www.ultragenyx.com

CaSSS Gene Therapy Forum

November 8, 2018

Unique Considerations for AAV Gene Therapy Manufacturing

K. Baradaran

Legal Warning

Cautionary note regarding forward-looking statements: This presentation contains forward-looking statements, including, but

not limited to, statements regarding our plans with respect to commercializing our product and product candidates, our translational

research program, the expected timing of release of additional data for our product candidates, plans to initiate additional studies for

product candidates and timing and design of these studies, plans regarding ongoing studies for existing programs, expectations

regarding the adequacy of clinical data to support marketing applications and approvals of product candidates, our intent to file

marketing applications and the timing of such filings, expectations regarding timing of receiving potential approval of product

candidates, and expectations regarding prevalence of patients. Such forward-looking statements involve substantial risks and

uncertainties that could cause our clinical development programs, future results, performance or achievements to differ significantly

from those expressed or implied by the forward-looking statements. Such risks and uncertainties include, among others, the

uncertainties inherent in the clinical drug development process, such as the regulatory approval process, the timing of our regulatory

filings and other matters that could affect sufficiency of existing cash, cash equivalents and short-term investments to fund

operations, the availability or commercial potential of our product and product candidates, and our ability to integrate acquired

businesses, which are more fully described in our most recent Form 10-Q or Form 10-K under the caption “Risk Factors” and

elsewhere in such reports. Any forward-looking statements made by us reflect our current views with respect to future events or to

our future financial performance and involve known and unknown risks, uncertainties, and other factors that may cause our actual

results, performance, or achievements to be materially different from any future results, performance, or achievements expressed or

implied by these forward-looking statements. Accordingly, our actual results may materially differ from our current expectations,

estimates, and projections. Given these uncertainties, you should not place undue reliance on these forward-looking statements.

Any forward-looking statements made by us in this presentation speak only as of the date of this presentation and represent our

estimates and assumptions only as of the date of this presentation. Except as required by law, we assume no obligation, and we

disclaim any intent, to update these statements to reflect actual results.

This presentation concerns drugs that are under preclinical and/or clinical investigation and which have not yet been approved for

marketing by the U.S. Food and Drug Administration (FDA). They are currently limited by Federal law to investigational use, and no

representations are made as to their safety or effectiveness for the purposes for which they are being investigated.

Ultragenyx, Ultragenyx Pharmaceutical, Ultragenyx Gene Therapy, and our logo are our trademarks. Any other trademarks

appearing in these slides are the property of their respective holders.

1

Ultragenyx rAAV Platform for Gene Therapy

• Multiple constructs

• Oversized, Self Comp

• Codon optimization

• Enhancers

• Promoters

Transgene

Cassette

Capsids Vector Peripheral Liver

Directed

• Multiple Serotypes

• Clad E capsids Library

• Neutralizing antibodies

• Mammalian Platform

• Multiple Analytics

• Characterization

• Non-clinical (primary KO) models

• Formulations

• Internal Development & External CMO/CRO Relationships

• High Throughput Development

• Scale-Up & Tech Transfer

• Primary Liver Focus

• Global Clinical Trials & Submissions

• Expanding Indications

• Personalized Patient Delivery

Manufacturing

2

Ultragenyx rAAV Manufacturing Platforms

3

HEK293 Adherent HEK293 Suspension HeLa Producer Cell

• Well-known

• Regulatory experience

• Transient tripletransfection

• Serum-containing production

• Limited scalability (Scale-Out)

• Well-known

• Established platform

• Transient triple transfection

• Serum free production

• Bioreactors

• Scalable up to 200 to 500L, potentially scalable to 2000L

• Well-known

• Clonal, high productivity

• Similar to CHO platform

• Serum-free production

• Large scale bioreactors

• Scalable up to 2000L

▪ Three active Gene Therapy CMC/IND programs

▪ Three active global hPOC clinical trials in US and Ex-US for rare diseases

▪ Three AAV manufacturing platforms in parallel production

▪ Three INDs in less than 18 months

▪ One major collaboration

▪ Multiple CDMO

▪ Multiple CRO & Academic Labs

▪ Multiple MFG Suppliers

▪ Multiple Biorepositories

▪ Strategic CRO/CMO for clinical distribution

Topics for Discussion

▪ Typical profiles of gene therapy products vs traditional biologics

▪ Unique considerations for gene therapies vs traditional biologics

– Manufacturing

– Quality

– Supply Chain and Delivery of Product

– Comparability strategies

▪ Questions and discussion

4

Typical Profiles of Gene Therapy Products

Attribute Traditional

Biologics

Gene Therapy Cell Therapy

Disease Profile Large Rare/Small Rare/Small

Delivery Repeated Single in-vivo Single ex-vivo

Administration Multiple Primarily IV or I/T Potentially

Leukapheresis &

Infusion

Presentation Multiple Frozen Cryopreservation

Supply Chain Inventory/Multiple Personalized

Shipment/

Cold Chain

Personalized

Medicine/Cold

Chain

Production Standardized Complex A batch a patient

Clinical Trial Profile Large

Healthy

Volunteers/

Placebo/

Comparator

Small

No Healthy

Volunteers/

Open Label

Small

No Healthy

Volunteers/

Open Label

5

Commonly Used Viral Vectors*P

art

icle

Ch

ara

cte

ristics

Attribute Adenovirus AAV Herpes Retrovirus Pox/Vaccinia

Genome dsDNA ssDNA dsDNA ssRNA dsDNA

Coat Naked Naked Enveloped Enveloped Enveloped

Genome size 30-38 kb 5 kb 120-200 kb 3-9 kb 130-280 kb

Ge

ne

Th

era

py P

rop

ert

ies

Infection/

tropism

Dividing and

non-dividing

cells

Dividing

and non-

dividing

cells

Dividing

and non-

dividing

cells

Dividing

cells**

Dividing and

non-dividing

cells

Host genome

interaction

Non-

integrating

Non-

integrating

Non-

integrating

Integrating Non-integrating

Transgene expression Transient Potential

long-

lasting

Potential

long-

lasting

Long-

lasting

Transient

Packaging capacity 7.5 kb 4.5 kb >30 kb 8 kb 25 kb

Immunogenicity High High High Low High

6

*Source: White Paper on Gene Therapies 2015 Smart Analyst

** Lentivirus vectors can also infect non-dividing cells

Manufacturing Strategies Vary

▪ Modified Cell Therapy manufacturing

– Lentivirus vector

– Autologous vs Allogeneic

• CAR-T: Individual patient T-cells modified and tested before being

administered to the patient

▪ AAV manufacturing strategies

– Baculovirus

– Helper-Free Transfection

• Adherent or Suspension Triple Plasmid transient transfection

– Helper virus (HSV, AdV)

• Producer Cell Lines vs. Packaging Cell Lines

– Single vs. multiple AAV vectors (eg, zinc finger gene editing strategy)

• Multiple serotypes

7

Finding the right CMO is challenging – no ‘one stop shop’

Critical Raw Materials: Traditional Biologics vs

Gene Therapy

Attribute Traditional

Biologics

Gene Therapy

MCB X X

WCB X X

Serum or Serum

Free Cell Culture

media

X X

Resins X X

Plasmids X

Viral vector(s)

stocks(X)* X

Viral Clearance X X

8

*Some viral vaccines also require virus stocks

MCB: Master Cell Bank; WCB: Working Cell Bank

MVB: Master Virus Bank; WVB: Working Virus Bank

Critical Raw Materials –

Plasmid and Helper Virus Banks

Manufacturing

Strategy

E.Coli

MCB/

WCB

E.Coli

MCB/

WCB

E.Coli

MCB/

WCB

Parent

MCB/

WCB

Product

MCB/

WCB

MVB/

WVB

Transient

transfectionx x x x

Helper virus x x x

Traditional

Biologicsx

9

Need to identify ‘enabling’ CMOs for plasmid or viral vector supply

MCB: Master Cell Bank; WCB: Working Cell Bank

MVB: Master Virus Bank; WVB: Working Virus Bank

CMC Challenges & Considerations

Attribute Gene Therapy Cell Therapy

Cell & Virus Banking High High

Process VariabilityqPCR assay

dependentHigh

Batch Success (or Failure) ModerateHigh

Process is the product

Sterility Moderate Very High

Vector Transduction and

replicationHigh High

Co-packaged host DNA

High for systemic

dosing, above

WHO level (10ng

DNA/dose)

Low/Moderate

Comparability ModerateHigh

One lot per patient

Critical Raw Materials High High

10

Ultragenyx AAV Platform Supply Chain

Plasmid

•Rep

•Cap

Plasmid

•Ad Helper

Plasmid

•Trans-gene

DS

• UPS

DS

• DSP

Media

•Liquid

•Pre-made

Buffers

•Liquid

•Ready-To-Use

SUS

•Bags & Compon.

•Manifolds

•ATF

Critical RM

•Nuclease

•Resins

•Membranes

Fill Comp

•Vials

•Stoppers

•Crimpers

•Labels

Critical RM

•Nuclease

•Resins

•Membranes

DP

• Filling

• Labeling

Testing

• CDMO

• CROs

E.Coli

•MCB

•WCB

E.Coli

•MCB

•WCB

E.Coli

•MCB

•WCB

Hela S3

• MCB

• WCB

Ad5

• MVB

• WVB

HelaPCL

• MCB

• WCB

HEK293

• MCB

• WCB

Quality Testing Considerations

▪ Use of multiple QC test labs to cover wide variety of technical methods –no ‘one stop shop’

– Multiple different PCR-based methods

– Cell-based infectivity methods +/- PCR or antibody-based detection

– ELISA methods

– Gel electrophoresis +/- blotting techniques

– ICH, USP/Ph. Eur. methods

▪ Minimal sampling and sharing of vials where possible to conserve material, minimize number of QC retains

▪ Media fill results must be summarized in IND and reports provided upon request

▪ PCR method must be validated and report submitted in IND

▪ Sensitivity of release methods should be summarized in IND

▪ Characterization assays are required for each lot – and there are a lot of them

A lot of hands-on, real-time sample management and data review

Unique QC Testing Strategies:

Example Testing for 1 Lot

▪ In-process testing

– Mycoplasma

– 28-day in vitro viral assay

– Bioburden

▪ Release and characterization testing

– General (pH, appearance, osmolality)

– Identity – could be multiple methods

– Purity

– Potency – could be multiple methods

– Concentration (eg, genome copies by PCR)

– Safety testing (bioburden (DS), sterility(DP), endotoxin)

– Impurities (eg, host cell protein, host cell DNA, process residuals such as

BSA, Benzonase, affinity resin leachates)

– In addition – residual plasmid DNA, ‘packaged’ host cell DNA – multiple PCR

assays to cover different DNA sequence targets

– Sequence of final gene therapy product

13

Comparability Strategies

▪ Comparability strategies are needed for major changes, for example:

– DNA sequence modifications – coding vs non-coding regions

– Cell substrate changes (eg, HEK293 vs PCL vs Baculovirus)

– Downstream purification changes

– CMO

– Presentation or formulation changes

– Other major changes

▪ Analytical comparability typically consists of in-process, release,

characterization and stability data vs historical trends

– Side by side testing vs individual read-outs

▪ If differences are seen, non-clinical or human studies may be needed

14

Conclusions

▪ There are a number of unique CMC considerations for cell and gene therapy

manufacturing

▪ There is no ‘one stop shop’ for manufacturing and testing

▪ Different CMOs and test labs have different capabilities; capacity may be

limited

▪ Additional ‘enabling CMOs’ may be needed for critical raw materials

▪ Supply chain is complex and highly patient-centric

▪ Comparability strategies are dynamic and need to be designed to be fit for

purpose

15

Questions for Discussion

16