1. Animal Genetics Div., INRA, France
A perspective on FAANG
Elisabetta Giuffra
Animal Genetics Div., INRA, France
Workshop on Animal genomics and breeding for sustainable production – Brussels, 10-11/10/2016

2. Why FAANG is important? Understanding the genotype to phenotype link:
Genomic selection
Improving fundamental understanding of biology
This needs:
Eliminare?
Challenges:
Many species and groups with limited resources
Variable quality of existing reference genomes and annotation
Workshop on Animal genomics and breeding for sustainable production – Brussels, 10-11/10/2016

3. Conception and start of FAANG
EU-US Animal Biotechnology Working Group (ABWG)
ABWG Workshops:
Washington DC, Nov 2011: Strategic Priorities to Realize the Promise of Genomics to Animal Health, Well-being & Production.
Hinxton, UK, Sept 2012: A shared international cyber-infrastructure dedicated to genomic and phenomic animal data.
S. Diego (PAG XXII), Jan. 2014: Agencode workshop - to develop a plan for a coordinated ENCODE-like project for food animals (AgEncode).
Preparative phase (since 2011) led by ABWG with a small group of scientists from 12 countries
June 2014: AgENCODE FAANG
Workshop on Animal genomics and breeding for sustainable production – Brussels, 10-11/10/2016

4. Lessons from ENCODE projects
Well established consortium rules and policies
Established technologies (= now, lower costs) and experimental and data standards of reference
Demonstrated the value of freely available reference datasets, and of integrating biochemical data alongside other evidence
The essential lessons
80.4% participates in at least one biochemical RNA - and/or chromatin-associated event in at least one cell type
 95% lies within 8 kilobases (kb) of a DNA –protein interaction (as assayed by bound ChIP-seq motifs or DNase I footprints )
 99% is within 1.7 kb of at least one of the biochemical events measured by ENCODE
 It is possible to correlate quantitatively RNA sequence production and processing with both chromatin marks and transcription factor binding at
Promoters
 indicating that promoter functionality can explain most of the variation in RNA expression.
 Many non - coding variants in individual genome sequences lie in ENCODE - annotated functional regions; this number is at least as large as those
that lie in protein - coding genes.
These modes of actions are followed by most large consortia for research
Workshop on Animal genomics and breeding for sustainable production – Brussels, 10-11/10/2016

5. FAANG ‘is a coordinated international action to accelerate genome to phenome’
AIMS:
Standardize core assays and experimental protocols
Coordinate and facilitate data sharing
Establish an infrastructure for the analysis of these data
Provide high quality functional annotation of animal genomes
Eliminare?
In adherence to the "FAANG Data Sharing Statement" 
Workshop on Animal genomics and breeding for sustainable production – Brussels, 10-11/10/2016

6. How achieving the goals of FAANG?
White Paper: Andersson et al. Genome Biol Mar 25;16:57 The ‘unique value’ of domesticated animal species across several topics of research and applications
First phase:
Obtain a biological reference for main farm species (i.e. with sufficiently annotated genomes)
Next phase:
‘Expansion’: different developmental stages, different physiological conditions, additional species…
‘Genotype-to-phenotype’: new breeds/phenotyped populations (involving industry)
To be shown at the end!!!!
Workshop on Animal genomics and breeding for sustainable production – Brussels, 10-11/10/2016

7. Working Groups Animal, Samples and Assays – AS&A
Elisabetta Giuffra and Huaijun Zhou
Bioinformatics and Data Analysis – B&DA
James Reecy and Mick Watson
Communications – Coms
Chris Tuggle and Jeff Silverstein
Metadata and Data Sharing – M&DS
Laura Clarke and Carl Schmidt
Working with the community by:
Periodic video-conferences and wiki
Reporting at workshops, e.g.
@faangomics
Workshop on Animal genomics and breeding for sustainable production – Brussels, 10-11/10/2016

8. FAANG events www.faang.org/Publications
Since 2014: dedicated meetings/workshops at PAG conferences (San Diego)
2015: GO-FAANG meeting (Washington DC)
Several representatives of Funding Agencies
Outcomes reported in: Animal Genetics (Vol. 47, Issue 5, pages , 24 JUL 2016)
2016: FAANG -ASAS-ISAG Joint Symposium (hosted by the 35th ISAG conference, Salt Lake City)
>400 participants
Workshop on Animal genomics and breeding for sustainable production – Brussels, 10-11/10/2016

9. Some elements for a discussion on FAANG perspectives
(and sustainability)
Wokshop on Animal genomics and breeding for sustainable production – Brussels, 10-11/10/2016

10. Joint ASAS/ISAG FAANG Symposium, 23 July 2016, Salt Lake City
Questionnaire* administered to the participants of the FAANG-ASAS-ISAG workshop (July 2016)
Are you a FAANG member?
* about 20% responders
Joint ASAS/ISAG FAANG Symposium, 23 July 2016, Salt Lake City

11. Joint ASAS/ISAG FAANG Symposium, 23 July 2016, Salt Lake City
Not FAANG members:
WHY?
16% Not doing/not planning to do –omics research with the main FAANG species
12% The genomic resources for the species of interest are still too limited
3% cannot adhere to FAANG policies
49% Still ‘exploring’, waiting to see the first outcomes of FAANG
20% Other reasons
Joint ASAS/ISAG FAANG Symposium, 23 July 2016, Salt Lake City

12. Joint ASAS/ISAG FAANG Symposium, 23 July 2016, Salt Lake City
FAANG members:
65% have joined the activities of at least one FAANG Working Group
65% are carrying out (or have submitted) a FAANG-related project
76% will submit samples and/or data to FAANG databases within a couple of years
Joint ASAS/ISAG FAANG Symposium, 23 July 2016, Salt Lake City

13. Joint ASAS/ISAG FAANG Symposium, 23 July 2016, Salt Lake City
FAANG-pilot: few animals, several tissues/assays; connected to ongoing research FAANG-related: several animals, usually less assays; part of ongoing research
Species
Leading Inst. & country
FAANG-pilot
FAANG-rel.
pig, cattle, goat, chicken
INRA
France X x
pig, cattle, chicken
UC-Davis US
horse
UC-Davis & Nebraska Univ.
cattle
Leibniz Inst. for Farm Anim. Biology
Germany
Sheep
Int. Sheep Genome Consortium & others
Australia & US
pig, chicken
Wageningen Univ.
The Netherlands
Dairy Futures Coop. Res. Centre, AgriBio & others
Australia
cattle, pig
Alberta & Guelph Univ. & others
Canada
cattle and zebu
Adelaide Univ.
sheep, buffalo
Roslin- Edinburgh Univ. UK
Washington State Univ.
‘Arctic Ark’
Natural Resources Institute
Finland
…………
………
…..
I got a lot of slides and I made an attempt to summarize! These definitions are temptative
(ongoing/recently funded/started)
Joint ASAS/ISAG FAANG Symposium, 23 July 2016, Salt Lake City

14. Joint ASAS/ISAG FAANG Symposium, 23 July 2016, Salt Lake City
New joining communities: Functional Annotation of All Salmonid Genomes (FAASG)
Opportunities
Develop comparative data sets to understand how genome functions evolve after whole genome duplication events in vertebrates and how genomic variation and expression translates into phenotypes
Develop new approaches and resources to facilitate the creation of solutions that enhance sustainable salmonid fisheries, conservation and aquaculture production worldwide
Approach: Coordinate the international salmonid community to acquire, standardize and share data for comprehensive mapping and characterization of the functional elements of salmonid genomes. f
From: talk of Caird E. Rexroad (ARS-USDA) talk at FAANG-ASAS-ISAG workshop - Salt Lake City, July 2016
Joint ASAS/ISAG FAANG Symposium, 23 July 2016, Salt Lake City

15. FAANG Networking and Data Coordination Centre
Leading Inst. & country
Networking Actions
DCC
Delaware Univ. US X
Roslin- Edinburgh Univ. UK
EMBL-EBI
data being produced now
Wokshop on Animal genomics and breeding for sustainable production – Brussels, 10-11/10/2016

16. ww.faang-europe.org/preview
ww.faang-europe.org/preview
@FAANGEurope
International networking & cooperation
Functional Annotation of Animal Genomes - European network (FAANG Europe) Cost Action CA Alan Archibald
Animal Genome to Phenome Research Coordination Network (AG2P) – NSF networks - Carl Schmidt
Wokshop on Animal genomics and breeding for sustainable production – Brussels, 10-11/10/2016

17. FAANG Europe (COST Action)
Experimental data
Improved function annotation
FAANG
annotation
pipeline
Re-analyse
Re-interpret
Exploit assay-by-sequence approaches (tissues, primary cells)
Optimize available resources (e.g. samples)
Prioritise assays
Standards (laboratory protocols, metadata, data analysis) to facilitate data re-use and metanalysis
Pre-publication data sharing based on The FAANG Data Sharing Statement (
Wokshop on Animal genomics and breeding for sustainable production – Brussels, 10-11/10/2016

18. FAANG Data Coordination Center
Grant awarded by BBSRC
EMBL-EBI and Roslin institute collaboration
Starts November 1st
Will provide
Submission and validation support
Data portal
Standard analysis results
Wokshop on Animal genomics and breeding for sustainable production – Brussels, 10-11/10/2016

19. How FAANG is going to develop?
(White Paper 2015)
1st phase
Obtain a biological reference for main farm species
2nd phase:
‘Expansion’: Biology-led projects (FAANG-related projects)
‘Genotype-to-phenotype’: new breeds/phenotyped populations (involving industry)…
Pilot projects since 2015
(only limited national funding)
An international and coordinated project to build FAANG reference(s) would act as a boost for ‘any’ research topic and avoid redundancies/fragmentations
This is well demonstrated by ENCODE and other recent consortia (e.g. BluePrint EC project)
But this is not supported (yet?) by main national and international agencies
Wokshop on Animal genomics and breeding for sustainable production – Brussels, 10-11/10/2016

20. How FAANG is going to develop?
(White Paper 2015)
1st phase
Obtain a biological reference for main farm species
2nd phase:
‘Expansion’: Biology-led projects (FAANG-related projects)
‘Genotype-to-phenotype’: new breeds/phenotyped populations (involving industry)…
Reinforcing the means for global coordination is a key need (interconnected Data Analysis Centers; expansion to additional groups; efficient links to other communities; etc.)
Biology-led projects (FAANG-related projects)
Suited to fit in multidisciplinary call topics
COST ‘FAANG Europe’ ; AG2P; DCC
Wokshop on Animal genomics and breeding for sustainable production – Brussels, 10-11/10/2016