Biobanking with PerkinElmer

For research use only. Not for use in diagnostic procedures.

APPLIED GENOMICS

Modular & Scalable

Automation

Single Source Integration

FLEXIBILITY TO MEET CHANGING DEMANDS

HIGH QUALITY

SAMPLE PROCESS TRACEABILITY

Nucleic Acid Extraction &

Analysis Expertise

Facing an ever-increasing demand, biobanks empower clinical, pharmaceutical, and basic research to increase our understanding of complex diseases by delivering the right resources, to the right researcher, at the right time. PerkinElmer enables biobanks to serve their customers’ needs by developing complete, validated workflow solutions providing high quality nucleic acid extraction, automation with flexible throughput, and sample process traceability ensuring the accurate identification of samples.

UNIQUELY POSIT IONED TO EMPOWER RESEARCH

REVOLUTIONIZE BIOBANKING

PerkinElmer is uniquely positioned to enable biobanks to empower research with high quality nucleic acid extraction and QC and analysis solutions, modular and scalable automation, and sole source integration, delivering the flexibility biobanks need to meet their changing demands.

PERKINELMERDELIVERS

Nucleic Acid Extraction ExpertiseInput Agnostic Nucleic Acid Extraction

Since the samples collected by biorepositories can be extremely diverse, the ability to isolate nucleic acids from an extensive range of sample types and volumes is critical. With the ability to extract nucleic acids from 10 µL to 10 mL of input samples, PerkinElmer’s chemagic™ reagents and automation solutions are agnostic for both starting materials and type of nucleic acid extracted(1 – 10).

High Quality Nucleic Acids

Nucleic acid quality is of major importance when conducting molecular analysis since factors causing degradation, presence of impurities, and enzymatic inhibitors, and long-term storage can have a significant impact on the quality of data. PerkinElmer’s chemagen™ technology addresses the challenges associated with extraction while offering high recovery of clean nucleic acids suitable for long-term storage and a variety of demanding downstream applications. The shaking and centrifugation steps typically resulting in nucleic acid denaturation and fragmentation are avoided with chemagen™ technology. This automated magnetic separation procedure uses chemagen™ M-PVA magnetic beads to isolate and purify nucleic acids from human sample material. The beads have a high affinity for nucleic acids and low inhibitor binding, resulting in ultra-pure DNA and RNA. chemagen™ technology features magnetizable rotating rods, combining the transfer and suspension of magnetic beads to extract DNA, preventing further fragmentation. There are optimized protocols available for high molecular weight DNA as well as for cell free DNA (cfDNA). The nucleic acids isolated are compatible with a wide range of downstream applications including NGS, PCR, and MLPA(1 – 10).

Sample Type Agnostic chemagic™ Nucleic Acid Isolation Solutions

BLOOD

BUFFY COAT

DBS

SALIVA

SWABS

CELLS

TISSUE/FFPE

URINE

STOOL

AND MANY MORE

Figure 1. chemagen™ technology. Automated magnetizable rotating rods, combining the transfer and suspension of magnetic beads, to isolate ultrapure, high molecular weight DNA.

LysisSample +

Lysis Buffer + Enzymes

BindingLysate + Binding Buffer + M-PVA Magnetic Beads

Washing Elution PureDNA

Transfer of magnetic beads and DNA/RNA

instead of liquids

Figure 2. High Quality DNA Extracted from Dried Blood Spots. DNA was extracted from dried blood spots using the chemagic™ 360 instrument and the chemagic™ DNA dried blood spot kit. DNA was analyzed using the Genomic DNA assay on the LabChip® GX Touch™ nucleic acid analyzer.

Figure 3. High Concentration DNA. DNA was extracted from 133 - 4 mL samples of whole blood using the chemagic™ 360 instrument with an elution volume of 500 µL. The mean concentration is 314 ng/µL with a mean yield of 157 µg. DNA isolated using this kit typically has an OD 260/280 >1.9, OD260/230 >2, and an average DNA yield of 20-50 µL per mL of blood.

Flexible Outputchemagic™ Nucleic Acid Isolation Solutions

GENOMIC DNA

cfDNA

METAGENOMIC DNA

mRNA / miRNA

HMW DNA

With the ability to isolate nucleic acids from 96 to 1,000 samples per day and the flexibility to isolate DNA or RNA from any other human sample type, the chemagic™ 360 Instrument is designed to meet labs high-throughput nucleic acid isolation needs.

INSTRUMENTchemagic™ 360

Figure 4. DNA is not Degraded During Extraction. DNA was extracted from 4 mL samples of whole blood using the chemagic™ 360 instrument and diluted 1:1000 for analysis of molecular weight using a Agilent® FEMTO Pulse™ system.

Figure 5. Extracted DNA is Suitable for NGS Applications Including Metagenomics Analysis.DNA was isolated from stool samples using the chemagic™ 360 instrument and the chemagic™ DNA stool kit. Libraries were prepared both manually and on a Sciclone® G3 NGSx workstation using the Illumina® Nextera™ DNA Flex kit. MetaQUAST genome assembly analysis was performed for a sub-set of the top abundant bacteria species detected in Illumina® Nextera™ DNA Flex libraries by Genius Metagenomics.

The chemagic™ Prime instrument offers high throughput primary sample transfer along with nucleic acid isolation for high throughput labs, isolating and processing nucleic acids from 96 to 1,000 samples per day per day.

INSTRUMENTchemagic™ Prime™

NUCLEIC ACID QUALITY ASSESSMENT & QUANTITATION EXPERTISE

Eliminate your nucleic acid QC and quantitation bottlenecks with seamless analysis solutions validated & tested as components of PerkinElmer’s biobanking workflow

MULTIMODE PLATE READERVICTOR Nivo™

NUCLEIC ACID ANALYZERLabChip® GX Touch™

For nucleic acid quantitation, the VICTOR Nivo™ multimode plate reader uses either UV-absorption at 260 nm and 260:280 nm ratios or the measurement of fluorescence intensity of a dye binding to double-stranded DNA (Qubit® assay kit, Thermo Fisher® Scientific) in 96- and 384-well microplate formats.

PerkinElmer’s LabChip® GX Touch™ nucleic acid analyzer delivers nucleic acid quality control analysis in about 30 seconds using microfluidics technology.

LabChip® GX Touch™

Modular & Scalable AutomationPerkinElmer’s automation solutions allow biorepositories to standardize procedures and implement best practices ensuring sample integrity and security, increasing throughput, and decreasing costs. PerkinElmer’s flexible instrumentation modules offer flexibility in throughput, capacity and dynamic volume range, high quality manufacturing standards, and outstanding customer service and support.

Single Source Integration

PerkinElmer’s explorer™ G3 workstations seamlessly integrate many of the critical biobanking processes across platforms. With integrated nucleic acid isolation, sample assessment and a modular approach for increasing throughput, a tailored explorer™ G3 workstation can be designed to align with any analytical pipeline inputs.

Increasing Throughput & Sample Security

PerkinElmer offers modular, scalable solutions addressing sample security requirements and changing throughput and workflow requirements to automate entire biobanking workflows.

Fast, Cost-effective Nucleic Acid Extraction from Flexible Input Volumes

With flexibility in throughput, capacity, and sample type, high quality manufacturing standards, and outstanding customer support, PerkinElmer’s chemagic™ nucleic acid extraction automation solutions process sample volumes ranging from 10 µL to 10 mL cost effectively and quickly.

JANUS® G3 Workstation• Track samples with barcode reader• Transfer samples from tubes to extraction labware• Prep for NA isolation

JANUS® G3 Workstation• Track samples with barcode reader• Transfer eluate to destination labware

Hotel• chemagic™ labware storage

Sealer

plate::handler™ Flex Collaborative Robotic Arm• Moving samples

chemagic® 360 Instruments• Nucleic Acid Isolation

Platestak™ Labware Stacker• Tip storage

CUSTOM explorer™ G3 WORKSTATION

Walk-away, seamless automation of nucleic acid extraction and preparation for analytical processing.

For more information, visit www.applied-genomics.com

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PerkinElmer, Inc. 940 Winter Street Waltham, MA 02451 USA P: (800) 762-4000 or (+1) 203-925-4602www.perkinelmer.com

Contact your local sales rep today to learn how to position your biobank for success by incorporating complete automated workflows designed to meet your lab’s specific needs. | perkinelmer-appliedgenomics.com/biobanking

For research use only. Not for use in diagnostic procedures.

References1. Beisani, M., Pappa, S., Moreno, P., Martínez, E., Tarascó, J., Granada, M. L., . . . Balibrea, J. M. (2019). Laparoscopic sleeve gastrectomy induces molecular changes in peripheral white blood cells. Clinical Nutrition. doi:10.1016/j.clnu.2019.03.012.2. Bittner, N., Jockwitz, C., Mühleisen, T. W., Hoffstaedter, F., Eickhoff, S. B., Moebus, S., . . . Caspers, S. (2019). Combining lifestyle risks to disentangle brain structure and functional connectivity differences in older adults. Nature Communications, 10(1).

doi:10.1038/s41467-019-08500-x.3. Fang, H., Xu, X., Kaur, K., Dedek, M., Zhu, G., Riley, B. J., . . . Moreno, T. A. (2019). A Screening Test for HLA-B*15:02 in a Large United States Patient Cohort Identifies Broader Risk of Carbamazepine-Induced Adverse Events. Frontiers in

Pharmacology, 10. doi:10.3389/fphar.2019.00149.4. Kappelman, M., Lange, A., Randell, R., Basta, P., Sandler, R., Laugesen, K., . . . Erichsen, R. (2018). Feasibility of salivary DNA collection in a population-based case–control study: A pilot study of pediatric Crohn’s disease. Clinical Epidemiology,

Volume 10, 215-222. doi:10.2147/clep.s143322.5. Mathay, C., Hamot, G., Henry, E., Mommaerts, K., Thorlaksdottir, A., Trouet, J., & Betsou, F. (2016). Method Validation for Extraction of Nucleic Acids from Peripheral Whole Blood. Biopreservation and Biobanking,14(6), 520-529. doi:10.1089/

bio.2016.0011.6. Miller, N. A., Farrow, E. G., Gibson, M., Willig , L. K., Twist, G., Yoo, B., . . . Kingsmore, S. F. (2015). A 26-hour system of highly sensitive whole genome sequencing for emergency management of genetic diseases. Genome Medicine,7(1). doi:10.1186/

s13073-015-0221-8.7. Mortensen, Ó, Lydersen, L. N., Apol, K. D., Andorsdóttir, G., Steig , B. Á, & Gregersen, N. O. (2019). Using dried blood spot samples from a trio for linked-read whole-exome sequencing. European Journal of Human Genetics, 27(6), 980-988.

doi:10.1038/s41431-019-0343-3.8. Schöfl, G., Lang, K., Quenzel, P., Böhme, I., Sauter, J., Hofmann, J. A., . . . Lange, V. (2017). 2.7 million samples genotyped for HLA by next generation sequencing: Lessons learned. BMC Genomics,18(1). doi:10.1186/s12864-017-3575-z.9. Tantoh, D. M., Wu, M., Ho, C., Lung, C., Lee, K., Nfor, O. N., . . . Liaw, Y. (2019). SOX2 promoter hypermethylation in non-smoking Taiwanese adults residing in air pollution areas. Clinical Epigenetics, 11(1). doi:10.1186/s13148-019-0647-8.10. Tantoh, D. M., Lee, K., Nfor, O. N., Liaw, Y., Lin, C., Chu, H., . . . Liaw, Y. (2019). Methylation at cg05575921 of a smoking-related gene (AHRR) in non-smoking Taiwanese adults residing in areas with different PM2.5 concentrations. Clinical

Epigenetics, 11(1). doi:10.1186/s13148-019-0662-9.

Primary Sample Scanned-in

• Register Rack ID & individual 2D elution tube barcodes

• Samples & reagents transferred to extraction plate

• Nucleic acid extraction

• Eluates transferred to 2D tubes (optional)

• 2D tube ID assigned in sample registry (optional)

• Print sample ID corresponding to rack & elution tube ID

• IMPROVE EFFECIENCY

• STANDARDIZE PROCEDURES TO ENSURE SAMPLE INTEGRITY & SECURITY

• INCREASE THROUGHPUT

• DECREASE COSTS

Leverage PerkinElmer’s Biobanking Workflows With expertise in nucleic acid extraction, automation, system integration, and qualitative and quantitative analysis, PerkinElmer’s automation team helps position biobanks for success by offering flexible, modular solutions improving their efficiency helping to do more with less.

Sample Process Traceability

Improved Reproducibility & Accuracy

Automation eliminates most human handling steps, which are a primary source of run-to-run variation. PerkinElmer’s automated solutions improve reproducibility and accuracy by eliminating errors including mislabeling or misplacing samples.

Sample Tracking

PerkinElmer’s biobanking solutions facilitate sample tracking by incorporating automated barcode scanning into every step of sample processing. Samples are received by a biobank and placed into a PerkinElmer automation solution, where they are scanned by the barcode reader which communicates with the Laboratory Information Management Systems (LIMS) and processed according to predefined work orders.

LIMS Integration

Laboratory Information Management Systems (LIMS) are necessary for biobanks which need to manage a diverse array of samples, integrate with electronic medical and health records and comply with relevant regulatory environments such as HTA, GCLP, MHRA, FDA 21 CFR Part 11. Compatible with all major LIMS, PerkinElmer’s automation solutions allow biobanks to easily import data into management systems.