PAPGI minutes by Cora and Maude 2011 5-7 Oct

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2ND PAPGI MEETING, BIOPOLIS, SINGAPORE, 6 OCTOBER 2011
 
Hosted by FAOBMB Conference Singapore (Poh-San Lai)
 
 
List of Attendees(Surname alphabetical order):

1
Jong
Bhak
jongbhak@genomics.org
2
Zilfalil
Bin Alwi
zilfalil@kb.usm.my
3
Eva Maria
Cutiongco-de la Paz
ecutiongcodelapaz@upm.edu.ph
4
Maria Corazon
De Ungria
mariadeungria@gmail.com
5
Vajira
Dissawayake
vajirahwd@hotmail.com
6
Takashi
Gojobori
tgojobor@genes@genes.nig.ac.jp
7
Boon Peng
Hoh
hohpeng@yahoo.com
8
Huanming
Yang
yanghm@genomics,org,cn
9
Poh San
Lai
paelaips@nus,ed,sg
10
Min
Lee
mlee@diagnomics.com
11
JJ
Liu
liuj3@gis.a-star.edu.sg
12
Carmencita
Padilla
cdpadilla@upm.edu.ph
13
Maude
Phipps
maudephipps@monash.edu
14
Ming
Qi
ming_qi@urmc.rochester.edu
15
Vinod
Scaria
vinods@igib,in
16
Shirlena
Soh
sohwl@gis.a-star.edu.sg
17
YY
Teo
statyy@nus.edu.sg
18
Sissades
Tongsima
sissades@gmail.com
19
Shuhua
Xu
xushua@gmail.com
20
Eric
Yap
earthsalt@gmail.com

 
Via skype connection (with intermittent interruptions) :
 
Fahd Al-Mulla  (Kuwait), Chien-Hsiun Chen (Taiwan), Daoroong Kangwanpong (Thailand); Timothy Ravasi (Saudi Arabia); Guoping Zhao (China)
 
 
2nd Draft of MINUTES OF MEETING
 
I. Meeting Proper (PAPGI members only)
 
1) The meeting started at 3:40pm.
Dr Lai Poh San conveyed Dr Ed Liu’s apologies for not being present and welcomed Dr Shirlena Soh who was sent by Ed to sit in on behalf of HUGO. All past members from PANSNPI (Pan-Asian SNP Initiative) and new members who have expressed interest in this consortium for Pan-Asian Population Genomics Initiative (PAPGI) have been invited to this meeting either in person or through online video-conferencing. Trade representatives will be invited at the end of the meeting to share on their technologies as resources available to members. Poh San also shared that Dr Yang Huanming and some members of BGI were also present at this meeting.
As a point of reference, it was noted that members physically present at this meeting had shared an update on work in their respective populations earlier in the afternoon during the FAOBMB conference on Asian Genomes (http://www.burnaby-solutions.com/faobmb2011/?page_id=565).
 
Dr Jong Bhak reminded everyone that this meeting is a continuation of an earlier meeting hosted during HGM 2011 in Dubai wherein the members had agreed to include other groups such as Africa and the Middle East in the PAPGI the consortium.
A list of topics was shown on the screen to guide the discussion for this meeting. Topics included the following:
■ Action protocol
■ Sampling from populations, sample preparation
■ Data deposition
■ Resolution
■ Budget: commercial sponsors and research grants
■Technology: Choice of Platform
■ Policy: Research Procedures incl Task Force and Ethics
■ Data Release
■ Analysis
 
2) The meeting started with the discussion on sample size needed per population/group.
Dr Vinod Scaria put forward the issue that we have not formulated the scientific questions that we want answered.
Dr Takashi Gojobori also asked that the objectives of the project be better defined. He mentioned problems encountered by scientists in the Human Genome Project HGP) wherein activists misunderstood the project’s objectives and believed that it was promoting racism. He further emphasized the importance of clarity in defining the goals of PAPGI in order to explain these more accurately to the general community.
Dr Jong addressed both questions posed by Dr Vinod and Dr Takashi by re-stating the overall objectives of PAPGI which are: to collect and to analyze Asian genomic data, to understand the history of migration, local adaptation, and genetic diversity associated with phenotypes and diseases, as the scientific topics were originally proposed by many members including Dr. Shuhua Xu before the meeting and during the construction of the PAPGI webpage.
Dr YY Teo suggested that we follow the HapMap Project which used an arbitrary sample size of 45 persons per group.
Dr Shuhua Xu volunteered his proposed strategy that he had shown in his presentation during the Asian Genome Session of the FAOBMB Conference.
 
 3) Discussion on the different sections of the strategy ensued:
■ Stage 1: Whole Genome Sequencing: New population and small sample size. This stage involves a preliminary screen of the population to obtain an overview of the genetic diversity characteristic of a population in relation to other populations.
 
■ Stage 2: Whole Genome Genotyping: Many populations and moderate sample size
 
■ Stage 3: Targeted Capture Sequencing: All populations and a large sample size
 
Dr Cora De Ungria requested clarification on the actual number which fit in the description ‘small sample size’. Dr. Shuhua responded by saying that the smallest sample size in any given population is 1 individualfor whole-genome sequencing and 10 would be ideal in theory to capture the alleles with frequency of 5%. Jong suggested to include three persons per group which means that for 71 groups which currently comprised member groups of PAPGI, there would be raw data for at least 210 persons. 
 
Dr YY then asked the different members about the number of personal genomes that are already available in their respective populations and how many more are expected for completion within 2011 early part of 2012. Rough estimate of generating the sequence of one person is US$3500. The response of the different members is listed below:
■ Korea: Dr Jong said that data for 70 Koreans are available. No more is needed.            
 
■ India: Dr Vinod Scaria that raw data for 30 Indian people from major large populations will be available in late 2012.
 
■ Sri Lanka: Dr Vajira Dissawayake said that one person genome is available. By the end of the year,   a better estimate of their funds and their plans will be made available.
 
■ Malaysia: Dr Boon Peng will look into sequencing of a few individuals.
Dr Falil said there would be two Malaysian genomes by the end of 2011.
Dr . Maude Phipps proposed to sequence a Negrito Trio and male and female (if trio is not available) from the Proto-Malays and the Senoi at end 2011/2012
 
■ Philippines: Dr Carmencita Padilla committed the sequence of a paternity trio next year.
 
■ Singapore: Dr YY said there are 100 Singaporean-Malay genomes which are already available. Thirty-eight (38) Singaporean-Indian genomes will be available by the end of the year. Two Singaporean-Chinese genomes are also being worked on.
Dr Eric Wang committed 1 trio of Han Chinese.
Dr Lai Poh San said that she has one complete genome generated using whole genome and exome sequencing technologies.
 
■ Thailand: Dr Sissades committed the sequencing of one contemporary Thai. Because of some concerns about using ethnic samples in Thailand, Dr Sissades said that he will propose the sequencing of one contemporary Thai to his colleagues in Thailand. It was unfortunate that at this time, Dr Daoorong, one of the first pioneering members in PanAsia SNP Consortium, the progenitor of PAPGI, was already disconnected from skype and the rest of the team.
 
■ Dr Huanming Yang of Beijing Genome Institute suggested that China, Japan, India and Korea should support struggling member nations for the sake of the project.
 
4) Funds
a) Participants wanted to contribute to the initiative but could not assure the group of its completion as this was subject to finding financing for the initiative.
 
b) Discussion of funding and support.
Dr Carmencita stated that the Asia Pacific Society of Human Genetics has supported the initiatives of PanAsia SNP in the past through its members. Dr Poh San identified HUGO, which was led by Dr Edison Liu, as another organization that had supported this initiative.
 
The following member and host- institutions have committed to working together to generate the required sequences:
            

Member country
Contact Person in Member Country
Project Leader
Preferred Host Institution for Platform Technology/ Informatics
Contact Person in Member Country
Thailand
Dr Sissades
 
Korea
Jong Bhak
Sri Lanka
Dr Vajira
 
India
Dr Vinod
UAE, Kuwait
Dr Fahd
 
Malaysia
 
Qatar
Dr Fahd
 
 CAS-MPG PICB, China
 Dr. Shuhua Xu
Other countries?
Saudi Arabia
 
Dr Tim Ravasi
 
BGI, China
Dr Huanming Yang

 
 
5) Ethics
a) Because of the increasing interest in generating Asian personal genomes, Dr Poh San reminded all member-nations of the need to obtain their own approval from their respective institutional ethics review boards.
Poh San reiterated the need to have the proper and comprehensive ethics approval from the very start.
Dr Eva in fact, reminded others that members might need a new ethical review because of the modification of procedures and scope of PAPGI compared to PanAsia 1 if previous DNA samples are used.
Dr Takashi agreed with Dr Eva and stated that ethics approvals are given for a specific objective.
Similar to the guidelines issued by the Policy Review Board of PanAsia SNP1, each member /institution is solely responsible for his/her approval.
 
b) More importantly, members/nations that will be conducting their lab work, in their host institution/s, were reminded that in principle, the samples do not leave the country of origin or be shipped out. This is to preserve the sovereign rights of the country and volunteers whose samples are utilized.
However, if platform technology cannot be accessed within a member’s country then samples can be physically taken by members or their RAs/Students from their original countries and worked upon in a ‘Host Lab’ that is ‘overseas’, within the consortium.
 
6) Platform technology
Dr Eva went on to ask if the PAPGI is prescribing a defined platform for all member institutes. Dr Jong said that it was agreed upon in an earlier meeting to not exclude any platform since some members have Illumina whereas others have the Solid, and Roche 454. What is more important is to formulate the SOPs for design and quality control for which all members will have to follow in submitting their sequences to PAPGI. 
 
 
II PAPGI engagement with Industry Reps
 
7) Further Discussion
At this stage of discussing finances and budgets, representatives of 5 commercial companies were asked to join the meeting in order for them to provide information about their products which may be useful for PAPGI as well as their ‘sales pitch’ as to how they can provide better financing/support for a larger-scale multi-center initiative.
Each company rep presented in turn.
 
■ Affymetrix that introduced their Human Origin Array which was specifically designed for determining human origins and ancient migrations
 
■ Illumina that highlighted the availability of solutions for every stage of the proposed strategy, e.g. from small scale screens to larger scale initiatives
 
■ Roche that talked about its 454 machine which can generate a sequence up to 1000 bp and is designed for generating genome sequences
 
■ Agilent Technologies that talked about target enrichment solutions which may be customized 
 
■ Life Technologies that highlighted its new Ion Torrent which is the cheapest way to sequence
 
A vote of thanks was given to the reps and PAPGI members acknowledged that they would ‘consider’ these options and choose the one/s best suited to their work and institution.
 
The meeting ended at about 5:30pm. Dr Cora had taken Minutes of the Meeting which would be circulated to all present and Jong will post the final Minutes on the PAPGI mailing list and website.
 
 
Minutes prepared by:
Dr. Cora De Ungria- Philippines (Oct 2011)
Edited by :
Dr. Maude E Phipps, Malaysia (16 Feb 2012)
Dr Lai Poh San, Singapore (20 Feb 2012)
Dr. Shuhua Xu, China (20 Feb 2012)
Posted to the web by:
Dr Jong Bhak, Korea (20 Feb 2012)
 
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