Nevada Institute of Personalized Medicine at UNLV

Transcription

1 UNIVERSITY OF NEVADA, LAS VEGAS NEVADA INSTITUTE OF PERSONALIZED MEDICINE Nevada Institute of Personalized Medicine at UNLV Quarterly Progress Report Reporting Period: October 1st to December 31th, 2015 February 16, 2016

2 Table of Contents Project Purpose Problem NIPM is trying to solve Expected impact... 0 Section I: NIPM Progress... 1 Section II: Performance... 5 a. Dashboard details for reporting external faculty hired... 6 b. Dashboard details for reporting grants and amount of research funding received... 6 c. Dashboard details for reporting donations in support of NIPM... 6 d. Dashboard details for reporting number of student internships... 7 e. Dashboard details for reporting number of patent applications... 7 Section III: Budget... 8 Section IV: Weekly/Monthly Logs of NIPM Progress for Reporting Quarter... 9 Section V: Appendix Appendix 1 Sales Pipeline Appendix 2 Scorecard Supporting Documentation Page 1

3 Project Purpose 1. Problem NIPM is trying to solve Approximately 1 in 10 suffer from a genetic disorder, yet Nevada has almost no in- state infrastructure to diagnose and treat affected patients. This health disparity in our state negatively impacts the health and well- being of many Nevadans, as well as our economy by the continued export of genetic healthcare services and related revenues to other states. 2. Expected impact The Nevada Institute of Personalized Medicine and an affiliated enterprise will help regional healthcare partners utilize and deliver clinical genetics services and educate a clinical genetics workforce for Nevadans. During the funding period starting July 1, 2015, our major long- term goal is to build a clinical genomics trial entity to provide services for Nevadans. The clinical genomics trial entity will engage Nevada healthcare providers in personalized medicine. To achieve this goal, NIPM has identified a set of stepwise intermediary milestones (Figure 1). Detailed justification for these goals is provided in the separate Knowledge Fund application document. Figure 1. Milestones, goals, and economic impact of NIPM. Our main goal is in the cyan box.

4 The milestones in Figure 1 have been given numbers for easier reporting (Table 1). Table 1: Milestones Milestone number Milestone 1 Milestone 2 Milestone 3 Milestone 4 Milestone 5 Milestone 6 Milestone 7 Milestone 8 Milestone 9 Milestone 10 Milestone 11 Milestone 12 Milestone 13 Milestone 14 Milestone 15 Section I: NIPM Progress Description IRB approval Implement a computer system Set up NGS pipeline Set up personalized medicine database Conduct SOAPS Trial Establish Omics core Validate Omics core Exercise service business plan Athletigen or similar agreement Exercise GWAS trial COBRE grant Exercise service UNLV School of Medicine Pathology CLIA Sequencing Lab Clinical genomics trial service During the reporting quarter, NIPM has made significant progress toward meeting proposed metrics. Major accomplishments for the current reporting period include: 1. Major Accomplishment 1: Writing COBRE application During this quarter, NIPM faculty continued writing a COBRE application for submission in Q A draft was reviewed by three external reviewers whom had previously received COBRE awards and qualified to review our proposal. The final version of our proposal was 741 pages long and viewed favorably by the reviewers. 2. Major Accomplishment 2: Write and revise GOED NIPM project in consultation with GOED Over this quarter, NIPM wrote and revised a NIPM reset proposal requested by GOED. This eventually also led to a budget request, once the proposal was complete. The proposal and budget were, in principal, approved by Steve Hill. We are now completing a description of the budget that was requested and are hopeful that our new project will be approved. We expected this would be done by now, but it has taken longer than anticipated. 3. Additional Accomplishments a. Activities related to commercialization and recruiting new commercial partners and customers. These include a seminar series, minisymposium on cell- free DNA, a Science Café presentation to public, an R- J story about NIPM and Athletigen, discussion with Spectrum Pharmaceutical Page 1

5 Co., a presentation to investor Ray Mazyka, and a story with Desert Companion. We also continued prosecution of several patent applications. b. Staffing. NIPM has had some setbacks in staffing. The NIPM Program Coordinator took another job this quarter, so NIPM interviewed and hired a replacement. This person is needed for basic administration to NIPM. Our Business Development Officer was also transferred to a different position. NIPM worked with GOED and our Office of Economic Development office to create a new staffing model for BDO in NIPM. A search was started this quarter. On more positive notes, NIPM also started a faculty search for two new NIPM faculty funded by UNLV. The subject areas of these faculty are relevant to both goals and milestones 1-4, 6, 7, and Commercialization / Partnering Industry partnerships, research collaborations, and IP licensing remain a priority for NIPM, although this activity slowed during the reporting quarter given the lack of a NIPM Business Development Officer to guide some of these efforts. During the reporting quarter, a total of four new contacts were made with companies and individuals regarding wither partnership or IP licensing opportunities. The most positive outcome of these efforts should soon result in a formalized partnership with a Canada- based company with a leading focus on sports genetics. Current discussions include the establishment of a Las Vegas- based presence for this company. A total of six additional industry partners remain interested in learning more about NIPM once additional proof of concept data is available. It is anticipated that partnering and commercialization efforts will increase in the first half of 2016 with the hiring of a new Business Development Officer and/or consultant. NIPM will continue to cultivate alliances with external colleagues and industry partners working in personalized medicine through: (1) direct communication; (2) industry outreach; (3) establishing formal and informal relationships with industry and academic partners; (4) engaging scientists in the NIPM seminar series; (5) hosting annual events; and (6) recruiting additional NIPM external advisory board members. Appendix 1 provides an anonymized listing of all partnering and commercialization contacts made during the reporting quarter. 5. Intellectual property During the reporting quarter, no invention disclosure reports were submitted to the UNLV Office of Economic Development by NIPM faculty and staff. No patent applications have been filed to date as a direct result of investment of Knowledge Fund funds in NIPM. A total of four patent application families, based on innovations developed by NIPM Executive Director Dr. Martin Schiller, are currently in active prosecution (see Table XXX). Some of the research that resulted in the innovations described in these patent applications was performed prior to the formation of NIPM, in anticipation of its formation. These patent applications are reported herein as Page 2

6 they (i) describe innovations made by a NIPM faculty member, and (ii) support the NIPM mission and objectives. Table 2 NIPM Intellectual Property Internal(ID Inventor Title Patent/Applciation(No. Change(since(last(report 2013=001 Martin(Schiller Genome(Surgery(with(Paired,(Permeant(Endonuclease( 13/937,860 PCT(applciation(converted(to(EPO(applciation Construct EPO= US(Applciation(13/937,944(was(abandoned 2010=003 Martin(Schiller Methods(and(Systems(for(Information(Search 14/328,316 PCT/US2015/ Reporting(filing(of(PCT 2014=034 Martin(Schiller Methods(and(compostions(for(screening(molecular( funcitons(compursing(chimeric(minimotifs PCT/US2015/ Non=provisional((PCT)(application(filed 2015=032 Martin(Schiller Compositions(Comprising(Talens(And(Methods(of(Treating( 62/140,048 HIV( 62/265,232 2nd(provisional(patent(filed 6. Programmatic & project changes Our previous quarterly report redefined the scope of work for NIPM. As part of this scope, NIPM purchased a genome sequencing instrument this quarter and have been working on designing a computer system to analyze genomic data. 7. Looking forward The relevance of each milestone to the two major goals is in Figure 1. The anticipated progress on each milestone is listed below. Milestone 1. IRB approval NIPM expects our IRB protocol to be approved this quarter, completing this milestone. Milestone 2. Implement a computer system NIPM expects the first node of our computer systems to be purchased, installed, and tested. If our GOED budget is approved, NIPM will proceed with the purchase of more computer nodes for the system. Milestone 3. Set up NGS pipeline NIPM expects to continue developing the pipeline this quarter, with a functioning version in two quarters (Q2 2016). NIPM has an ongoing faculty search for an additional expert in this area. NIPM expects to conduct interviews during Q Milestone 4. Set up Personalized Medicine database NIPM expects the database will reach a point of functionality for genome interpretation this quarter. NIPM has an ongoing faculty search for an additional expert in this area. NIPM expects to conduct interviews during Q Milestone 5. Conduct SOAPS trial NIPM expects this will start in two quarters in Q Milestone 6. Establish Omics core Page 3

7 NIPM expects that the design of the renovation will be completed and that demolition and the start of the renovation will occur this quarter. In the meantime, NIPM expects the use a temporary location to start setting up the Omics core. NIPM will order additional equipment, install the NextSeq, and get training for the NextSeq. NIPM will work on a model for a staff member to prepare libraries and run the sequencing machine. NIPM also has started a faculty search for an expert in this area and will interview candidates during this quarter. Milestone 7. Validate Omics core NIPM does not plan to start this yet. Milestone 8. Exercise service business plan NIPM does not plan to start this until Q Milestone 9. Athletigen or similar agreement NIPM has a signed MOU with Athletigen and the Office of Economic Development is working on an agreement that should be completed Q NIPM has also identified two other potential partners to explore similar agreements with. An annual retreat event will be used for recruiting new partners and customers. Milestone 10. Exercise GWAS trial NIPM does not plan to start this until Q Milestone 11. COBRE grant NIPM plans to complete this grant and submit it to NIH. This is a key step for this milestone. NIPM anticipates a decision in the Fall of 2016, resubmission next January, and funding in the Fall of Milestone Page 4

8 Section II: Performance Table 3: Progress toward Metrics Nevada&Ins*tute&of&Personalized&Medicine&(NIPM)& Progress&Dashboard& KNOWLEDGE&FUND& GOED&Requested&Metrics& Current&Result&/&YearFend&Target&& To&6/30/15& By&12/31/15& By& 12/30/17& Number%of%Companies%that%moved%to%Nevada%as%a%result% of%nipm%kf%project% 0/0% %0%/%0% %0%/%0% Number%of%startBups% 0/0% %0%/%0% %0%/%1% Number%of%jobs%created% 0/0% %0%/%0% %0%/%0% Intellectual%property%licenses%/%opCons%% 0/0 A % 0/0 B % 0%/%0 A % 0%/%1 B % %0%/%1 A % 0%/%1 B % Intellectual%Property%Revenue%Received%by%University% 0/0% %0%/%$0% %0%/%$25k% Amount%of%research%grants%awarded%to%%(and%received)% the%nipm%research%teams%and%faculty C % Amount%of%research%funding%received%by%NIPM%research% team%from%industry%of%public%sector%agencies D% Number%of%sponsored%research%contracts%executed%on% behalf%of%nipm%research%team% $1M/ $500K% 0%/%$0K% 0/0% %$0K%/% $3.3M% 0%/%$205K% 0%/%0% %0%/%$3.3M% %0%/%$205K% %0%/%0% Number%of%patent%applicaCons%filed% %0/0% %0%/%2% %0%/%2% Number%of%issued%patents% %0/0% %0%/%0% %0%/%0% Number%of%students%placed%with%companies%%% 0/0% 0%/%0% 0%/%0% Number%of%external%faculty%hired% 3/3% 4%/%3% 4%/%3% Amount/value%of%giMs/donaCon%received%by%UNLV%in% support%of%nipm% $25K%/ 200K% $28K%/% $200K% $28K%%/% $200K% Total%number%of%student%internships%% 0/0% 2%/%0% 2%/%0% A. Number%of%IP%licenses% B. Number%of%opCons% C. Excludes%sponsored%research%and%KF%funding% D. This%category%also%inclused%clinical%reventue% Note%that%the%To%6/30/15%column%if%for%phase%I%of%this%project,%The%other%columns%are%for%phase%II% % n/a%or%target%of% Color&Key& zero% Too%early%to%tell% Goal%not%met% Close%to%achieving% goal% Goal%achieved% Page 5

9 Project Scorecard Narrative For each detail category, all progress for Q is summarized. a. Dashboard details for reporting external faculty hired NIPM needs to hire experts in many different areas to achieve its two goals. Some of the regular faculty receive direct support from GOED (Martin R. Schiller, executive director and professor; Qing Wu, associate professor; Xiangning Chen, professor; Jingchun Chen, assistant professor; and Michael Nasiak, professor). These faculty are reported as the four hires on the dashboard table (executive director excluded). Two other regular faculty spend the majority of their research effort working with NIPM and have been approved as regular faculty (Mira Han, assistant professor and Justin Zhan, associate professor). For reporting, NIPM only reports metrics for GOED- funded faculty in the dashboard, but provides information for other categories where it is relevant. For example, it does not make sense for us to leave out Mira Han because she is located with NIPM faculty, works with NIPM daily, and is an essential person in the COBRE grant application and other milestones. b. Dashboard details for reporting grants and amount of research funding received Research funding is needed to leverage GOED dollars to hire the personnel needed to achieve Goal 1. For example, NIPM needs a postdoctoral fellow to analyze genome sequence data of participants in the clinical trial, a necessary capability in the proposed clinical service. Research funding is also needed, as NIH does not award large programmatic grants to teams that have not demonstrated previous consistent funding. The number of grants received was not a metric in the original proposal. NIPM faculty receiving salary from GOED received four research grants for ~$1.1 M (Table 3). Two of these grants were to Dr. Xiangning Chen, and transferred or being transferred from Virginia Commonwealth University. These are not included in the reported metric for Q Hiring a faculty that brings in their own personalized medicine grants is a good way to leverage GOED funds. c. Dashboard details for reporting donations in support of NIPM NIPM to date had previously received $25,000 of an in- kind mammalian cell culture incubator equipment donation to NIPM faculty. NIPM received a $3,000 donation during Q by the biggest sequencing company in the world, Illumina. Page 6

10 d. Dashboard details for reporting number of student internships Trainees are critical for performing the work needed for goals 1 and 2, as well as providing trained individuals for the workforce. NIPM is reporting 0 trainees supported by GOED funding. However, many students in NIPM are working on NIPM projects. There are four new graduate students working under NIPM regulation faculty (Drs. Schiller, Han, and Wu). One of these receives a stipend from GOED funds. Furthermore, Drs. Schiller, Wu, and Han have more than 20 undergraduate students being trained. Many of these are working on parts of goals 1 and 2. e. Dashboard details for reporting number of patent applications A total of five patent applications / families, based on three innovations developed by NIPM regular faculty receiving GOED funding, remain in active prosecution (Table 1). However, NIPM reports none for the dashboard metric because all of these projects, at least in part, had their origins prior to the appointment of Dr. Schiller as executive director of NIPM. Two applications have been updated during Q In our application for the chimeric minimotif decoy technology, much of the research, and grant application and funding occurred during, and was supported in part by, GOED funding. Furthermore, this technology is relevant to variant interpretation, which is particularly relevant to personalized medicine and the clinical genome trial company. Nevertheless, NIPM does not report this on the dashboard as it does not meet the criteria for the GOED reporting metric. Page 7

11 Section III: Budget The Institute recognized expenditures of $853,276 during the reporting quarter. The largest single expenditure was for the purchase of a DNA sequencing machine. In all categories, total expenditures recognized were below estimates for the quarter. Detailed NIPM expenditure information is provided in Table 4: Table 4: NIPM Expenditures NIPM Expenditures For Reporting Period October 1 December 31, 2015 Estimate (Year 1) July 1, 2015 June 30, 2015 Expenditures Inception to Date July 1, 2015 December 31, 2015 Expenditures Current Period October 1- Decmber 31, 2015 Total Salary & Benefits $908,250 $397,653 $220,733 Equipment $702,785 $231,769 $216,884 Travel $8,678 $5,657 $2,553 Other Direct Costs $270,275 $215,513 $238 Graduate Tuition $1,584 $1,584 $1,584 Total $ 1,891,572 $852,276 $441,754 Detailed income information is provided in Table 5. Table 5: NIPM Income NIPM Income For Reporting Period October 1 December 31, Estimate Income (Year 1) Inception to Date July 1, 2015 July 1 1, 2015 June 30, 2015 December 31, 2015 Grants / Contracts 2 $1,175,486 $488,096 $488,096 Gifts $53,000 $3,000 $3,000 Cont. ED/ Outreach $0 $0 $0 Other Contributions 3 $1,042,149 $752,624 $603,184 Knowledge Fund $1,908,571 $852,176 $441,992 Income Current Period October 1- December 31, 2015 Total $ 4,179,206 $2,095,896 $933,088 1estimates are for gross revenue. 2grants include only those awarded after that date. Reported income is for a single grant on personalized medicine transferred from Virginia Commonwealth University. Transfer of a grant is considered a new contract by NIH. This grant is not included in the scorecard. 3Other contributions are from UNLV. Page 8

12 Section IV: Weekly/Monthly Logs of NIPM Progress for Reporting Quarter All progress is related to the 15 milestones identified in Table 1. Monthly Report October 2015 Milestone 1. IRB approval NIPM is waiting for the UNLV IRB to give a decision about our submitted protocol. Milestone 2. Implement a computer system Small scale testing is being done for variant imputation on Cherry Creek. Milestone 3. Set up NGS pipeline The pipeline involves setting up and testing a large set of software and is a moving target as new versions are released frequently. NIPM has started the process of installing and testing some of the software NIPM will be using to analyze genomes. Milestone 4. Set up personalized medicine database Our team is progressing in building this large database. Milestone 5. Conduct SOAPS trial NIPM has been meeting weekly with the PeopleSeq project consortium. NIPM cannot start this until milestone 1 is complete. However a Clinical Geneticist was hired last month and is needed to interact with the trial participants. Milestone 6. Establish Omics core Waiting for renovation of lab to start and approval of GOED budget to buy equipment. Milestone 7. Validate Omics core Milestone 8-10 Milestone 11. COBRE grant NIPM started writing the COBRE grant. Milestone Page 9

13 Monthly Report November 2015 Milestone 1. IRB approval The IRB requested revision to the submitted protocol. Milestone 2. Implement a computer system Small scale testing continued for variant imputation on Cherry Creek. Other software has been installed. NIPM started the process of designing the computer system. NIPM is working with consultant Ronald Nowling and hired a new NIPM faculty to help with computation, Justin Zhan. This was at no cost to NIPM, as he was hired by the UNLV Computer Science department. Milestone 3. Set up NGS pipeline The pipeline involves setting up and testing a large set of software and is a moving target as new versions are released frequently. NIPM has started the process of installing and testing some of the software NIPM will be using to analyze genomes. Milestone 4. Set up personalized medicine database Our team is progressing in building this large database. Milestone 5. Conduct SOAPS Trial NIPM has been meeting weekly with the PeopleSeq project consortium. NIPM cannot start this until milestone 1 is complete. However a Clinical Geneticist was hired last month and is needed to interact with the trial participants. Milestone 6. Establish Omics core Waiting for renovation of lab to start and approval of GOED budget to buy equipment. Milestone 7. Validate Omics core Milestone 8-10 Not started yet Milestone 11. COBRE grant NIPM continued writing of the COBRE grant. A draft was assembled on Thanksgiving holiday and sent out to an External Review panel. Milestone Page 10

14 Monthly Report December 2015 Milestone 1. IRB approval NIPM worked on revisions for the UNLV IRB concerning our submitted protocol. There were some changes in the protocol that caused a delay because NIPM hired a Clinical Geneticist and this changed the procedure. NIPM is hopeful for an approval in the next 2 months. Milestone 2. Implement a computer system The new computer system was designed, NIPM received quotes and order for the first node was forwarded to purchasing for their competitive bidding process. Milestone 3. Setup NGS pipeline Testing primarily using Cherry Creek continued. NIPM had a problem in that it did not have privileges to install software on Cherry Creek. NIPM is working on fixing this problem as it slows progress. Milestone 4. Setup Personalized Medicine database Our team is progressing in building this large database. Milestone 5. Conduct SOAPS Trial NIPM has been meeting weekly with the PeopleSeq project consortium. NIPM cannot start this until milestone 1 is complete. Milestone 6. Establish Omics core Waiting for renovation of lab to start and approval of GOED budget to buy equipment. NIPM also negotiated a larger room for the Omics core if our COBRE grant is funded (milestone 11). Milestone 7. Validate Omics core Milestone 8-10 Milestone 11. COBRE grant Our COBRE grant draft was reviewed by external panel and NIPM worked on the changes they suggested. NIPM does not anticipate any trouble meeting the Jan 28 submission deadline. Milestone Page 11

15 Section V: Appendix Appendix 1 Sales Pipeline Company(Name Company(Type Opportunity(Type Status Notes((Progression(and(Next(Step) Leads(:(Awareness((0(:(24) DS#0002 Diagnostic.Lab General.Partnership On#Hold Potential.user.of.NIPM.services DS#0004 Diagnostic.Lab General.Partnership On#Hold Potential.user.of.NIPM.services DS#0005 Diagnostic.Lab General.Partnership Initial.Contact Potential.user.of.NIPM.services DS#0007 Diagnostic.Lab General.Partnership On#Hold Potential.user.of.NIPM.services IP#0001 Biotech IP.Licensing Awaiting.Response HIV.tech..licensing IP#0002 Biotech IP.Licensing Awaiting.Response No.Response IP#0003 Biotech IP.Licensing Awaiting.Response HIV.tech..licensing IP#0007 Biotech IP.Licensing./.Collaboration On#Hold Too.early.#.contact.in.6.months IP#0008 Biotech IP.Licensing./.Collaboration On#Hold Technology.licensing.opportunity IP#0011 Pharmaceutical IP.Licensing./.Collaboration On#Hold CMD./.HIV.tech.licensing IP#0012 Pharmaceutical IP.Licensing Awaiting.Response CMD./.HIV.tech.licensing IP#0018 Pharmaceutical IP.Licensing./.Collaboration Initial.Contact Awating.response. IP#0024 Biotech IP.Licensing Initial.Contact Local.start#up.looking.for.IP IP#0025 Biotech IP.Licensing Initial.Contact Not.in.strategic.area.of.focus.but.will.respond IP#0029 Technology.Co. IP.Licensing./.Collaboration Initial.Contact No.response IP#0033 Technology.Co. IP.Licensing./.Collaboration Initial.Contact Info.sent.to.different.internal.unit MC#0003 Medical.Center General.Partnership On#Hold Data.sharing/.Patient.referral.partnership MC#0004 Medical.Center General.Partnership Initial.Contact Data.sharing/.Patient.referral.partnership Prospects(:(Interest(((0(:(14) CO#0002 Biotech Research.Partnership Early.Discussion Nutrigenomics.and.aging DS#0006 Diagnostic.Lab General.Partnership Early.Discussion Potential.user.of.NIPM.services IP#0006 Biotech Research.Collaboration Early.Discussion PM.partnership IP#0023 Start#up IP.Licensing./.Collaboration Initial.Contact Local.start#up.looking.for.IP MC#0002 Medical.Center General.Partnership Early.Discussions Data.sharing/.Patient.referral.partnership Univ#0003 Consortium General Early.Discussion PM.consortium.group Qualified(:(Desire((0(:(6) CO#0004 Biotech Research.Partnership Early.Discussion Local.start#up.looking.for.IP CO#0005 Biotech Research.Partnership Early.Discussion Potential.CSR.and.company.relocation IP#0030 Technology.Co. IP.Licensing./.Collaboration Initial.Contact Potential.for.research.collaboration IP#0031 Biotech IP.Licensing./.Collaboration Early.Discussion Presented.in.person,.awaiting.response MS#0003 Services.Company General.Partnership Early.Discussion NIPM.qualified.service.provider MS#0005 Medical.Clinic General.Partnership On#Hold NIPM.qualified.service.provider Negotiation(:(Action((0(:(2) CO#0001 Biotech Research.Partnership Interest.Indicated Potential.CSR.and.company.reloaction.to.Nevada MC#0001 Medical.Center General.Partnership Interest.Indicated Clinical.trial.partnership MS#0004 Hospital Research.Collaboration Interest.Indicated NIPM.clinical.facility./.collaborator Won(or(Lost*(0(:(14) MS#0001 Medical.Clinic Services.Provider Partner/Licensee NIPM.qualified.service.provider Univ#0002 University Pers.Med.Consort. Partner/Licensee PM.consortium.group..No.agreement.but.partnership.ongoing IP#0004 Biotech IP.Licensing Declined Not.in.strategic.area.of.focus IP#0010 Biotech IP.Licensing./.Collaboration Declined Technology.licensing.opportunity IP#0019 Pharmaceutical IP.Licensing./.Collaboration Declined Initially.not.in.strategic.area IP#0026 Generics IP.Licensing Declined Suggested.not.fit.with.new.structure IP#0032 Biotech Declined Sent. .regarding.license;.no.response CO#0002 Biotech Research.Partnership Declined Not.good.fit.for.NIPM DS#0001 Diagnostic.Lab General.Partnership Declined Perhaps.wrong.avenue.into.organization MS#0002 Medical.Clinic General.Partnership Declined Not.in.area.of.focus Page 12

16 Appendix 2 Scorecard Supporting Documentation No documentation for this report. Page 13