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About Swift

Swift Biosciences develops and commercializes NGS

Library Preparation Kits that enable technologies for

genomics, translational, and clinical research. Our

proprietary technologies expand the range of sample

inputs to extend the applications of next-generation

sequencing (NGS). Swift Library Kits are designed to

maximize data output, provide the most comprehensive

coverage available on the market and reduce sequencing

costs. Our products are designed to facilitate library

normalization and to analyze DNA and RNA samples for

applications including Liquid Biopsy (circulating, cell-free

DNA), Methylation Sequencing, Whole Genome, Exome

and Transcriptome Sequencing as well as Chromatin

studies, from low input quantities and from Formalin-

Fixed, Paraffin-Embedded samples. The mission of Swift

is to provide research tools for long term improvements in

the health of individuals and their communities all

around the world, specifically in the fight against cancer

and understanding the complexities of inherited

diseases. The tools developed in our efforts are directly

applicable to research in agrigenomics, biotechnology,

metagenomics, and the pharmaceutical industry.

Swift Solutions

DNA and RNA Library Prep Kits

Optimize Your Workflow for Automated, High

Throughput NGS Library Construction Using Your

Choice of Highly Validated Products

Swift 2STM Turbo Kits-Consistent quality genomes &

exomes with quick 2-hour workflow

Swift RNA and Rapid RNA Kits-Comprehensive RNA-

Seq from 1st strand cDNA down to 10 ng total RNA

Swift Hybridization Capture Panels-Highest on target

rate with efficient 12-plex pooling

Swift Indexing Kits-96 UDI and up to 768-plex

Combinatorial Dual Indexing, Molecular Identifiers

(MIDs) for accurate de-duplication & variant analysis

Accel-NGS® Methyl-Seq Library Kit-Best in class

Methylation sequencing from lowest DNA input down

to single cell when using Adaptase® Module

Accel-NGS® 2S Library Kit-Best performance from low

cell number ChIP, HiC, Metagenomes and FFPE

Accel-NGS® 1S Plus DNA Kit-Sequence damaged DNA

& accurately represent ss/dsDNA viromes

Accel-Amplicon® NGS Panels-Overlapping primers in a

single tube for contiguous target coverage in 2 hours.

Oncology, Genotyping, Bacterial 16S & Custom Panels

Swift NormalaseTM Kits-Streamlined library

normalization that minimizes read depth variation

For Research Use Only. Not for use in diagnostic procedures.

Customer Service and Affordability Down to a Science

Swift Configuration

• Custom Packaging for a wide range of options

o Bulk

packaging

o Lot specific

builds

o Pre-

packaged

plates

o Labels

o Barcodes

o Fill volumes

o Batch Sizes

• Client use processes

• QC-Quality control

specification

Swift Offers

• Assurance of supply of reagents

• ISO 13485 Certification

• Supply chain for worldwide access

• Supply and quality agreements

• Standing orders and competitive pricing

• Automated protocols for all kits

Automation Abilities for

Multi-Batch Processing

Swift Biosciences acknowledges the need to increase

throughput while minimizing variability and errors by

employing a team of highly technical automation

specialists. Our automation team will become an

extension of your team, customize your protocol and

workflow to deliver high quality, cost effective and

consistently reproducible results.

This service is provided free of charge to Swift customers

Swift NGS workflows can be automated on most liquid

handlers – here is a list of platforms where we have

automated our preps

• Opentrons

• Biomek Legacy Series

• Biomek i-series

• Hamilton STAR

• Hamilton STARlet

• Agilent Bravo

• Eppendorf epMotion

• Perkin Elmer Sciclone

Your Automation Experience

What your project will look like

• Swift FAS will conduct a pre-visit consultation

call or meeting

• Necessary materials will be sourced and

shipped

• Swift FAS will meet on site at your laboratory

• Protocol, Script Writing, Verification, Custom

Barcoding Strategies, QC

• Each protocol will be verified with Swift

control samples and chemistry

• Reagents can be custom packaged in the

labware of your choice

GAT AATCTGGTCTAGAT AATCTGGTCTA

GAT AATCTGGTCTA

ATTTCCGATAATCTT

AGGCCAGCGTGAC

AATGGACGCCCTTG

CTGGTCTTATTTCCT

P R E-V I S I T A U TO M AT I O N Q U E S T I O N N A I R E

Thinking of Automating? Swift is happy to help; if you elect to adopt the

Swift workflows, we would like to offer one free-of-charge 96 reaction kit to facilitate validation of our automated solution

To help us prepare for the upcoming Swift FAS on-site visit to your lab, please provide the following information.

1. Specify which Swift kit(s) and protocol(s) to automate?

2. Quantity of samples per run?

4. Specify your automation instrument make and model

5. Select all relevant off-deck instruments and equipment

3. Quantity of runs per month?

a. Thermocycler

b. Sample and Library QC Instrumentation

i. Electrophoretic Instrument (e.g. Bioanalyzer, TapeStation, etc…)

ii. qPCR Machine

iii. Plate-Reader or Fluorometric

Quantification

c. Sequencing Instrument

i. Illumina

1. iSeq

2. MiniSeq

3. MiSeq

4. NextSeq

5. HiSeq

6. NovaSeq

ii. Ion Torrent

1. PGM

2. S5

3. Proton

P R E-V I S I T A U TO M AT I O N Q U E S T I O N N A I R E

Most automation projects require:

1. Definition of relevant milestones for a “Job Complete” a. Writing of script(s)

b. Perform volume testing

2. Perform qualification of the script(s) a.Listanyspecificqualificationrequirements

b.Pleasedefinequantitativesuccesscriteriaofthefunctionaltest (e.g. library yield, fragment size, sequencing metrics, etc…)

Your answers to the above questions will be very helpful to expediting the automation of Swift protocols at your laboratory.

Thank you and we look forward to working with you!

The Swift Automation Team

Supply of Swift Kits

Protecting your investment in assay

validation for a new library preparation

workflow is a significant and important final

step to securing and maintaining

implementation. Swift acknowledges the

pressures production labs face to meet

pricing constraints and manage the risks

associated with relying on a consistent

supply of product for years into the future.

Following validation work to ensure

satisfactory performance, ergonomic product

format, and lot consistency, competitive

pricing and the guarantee of a multi-year

supply from Swift, can be provided through

a formal Supply Agreement, and if needed a

Quality Agreement.

Swift also offers flexibility through alternate

available mechanisms to meet demand

forecasts and delivery, such as Standing

Order agreements. Swift provides long-term

assurance of its reagents through vertical

integration of component manufacturing

and business practices to warrant the

continuity of supply. In addition, Swift has

achieved and maintained ISO 13485

Certification and developed shipping and

logistics procedures for worldwide access to

its products.

Swift Manufacturing and QC

Swift is committed to providing high-quality products to

our customers. All products are manufactured in

environmental-controlled manufacturing suites. While all

air flow into the rooms are HEPA filtered and all

personnel are fully gowned while entering the

manufacturing suites, Swift takes extra precautions by

only handling open materials within PCR hoods ensuring

physical separation of all materials.

Swift performs functional QC on each production lot to

ensure the products perform to the specifications with lot-

to-lot consistent performance. The library preparation

products are tested across the full range on recommended

input quantities and libraries are sequenced to complete

functional analysis.

Swift’s Quality Management System is 13485:2016

Certified.

Figure 1: 2S Turbo QC lot comparison for NGS Mean Insert Size for targeted 200bp and 350bp fragmentation size at different input DNA quantities.

SWIFT SUCCESS

Excellent Performance and Consistency

CASE STUDY

Swift 2STM

Turbo & ®

Case Study Summary

The process and requirements to evaluate and adopt a new library preparation workflow at

scale can be streamlined by collaborating with the Swift Team. In this Case Study, we review the

following stages undertaken by Helix in collaboration with Swift Biosciences to expedite

adoption of the Swift 2S Turbo DNA Library Kit for Whole Exome Sequencing at its Southern

California production facility:

• Swift Kit Selection• Technical Evaluation • High Throughput Implementation and Automation Support

• Custom Product Format

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Swift Kit Selection

Enzymatic fragmentation increases sample throughput, decreases time, and reduces cost of

capital equipment and consumables when compared to physical shearing methods.

Tagmentation-based chemistries produce inconsistent fragment size and require cumbersome

optimization and precise input quantities to produce consistent results.

Recognizing such pain-points as obstacles to achieving consistent and reproducible results,

Swift’s expertly designed its 2S Turbo chemistry and innovative tools such as the Swift

Deceleration Module, produce consistent aligned insert size and minimize lot to lot variation.

These features accommodated Helix’s unique laboratory setup and automation needs, making

Swift 2S Turbo their ideal choice for library preparation.

Swift 2S Turbo was also designed with automation compatibility in mind and is supplied with

sufficient overage volumes required for liquid handling systems. These specifications can be

customized which was also a required feature in order to meet the needs of Helix’s clinical-

grade high throughput processing.

Certificate of Analysis to Minimize Lot to Lot Optimization

Swift 2S Turbo chemistry produces consistent performance across a wide range of inputs, GC

base composition and sample types. While minor lot-to-lot variation of enzymatic

fragmentation time can be expected, Swift’s state of the art manufacturing and rigorous

incoming quality control and carefully sourced raw materials aim to reduce this variation.

Additionally, each lot comes with a Certificate of Analysis (CoA) outlining the fragmentation

time for common insert sizes for fragment targets of 200 bp and 350 bp routinely used in whole

genome and exome sequencing applications. This unique feature reduces incoming QC time

and cost while expediting time to result.

While Helix has a dedicated team of experts performing rigorous incoming QC for each lot, the

accompanying CoA served as an additional reference point to support their work, which was

key to their kit adoption.

Controlled Enzymatic Fragmentation with Swift Deceleration Module

To further improve enzymatic fragmentation, Swift developed ‘Reagent DE’ supplied in the

Swift Deceleration Module. This component is designed to achieve longer insert size, control

fragmentation time for manual sample processing and on-deck automated platforms and adjust

incoming sample buffers (e.g. 10 mM Tris or water). The availability of this module was a key

feature in Helix’s selection of Swift 2S Turbo.

Figure 2. Using Reagent DE to control fragmentation for preparation at room temperature. In detail, six

Swift 2S Turbo libraries were prepared with 100 ng of Coriell NA12878. Four of the libraries were

prepared at room temperature with 5 microliters of Reagent DE in the fragmentation reaction, no Reagent

K2, and a 15 min fragmentation. For comparison, two libraries were also prepared on ice without Reagent

DE, 1.5 microliters of Reagent K2, and 8 min fragmentation. Measured on a MiSeq, libraries provided a

mean aligned insert size of 380 bp.

Technical Evaluation to Confirm Baseline Performance

Production laboratories work with highly complex and interconnected workflow steps that

require synergy and compatibility with preceding and subsequent steps from sample

preparation to data analysis. Swift recognizes the importance of ensuring a seamless transition

with minimal impact to the users’ existing tools and operating procedures and strives to

improve and innovate to support customer success.

During an initial technical evaluation of the Swift 2S Turbo technology, Swift performed library

preparation and exome sequencing on an initial set of samples provided by Helix,

demonstrating excellent data quality at small scale to serve as a baseline proof of performance.

Helix subsequently performed a larger scale evaluation across many samples and product lots

to further evaluate data quality and compatibility with their laboratory procedures.

The following sections highlight a few areas, where both company’s willingness to collaborate

and partner together facilitated a successful product evaluation, customization and

implementation at great scale.

High Throughput Implementation and Automation Support

Swift and Helix closely collaborated to understand Helix’s requirements and leverage Swift’s

deep knowledge of molecular biology tools and innovative technology to customize and

optimize the library preparation step to meet Helix’s unique needs.

Based on initial evaluation of the standard 2S Turbo protocol, custom workflow requirements

were defined by Helix, which included:

• Customize enzymatic fragmentation to produce the insert sizes

• Adjust chemistry for a longer automation-friendly incubation for this fragmentation size

• Adjust chemistry to enable room temperature setup of enzymatic fragmentation reaction

with ample time for multi-plate processing to avoid need for on deck chiller

• Produce consistent fragmentation using a single incubation time to avoid lot-specific

adjustment of the thermocycler program

• Offer 768-plex Combinatorial Dual Indexing with high fidelity demultiplexing

performance

• Produce uniform library insert size, yield and complexity for consistent, high quality

exome sequencing data

The implementation was completed by the following processes:

• FAS and Swift R&D provided support to Helix during optimization of the kit reagents

and automation script for desired enzymatic fragmentation and overall library output

• Swift worked with Helix’s team of wet-lab and automation professionals to leverage the

Reagent DE supplied in the Swift Deceleration Module to control fragmentation time to

accommodate ambient set-up for high throughput processing

• Swift FAS provided onsite support to establish successful single plate processing

followed by multiple plate processing

• For all functional testing, quantitative success criteria consisted of uniform insert size,

library yield and exome data quality

Reproducible Fragmentation Performance Across Lots

Consistent sample fragmentation profile is key to achieving reproducible data output; therefore,

Helix evaluated reproducibility of fragmentation profile for multiple Swift 2S Turbo lots

leveraging Reagent DE on their automation systems. The results of three lots shown below

demonstrates the highly reproducible library and pool average sizes.

Figure 2. Insert size tested with three separate lots of Turbo, using three separate sample types.

Experiments were performed and analyzed by Helix.

Custom product format to fit form and function of production lab

Maximizing throughput and speed while achieving excellent data quality are central to

production labs’ success. With the goal to reduce in-lab preparation time and cost and ensure

optimal automation performance, Swift and Helix collaborated closely to customize and

configure reagents and plate formats to meet their specific needs. As an example, the joint team

modeled multiple configuration options and automation procedures to minimize necessary

plate overages to develop the lowest cost solution. This work resulted in custom plate

configurations for fragmentation, ligation and indexing PCR for processing 384 samples at once.

Indexing PCR

To accommodate Helix’s high-throughput sample processing, Swift’s 768 Combinatorial Dual

Indexing primers are pre-plated by Swift into single use 96-well plates tailored for automated

use. The plates are designed to have the post-ligation DNA samples and PCR mastermix added

directly to each indexing primer well for minimal set up required by the Helix laboratory staff

(layouts not shown).

Press Release

Helix Selects Swift Biosciences to Power Exome+™ Assay with Swift 2S™ Turbo DNA

Library System

(ANN ARBOR, Mich. – February 4, 2020) Swift Biosciences, Inc (“Swift”) and Helix OpCo, LLC

(“Helix”) today announced a Partnership Agreement to leverage Swift’s 2S™ Turbo DNA

library preparation for Helix’s Exome+™ assay. Helix, a population genomics company, uses

the Exome+™ assay to power population health programs focused on accelerating the

integration of genomics into clinical care and facilitating novel genetic discovery.

Swift 2S Turbo launched in the summer of 2018 and was Swift’s first foray into the high-

throughput laboratory market. Building its brand on low input and precious DNA samples.

Swift disrupted the large production market segment by solving client’s pain points. Turbo

delivers a high quality and automation friendly kits at a competitive price, by leveraging robust

enzymatic fragmentation and a 2-hour workflow.

Helix has been continually optimizing its Exome+™ assay and as it prepares to launch its latest

version, it was apparent that the synergies between these two new products were going to

create a superior workflow when used together. The Exome+™ assay gives clinicians and

researchers the benefits of a targeted panel, the breadth of a microarray, and the completeness of

an exome – all from one sample and one assay. The Healthy Nevada Project, powered by

Renown Health, is an example of how the Exome+™ assay is being used in combination with

environmental data and longitudinal EHRs to improve health outcomes and accelerate

innovative research.

Through this partnership agreement, Swift supplies Helix with high-quality library prep

reagents customized, packaged, and configured to Helix’s unique technical specifications, plate

format with high-throughput indexing, and automation requirements. These customizations

significantly reduce the in-lab set up time and costs for Helix to run their services.

During the evaluation phase, Swift personnel worked closely with counterparts at Helix to

provide technical support and facilitate efforts between the two companies to achieve consistent

and reproducible data. Helix’s dedicated quality control team was able to leverage Swift 2S

Turbo’s pre-optimized enzymatic chemistry for fast and robust fragmentation, supplementing it

with a lot-based certificate of analysis to dial-in the optimal fragmentation time.

“We look forward to our strategic relationship with Helix moving forward. It is wonderful to

work with a company that helps health systems and research institutes more deeply integrate

genomics into clinical care and accelerate genomic research.” said Nathan Wood, Swift’s

President and CEO

Helix chose 2S Turbo because of its superior coverage uniformity and on-target performance

with minimal base composition bias and excellent data reproducibility, which were of critical

importance to Helix’s product integrity. Furthermore, Helix applied their team’s deep

knowledge of genomics and bioinformatics to ensure a seamless integration into their existing

sample preparation and target capture pipeline.

“In designing the Exome+™ assay, one of the most important things to us was ensuring there

were no gaps in coverage for clinically relevant regions. Swift’s coverage uniformity and on-

target performance helped significantly here.” said David Becker, Helix’s VP of Quality and

R&D. “We look forward to our continued partnership with Swift, which has played a role in

helping us develop one of the most versatile whole exome assays on the market capable of

supporting both clinical and research applications.”

About Helix

Helix is a population genomics company with a mission to empower every person to improve

their life through DNA. Helix is accelerating the integration of genomic data into clinical care

and broadening the impact of large-scale population health programs by providing

comprehensive expertise in DNA sequencing, bioinformatics, and individual engagement.

Powered by their proprietary Exome+™ assay—a panel-grade clinical exome enhanced by more

than 300,000 informative non-coding regions—Helix partners with health systems to provide a

scalable solution which enables the discovery of medically relevant, potentially life-saving,

genetic information. Additionally, Helix offers a suite of DNA-powered products for continued

individual engagement and discovery.

Helix is headquartered in the San Francisco Bay Area and has one of the world’s largest CLIA-

certified, CAP-accredited Next Generation Sequencing labs, located in San Diego, California.

Learn more at www.helix.com.

Helix, the Helix logo, and Exome+ are trademarks of Helix OpCo, LLC

About Swift Biosciences

Swift Biosciences develops enabling technologies for genomics, translational, and clinical

research. Our technologies expand the range of sample inputs to extend the applications of

next-generation sequencing (NGS).

We have developed unique intellectual property (IP) to enhance adapter ligation to both single

and double-stranded DNA, improve multiplexed PCR for targeted sequencing and enable novel

solutions for NGS workflows and our RNA is the fastest on the market using Adaptase®

technology.

Using its proprietary technologies, Swift has developed DNA and RNA library preparation kits

and library normalization for NGS.

Our high-quality product portfolio features fast, easy and reliable solutions for many lab

workflows. For more information, visit SwiftBioSci.com and follow Swift Biosciences on Twitter

(@SwiftBioSci).

PARTNER WITH US

674 S. Wagner Road, Suite 100 • Ann Arbor, MI 48103

734.330.2568

www.swiftbiosci.com