PAPGI steering committee meeting 5-6th July meeting minutes
MINUTES OF HUGO - PAPGI STEERING COMMITTEE & Malaysian Chapter MEETING
DATE: 5TH – 6TH JULY 2012
VENUE: JEFFREY CHEAH SCHOOL OF MEDICINE AND HEALTH SCIENCES, MONASH UNIVERSITY SUNWAY CAMPUS, KUALA LUMPUR, MALAYSIA
1.0 Preamble :
A two day meeting focused on HUGO PAPGI was organized by Prof. Dr Maude E. Phipps (SC Co-chair), Associate Professor Dr Rakesh Naidu and team at Monash University (Sunway Campus). All conference facilities, meals, accommodation at the Sunway Monash residences and dinner at Old China Restaurant, Central Market, KL were supported by MOSTI Malaysia grant RM1/BIOTEK16/6/2B awarded to ME Phipps, Jeffrey Cheah School of Medicine & Health Sciences and Science Vision Sdn. Bhd.
Malaysia : Monash University - ME Phipps, R Naidu, F. Aghakhanian
UiTM - BP Hoh (recorded minutes), Siti Shuhada Mokhtar, Yushimah Yunus
UMS - V. Kumar, C. Voo, Yew Chee Wei
USM - Z. Alwi,
UM – M. Ameen, J. Edo, XX (Saudi Arabia)
China : CAS - SH Xu
Saudi Arabia : KAUST – T. Ravasi
Singapore : NUS – YY Teo
Philippines : UP - E M Cutiongco
UK: Camb.U – A. Manica
MUSC Technical team : TY Tee and YC Mah
PAPGI members who were not present would have emailed messages and further information so their names would appear as part of discussions although they were not physically present.
3.0 Overview of PAPGI SC Meeting Programme & Objectives (Chaired by MEP)
- Ratification of Teleconference minutes on April 2012
- Agreement on the structure, composition, policy and modus operandi of PAPGI
- Presentations from new consortium members regarding additional ethnicities and their institutional facilities
- Discussion of latest ethical and technical considerations
- Formulation of resolutions, timeline, project milestone and ways to move PAPGI forward.
4.0 PAPGI Vision statement as articulated in the document on papgi.org was confirmed.
PAPGI philosophy is
• Guided by PASNP spirit of collaboration, transparency and ‘guest host’ partnership
• A purely scientific endeavour in population genomics project
• Non-commercial, Non-profit
• Data to be free of charge and accessible to all legitimate researchers / individuals
through data management mechanism
5.0 Modus Operandi:
Based on the spirit of respect, mutual trust, transparency and accountability.
Purely meant knowledge generation and greater good.
No MoUs, MoA, NDA etc for PAPGI members.
5.1 “Host-Guest” partnerships are essential: -
DNA should be BROUGHT BACK to the host country; knowledge and technology transfer: - supported by institutions like GIS/NUS, KAUST and/or CAS (Shanghai).
From communications between members, it was apparent that Nepal, Indonesia, and some other members required technical support and may not be able to obtain grants for WGS.
Jong (Korea) pledged to support WGS of 50 genomes and Tim (KAUST) pledged support for 10 WGS. PS Lai is in communication with BGI and will update at INCOB 2012 Bangkok in October.
Maude will communicate with Dr. Ed Liu as HUGO president and senior advisor of PAPGI to provide a letter of support which PAPGI members can use in their applications for funding. A statement “… towards the implication of healthcare and medicine..” could be added in the PAPGI goal – for the ease of justification to the funders.
5.2 Ethical issues (Co- Chaired by EMC & MEP)
Important information : It is compulsory that members from each county / institution send copies of IRB approval document, example of information to participants and a signed consent form (one should be enough) to Maude and PS Lai for secretariat records and subsequent publication of papers. Any member who is not able to provide evidence of these documents, will not be included in final papers.
Tim briefed that all human research and data in Saudi Arabia falls under the authority of the Saudi Military for political reasons. He recommended that PAPGI invite a senior member of the SM to join. Tim will update during INCOB2012.
All PAPGI members will follow their own institutional/national regulations on all ELSI issues. Should some countries not have these in place, we recommend UNESCO and WHO guidelines on human genomics research to be followed.
e.g. Malaysia – regulations by Unis, MoH (where applicable) and Bioethics Council. Maude will inform Msian Bioethics Council should the need arise.
6.0 Choice of ethnic groups / populations:
All populations were identified by members present or thru communication:
Saudi Arabia – TR : Bedouin / Arabs
Kuwait – FAM : Kuwaitis
Philippines – EMC : Metro Manila & Philippine Negritos from Luzon, Visayas, Mindanao
Malaysia - VK : Borneo Dusun, Rungus, Orang Sungai
HBP : Mendriq, Bateq, Semai
MEP : Jehai, Kintak, Orang Seletar, MahMeri, Temuan
ZFA : 3 Malay groups, Kelantan, Minang, Central
Singapore – YYT : Cosmopolitan Malay, Chinese, Indian
China – SHZ : Northern Han, Southern Han, Dai, Mongolian, Uyghur, Kazakh, Tibetan, Hui
Korea - JB : Korean
Sri Lanka – V: Sinhalese
Members volunteered to contact the various ethnicities living in Msia :
Iraq– MA- : Iraqis (in M’sia)
Iran – FA : Iranians (in Msia)
Myanmar – KKTha (MUSC) : Myanmarese in Msia
Vietnam – YYT’s contact
Russia – UITM Russian lecturers
Funds to genotype these additional groups are still to be determined.
A new member, Halabi who attended with Mahmood Ameen suggested PAPGI SC chairs approach the Prince Al-Waleed Foundation for funds.
6.1 All other SCs / PIs that were absent namely :
- Ingrid (Aust), Herawati (Indo), Sissades (Thailand), Chen(Taiwan), Sumio (Japan), Vinod (India), etc are required to communicate to SC co- chairs Jong, PS Lai and Maude asap :
- identify and confirm ASAP ethnic groups they intend to investigate
- provide names and contact details of alternate SC members of their country to attend meetings or Teleconfs.
- state explicitly if they wish to be a host lab or be hosted
- state explicitly whether they will need WGS support.
PIs to identify respective geographic coordinates and language family, how homogenous are the samples in geography/location?
By Sep/Oct 2012, Jong is requested setup a registration (committed populations) in the PAPGI website.
Andrea Manica’s presentation on ‘Lessons learnt from other WGS projects’ was lucid, insightful and candid. His analyses of the weaknesses in those projects and subsequent publications was helpful and served to inform the design and approach of PAPGI
6.2 Aspects/Phases of PAPGI (Chaired By SHX)
Phase I* : Whole genome sequencing
Min 30X coverage
Strongly recommended: Illumina Hi-Seq
If members really cannot access the Illumina platforms, then others platform are allowed
Phase II* : SNP array genotyping
Strongly recommend : Illumina Omni 2.5
Affymetrix SNP6.0 are allowed
Special pricing for PAPGI to be confirmed by industry and platform providers. To prevent confusion and problems or official PAPGI reps to engage industry are :
Illumina: YYT, Affymetrix: SHX, BGI: PS Lai
Illumina: YYT, Affymetrix: SHX, BGI: PS Lai
* P1&2 may run concurrently dep. on ind member’s research activities and KPIs
Phase III : Targeted re-sequencing of regions of interest
e.g. MHC, pharmacogenomic importance, infectious disease associated, etc. Suggested samplesize 30-45 individuals
6.3 Computational analysis and data storage (Chaired by SHX & TR)
Raw data from Saudi Arabia has to be stored in the country only. Tim offers to access and perform data analysis in KAUST. Should be discussed in detail at INCOB.
Data analysis can be housed alternatively at: CAS, NUS, Korea
Question: Data analysis for primary paper – how to pool data for central analysis?
Suggestion: vcf files to be transported and released. To be sorted out during INCOB2012
IP: no engagement with commercial entities without prior approval from 70% of the steering committee attending the particular meeting
Centre repository: Raw data mirroring at multi-sites:
Suggestion: 1 centre, 4 mirrors.
BioIT working group will test the fastest site for storage (Jong and Sissades).
Bandwidth testing: to test by using 1000Genomes.
* Bandwidth testing output: too slow.
Suggest to share the sam @ bam files.
No data access application. Once users registered, there will be no restriction.
YY will write a draft of agreement on the data access. BioIT TF will take a look.
6.4 Publication Policy (chaired by YY Teo) :
Data unique to each country/ institution as part of ongoing investigations, can be published first if generated ahead,. When the data is submitted for combined analysis with other PAPGI members data, it will be PAPGI Consortium paper/s. There will be a ‘No Surprises’ rule.
There will be a timeline set, by that timeline, paper will be published. Core members of PAPGI will appear in all publications as co-authors. Subsequent papers can have additional members.
6.5. PAPGI Concept Paper
It was suggested by YYT and agreed by members that writing the PAPGI concept paper should be our first publication.Dateline of concept paper draft: 1st August preferably
The concept paper would generally have 3 major sections drafted. These are
1) Developing an Asian genomics network (YY, SHX, BP)
- Aims and goals of PAPGI
- How to address the aims and goals (Three phases of PAPGI)
- Capacity building
- Guest-host structure
2) Data issues and Bioinformatics (Jong, SHX, TR, AM)
- Data generation and access (members and non-members)
- Intellectual property
- Bioinformatics challenges in storage and sharing
3) ELSI and Sustained Community Engagement (LPS, EMC, MEP, ZFA)
Other PAPGI members can choose to participate in any of these sections.
6.6 Timeline of the study & Future meetings :
Gantt Chart as provided in Appendix A
Next PAPGI teleconf / meetings/discussions :
- YYT has undertaken to organize SC teleconfences at NUS for months in between meetings
- INCOB 2012 meeting, 4&5 Oct 2012, Bangkok. (Contact Sissades for details)
- 10th Asia Pac Congress of Hum Gen., Dec 2012, Kuala Lumpur (Contact Zilfalil Alwi for details)
Minutes taken by HBP, July 2012
Edited by MEP, Sep 2012