10th APCHG in Kuala LumpurPAPGI Members Meeting
Notes/Minutes of PAPGI Members Meeting during 10th APCHG in Kuala Lumpur
Date: 7 December 2012
Time : 11 am
Venue : Crowne Plaza Hotel, KL
10th Asia Pacific Conference of Human Genetics
Mitali (India), Shuhua (China), Chen Chien-Hsiun (Taiwan), Poh San (Singapore), Vinod (India), Vijay Kumar (Sabah, Malaysia), Mohd Zahirul (Bangladesh), Saovaros Svasti (Thailand, representing Sissades), Chee Wei (VJ’s student, Sabah, Malaysia), Gregorio Alanis (Tim’s PhD student), Tim (Saudi Arabia), Maude (Malaysia), Ming Qi (BGI, China), Eva (Philippines), YY (Singapore), Anders Eriksson (Cambridge, to represent Andrea Manica), Ming Qi (China), Maude (Malaysia), Carmencita Padilla (Philippines), Endom Ismail (UKM, Malaysia), Zilfalil (Malaysia), Rakesh Naidu (Malaysia), Xiozhen Jenny Lin (observer)
Notes/Minutes of the Meeting
1. Poh San (PS) gave a brief introduction to all participants on the set-up and aims of PAPGI,
including the task force, Steering Committee and the relevant teams (Ethics, Analysis).
The Steering Committee member or alternate would be the representative or point of
contact for the research groups in each country. The names of the contacts were recapitulated:
India: Vinod /
China: Shuhua and Ming Qi
Malaysia: Maude and Boon Peng
Singapore: Poh San and YY
Saudi Arabia: Timothy
Sri Lanka: Vajira
Bangladesh: Dr Mohammad ZahirulHoque (firstname.lastname@example.org)
Taiwan: Chen Chien-Hsiun
2. IRB Issues
PS reminded everyone to pay particular attention to getting proper IRB approval and community engagement for their population samples to safeguard the overall scientific repute of the PAPGI consortium and to ensure compliance to internationally accepted ethical standards. She reported that no member has submitted a copy of their IRB documents as yet.
3. Discussion points
1) Maude and PS updated everyone about the concept paper, where Myles Axton has expressed in-principle interest from Nature in publishing the concept paper. Poh San will take the lead in communicating with the Editors from Nature. Currently, a number of members had already edited on a draft Concept paper which Jong, Vinod, YY, etc. had put together. Poh San reminded everyone that the population ethnic group descriptions were necessary for inclusion in the paper.
2) Maude updated everyone that she had already circulated a HUGO letter about PAPGI signed by Edison Liu, and this letter can be used by all participants to help obtain the necessary funding and ethics approval from their respective institutions.
3) Maude reminded everyone that data that is submitted for PAPGI will be made publicly available.
4) All members who already have IRB approval are requested to send a copy of the document along with a copy of the informed consent form to Maude and Poh San for records and filing with the PAPGI Ethics committee . Mitali asked what should the ethics cover? As we do not want to be too prescriptive taking into account the varying situations in different countries, PS mentioned the Policy & Ethics committee will draw up and circulate the minimum requirements for, consensus to all members of the Steering Committee will have to reply by 31 December 2012
a. PS to send out a draft of the minimum requirements for the IRB coverage by 14 December 2012 to the Steering Committee for discussion and finalization
b. All SC members to reply back to PS by 31 December 2012.
c. All PAPGI members will be informed on the final agreed requirements for the IRB coverage. They will need to reply on their IRB status – ie. approved, pending or in process of application – by mid-Jan 2013.
5) Countries with available and completed WGS data: Singapore (1 male and 1 female Malays and Indians, 2 Chinese males), China (Tibetan, Yao, Han, Dai, Mongolian, Ughur, Kazak, Tajik, Hui, Miao-to be confirmed), India (1 male from Northern (Indo-European), 1 female from Southern (Dravidian)), Taiwan (Min-Nan, Hakka – need re-consent for PAPGI sharing, 5 more pending from Taiwan aborigines), Malaysia (1 Kelantan male Malay), Thailand (2 cosmopolitan Thais, 1 male and 1 female), Sri Lanka (Sinhalese, 1 male)
6) Countries with available microarray data completed: Singapore (Chinese, Malays and Indians – 2.5M), China (Tibetan, Ughur, Kazak, Tajik, Hui – Affy6), India (from IGV – Illum1M, 20 from 5 groups), North Borneo/Sabah (32 ethnic groups, Sungei, Rungus - Omni 2.5M), Malaysia (4 Malay subgroups Kelantan Malays, Kedah, Minang, Champah, Senoi, Jehai-Negrito, Orang Seleta-Proto Malay, Mandrike-Negrito, Jakun-Proto Malay, Kintak-Negrito– 2.5M), Kuwait (56 samples – Affy6)
7) Countries that will need to perform more sequencing: Saudi Arabia (Arabs from 5 geographical regions 13 provinces but same language), Malaysia (1 Kelantan female Malay, Kedah, Minang, Champah, Orang Asli)
8) Countries who need support for sequencing but with samples: Thailand (4 groups across Thailand, from Sissades PCA work), Philippines (15 ethno-lingo groups identified by anthropologists but non-indigenousand around 36(?)Negrito groups-to be prioritized by Philippines SC rep, Tim’s lab will support 6 groups/12 people), North Borneo/Sabah (3 groups: Sungei, Rungus, Songsogon, Jong’s lab will support 6 samples), PenisulaMalaysia (Senoi, Jehai-Negrito, Orang Seletar-Proto Malay, Mandriq-Negrito, Jakun-Senoi, Kintak-Negrito, Jong’s and YY’s labs will support some sequencing here), Bangladesh (Chakmah, Dhaka Bangladesh: 4 samples, pending IRB clearance), Kuwait (Tim’s lab will support 2 samples), Sri Lanka (Sinhalese, 1 female)
9) Maude raised the point about including samples from a hosting country, such as Russians in Malaysia. The consensus is that PAPGI will not do this, but will only work via a PI from the respective country.
10) Maude and PS encouraged all PAPGI members to attend HGM/ICH 2013 conference in Singapore where a PAPGI oral presentation session followed by discussion meeting have been arranged. Poh San said that following majority consensus and preference, she had informed Shirlena from HUGO secretariat that the preferred date was 16 April (2 to 4 pm) as many people may not be available on the last day of 18 April from 1.30 to 3.30 pm. However, Falil highlighted the clash with the HVP session on 16 April. Members agreed to let Falil explore an alternative date from the programme within a week so that any changes can be conveyed immediately to Shirlena.
11) Maude mentioned that there will be a special registration rate for PAPGI members. PS also informed members that PAPGI members will have the opportunity to present their work during the PAPGI session and she will check with HUGO office about the abstract submission process when she is back in Singapore. Any PAPGI members who are interested should contact PS so that a formal list of speakers can be drawn up.
12) PS urged for Steering Committee members to respond to emails, so as to allow the concept paper to move forward, especially in terms of community engagement and IRB approval. This will be important for the Consortium to move forward. All PAPGI members were asked to actively contribute in either starting or completing their sequencing as soon as possible in order for the data to be relevant and timely for publication.
13) The Bioinformatics task force will try to look at all available WGS data to produce the first population genetics paper. (Jong to lead the Bioinformatics Committee)
14) Maude reminded everyone about the Publication Policy, that there is the No Surprise Rule for any use of consortium data.
15) Taiwan will do the genotype QC for microarray data. Every group will send all the genotype data to Taiwan. Chien-Hsiun will send a checklist to everyone with regards to the required files and information to be sent. After the QC is performed, Chien-Hsiun will send out the files to the five analysis sites below (see 16 below).
16) China CAS (Shuhua) will be the primary host of the WGS data upload (to be assisted by dedicated staff from BGI-Ming Qi to identify), and his lab will be in charge of the primary data QC and alignment. Subsequently the data will be transmitted to the following 5 sites:
d. Saudi Arabia
17) PS noted that PAPGI is an initiative officially under HUGO, and also co-supported by Asia-Pacific Society of Human Genetics with a number of PAPGI members being active in both organizations. She brought up a proposal from some members for PAPGI to have some form of collaboration or link with Human Variome Project (HVP). Mitali suggested that as most members will also have phenotype data, it will be useful to be involved in HVP. There is general consensus that it will be advantageous for PAPGI to be linked with HVP with regards to disease gene variants .
18) Maude reminded all that it is important that any communications with the media or third parties about PAPGI, espc with regards to population groups, sample collection or ethics issues should be raised to the Steering Committee, as any comments made by an individual will be representative of the whole consortium. As such, it will be good to follow the “No Surprises Rule” when it comes to media/external engagement.
19) PS raised the issue of teleconferencing meetings. It will be useful to have semi-regular updates via teleconferences, with at least one teleconferencing (tc) meeting for Steering Committee members before the HUGO meeting. Generally, the consortium can be kept updated via emails but it will be useful to have one call for updates of progress. Target to have one tc in mid/end January. PS also noted that YY had been hosting the cost of the t/c calls and expressed appreciation on behalf of the members. While it is acknowledged that it will be costly for some members to make local call connection to the t/c, it was felt that skype conferencing was not reliable when multiple calls were hosted. As an alternative, members who could not join the t/c can communicate simultaneously using emails.
Meeting ended at: 1.45pm
Prepared by: YY Teo
Vetted by: Maude Phipps and Poh San
Vetted by: Maude Phipps and Poh San
1) IRB minimal requirements - PS to send out by 14 December 2012 to the Steering Committee
2) PS will liaise with HUGO about registration and abstract submission for PAPGI members, and following-up on the special registration rate 3) PS will draw up and send out a form asking members to fill in information on the population samples , IRB and consent process, and community engagement activities for the Concept Paper
1) To send a checklist to the Steering Committee with regards to the files and information required for uploading the microarray data
1) To direct the Bioinformatics Committee on the pipeline to analyse the available WGS data.
1) To identify a point person to work with Shuhua on collating and QC of the available WGS data.
1) To send a copy of sample consent and IRB documents (requirements and masking of info, etc.)
1) PAPGI session - To identify another slot in the HUGO 2013 programme as an alternative to the proposed date of 16 April.