making prescriptionsppersonal - pharmacogenomics reports - software in medicine
TRANSCRIPT
THE THESIS - September 12, 2015.
“Egyes szakértők szerint 10 éven belül valóra válhatna az a még kissé futurisztikusnak tűnő kép, hogy mindenkiről egy genetikai polimorfizmus adattár áll rendelkezésre mondjuk a háziorvosnál, az beírja a komputerébe, hogy milyen hatású gyógyszert szeretne felírni az adott betegnek, majd a gép megadja, hogy melyik konkrét gyógyszer vagy gyógyszerek a leghatásosabbak, vagy lesz a legkevesebb, és legkevésbé veszélyes mellékhatásuk az
adott genetikai mintázattal rendelkező betegnél.”1
Prof. Dr. Szalai CsabaSemmelweis Egyetem, Általános orvostudományi Kar,
Genetikai, Sejt - és Immunbiológiai Intézet Intézetvezető helyettes
1. According to publication of Prof. Dr. Csaba Szalai (http://gyogyhirek.hu/farmakogenomika-a-jovo-igerete/)
Judit AlföldiInvenshure Hungary LLC.
OUTLINE
● Introduction ● OneOme solution - Patient's perspective● OneOme Pharmacogenomics Report (PGx)● OneOme solution - Doctor's perspective● Technical background● About Invenshure and Invenshure Hungary LLC.
DEFINITIONS
● Genetics - the study of genes and genetic variation - mostly one gene
● Genomics - study of the whole genome - mostly more than one gene
● Pharmacogenetics - the study of the role of genetics in drug response - mostly one gene
● Pharmacogenomics - the study of the role of genetics in drug response - mostly more than one gene
GOALS OF PHARMACOGENOMICS
● Drug discovery and development
● Reveal adverse drug reaction
PHARMACOGENOMICS
Human genome project (1999-2003) 1
~ 3 300 000 000 DNA base pairs~ 20.000 genes~ 400 are target genes for drugs~ 23 genes covering around 340 drugs
1. http://www.ensembl.org/Homo_sapiens/Info/StatsTable
THE PROBLEM - DRUGS
>4 Billion 1
~48% Do not work as intended2
>95% of drug - response variability and susceptibility depends on genetic factors
1. According to IMS Institute for Healthcare Informatics2. Spear BB, Heath-Chiozzi M, Huff J. Trends Mol. Med.7, 201–204 (2001).
THE PROBLEM - ADR’s
NIH estimates ADR’s account for as much as● ~7% of all admissions● > 20% readmissions
● 4th leading cause of death● > $130B the annual cost of ADR’s (estimated
by the FDA) 1
1. http://www.fda.gov/Drugs/DevelopmentApprovalProcess/DevelopmentResources/DrugInteractionsLabeling/ucm110632.htm
OUR MISSION
Provide the ● Most Cost-effective, ● Comprehensive,● Personalized,Pharmacogenomics analysis that identifies optimal drug therapy for individual Patients.
OUTLINE - STEP
● Introduction ● OneOme solution - Patient's perspective● OneOme Pharmacogenomics Report (PGx)● OneOme solution - Doctor's perspective● Technical background● About Invenshure and Invenshure Hungary LLC.
PATIENT’S PERSPECTIVE
STEP 1:Doctor orders the
test
STEP 2:Patient provides
cheek swab sample
STEP 3:Patient or doctor activates the kit
online
STEP 4:OneOme processes the sample & returns report to the doctor
OneOme video
OUTLINE - STEP
● Introduction ● OneOme solution - Patient's perspective● OneOme Pharmacogenomics Report (PGx)● OneOme solution - Doctor's perspective● Technical background● About Invenshure and Invenshure Hungary LLC.
OneOme REPORT - USE WITH CAUTION
Content:● Patient’s personal information● Main categories with those drugs which
must be used with great caution according to patient’s genotypes
● Main categories with those drugs which must be used with caution according to patient’s genotypes
● L1, SL, SH, T marks
OneOme REPORT - USE AS DIRECTED
Content:● Main categories with those drugs which
can be used as directed according to patient’s genotypes
OneOme REPORT - GENOTYPES
Content:● Genes with their genotypes which might
affect phenotype and metabolism,○ metabolism (CYP) could be normal,
decreased or increased○ Genotype might cause normal
response or increased risk in phenotype
○ CYP3A4, CYP3A5, CYP2C9, CYP2D6
OneOme REPORT - CYP ENZYMES
Content:● CYP enzymes are encoded by CYP
genes responsible for metabolism and elimination of clinically used drugs
● CYP enzymes could be inducers or inhibitors
● Relation between examined drugs and CYP enzymes are shown in the list
OUTLINE - STEP
● Introduction ● OneOme solution - Patient's perspective● OneOme Pharmacogenomics Report (PGx)● OneOme solution - Doctor's perspective● Technical background● About Invenshure and Invenshure Hungary LLC.
THE WEB PORTAL
Provides a web interface for ○ Institution (Institutional teams),○ Providers,○ Patients
to○ View,○ Order,○ Activate,○ Interact
with the report of genetic result.
THE WEB PORTAL - SIGN IN
● Different login form for○ Provider,○ Patient and○ Admin
● User Session management provided by Flask-Login
● OAuth2 authentication for Admins (LIMS, Scientists)
● Password meets HIPAA regulations
● Users are stored in database
THE WEB PORTAL - ORDERS
● List all orders associated with Provider’s clinical team
● The list is searchable● The doctor can
○ create an order,○ review an order,○ manage an order and○ interact with the result of the
PGx report.
THE WEB PORTAL - ORDER STATUSES
● Each orders has statuses,○ Test ordered○ Payment pending / received○ Kit shipped ( if necessary )○ Kit activated○ Arrived at laboratory○ Sample is processing○ Report generated
● Doctor can○ Download the generated report,○ Explore the generated report (Drug explorer)
THE WEB PORTAL - DRUG EXPLORER
● Drugs are grouped by diseases● List drugs which are correspond to
the patient’s PGx Report● Search and add drugs by name or
indication● Search and review patient’s
Medication history provided by SureScripts
● Indications are marked with icons● Possibility to generate report
THE WEB PORTAL - DRUG ALTERNATIVES
● Drug overview explains the reason of caution● Offers alternatives of the selected drug,
○ Use as directed,○ Use with caution○ Use with great caution
● Possibility to add alternative drugs to drug list
THE WEB PORTAL - DRUG TO DRUG INTERACTION
● Drug / Drug interaction information from Wolters Kluwer database
● Summary view of all drug / drug interactions
● Detailed view of each drug / drug interaction
OUTLINE - STEP
● Introduction ● OneOme solution - Patient's perspective● OneOme Pharmacogenomics Report (PGx)● OneOme solution - Doctor's perspective● Technical background● About InvenShure and Invenshure Hungary LLC.
TECHNICAL BACKGROUND - ENVIRONMENTS
● Development○ Local environment○ Docker-compose / Docker○ MariaDb
● Staging / Testing and Production○ Cloud environment (Amazon services)
■ Elastik (Load Balancer)■ Private Subnet for Web portal■ RDS for MariaDB
THE SYSTEM
● Web portal with LIMS (Laboratory Information Management System) are the basic interfaces
● Salesforce is a CRM● BrainTree responsible for
payments● SureScripts responsible for
medication history● Databases
THE WEB PORTAL - SOFTWARE INFRASTRUCTURE
● Utilizes the Python 3 framework and uses MariaDB● Uses the following packages
○ Flask - a microframework for Python based on Werkzeug, Jinja 2○ Flask-Bootstrap - HTML, CSS, and JavaScript framework for Flask○ Flask-Login - provides user session management for Flask○ Flask-Mail - provides an interface to set up SMTP and send messages○ Flask-OAuth2-Login○ Flask-Script - provides support for writing external scripts in Flask○ Flask-SQLAlchemy - adds support for SQLAlchemy○ Flask-Admin - provides support to building an admin interface on top of
an existing data model○ SQLAlchemy - Python SQL toolkit and Object Relational Mapper ○ WTForms, Jinja2 , NodeJs
OUTLINE - STEP
● Introduction ● OneOme solution - Patient's perspective● OneOme Pharmacogenomics Report (PGx)● OneOme solution - Doctor's perspective● Technical background● About Invenshure and Invenshure Hungary LLC.
THE COMPANY
QUESTIONS?
Confidential. OneOme 2016.