INCOB 2012 Thailand PAPGI Meeting Minutes
PAPGI meeting 4-5 Oct 2012, Bangkok, Thailand
The 4th PAPGI session was held on 4th – 5th October 2012 at Grand Centara Hotel, Bangkok as part of the INCOB 2012. This was made possible by SC representative from Thailand Dr. Sissades Tongsima and his team. There were 7 presentations by members on the 4th in a session chaired by ME Phipps, followed by 2 presentations and a general discussion on 5th chaired by PS Lai. The aim was to follow up on the project timelines, issues and updates from the 3rd meeting at MUSC in July.
2.0 Attendees (as listed in attendance list, extra details for “new” attendees/members)
1. Zilfalil Alwi (ZFA)
2. Fahd Al- Mulla (FAM)
3. ShuHua Xu (SHX)
4. Rick Twee Hee Onn (RO)
5. Jiraporn Mongkolpiyawat (JM, Govt. Pharmaceutical Organization, Thailand)
6. Sissades Tongsima (ST)
7. Philip Shaw (PS, Biotec, Thailand) – Philip@biotec.org,th
8. Mahmoud Elltofil (ME, National Research Centre, Egypt) – firstname.lastname@example.org
9. Maude Phipps (MEP)
10. Lai Poh San (LPS)
11. Tim Ravassi (TR)
12. Suthat Fuchearon (SF)
13. Thipparat Nasrisok (TN,Mahidol University, Thailand) – email@example.com
14. Metawee Srikummol (MS, Nrasuan University, Thailand) – firstname.lastname@example.org
15. Saovaros Svasti (SS Mahidol Uni) – email@example.com
16. Vijay Kumar (VK)
17. Wasun Chantratita (WC, Mahidol Uni) – firstname.lastname@example.org
18. Kha Dhana Chandra Singh (KDCS, Alagappa University, India) – email@example.com
3.0 The Issues raised and addressed on during discussion on 5th Oct was as follows:
3.1 Ratification of Consensus Agreement –
Unanimous ratification on this consensus agreement ,
It was agreed that PAPGI will continue with our official affiliation with HUGO and that formal endorsement and statement of support will be sought from current HUGO President Dr. Edison Liu. A write-up document about PAPGI for the purpose of IRB application will be drawn up. This will be emailed to all members and will be useful for IRB and research fund applications.
We will also formalize our affiliation with the Asia Pacific Society of Human Genetics.
3.2 Sample selection
This issue was raised by FAM as to the nature and quantity of samples to be collected The response was that we stick to the earlier recommendations as in pansnp such as
- Preferably 3 generations of same ethnic group
- Main populations and indigenous populations
- Unrelated, distinct language & geographical location
- Age depends on specific community preference and PI’s opportunity. Only adult to be sampled.
- 10 ug of DNA for NGS
SHX will prepare a list / general guidelines draft by 26 Oct 2012 to be posted on the website. PAPGI encourages collection of as much phenotype data in each population
- SF, ST and Thai researchers will discuss the Thai ethnic groups to be included and confirm with PAPGI by 15th Dec 2012.
- lab facilities, etc.
FAM – To start collection Kuwait, Bahrain, UAE , Qatar, Lebonon (20 ea) +- Palestine, April 2012
TR – 120 out of 200 collected, diff geographical location, April 2012
ZFA – Collection completed, 3 Malay gps
SHX – Collection NW Chi Uigher, Tjik, Tibetians,sep 2012 sample collection complete
Ming Qi – commit to some Chinese pops., in 2 wk
RO – WGS and snp array genotype available for 100 Malays (Omni1 Quad), 38 Indians and 2 Chinese (Omni2.5M)
Egypt – Seena, Said, Alexandria (10 each, same males and females), collection date, April 2012, - will be hosted / supported by FAM’s lab in Kuwait
Japan – Thru MEP who communicated with Prof. Tokunaga (Uni Tokyo), confirmed samples from metropolitan Tokyo population. (Not sure about Okinawa or Ainu yet)
- Other attendees confirmed the ethnic groups they listed from the previous meeting. Some stated that they will be using archival samples from previous studies
3.3 Ethics and IRB
LPS reminded members to seek and submit the documents related to consent and IRB to the PRB as soon as possible. The guidelines for the ethics and IRB approvals are given in the Consensus Agreement. All members are advised to provide full disclosure on the nature of the work to their respective IRBs and to ensure informed consent are obtained for their samples
3.4 Expression of interest / New members / Collaborations
- Mahmoud al Hafnawi (Uni of Cairo, Egypt) expressed interest in joining the consortium. He was advised to write formally to the three co-chairs providing his further details of his specific intentions to contribute in terme of ethnicities, expertise, Japan
- Saitou Naruya (Natl Inst. Of Genetics, Japan) a population geneticist and collaborator of Tokunaga, Phipps and Jinam, wrote officially to S Sugano (SC representative form Japan) expressing interest to join. SS has accepted and PAPGI welcomes Dr. Saitou into the consortium.
- FAM suggested that PAPGI collaborate with Human Variome Society (HVS) due to some shared interests, members and potential benefits. Also HVS is supported by WHO and UNESCO.
Members agreed to this collaboration but asserted the independence of PAPGI
- TR stated that in order to freely use the Saudi genome sequences under the consortium umbrella MY collaborator and Saudi samples provider, Prof. Mohammed Ali Al Jumah from the Saudi National Guard hospital and the King Abdullah International Medical Research Center needs to be officially invited to join the consortium (http://www.ksauhs.edu.sa/English/AboutUs/Pages/MohammedAliAlJumah.aspx)
TR already introduced Prof. Al Jumah to the PAPGI structure, objectives and philosophy but an official letter of invitation from the Chairs of the steering committee is NECESSARY to move forward with the Saudi samples.
3.5 BioIT Pipeline & IT training
TR, ST, SHX and members of the Bioinf Working Group will be discussing in consultation with Jong Bhak in detail. The BioIT pipeline strategy and implementation will be confirmed by the nx PAPGI meeting planned during the 10th Asia Pacific Congress of Genetics, KL on 4-6th Dec 2012.
The BioIT WG strongly recommends the Iluminina platform for all members
Research BioIT capacity building (After March 2013) – Eva Maria Cutiongco has communicated regarding the genomic lab developments in Philipines and will work wih the relevant PAPGI members to organize a Manila Bioinformtics workshop in 2013,
3.6 Concept paper update
The ELSI section of CP has already been drafted by LPS and will be further detailed by members in ELSI working group such as EMC, MEP, CP, etc.
The BIoIT section has yet to be drafted and TR, AM, ST,Chris Voo, BioIT group members will need to draft as soon as possible
The overview will be drafted by YY Teo, BP Hoh and other members who had volunteered.
The first draft of the complete concept paper should be ready by 1 Dec 2012. YY Teo to oversee
3.7 Data Depository
(a) After Bandwidth testing, the decision is to send hard drives between ‘host’ IT labs with high IT platforms and computing facilities to ‘guest labs’ because the internet would take too long.
(b) All members were reminded to send copies of their IRB approval documents and samples of signed Informed Consent forms to LPS and MEP for archiving and storage. This is of paramount importance for any PAPGI publication
3.8 Third Party (non-collaborating queries)
Of late, various members have received emails form external parties requesting information or interviews about community engagement and ELSI issues for PANSP and PAPGI. Due to the fact that it would be very difficult to ascertain the motives for these interviews or how the information will be eventually used, members agreed that a cautious approach would be taken to prevent any negative or unfavourable consequences. This has happened in the past with other large scale genome projects where some researchers were quoted out of context, which lead to aspects of the project being jeopardized.
It was agreed that PAPGI members engage with external parties who had any queries about the issues mentioned only in their own capacity and on their own personal research.
Any request for PAPGIPANSP or PAPGI information would require formal application to Steering Committee thru’ the CoChairs and will be discussed before any decision is taken.
3.9 Sourcing External Funds
Mr. Halabi, a Saudi Ph.D. student of PAPGI member Mahmood Ameen has suggested that PAPGI apply for research funds to the Prince Al Waleed bin Talal Foundation. The Princess, consort of the prince, administers some philanthropic fund from the foundation which may be open to international projects which involve Saudi Arabia.
TR will liase with Halabi and contact the foundation. He will update PAPGI when he has the full information before December.
FAM suggested the ‘Kuwait Foundation for the Advancement of Sciences’ for PAPGI support. He will also be making enquiries and inform the SC. PAPGI's Co-Chairs should contact KFAS officially requesting support through a project and International collaboration.
4.0 Upcoming meetings :
APCHG 5-7 Dec 2012 in Kuala Lumpur
HGM /ICG 13-18 April 2013 in Singapore.
Teo Yik Ying will be requested to host a SC teleconference in November 2012 for additional updates.
Members were encouraged to host PAPGI meetings if they are organizing any future genetics/genomics meeting in their countries and to provide the necessary support for members to attend.
The meeting ended at 4.30pm with a vote of thanks to the local organizers & hosts, and all members who participated and VK who took notes.
Document prepared by and finalized by MEP with edits from LPS, FAM, SHX, RO, ST, TR 18 October 2012