8-K

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

FORM 8-K

CURRENT REPORT

PURSUANT TO SECTION 13 OR 15(D)

OF THE SECURITIES EXCHANGE ACT OF 1934

Date of Report (Date of earliest event reported): August 11, 2020

APPLIED GENETIC TECHNOLOGIES CORPORATION

(Exact Name of Registrant as Specified in Charter)

Delaware	001-36370	59-3553710
(State or other jurisdiction of incorporation)	(Commission File Number)	(IRS Employer Identification Number)

14193 NW 119^th Terrace

Suite 10

Alachua, Florida, 32165

(Address of principal executive offices) (Zip Code)

(386) 462-2204

(Registrant’s telephone number, including area code)

Not Applicable

(Former Name or Former Address, if Changed Since Last Report)

Check the appropriate box below if the Form 8-K filing is intended to simultaneously satisfy the filing obligation of the registrant under any of the following provisions (see General Instruction A.2. below).

☐ Written communications pursuant to Rule 425 under the Securities Act (17 CFR 230.425)

☐ Soliciting material pursuant to Rule 14a-12 under the Exchange Act (17 CFR 240.14a-12)

☐ Pre-commencement communications pursuant to Rule 14d-2(b) under the Exchange Act (17 CFR 240.14d-2(b))

☐ Pre-commencement communications pursuant to Rule 13e-4(c) under the Exchange Act (17 CFR 240.13e-4(c))

Securities registered pursuant to Section 12(b) of the Act:

Title of each class	Trading Symbol(s)	Name of each exchange on which registered
Common Stock, $0.001 par value	AGTC	Nasdaq Global Market

Indicate by check mark whether the registrant is an emerging growth company as defined in Rule 405 of the Securities Act of 1933 (§230.405 of this chapter) or Rule 12b-2 of the Securities Exchange Act of 1934 (§240.12b-2 of this chapter).

Emerging growth company  ☐

If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for complying with any new or revised financial accounting standards provided pursuant to Section 13(a) of the Exchange Act.  ☐

Item 7.01. Regulation FD Disclosure.

Applied Genetic Technologies Corporation (the “Company”) from time to time presents at various industry and other conferences a summary of recent corporate and clinical developments. A copy of the slide presentation that will be used by officers of the Company in connection with such presentations (the “Corporate Presentation”) is attached to this Current Report on Form 8-K as Exhibit 99.1. The Corporate Presentation is current as of August 11, 2020, and the Company disclaims any obligation to correct or update this material in the future.

The Corporate Presentation attached as Exhibit 99.1 is intended to be furnished and shall not be deemed “filed” for purposes of Section 18 of the Securities Exchange Act of 1934 (the “Exchange Act”) or otherwise subject to the liabilities of that section, nor shall it be deemed incorporated by reference in any filing under the Securities Act of 1933 or the Exchange Act, except as expressly set forth by specific reference in such filing.

Item 9.01. Financial Statements and Exhibits.

    (d) Exhibits.

Exhibit No.	Description
99.1	Corporate Presentation current as of August 11, 2020

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SIGNATURES

Pursuant to the requirements of the Securities Exchange Act of 1934, the Registrant has duly caused this report to be signed on its behalf by the undersigned thereunto duly authorized.

APPLIED GENETIC TECHNOLOGIES          CORPORATION
By:	/s/ William A. Sullivan
	William A. Sullivan
	Chief Financial Officer

Date: August 11, 2020

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EX-99.1

August 2020 Investor Presentation Exhibit 99.1

Forward-Looking Statements This presentation contains forward-looking statements that reflect AGTC's plans, estimates, assumptions and beliefs. Forward-looking statements include statements regarding the timing for and expected expansion of its XLRP clinical development program, the timing for reporting data in its XLRP and ACHM clinical programs, and its ability to enroll patients, effectively design and successfully complete its ongoing clinical trials, financial guidance, business strategies and operations, regulatory progress, potential growth and market opportunities, and the effects of competition. Forward-looking statements include all statements that are not historical facts and can be identified by terms such as "anticipates," "believes," "could," "seeks," "estimates," "expects," "intends," "may," "plans," "potential," "predicts," "projects," "should," "will," "would" or similar expressions and the negatives of those terms. Actual results could differ materially from those discussed in the forward-looking statements, due to a number of important factors. Risks and uncertainties that may cause actual results to differ materially include, among others: AGTC cannot predict when or if it will obtain regulatory approval to commercialize a product candidate or receive reasonable reimbursement; uncertainty inherent in clinical trials and the regulatory review process; risks and uncertainties associated with drug development and commercialization; risks related to the COVID-19 outbreak that may delay clinical trials; gene therapy is still novel with only a few approved treatments so far; factors that could cause actual results to differ materially from those described in the forward-looking statements are set forth under the heading "Risk Factors" in the Company's Annual Report on Form 10-K for the fiscal year ended June 30, 2019 and subsequent periodic reports filed with the SEC. Given these uncertainties, you should not place undue reliance on these forward-looking statements. Also, forward-looking statements represent management's plans, estimates, assumptions and beliefs only as of the date of this presentation. Except as required by law, we assume no obligation to update these forward-looking statements publicly or to update the reasons actual results could differ materially from those anticipated in these forward-looking statements, even if new information becomes available in the future.

Industry Leading Gene Therapy Company Poised for Success XLRP: Lead Product Candidate Advancing Toward Phase 2/3 Trial in Q1 2021 Sustained Improvements in visual function for centrally dosed patients Expanding ongoing Phase 1/2 trial; expect dosing to begin in Q4 2020 ACHM: Early Evidence of Biological Activity in Both ACHM Trials Dose escalation completed in adult patients Best-in-Class Technology Platform Process and scale expected to support late-phase development and commercialization Expertise in product design allows for best capsid, promoter and gene cassettes for each indication Robust use of disease specific animal modeling to guide clinical dosing Deep expertise and capabilities to support robust pipeline in ophthalmology, CNS, and otology

Positioned for Success in a Changing Landscape XLRP: Direct Path to Phase 2/3 in Q1 2021 Expanding Phase 1/2 trial to increase total data set Industry-leading data package Manufacturing of Phase 2/3 material on track Redundant manufacturing options contracted; CDMOs are considered essential businesses in their locations ACHM Adult enrollment complete in both trials 8 of 18 pediatric patients across both trials enrolled DSMC approval to highest pediatric dose Developing creative solutions for additional data collection Local ophthalmology clinics, mobile vision centers, software applications all under review Remain on track for 2H 2020 data release for all three programs Strengthened cash balance with February 2020 financing of $34.8M Extends cash runway and secures financing to start XLRP Phase 2/3 trial

A Pipeline with Significant Clinical and Commercial Potential   DISCOVERY IND ENABLING PHASE 1/2 PHASE 3 NEXT MILESTONE* XLRP RPGR         High Dose Data 2H 2020/Start Phase 2/3 Trial in Q1 2021 ACHM CNGB3         Interim Data New Adult Groups 2H 2020 ACHM CNGA3         Interim Data New Adult Groups 2H 2020 Optogenetics Unique ChR         Partnership with Bionic Sight; Complete Dosing Otology GJB2         Partnership with Otonomy; IND filing 2 CNS Indications Frontal Temporal Dementia, ALS Final product construct testing ALD ABCD1 IND enabling Studies Dry AMD Not yet disclosed Final product construct testing Stargardts ABCA4 IND Enabling Studies * Milestones based on calendar year and not AGTC’s fiscal year

Interim data new dose groups: XLRP Interim data new adult groups: ACHM B3 ACHM A3 Six-month data, initial dose groups: ACHM A3 ACHM B3 XLRP Complete enrollment new dose groups: XLRP Complete enrollment new adult groups: ACHM A3 ACHM B3 Bionic Sight doses first patient: Optogenetics End of Phase 2 response from FDA: Healthy Financial Position to Fund Upcoming Milestones Final data release Phase 1/2: ACHM A3 ACHM B3 XLRP 2021 1st Half 2020 1st Half 2nd Half XLRP Milestones based on calendar year and not AGTC’s fiscal year * Cash and investment balance based on March 31, 2020 includes $34.8M in net proceeds from February 2020 financing; not inclusive of debt Strong Balance Sheet: Cash and Investments of $84.5M* XLRP Start Phase 2/3 Trial ü ü ü ü ü

Leading the Commercial Production of Customized Gene Therapies

Patients are at the Forefront of What We Do  “It’s something I am not allowed to forget – crossing the street or realizing that I am putting my life into a person’s hands who is driving down the road because I cannot see inside the cab of a car.” “The way I describe my vision is that I can’t notice any difference in the scene in The Wizard of Oz when Dorothy leaves her house and the film shifts from black and white to color.” “Sometimes my friends get annoyed… they ask, ‘can’t you get glasses?’ I have to tell them that I have trouble perceiving color and light and it’s not something that a corrective lens can fix.”

AGTC’s Comprehensive Technology Platform We integrate vector biology, genetic engineering, manufacturing and unmet patients needs to develop transformative therapies with substantial clinical and commercial potential. Capsid Diversity Promoter Gene Cassette Formulation Manufacturing Vector Administration Characterization Validated technology program that has supported development of industry-leading data for inherited retinal disease indications

Customization Enables Vectors with Superior Properties Expertise in genetic and vector engineering improves targeted cell-specific transduction and expression: Literature cone promoter (PR2.1) AGTC proprietary cone promoter (PR1.7) Improved promoter activity drives higher, specific transgene expression Red: Cones; Green: Reporter Red: Cones; Green: Reporter Enhanced transduction of photoreceptors in non-human primates following subretinal injection of AAV-TYF AGTC AAV-TYF AAV-TYF

Unmatched AAV Manufacturing Productivity Proprietary, pivotal-stage manufacturing platform Unmatched productivity, characterization Highly scalable, extensive regulatory vetting Up to 2000 ophthalmic doses from 50 L Up to 300 doses from 2000 L for systemic diseases like SMA and DMD Compared to early phase AAV manufacturing method Productivity Increase 100X COGs Decrease 90X Achievable with aggressive scaling Fold decrease in estimated COGs Fold productivity relative to TFX Sedimentation Coefficient and Peak Area Determination: Nearly 90%, full-length genome final product encapsidation ~90% Full

Program Overviews

The Eye THE RETINA: A highly organized tissue Retinal pigment epithelial cell Rod cell Cone cell Mueller cell Horizontal cell Bipolar cell Amacrine cell Ganglion cell Pupil Iris Cornea Lens Retina Fovea Cone diseases Rod diseases Optogenetics Optic nerve Vitreous humour LIGHT ENTERS RETINA

X-linked Retinitis Pigmentosa (XLRP) Missing protein results in degeneration of rods and cones ~20,000 patients in US and EU No current treatments Early night blindness, progressive constriction of visual fields Legally blind by age 45 IMPACT OVERVIEW Blindness is devastating - it robs you of so many things. Number one your freedom. It robs you of your independence.”

Leading XLRP Program Moving Toward Q1 2021 Phase 2/3 Sustained treatment effect, favorable safety profile Evidence of increase and expansion in central visual sensitivity Encouraging improvements in visual acuity Quality of life survey results support meaningful impact on patients’ lives Enrollment complete—28 patients across six dose groups All patients dosed continue to demonstrate a favorable safety profile Expanding Phase 1/2 Trial with dosing expected to begin in Q4 2020

Designed to Restore RPGR Gene Activity AGTC’s XLRP program is designed to provide a functional copy of the RPGR gene to cone and rod photoreceptors Engineered capsid more efficiently transduces photoreceptors in primates compared to competitors Promoter directs cell-specific transgene expression Codon-optimized human RPGR gene enables stable expression Patent-protected capsid, gene and manufacturing process AAV-TYF ITR RPGRco ITR GRK1 SV40 pA SV40 SD/SA 4483 bp

Strong XLRP Competitive Position Six dose groups over a 100-fold range in concentration Favorable safety profile No product related SAEs No recurrent inflammation Earlier groups now 12-24 months past enrollment date with continued safety Meaningful improvements in visual function sustained over time Expanding Phase 1/2 Trial with dosing expected to begin in Q4 2020 AGTC BIIB MeiraGTx Patients Dosed 28 18 10 BCVA + - Unknown Construct ++Expression +Stability -Expression +Stability -Expression -Stability Sensitivity ++ + + Safety ++ Secondary Inflammation Secondary Inflammation Competitive Comparison* *Based on publicly available information

Centrally Dosed Responders Show Sustained Increase in Visual Sensitivity (4 of 8 Evaluable Patients) = standard deviation Treated Untreated Baseline Month 1 Month 2 Month 3 Month 6 Change from Baseline Mean Sensitivity (dB)

50% of Treated Eyes Show Sustained Increase in Visual Sensitivity Compared with Untreated Eyes UNTREATED EYE TREATED EYE Mean Sensitivity (dB) Mean Sensitivity (dB) Change of ≥ 2 dB for an individual patient is statistically outside the limits of test-retest variability Baseline Month 1 Month 2 Month 3 Month 6 Change from Baseline Change from Baseline Baseline Month 1 Month 2 Month 3 Month 6 Responder Non-responder Responder Non-responder * * Patient required ocular surgery prior to Month 3 test

Treated Eyes Show Positive Trends in Visual Acuity 7/9 patients show improving visual acuity UNTREATED EYE TREATED EYE BCVA (ETDRS letter score) BCVA (ETDRS letter score) Change from Baseline Change from Baseline Baseline Month 1 Month 2 Month 3 Month 6 Baseline Month 1 Month 2 Month 3 Month 6

Treated Example Responder Shows Improvement in Visual Sensitivity at All Time Points Compared with Untreated Eye UNTREATED TREATED Improvements in the intensity and area of sensitivity for the treated eye (top row) versus untreated eye (bottom row) Bleb covered all but the far left area 5.84 dB 7.80 dB 8.06 dB 7.28 dB 5.82 dB 5.78 dB BASELINE MONTH 3 MONTH 6

XLRP Moving Forward to Phase 2/3 Trial in Q1 2021 On track to finalize Phase 2/3 protocol for initiation in Q1 2021 Overview of trial design Clinical trial material fully contracted Overlapping CDMOs and GLP testing labs—on track to support trial initiation in Q1 2021 Next data report 2H 2020 Twelve-month analysis for Groups 1-4—evaluate durability of effect and continued safety Interim analysis for Groups 5 and 6—evaluate safety and efficacy at higher doses 1st EYE INJECTED, Dose 1 2ND EYE INJECTED FOLLOW-UP VISITS Crossover to Active Treatment Primary Endpoint at 1 Year Eligibility Screening Randomization (1:1:1) Untreated CONTROL BASELINE TESTING Both EYES INJECTED 1st EYE INJECTED, Dose 2

Achromatopsia (ACHM) AGTC focused on A3 and B3 gene mutations, which account for at least 70% of ACHM Severely impaired vision and day blindness due to loss of cone photoreceptor function Affects ~27,000 patients in US and EU No current treatments Extremely poor vision, legally blind Extreme light sensitivity (day blind) Complete loss of color discrimination IMPACT OVERVIEW The bright light makes it really hard for her, so she tends to freeze up and doesn't want to walk anywhere because she's afraid she might injure herself.  She gets more cautious in new or bright environments."

ACHM Clinical Trials Overview Early signs of biologic activity supported by patient-reported outcomes No dose-limiting toxicity observed DSMC-approved dosing of pediatric patients to highest dose Adult enrollment complete 22 adult patients enrolled in ACHM B3 15 adult patients enrolled in ACHM A3 Pediatric enrollment ongoing 4 of 9 patients enrolled in ACHM B3 4 of 9 patients enrolled in ACHM A3 Data on File

ACHM Trial Design: Similar Across Both Trials DOSE LEVEL Low Middle High Higher Highest Age: ≥18 years Group 4 N=3 (6-17) Group 6 N=3 (≥ 18) Group 5 N=3 (≥ 18) Group 1 N=3 Group 2 N=3 Group 3 N=3 PAUSE PAUSE PAUSE Group 6a N=3 (≥ 6) PAUSE PAUSE Group 5a N=3 (6-17) DSMC Review PAUSE Data from adult groups expected 2H 2020

Addressing the Underlying Cause of Achromatopsia AAV-TYF ITR CNGB3co or CNGA3co ITR PR1.7 SV40 pA SV40 SD/SA AGTC’s ACHM program is designed to provide a functional copy of the CNGB3 or CNGA3 gene to cone photoreceptors Engineered capsid more efficiently transduces photoreceptors in primates compared to competitors Promoter directs cell-specific transgene expression in all three primate cone types Codon-optimized human gene enables stable expression Patent-protected capsid, promoter and manufacturing process

Indications of Improvement in Light Discomfort Data on File Month 3 Post-Treatment Group 1a: LOW DOSE Group 2a: MID DOSE Group 0b: MID/HIGH DOSE Group 3a: HIGH DOSE Group 1b: LOW DOSE Group 2b: MID DOSE Group 3b: HIGH DOSE Treated Eye Untreated Eye

Encouraging Early Data Support Continued Development Robust body of pre-clinical data, improvement in key symptom for patients, and favorable safety profile in both trials builds confidence in product potential Product generally safe and well-tolerated Supported across both ACHM and well as XLRP trials with same capsid Preliminary signs of biologic activity Based on light discomfort testing at Month 3 across both trials Literature and KOL support suggests more time could lead to improvements in additional outcome measures Patient reported outcomes support meaningfulness of improvements in light discomfort—the outcome most important to majority of patients

Innovative Optogenetics Approach to Restore Vision Loss Partnership with Bionic Sight to combine AGTC gene delivery expertise with a novel neuroprosthetic device with a unique retinal coding algorithm Innovative and exciting technology - device performs the same processing as the normal retina sending signals to the brain that are critical to forming normal visual perceptions. Potential to provide clinical benefit to a broader population of patients regardless of cause Opportunity to leverage investment in current technology into additional applications IMPACT OVERVIEW (Transducer) Photoresponsive ganglion cells Image code sent to the brain Light Encoder Blind Normal Vision Bionic Sight Current Prosthetic Bionic Sight Retinal Coding Algorithm No Image

Optogenetics Clinical Development Initiated IND cleared and first patient dosed AAV-ChR Treatment Approach AAV gene therapy is targeted to the retinal ganglion cells, that form the optic nerve, instead of the photoreceptors The gene therapy delivers a light-sensitive protein to the retinal ganglion cells, which enables them to receive light and respond by transmitting electrical signals to the brain ITR Unique ChR Promoter Enhancer ITR

DISCOVERY IND ENABLING PHASE 1/2 PHASE 3 Milestone/Product Differentiation* Dry AMD Not yet disclosed Final product construct testing Stargardts ABCA4 IND Enabling Tox Studies Otology GJB2         Novel capsid and promoter targeting; IND filing; partnered with Otonomy ALD ABCD1 IND Enabling Tox Studies 2 CNS Indications Frontal Temporal Dementia, ALS Final product construct testing; novel trivalent gene cassette Exciting Preclinical Pipeline Advancing multiple important pipeline candidates in ophthalmology, otology and central nervous system disorders Manageable short-term capital investment for potential long-term significant value creation

Positioned for Success

A Pipeline with Significant Clinical and Commercial Potential   DISCOVERY IND ENABLING PHASE 1/2 PHASE 3 NEXT MILESTONE* XLRP RPGR         High Dose Data 2H 2020/Start Phase 2/3 Trial in Q1 2021 ACHM CNGB3         Interim Data New Adult Groups 2H 2020 ACHM CNGA3         Interim Data New Adult Groups 2H 2020 Optogenetics Unique ChR         Partnership with Bionic Sight; Complete Dosing Otology GJB2         Partnership with Otonomy; IND filing 2 CNS Indications Frontal Temporal Dementia, ALS Final product construct testing ALD ABCD1 IND enabling Studies Dry AMD Not yet disclosed Final product construct testing Stargardts ABCA4 IND Enabling Studies * Milestones based on calendar year and not AGTC’s fiscal year

Sue Washer Chief Executive Officer Stephen Potter Chief Business Officer Mark Shearman, Ph.D. Chief Scientific Officer Bill Sullivan Chief Financial Officer Brian Krex General Counsel Matt Feinsod, M.D. Exec. VP Global Strategy and Development Nnenna Ihekoromadu, M.D. VP, Clinical Research Karen Carroll, RN VP, Clinical Operations Ellery Mangas Exec. Dir. Regulatory Dave Knop, Ph.D. Exec. Dir. Process Dev Experienced Team

August 2020 Investor Presentation