS) has posed significant challenges. This application note presents Revvity’s optimized workflow for targeted sequencing of DNA extracted from DBS, which addresses these challenges effectively.
The workflow begins with the DBS Puncher™ instrument, which punches samples into 96-well microtitration plates. DNA is then isolated using the chemagic™ DNA CS200 DNA Kit on the chemagic™ 360 instrument, capable of processing up to 1,000 samples per day. Central to this process is chemagen™ Technology, which employs an automated magnetic separation procedure to isolate high molecular weight (HMW) genomic DNA (gDNA) without denaturing or fragmenting nucleic acids. Quality control is ensured using the LabChip® GX Touch™ nucleic acid analyzer. The DNA is sheared to a target size of 150-200 bp, and libraries are prepared using Agilent® SureSelect® XT kits. The entire process is automated on the Sciclone® G3 NGSx workstation, and sequencing is performed on an Illumina® NovaSeq® sequencer.
The results demonstrate high-quality sequencing data with over 99% of reads mapped and low duplicate read percentages, confirming the effectiveness of Revvity’s workflow in producing pure, high-quality DNA suitable for NGS analysis. This optimized workflow facilitates the use of DBS in various research and biobanking applications, overcoming previous limitations in DNA extraction and sequencing.
Revvity is a trademark of Revvity, Inc. All other trademarks are the property of their respective owners.
<em>For research use only. Not for use in diagnostic procedures.</em>
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Automated nucleic acid isolation fulfilling biobanking needs
Biobanking core laboratories and biospecimen repositories are facing the demanding task to extract high-quality DNA and RNA for long-term storage from diverse sample materials like whole blood, buffy coats, and fresh, frozen or fixed tissues. To fulfill the needs of sensitive genetic research applications such as whole genome sequencing, real-time and digital PCR, and methylation analysis, the extraction of high yields of ultra-pure nucleic acids is an essential initial step. The purity of nucleic acids is especially critical when it comes to long-term storage of the extracted DNA and RNA samples. We offer full workflow solutions optimized for biobanking and biorepository demands, including high-throughput DNA and RNA isolation solutions, liquid handling robotics, and nucleic acid quality control and analysis. With its exhaustive offering of instrumentations and kits, we are your experienced biobanking application support from nucleic acid extraction to data.
<em>For research use only. Not for use in diagnostic procedures.</em>
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High quality DNA isolation suitable for ultra rapid sequencing
A major challenge of using Whole-Genome Sequencing (WGS) for high-throughput genomic analysis is the amount of time required to perform the entire procedure from DNA isolation from the primary samples to analysis of the sequencing results. Fast next-generation sequencing requires the isolation of high-quality nucleic acids in a very short time frame and the optimization of the downstream pipeline. In the application note below, we describe how fast DNA isolation from high volumes of blood coupled to modifications to an Illumina® HiSeq®2500 instrument and optimization of base-calling and variant detection using Isaac software v1 can decrease the time from sample preparation to sequence analysis to less than 35 hours.
Revvity’s chemagic™ research instrumentation and kits offer optimal solutions for high-throughput DNA extraction from a wide variety of sample types by providing:
<ul>
<li>High DNA yields– e.g., up to 50 µg DNA/ml blood</li>
<li>Capacity to handle large volumes of primary samples – more DNA available for testing</li>
<li>Fast processing times– e.g., 24 blood samples in 50 min</li>
<li>Tested sample handling technology – lower cross-contamination occurrences</li>
<li>Full or partial automated systems – less hands-on time during the nucleic acid purification procedure</li>
<li>High levels of DNA integrity – up to 200 kb fragments suitable for the most complex genomic analyses</li>
<li>Long-term stable nucleic acids – ideal for biobanking and clinical research applications</li>
</ul>
For more information, please download the application note or contact us.
<em>For research use only. Not for use in diagnostic procedures.</em>
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References:
- Lang K, Wagner I, Schöne B, et al. ABO allele-level frequency estimation based on population-scale genotyping by next generation sequencing. BMC Genomics. 2016;17:374. Published 2016 May 20.
- Beyter D, Ingimundardottir H, Oddsson A, et al. Long-read sequencing of 3,622 Icelanders provides insight into the role of structural variants in human diseases and other traits. Nature Genetics. 2021 Jun;53(6):779-786.
- Steiert TA, Fuß J, Juzenas S, et al. High-throughput method for the hybridisation-based targeted enrichment of long genomic fragments for PacBio third-generation sequencing. NAR Genom Bioinform. 2022;4(3):lqac051. Published 2022 Jul 13.
- Schmidt J, Berghaus S, Blessing F, et al. Genotyping of familial Mediterranean fever gene (MEFV)-Single nucleotide polymorphism-Comparison of Nanopore with conventional Sanger sequencing. PLoS One. 2022;17(3):e0265622. Published 2022 Mar 17.
- Watson CM, Crinnion LA, Hewitt S, et al. Cas9-based enrichment and single-molecule sequencing for precise characterization of genomic duplications. Lab Invest. 2020;100(1):135-146.
- Watson CM, Crinnion LA, Simmonds J, Camm N, Adlard J, Bonthron DT. Long-read nanopore sequencing enables accurate confirmation of a recurrent PMS2 insertion-deletion variant located in a region of complex genomic architecture. Cancer Genet. 2021;256-257:122-126.
- Valentin N, Camilleri M, Carlson P, et al. Potential mechanisms of effects of serum-derived bovine immunoglobulin/protein isolate therapy in patients with diarrhea-predominant irritable bowel syndrome. Physiol Rep. 2017;5(5):e13170.
- Kousathanas A, Pairo-Castineira E, Rawlik K, et al. Whole-genome sequencing reveals host factors underlying critical COVID-19. Nature. 2022;607(7917):97-103.