stoke therapeutics

Stoke TherapeuticsNovember 2020Nasdaq: STOK

© Copyright 2020 Stoke Therapeutics, Inc. All rights reserved.

Disclaimer

2 © Copyright 2020 Stoke Therapeutics, Inc. All rights reserved

This presentation has been prepared by Stoke Therapeutics, Inc. (“Stoke” or “our”) for informational purposes only and not for any other purpose. Nothing contained in this presentation is, orshould be construed as, a recommendation, promise or representation by the presenter or Stoke or any officer, director, employee, agent or advisor of Stoke. This presentation does not purport tobe all-inclusive or to contain all of the information you may desire. Information provided in this presentation speaks only as of the date hereof. Stoke assumes no obligation to publicly update anyinformation or forward-looking statement, whether written or oral, that may be made from time to time, whether as a result of new information, future developments, subsequent events, orcircumstances after the date hereof, or to reflect the occurrence of unanticipated events.

This presentation contains “forward-looking” statements within the meaning of the “safe harbor” provisions of the Private Securities Litigation Reform Act of 1995, including, but not limited to:preclinical data and study results regarding OPA1, future operating results, financial position and liquidity, the direct and indirect impact of COVID-19 on our business, financial condition andoperations, including on our expenses, supply chain, strategic partners, research and development costs, clinical trials and employees; our expectation about timing and execution of anticipatedmilestones, responses to regulatory authorities, expected nomination of future product candidates and timing thereof, our ability to complete lead optimization of ASOs for ADOA, the timing andresults of ADOA preclinical studies, our ability to develop ASOs treat the underlying causes of ADOA, our ability to advance OPA1 as our next preclinical target, and our ability to use study data toadvance the development of STK-001; the ability of STK-001 to treat the underlying causes of Dravet syndrome; and the ability of TANGO to design medicines to increase protein production andthe expected benefits thereof. These forward-looking statements may be accompanied by such words as “aim,” “anticipate,” “believe,” “could,” “estimate,” “expect,” “forecast,” “goal,” “intend,”“may,” “might,” “plan,” “potential,” “possible,” “will,” “would,” and other words and terms of similar meaning. These forward-looking statements involve risks and uncertainties, as well asassumptions, which, if they do not fully materialize or prove incorrect, could cause our results to differ materially from those expressed or implied by such forward-looking statements. Thesestatements involve risks and uncertainties that could cause actual results to differ materially from those reflected in such statements, including: our ability to develop, obtain regulatory approvalfor and commercialize STK-001, OPA1 and future product candidates; the timing and results of preclinical studies and clinical trials; the risk that positive results in a clinical trial may not bereplicated in subsequent trials or success in early stage clinical trials may not be predictive of results in later stage clinical trials; risks associated with clinical trials, including our ability to adequatelymanage clinical activities, unexpected concerns that may arise from additional data or analysis obtained during clinical trials, regulatory authorities may require additional information or furtherstudies, or may fail to approve or may delay approval of our drug candidates; the occurrence of adverse safety events; failure to protect and enforce our intellectual property, and otherproprietary rights; failure to successfully execute or realize the anticipated benefits of our strategic and growth initiatives; risks relating to technology failures or breaches; our dependence oncollaborators and other third parties for the development, regulatory approval, and commercialization of products and other aspects of our business, which are outside of our full control; risksassociated with current and potential delays, work stoppages, or supply chain disruptions caused by the coronavirus pandemic; risks associated with current and potential future healthcarereforms; risks relating to attracting and retaining key personnel; failure to comply with legal and regulatory requirements; risks relating to access to capital and credit markets; environmental risks;risks relating to the use of social media for our business; and the other risks and uncertainties that are described in the Risk Factors section of our most recent annual or quarterly report and inother reports we have filed with the U.S. Securities and Exchange Commission. These statements are based on our current beliefs and expectations and speak only as of the date of thispresentation. We do not undertake any obligation to publicly update any forward-looking statements.

By attending or receiving this presentation you acknowledge that you are cautioned not to place undue reliance on these forward-looking statements, which speak only as of the date suchstatements are made; you will be solely responsible for your own assessment of the market and our market position; and that you will conduct your own analysis and be solely responsible forforming your own view of the potential future performance of Stoke.

Stoke Therapeutics

Amplifying Science to Transform the Experience of Life

Stoke is making a new generation of RNA-based genetic medicines that upregulate protein expression to restore human health.


Foundational Elements of Stoke


Experienced Leaders in Innovation

Differentiated Platform with Broad

Applicability

Strong Financial Position to Support

Growth

Focused Development

Program

to transform the experience of life.

Amplifying Science


TANGO Restores Protein Levels by Stoking Output From Healthy Genes

• Stoke’s ASOs bind to specific stretches of pre-mRNA to reduce non-productive mRNA and increase productive mRNA

• The increased levels of productive mRNA from the functional copy of the gene result in increased protein production

• For haploinsufficiences, TANGO restores the target protein to near-normal levels

TANGO: An RNA-Based Genetic Medicine Platform for Protein Upregulation


Targeted Augmentation of Nuclear Gene Output

• Addresses underlying cause of disease

• Applicable to most loss-of-function mutations

• Applies equally to small or large gene targets

• Gene and tissue specific

• Controllable dose and duration

• Can address wide array of diseases

• Simple and scalable manufacturing

TANGO

Stoke uses RNA science to restore

missing proteins by increasing – or stoking –

protein output from healthy genes.

Transformative Potential of TANGO Technology for Gene Upregulation


Source: Lim, K.H., Han, Z., Jeon, H.Y. et al. Antisense oligonucleotide modulation of non-productive alternative splicing upregulates gene expression. Nat Commun 11, 3501 (2020).

Robust Target Identification Process Utilizing Proprietary Bioinformatics

• Approximately 50% of human genes contain a TANGO signature

• Cross-referencing with genetic disease databases identifies approximately 2,900 monogenic diseases amenable to TANGO

• Enables rapid and systematic identification of clinically relevant targets

RNA sequencing and in silico discovery datasets

Proprietary bioinformatics analysis

Universe of non-productive splicing events

Genetic disease databases

TANGO amenability assessment

TANGO targets

Cell and tissue validation

Hit identification

Candidate evaluationand prioritization

Source: Stoke data

Target identification process


TANGO is Applicable to a Broad Range of Targets


Genetic epilepsy – haploinsufficiency

- 30 60 120 30 60 1200

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SYNGAP1non-productive event productive mRNA protein

NT ASOnM

NT ASOnM

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Pathway target – wild type

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NT ASOnM

CD274 (PD-L1)non-productive event productive mRNA protein

0 20 40 60 80 1000123456789

Fold

upr

egul

atio

n

R2 = 0.94p = 0.03

% non-productive event

Correlation between event abundance (+CHX) & upregulation

SCN1ASYNGAP1

CD274PCCA

NT: non-targeting ASO control, all experiments n = 3, in vitro

Liver target – autosomal recessive

PCCAnon-productive event productive mRNA protein

NT ASOnM

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Dravet Syndrome: A Severe, Progressive Genetic Epilepsy


85%

1 out of

16,000 babies are born with Dravet syndrome

20%

Note: 1 Sudden Unexpected Death in Epilepsy Sources: 2018 Health Advances Report; Djémié et al., Molecular Genetics & Genomic Medicine 2016; Lagae et al., Developmental Medicine & Child Neurology 2017; Nabboutet al., Orphanet Journal of Rare Diseases 2013

of children and adolescents with Dravet die before adulthood, due to SUDEP1, prolonged seizures, seizure-related accidents or infections

~35,000

Seizures are not adequately controlled in

90% of people with Dravet

of cases caused by a haploinsufficiency of the SCN1A gene 50%

NaV1.1 protein expression

results in

people affected in the U.S., Canada, Japan, Germany, France and the UK

Up to

Dravet syndrome is not concentrated in a particular geographic area or ethnic group.

Non-Seizure Comorbidities of Dravet Syndrome Are Not Addressed by Current Therapies


Dravet is Not Limited to Seizures:More than 90% of patients suffer from at least one non-seizure comorbidity, including:

• Intellectual disability• Developmental delays• Movement and balance issues• Language and speech disturbances• Growth defects• Sleep abnormalities• Chronic infections• Disruptions of the autonomic nervous

system• Mood disorders

High Incidence of Premature Death:Up to 20% of children and adolescents die before adulthood, due to:

• SUDEP

• Prolonged seizures

• Seizure-related accidents

• Infections

Sources: Antisense oligonucleotides increase Scn1a expression and reduce seizures and SUDEP incidence in a mouse model of Dravetsyndrome Han et. al., Science Translational Medicine 2020; Shmuely et al Epilepsy & Behavior 2016

STK-001 Increases Scn1a mRNA and NaV1.1 Protein in Wild-type Mice

12 © Copyright 2020 Stoke Therapeutics, Inc. All rights reserved.

Decrease in non-productive Scn1a mRNA

Increase in productive Scn1a mRNA

C o n t r o l 0 . 3 1 . 0 3 . 0 1 00

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Fo

ld c

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Perc

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RNA

Source: Stoke data

Increase of NaV1.1 protein

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STK-001 Restores NaV1.1 to Near Normal Levels for >3 Months in Dravet Syndrome Mice

Note: Nav1.1 protein quantification based on standard curve obtained from untreated wild-type mouse brain as a reference control Source: Stoke data; University of Michigan (in-life study)

In preclinical studies, STK-001 exhibits long-lasting exposure, suggesting the potential for a favorable dosing regimen of as few as two to three administrations per year in humans

10

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Wild type Dravet mouse Wild type Dravet mouse

Placebo 7 weeksSTK-001 7 weeks

7 weeks 14 weeks

Increase in Nav1.1 protein expression after 7 and 14 weeks

Placebo (7 weeks)

STK-001 (7 weeks)

Placebo (14 weeks)

STK-001 (14 weeks)

Wild-type mice

Wild-typemice

Dravet syndrome mice

Dravet syndrome mice

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STK-001 Significantly Reduces Premature Mortality in Dravet Syndrome Mice


STK-001 DS mouse (n = 34)

0 10 20 30 40 50 60 70 80 900

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Placebo DS mouse (n = 62)

STK-001 Wild-type****

Significant improvements in survival among Dravet syndromemice after STK-001 administration (20µg) at postnatal day 2

****p<0.0001

Source: Z. Han, C. Chen, A. Christiansen, S. Ji, Q. Lin, C. Anumonwo, C. Liu, S. C. Leiser, I. Aznarez, G. Liau, L. L. Isom, Antisense oligonucleotides increase Scn1a expression and reduce seizures and SUDEP incidence in a mouse model of Dravet syndrome. Sci. Transl. Med. 12, eaaz6100 (2020).

Source: Stoke data, presented at AES 2019

STK-001 Significantly Reduces Spontaneous Seizures in Dravet Syndrome Mice


76% of mice treated with STK-001 were seizure-free compared to 48% of placebo-treated mice

0 1 20

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10

15

20

Number of seizures

Num

ber o

f mic

e

PlaceboSTK-001

≥

48%

76%

38%

14%

80% reduction in the average number of spontaneous seizures compared to placebo (p<0.05)

As measured between postnatal days (PND) 22 and 46 in Dravet syndrome mice after a single 20 µg injection of STK-001 at PND 2

PBS STK-0010

5

10

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Numb

er of

seizu

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Placebo

* = p<0.05

STK-001 Achieves Broad Distribution and Increases Nav1.1 Protein Expression in NHPs (n=3)


Exposure of STK-001 observed in all brain regions except pons and thalamus Nav1.1 protein levels increased up to 3-fold

Cerebell

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Hypothala

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Limbic

Lobe

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xPons

Prefrontal

Cortex

Temporal

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-001

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Cortex

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g)/T

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g)

PlaceboSTK-001

* *

Source: Stoke data, presented at AES 2019

.* = p<0.05

Pivotal Preclinical Single and Multiple-Dose Toxicology Studies in NHPs Showed STK-001 Well-Tolerated

Key safety findings from GLP studies*

No observed adverse events at highest dose tested

No change in platelet counts or renal/hepatic function

No adverse histopathology in brain, spinal cord, liver and kidney

17 © Copyright 2020 Stoke Therapeutics, Inc. All rights reservedSource: Stoke data

IT=Intrathecal, NHP= non-human primate

The no observed adverse effect level (NOAEL) in the GLP studies in NHPs exceeds the highest human equivalent dose that we plan to administer in our Phase 1/2a clinical study

* In non-GLP studies in NHPs, at levels above the NOAEL, hind limb paresis was observed; at extremely high dose levels, acute convulsions were observed.

STK-001 Has Potential to Address the Genetic Cause of Dravet Syndrome


Preclinical data support the use of STK-001 in Dravet syndrome:

Single dose restores NaV1.1 from 50% to near normal levels for >3 months in Dravet syndrome mice

Significantly reduces mortality and seizure frequency in Dravet syndrome mouse model

Selective target engagement may limit potential off-target effects

Broadly distributes in the brains of non-human primates with intrathecal delivery

Well-tolerated at pharmacologically-active dose levels in non-human primates

Able to dose titrate with wide therapeutic window

BUTTERFLY Observational Study Ongoing


• Two-year observational study of children and adolescents ages 2-18

• Designed to evaluate seizure frequency and non-seizure comorbidities associated with Dravet syndrome, including:

- Intellectual disabilities

- Developmental disabilities

- Motor impairment

- Speech impairment

- Behavioral problems

- Sleep abnormalities

Enrollment and Dosing in MONARCH Phase 1/2a Trial is Ongoing

• Open-label study of children and adolescents ages 2-18 with Dravet syndrome

First patient dosed August 2020 Plan to enroll ~48 patients at ~20 sites in the U.S. Primary endpoints: safety and tolerability of a single-ascending dose, characterize human

pharmacokinetics

Secondary endpoints: change in seizure frequency over 12-weeks, quality of life

• Two-part trial design:

Single ascending dose (SAD) portion (previously, Part A) will now be designed to evaluate three dose levels: 10mg, 20mg and 30mg; higher doses remain on FDA partial clinical hold

Subject to FDA review, a multiple ascending dose portion (MAD) will be added to the study to evaluate monthly doses up to 30mg for three months

For each dose level, sentinel group ages 13-18, followed by group ages 2-12

• Preliminary data expected in 2021


TANGO is Well Suited for Treatment of Eye Diseases

Benefits of focusing on the eye for ASOs• Localized delivery• Immune privileged and small treatment space (0.05% of total body weight) • Contralateral control for clinical trials• Availability of non-invasive measurements that reflect functional outcome (e.g. OCT)Advantages of TANGO for the eye • Intravitreal delivery has safety & patient acceptance advantage over subretinal delivery• Stoke preclinical data demonstrates long-term effects of up to 12 months• Tunable and reversible control of level and specificity of protein expression • No formulation or viral vector requirement• Approved product precedence (Vitravene for cytomegalovirus retinitis)• Potential to target large genes


OPA1 Protein Deficiency is the #1 Cause of Autosomal Dominant Optic Atrophy (ADOA), the Most Common Inherited Optic Nerve Disorder

• Autosomal dominant optic atrophy (ADOA) is the most common inherited optic nerve disorder seen in clinical practice

• ADOA causes progressive and irreversible vision loss in both eyes starting in the first decade of life. Many children progress to blindness

• The disease affects 1/30,000 people globally with a higher incidence of ~ 1/10,000 in Denmark due to a founder effect

• 65%-90% of ADOA is caused by loss of function mutations in one allele of the OPA1 gene which leads to haploinsufficiency and disease manifestation

• >400 different OPA1 mutations reported in ADOA patientsSources: Yu-Wai-Man P et al. The Prevalence and Natural History of Dominant Optic Atrophy Due to OPA1 Mutations. Ophthalmology. 2010 August; 117(8): 1538-1546; Yu-Wai-Man P, Chinnery PF. Dominant Optic Atrophy: Novel OPA1 Mutations and Revised Prevalence Estimates. Ophthalmology. Vol. 120, Number 8, August 2013: 1712-1712; 3. P. Amati-Bonneau P et al. OPA1-associated disorders: phenotypes and pathophysiology. The International Journal of Biochemistry & Cell Biology 41, 1855-1865 (2009); “What is ADOA?” Autosomal Dominant Optic Atrophy Association. Accessed May 6, 2020, from https://www.adoaa.org/what-is-adoa; Lenaers G, Hamel C, Delettre C, et al. Dominant optic atrophy. Orphanet J Rare Dis 7, 46 (2012); Chun BY and Rizzo JF III. Dominant optic atrophy: updates on the pathophysiology and clinical manifestations of optic atrophy 1 mutation. Curr Opin Ophthalmol 2016; 27:475-480; Le Roux B, Lenaers G, Zanlonghi X et al. OPA1: 516 unique variants and 831 patients registered in an updated centralized Variome database. Orphanet J Rare Dis 14, 214 (2019).


https://www.adoaa.org/what-is-adoa

TANGO ASOs Have the Potential to Be a First-In-Class Precision Medicine for ADOA

• There are currently no available treatments for autosomal dominant optic atrophy

• Corrective aids such as glasses or contacts do not help improve vision lost to the disease

• ADOA causes deterioration of the optic nerves (arrow in A), which can be observed on OCT (B)

• Stoke’s TANGO ASOs target the underlying cause of ADOA by utilizing a non-productive splicing event in the OPA1 gene to increase productive OPA1 mRNA & protein expression in retinal ganglion cells

Source: Lenaers et al. Dominant optic atrophy. Orphanet Journal of Rare Diseases 2012, 7:46


OCT

retinal nerve fiber layer thickness

OPA1 is Critical for Normal Mitochondrial Function and Cellular Metabolism

• OPA1 encodes a dynamin-like mitochondrial GTPase that is a key mediator of mitochondria fusion/fission which is critical for ATP synthesis and other important mitochondrial functions.

• Insufficient OPA1 activity causes mitochondria dysfunction with consequent insufficient ATP production, excess reactive oxygen species (ROS) production and eventual cell death.

• Retinal ganglion cells are high energy demanding cells and particularly susceptible to loss of ATP production and mitochondrial dysfunction


• Novel exon inclusion event (Exon X) identified in the OPA1 gene introduces a premature termination codon (PTC)

• Exon X inclusion produces a non-productive mRNA that is degraded by non-sense mediated decay (NMD), producing no protein

• Inhibition of NMD with cycloheximide allows for evaluation of the abundance of this event in vitro

protein

Exon A

productive mRNA protein

XNon-productive mRNA

Exon BExon X

*PTC


DMSO 10ug/mL 50ug/mLCycloheximide

A B

A BX

Human embryonic kidney 293 (HEK293) cells

OPA1 non-productive splicing event was detected in vitro in various cell lines

A Non-Productive mRNA Splicing Event in OPA1 Was Identified and Validated

Rabbit ASO Demonstrates Dose-Dependent OPA1 Protein Increase in Rabbit Retina

• Retinal exposure of ST-1102 ASO was elevated with increased dosing• Dose-dependent target engagement seen at all three time-points examined• Protein increase of OPA1 protein observed at both Day 15 and Day 29 of study

Target engagement; Day 29 OPA1 protein; Day 29ASO exposure in retina; Day 29

PBS ST-1102; 0.23mg

OPA1

Actin

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*

* *

*

*

*P<0.0005 by one-way ANOVA compared to PBS groupOD: oculus dextrus (right eye), OS: oculus sinister (left eye)

Day 15 Day 29

Day 1

Euthanize and collect retinal tissueFemale NZW rabbits

Single intravitreal (IVT) injection of vehicle/ASO (n=3/group)

Day 8


Human ASO Demonstrates ATP Upregulation in OPA1 Haploinsufficient HEK293 Cells

N= 3

• Adenosine triphosphate (ATP) is produced by the mitochondria and is the key energy carrying molecule in cells

• OPA1 protein is a crucial mediator of mitochondria health

• Here we evaluated the impact of restoration of OPA1 protein in haploinsufficient HEKs

• A 20% ATP deficit was observed in OPA1 +/- HEK293

• Treatment with ASO-14 restored ATP levels to ~90% of control cells

*one-way ANOVA# t-test

Mock

ASO-14Mock

ASO-140.0

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25

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75

100

125

150

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actin

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on

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******

###


** = P value 0.0006

*** = P value <0.0001

### = P value 0.0006


Dose-dependent decreases in non-productive OPA1 mRNA and increases in OPA1 protein expression in vitro and in vivo.

Increases in OPA1 protein levels in the retina of wild-type rabbits that correlated with increases in the level of the test ASO.

An increase in OPA1 protein expression to approximately 75% of wild-type levels in an OPA1 haploinsufficient (OPA1 +/-) cell line.

The rabbit surrogate ASO was well tolerated for up to 29 days (maximum days evaluated) after intravitreal injection.

Approach leverages upregulation of the wild-type allele and can potentially be used to treat ADOA due to loss of OPA1 activity in a mutation-independent manner.

Preclinical Data Support the Use of Stoke’s TANGO Technology to Treat ADOA

Increase in OPA1 protein levels in OPA1+/- cells correlated with a substantial restoration of mitochondrial function as measured by ATP synthesis.

We plan to initiate Lead Optimization to potentially identify a Clinical Candidate in 2021

2020

Early 2020: FDA communicated that Part A of MONARCH may proceed with dosing

2H 2020: Began enrollment and dosing of patients in MONARCH in Aug. 2020

2H 2020: Nominate new candidate for preclinical development in an additional genetic disease

Continuously evaluate potential collaborations to expand the pipeline

Build the organization and capabilities to scale as a clinical-stage company

Stoke Becomes a Clinical-Stage Company

Rapidly Scaling Stoke to Support Growth as a Clinical-Stage Company


2019

2018

Stoke is Poised to Enter the Clinic

Stoke is Launched • Closed $40M Series A financing

• Nominated Dravet syndrome as lead program; generated in-vivo proof of concept

• Completed FDA pre-IND meeting

• Closed $90M Series B financing

• Built robust intellectual property estate

• Completed $163.3M Initial Public Offering

• Received FDA orphan drug designation for STK-001, a potential disease modifying medicine for Dravet syndrome

• Enrolled first patient in the BUTTERFLY observational study

• Presented preclinical data supporting efficacy of STK-001

• Submitted IND for STK-001 to the U.S. FDA

Current Financials Anticipated to Fund Operations into 2023


Cash, Cash Equivalents and Restricted Cashas of 09/30/2020 $191.7 million

Common Shares Outstandingas of 09/30/2020 33,361,188

The Commitment that Drives Stoke


stoke therapeutics

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