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HIGH THROUGHPUT SEQUENCING, BIOINFORMATICS AND COMPUTATIONAL GENOMICS AND INTERNATIONAL ANIMAL HEALTH INFORMATION THE OIE STRATEGY Vincenzo Caporale Incheon, 15 October, 2014

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Page 1: HIGH THROUGHPUT SEQUENCING, BIOINFORMATICS AND ... · Pharmaceutical Products and Veterinary Diagnostic Systems using Biotechnology ... CENTRAL INSTITUTIONAL ROLE b. the development

HIGH THROUGHPUT SEQUENCING, BIOINFORMATICS

AND COMPUTATIONAL GENOMICS

AND INTERNATIONAL ANIMAL HEALTH INFORMATION

THE OIE STRATEGY

Vincenzo Caporale Incheon, 15 October, 2014

Page 2: HIGH THROUGHPUT SEQUENCING, BIOINFORMATICS AND ... · Pharmaceutical Products and Veterinary Diagnostic Systems using Biotechnology ... CENTRAL INSTITUTIONAL ROLE b. the development

ACKNOWLEDGEMENT

Page 3: HIGH THROUGHPUT SEQUENCING, BIOINFORMATICS AND ... · Pharmaceutical Products and Veterinary Diagnostic Systems using Biotechnology ... CENTRAL INSTITUTIONAL ROLE b. the development

OIE-AD HOC GROUP ON HIGH THROUGHPUT SEQUENCING,

BIOINFORMATICS AND COMPUTATIONAL GENOMICS (HTS-BCG)

Dr Sándor Belak

Dr Carlos Barroso

Dr Peter Daniels

Prof Massimo Palmarini

OIE - Collaborating Center for Viral Genomics and Bioinformatics

OIE – Collaborating Center for Development and Production of Vaccines,

Pharmaceutical Products and Veterinary Diagnostic Systems using Biotechnology

OIE – Collaborating Center for Biotechnology-based Diagnosis of Infectious

Diseases in Veterinary Medicine

OIE – Reference Laboratory for Bluetongue

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PILOT PROJECT & MOCK UP

Prof Massimo Palmarini

Dr Robert Gifford

Dr Antonino Caminiti

Dr Emiliana Brocchi

Dr Marco Caporale

Dr Silvano Galasso

University of Glasgow Centre for Virus Research - Glasgow

Istituto Zooprofilattico della Lombardia e Emilia Romagna - Brescia

Page 5: HIGH THROUGHPUT SEQUENCING, BIOINFORMATICS AND ... · Pharmaceutical Products and Veterinary Diagnostic Systems using Biotechnology ... CENTRAL INSTITUTIONAL ROLE b. the development

The role of genetic material profiling and complete genome sequencing in microbial infections is increasing a. pathogenesis and immunity b. diagnosis c. management d. characterisation of infectious agent e. likely distribution of their spread in time and space

In the current and future scientific environment a microorganism is not identified satisfactorily unless essential features of its genome are described

GENETIC PROFILING AND ANIMAL HEALTH

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The increasing reliance on generating and using sequence information, in particular the trend toward whole genome sequencing and metagenomics

The inevitable introduction of devices and systems for the generation of sequence data away from the laboratory and closer to the point of sampling on the farm or at other points along the “value chain”

a. THE ROLE, DESIGN AND MANAGEMENT OF VETERINARY LABORATORIES

The ever increasing trend toward global open information systems

b. THE NOTIFICATION AND MANAGEMENT OF INFECTIOUS DISEASES AND FOOD-BORNE INFECTIONS

HIGH THROUGHPUT SEQUENCING, BIOINFORMATICS AND COMPUTATIONAL GENOMICS

HAVE CRUCIAL AND FAR REACHING IMPLICATIONS FOR

Page 7: HIGH THROUGHPUT SEQUENCING, BIOINFORMATICS AND ... · Pharmaceutical Products and Veterinary Diagnostic Systems using Biotechnology ... CENTRAL INSTITUTIONAL ROLE b. the development

OIE RESPONSIBILITY AND INSTITUTIONAL ROLE IN

THE GLOBAL MANGEMENT OF ANIMAL

HEALTH AND FOOD SAFETY

Page 8: HIGH THROUGHPUT SEQUENCING, BIOINFORMATICS AND ... · Pharmaceutical Products and Veterinary Diagnostic Systems using Biotechnology ... CENTRAL INSTITUTIONAL ROLE b. the development

THE OIE HAS THE RESPONSIBILITY OF A LEADING AND CENTRAL INSTITUTIONAL ROLE

b. the development and adoption of international standards for animal health and welfare including diagnostic tests and vaccines

a. the animal health information collection and distribution worldwide

OIE RESPONSIBILITY IN THE GLOBAL MANGEMENT OF ANIMAL

HEALTH AND FOOD SAFETY

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THE OIE STRATEGY

Page 10: HIGH THROUGHPUT SEQUENCING, BIOINFORMATICS AND ... · Pharmaceutical Products and Veterinary Diagnostic Systems using Biotechnology ... CENTRAL INSTITUTIONAL ROLE b. the development

THE OIE STRATEGY

1. ADOPTION OF STANDARDS FOR SEQUENCE PRODUCTION, ASSEMBLY AND USE IN THE LABORATORY, ON THE FARM AND AT ANY POINT ALONG THE “VALUE CHAIN” LINKING ANIMALS TO CONSUMERS

2. CREATION OF AN OIE PLATFORM FOR THE COLLECTION AND MANAGEMENT OF PATHOGEN GENOMIC SEQUENCES AND RELATED METADATA INTEGRATED WITH EXISTING WORLD ANIMAL HEALTH INFORMATION SYSTEM (WAHIS)

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DEVELOPING THE OIE

STANDARDS

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1. Sequence and sequence analysis data should be considered an integral and necessary part of the reporting of cases and outbreaks to the OIE

THE OIE STRATEGY DEVELOPING THE OIE STANDARDS

The use of new technological tools, such as HTS-BCG, in the management of diseases of animals

2. Standards for sequence production and assembly should be generated

a. adopted within the context of tried and accepted processes for the management of animal health and food safety, including the laboratory quality assurance system

b. appropriate to the purpose of the investigation

c. sampling and the interpretation of the results have to be in context with the pathogenesis and epidemiology of the infection in the animal species under study carried out by appropriately qualified veterinary investigators within the appropriate regulatory framework

Methods to obtain pathogen genomic sequences - including HTS - Sequencing quality (quality of reads has to be appropriate to the purpose) Procedures for sequence assembly Reference genomes

Page 13: HIGH THROUGHPUT SEQUENCING, BIOINFORMATICS AND ... · Pharmaceutical Products and Veterinary Diagnostic Systems using Biotechnology ... CENTRAL INSTITUTIONAL ROLE b. the development

DEVELOPING AN INFORMATION

PLATFORM

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THE OIE STRATEGY

1. To create the OIE platform for the collection and management of pathogen genomic sequences and related metadata

Policy of data governance Property rights Accessibility Proper use

Data standards to describe sequences production and assembly

File formats for storage

Policy to support the use of open source software and licensing

2. To implement a process to reach consensus to define

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The OIE Reference Centres and other national sources should provide, the expertise for:

developing policies, practices and standards to generate, manage and use sequence information in animal diseases and related food safety infections, diagnosis and management

the scientific understanding of the use of sequence information of microorganisms, in relation to animal health and food safety

THE OIE STRATEGY THE ROLE OF THE GLOBAL NETWORK OF OIE REFERENCE CENTRES

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THE PILOT PROJECT

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OBJECTIVES OF THE PILOT PROJECT

4. Facilitate the participation of non-OIE Reference Laboratories in the platform and uploading of their own sequences

3. The network of OIE Collaborating Centres will be the main players in creating the platform and in defining the standards

1. Provide the blueprint for the creation of an open access platform for the collection and management of pathogen genomic sequences and related metadata managed and coordinated by the OIE and fully integrated into the World Animal Health Information System (WAHIS), defining among other property rights, accessibility and proper use of data

2. To update the OIE Manuals

defining reference genomes

defining standards for production, assembly and storage of genomic sequences to be integrated into the Manuals

A Pilot projects has initiated

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THE PLATFORM

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THE OIE PLATFORM THE PLATFORM

The open access platform for the collection and management of pathogen genomic sequences and related metadata will

Provide assistance and expertise for sequence assembly and data analyses within and outside the OIE Reference Laboratory network

Gather genomic sequences from the OIE Reference Laboratories, national laboratories, scientific institutions laboratories , etc.

Provide services for data storage

Provide sequencing information within and outside the OIE Reference Laboratory network

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THE OIE PLATFORM OVERVIEW

EPIDEMIOLOGICAL DATABASE

SEQUENCE DATABASE

OIE-REFERENCE LABORATORIES WITH LOCAL DATABASE

EPIDEMIOLOGICAL DATABASE

SEQUENCE DATABASE

SERVICE CENTER OIE-HEADQUARTERS

OIE-REFERENCE LABORATORIES WITHOUT

LOCAL DATABASE

WEB

SERVICES

EPIDEMIOLOGICAL DATABASE

SEQUENCE DATABASE

OTHER LABORATORIES WITH LOCAL DATABASE

WEB

SER

VIC

ES

OTHER LABORATORIES WITHOUT LOCAL

DATABASE SEQUENCE

EPIDEMIOLOGICAL DATA

EPIDEMIOLOGICAL DATA

SEQUENCE

REPORTS

USERS

OIE-WAHIS

OTHER GENOME & EPIDEMIOLOGICAL DATA

DATABASES (i.e. GMI, FAO, etc)

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THE SERVICE CENTER &

THE PERIPHERAL NODES

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THE OIE PLATFORM THE SERVICE CENTER AND THE PERIPHERAL NODES

Data exchange and services (such as those for sequence assembly, sequence comparison and data analysis, etc.) will be assured by the Service center to all laboratories within the system

Access and property rights will be ensured to the laboratory that has provided them, regardless of where data are stored physically

THE SERVICE CENTER IS LOCATED AT THE HEADQUARTER

to assure any other information exchange within and outside the platform

to manage the distributed database of the genomic sequences

to link the database and WAHIS

to provide access to data

THE KEY PERIPHERAL NODES ARE THE OIE –REFERENCE LABORATORIES

to supply the genomic sequences and the epidemiological data to the Service center

to provide assistance and expertise for sequence assembly and data analyses within and outside the OIE Reference Laboratory network

Page 23: HIGH THROUGHPUT SEQUENCING, BIOINFORMATICS AND ... · Pharmaceutical Products and Veterinary Diagnostic Systems using Biotechnology ... CENTRAL INSTITUTIONAL ROLE b. the development

THE ARCHITECTURE

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THE OIE PLATFORM THE ARCHITECTURE

OIE PAHOGEN GENOMICS PLATFORM

DATABASE STORE EPIDEMIOLOGICAL & SEQUENCE DATA

INDEX SEARCH RETRIEVE

CONNECTION MODULE LINK TO WAHIS

INTEROPERABILITY & SERVICES

AUTHENTICATION & AUTHORIZATION MANAGEMENT

AMINISTRATION MODULE VISIBILITY AND RIGHTS

MANAGEMENT WORKFLOW

MANAGEMENT

ANALYTICAL MODULE

SEQUENCE ASSEMBLY

OTHER TOOLS FOR DATA ANALYSIS

SEQUENCE COMPARISON HEADQUARTERS

OIE-REFERENCE LABORATORIES

OTHER LABORATORIES

OTHER USERS

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THE BASIC COMPONENTS

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The genomic sequence database will allow the storing, indexing and searching of genomic sequences

THE OIE PLATFORM THE BASIC COMPONENTS

The database will be characterized by a high degree of flexibility

to manage to manage files that differ in structure (type and organisation of the information in the file), format (plain text, compressed formats, etc.)

size (from a few megabytes to many gigabytes)

to allow pipelines to be run with variable programming language data input scope (sequence assembly, quality evaluation, phylogeny, etc.)

For each genomic sequence, the database will collect and store data on the sequencer equipment used the pipelines chosen the epidemiological findings

1. GENOMIC SEQUENCE DATABASE

Page 27: HIGH THROUGHPUT SEQUENCING, BIOINFORMATICS AND ... · Pharmaceutical Products and Veterinary Diagnostic Systems using Biotechnology ... CENTRAL INSTITUTIONAL ROLE b. the development

THE OIE PLATFORM THE BASIC COMPONENTS

The database will be distributed over a network of interconnected computers located in the laboratory network

In all cases responsibility for data quality and data property will belong to the laboratory inputting them.

Laboratories that do not possess their own database will have the possibility of participating in the worldwide OIE genomic database that will provide them with the necessary infrastructure for raw data management

c. Each laboratory system must guarantee the same standardised services and functions to assure the platform interoperability

a. Each laboratory represents an independent node with its own system

b. Each laboratory maintains control over the data produced locally and it accesses the entire database – as if it was centralised – to carry out analyses and reporting

1. GENOMIC SEQUENCE DATABASE

Page 28: HIGH THROUGHPUT SEQUENCING, BIOINFORMATICS AND ... · Pharmaceutical Products and Veterinary Diagnostic Systems using Biotechnology ... CENTRAL INSTITUTIONAL ROLE b. the development

THE OIE PLATFORM THE BASIC COMPONENTS

Assures the connectivity of the various components within the platform and other relevant information systems

It has two main functions accessible by the operator at the laboratory level

1. sequences are linked to the related immediate notifications, follow-ups and other types of official reports stored in WAHIS

2. the enrichment of genomic sequences with epidemiological data

2. THE CONNECTION MODULE

The epidemiological data enriching the sequence data will be

1. those present in WAHIS, in cases where the sequences are related to an immediate notification

2. a minimal set of epidemiological data to be defined in all other cases

Epidemiological data not related to official reporting will be subject to verification by the OIE before being publicly available to assure compliance to the existing international veterinary standards

Page 29: HIGH THROUGHPUT SEQUENCING, BIOINFORMATICS AND ... · Pharmaceutical Products and Veterinary Diagnostic Systems using Biotechnology ... CENTRAL INSTITUTIONAL ROLE b. the development

The OIE platform for pathogen genomics will collect and store sensitive information with related security challenges

3. THE ADMINISTRATION MODULE

THE OIE PLATFORM THE BASIC COMPONENTS

An Administration module and appropriate standard must be implemented

To manage visibility and access of data

To guarantee compliance with quality requirements during the uploading of the sequences

To ensure the respect of property rights

To trace information on the use of data

The administration module will integrate specific mechanisms to expand the platform with new services and functions by adding or update modules.

Page 30: HIGH THROUGHPUT SEQUENCING, BIOINFORMATICS AND ... · Pharmaceutical Products and Veterinary Diagnostic Systems using Biotechnology ... CENTRAL INSTITUTIONAL ROLE b. the development

MODULES FOR SEQUENCE ASSEMBLY

AND COMPARISON &

DATA ANALYSIS

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THE OIE PLATFORM MODULES FOR SEQUENCE ASSEMBLY & COMPARISON AND DATA ANALYSIS

The development and sharing of common tools would promote not only knowledge exchange but also the participatory development of standards

The OIE platform for genomics will offer a set of modules accessible to laboratories participating in the platform for sequence assembly sequence comparison data analysis

The modules could be developed by a single Laboratory or a group of Centres within the platform, and then offered to the other members of the platform

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DATA FLOW

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THE OIE PLATFORM DATA FLOW

The OIE requires that Member Countries

Official communications between Member Countries and the OIE are subject to strict procedures, and the publication of data follows a series of VERIFICATION AND VALIDATION steps before information is made public

a. notify any event of epidemiological significance (immediate notifications and follow-ups)

b. transmit periodic reports on the presence or absence of OIE listed diseases (6-monthly

Page 34: HIGH THROUGHPUT SEQUENCING, BIOINFORMATICS AND ... · Pharmaceutical Products and Veterinary Diagnostic Systems using Biotechnology ... CENTRAL INSTITUTIONAL ROLE b. the development

VETERINARY SERVICE

LABORATORY DELEGATE** OIE-REFERENCE

LABORATORY OIE WAHIS/WAHID/

INTERFACE

-

DATA PUBLICATION

DATA VERIFICATION & VALIDATION

SAMPLE ANALYSIS

CONFIRMATION

CONFIRMATION

CONFIRMATION

SAMPLE

CONFIRMATION

IMMEDIATE NOTIFICATION

DATA VERIFICATION & VALIDATION

SAMPLE ANALYSIS

SAMPLE*

EPIDEMIOLOGICAL DATA

* Confirmation from an OIE Reference Laboratory is required in case of certain diseases (e.g. FMD) **Chief Veterinary Officer

THE OIE PLATFORM OIE IMMEDIATE NOTIFICATION DATA FLOW

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VETERINARY SERVICE

LABORATORY CVO** OIE-REFERENCE

LABORATORY OIE WAHIS/WAID

/ INTERFACE

-

DATA PUBLICATION

DATA VERIFICATION & VALIDATION

SAMPLE ANALYSIS

CONFIRMATION

CONFIRMATION

CONFIRMATION

SAMPLE

CONFIRMATION & SEQUENCE

IMMEDIATE NOTIFICATION

DATA VERIFICATION & VALIDATION

SAMPLE ANALYSIS

SAMPLE*

EPIDEMIOLOGICAL DATA

* Confirmation from an OIE Reference Laboratory is required in case of certain diseases (e.g. FMD) **The relationship between laboratory and OIE-Reference Laboratory regarding sequences transmission needs to be defined

EPIDEMIOLOGICAL DATA

SEQUENCE & EPIDEMIOLOGICAL

DATA**

SEQUENCE GENERATION

THE OIE PLATFORM SUGGESTION FOR IMMEDIATE NOTIFICATION AND SEQUENCE

TRANSMISSION DATA FLOW

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LABORATORY/ OIE-REFERENCE LABORATORY

OIE WAHIS/WAHID/INTEFACE

DATA PUBLICATION

DATA VERIFICATION & VALIDATION

CVO

- DATA VERIFICATION

& VALIDATION

SAMPLE ANALYSIS

SEQUENCE & EPIDEMIOLOGICAL DATA SEQUENCE

GENERATION

THE OIE PLATFORM GENERIC TRANSMISSION OF SEQUENCES AND

EPIDEMIOLOGICAL DATA

VERIFICATION IF REQUIRED

Page 37: HIGH THROUGHPUT SEQUENCING, BIOINFORMATICS AND ... · Pharmaceutical Products and Veterinary Diagnostic Systems using Biotechnology ... CENTRAL INSTITUTIONAL ROLE b. the development