PAPGI Project Timeline

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Item Activity Timeframe Member/s Responsible Notes
1 Identification and Commitment of populations By 1 Aug 2102 TimR Saudi Arabia-Bedouin  - Gps from 13 regions ?
  *Confirmation of ethic gps proposed by those present at meeting   EvaM Philippines -  Luzon, Visayas, Mindanao - Negritos &  Non Negritos (6 gps)
      VJ Malaysia - Dusun, Rungus, Org Sungai (Borneo) - 3 gps
  Additional pops/ethnic gps fr other PAPGI members. Pls confirm   HBP  Mendriq,Jehai, Kintak, Bateq (Negrito) - 4 gps
  Jong - Korean   MEP Mah Meri, Semai (Senoi) - 2 gps
  Sumio - Japanese ( how many gps?)   MEP Org Seletar, Temuan (Proto Malay)- 2 gps
  Chen - Taiwanese (how many gps?))   ZFA Kelantan Malays, Minang Malays, Java Malays -3 gps
  Fahd - Lebanese, Kuwaiti,Bahrain, Emirati, Qatar   Samir Dixit Nepal - Nepalese - 1 gp
  Vajira - Sinhalese   YY Singapore - Cosmopolitan Malays, Indians, Chinese - 3 gps
  Sissades - Thai, how many gps ?   SHX China - N'thern Han, S'thern Han, Dai, Mongolian, Uyghur, Kazakh, Tibetian - 7 gps
  Vinod - Indian, how many groups ?     Others to be confirmed thru papgi mailing list
        How homogenous is a sample/ethnicity in geography/location ?  same village? Etc
        Geographical Coordinates
         
        Additional Interesting populations / new contacts
        India Vietnam, Cambodia, Laos - YY will contact Binay, others
        Myanmar - Vijay, Maude to contact Kyi Kyi Tha, Zilfalil, HBP thru Myanmarese staff in Msian Unis
        Russia, Pakistan - SH to contact
        Autralia, New Zealand - To reconnect with Ingrid Winship
      Mahmood Ameen Kurdistan - Mahmood Ameen to contact Kurdish in Msia  - 1 gp
      Farhang Aghakanian Iran - Farhang to contact Iranians (Persian eth) in Msia - 1 gp
         
2 Sample Collection 10-Jan-13 All PI Min : 10 inds/ethnicity,
        Recommended :  20 ind/ethnicity
        Best : 40 ind
         
         
3 Phase 1 WGS     Min 1 male & 1 female /ethnicity, unrelated ind, 4 grandparents of same ethicity
  Guest - host partnership 30-Jun-13 All PI JBhas offered to do 50 & TR 10 samples f.o.c. WGS 
  ILLUMINA Hi Seq (strongly recommended) 1st wave samples/data   Offers taken up by Eva, Maude, VJ, BP,MA,  others to be determined
  Other platforms (allowed)     LPS in talks with BGI  - result tba later
         
4 Phase 2 GWAS 30-Jun-13 All PI Special Pricing by Illumina for PAPGI - contact YY
  Guest - host partnership     Special Pricing by Affymetrix for PAPGI - contact SHX
  Illumina OMNI 2.5M (strongly recommended)      
  Affy 6.0 (recommended alternative)      
  Other platforms (allowed)      
         
5 BioIT pipeline 1st Oct 2012 BioIT working group  
         
6 data analysis      
  a) primary data analysis - NGS 1st Sept 2013 BioIT working group  
  b) population genetics analysis  end of 2013    
         
7 publications      
  a) concept paper last week of Sept 2012 Co-chairs of the SCs, 1st draft completed before meeting INCOB2012
       YY, Shua Hua, ZFA, Tim  
      Andrea  
  b) 1st main consortium paper Mac 2014 BioIT working group, PIs established writing group: Shuahua, YY, Tim, Jong, Andrea, Vinod, Sissades
  c) many other papers      
         
         
8 Research capacity building in developing countries   Mooted by Eva, YY  
  Suggestions: 1) short term (~ 3-5 day) training courses for bioIT Analysts/members after Mac 2013   The Philippines as the 1st site for the capacity building. Eva will feedback reg
  2) ELSI education & Community engagement by PRB members     suitable time in 2012 wshop
         
9 Data repository       
  a) bandwidth testing 31st July 2012 Tim, YY, Shuhua, Jong, Sissades 4 Data repository labs labs , Jong/Korea, Tim/ KAUST, YY/NUS and Xu/CAS 
        will send HGDP data to test sites : Eva/UPhil, BP/UiTm and VJ/UMS Msia.
      Eva, VJ, BP  
  b) database website 30th Oct 2013 Shuhua, Jong, Sissades, Tim Feedback will be given reg timeliness of data transfer & other details
        Option to use CD and FedEx courier for data transfer if online is unsatisfactory
         
         
  * meetings      
  a) INCOB2012 - Bangkok; 3rd-5th Oct 2012      
  b) APCHG 2012 - KL; 5th-8th  Dec 2012      
  c) monthly teleconference updates: Aug, Sept & Nov 2012   YY will provide details
         
  Teleconf 1200, July 2012 - New member fromIndia Binay, others and updated on populations  
         
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