About Us

From Papgi.org

Jump to: navigation, search

 The Purpose of HUGO PAPGI

The primary mission of this HUGO PAPGI consortium is to collect and analyze Asian genomic data to understand the history of human migration, local adaptation, and genomic diversity associated with phenotypes and diseases in Pan-Asia area. Pan Asian data will be made and publically available to the worldwide scientific community for further studies on human evolution and medical applications.

 

Ed Liu 2008 nature news.jpg Nature news on PASNP with Edison Liu's interview: 2008. 

"Scientists in Asia have a tendency to look past each other and focus on collaborations with the United States or Europe, partly because these collaborations get them more credit from their school administrations. Also, in Asia, most countries see each other as competitors. Just getting people together is an accomplishment."

- Ed Liu


 

Contents

Introduction

On the 15th of March 2011, Pan Asia SNP consortium participants held a HUGO working summit session for the next stage, PASNP project (PASNP 2.0).
The main focus of proposal was to investigate the Asian genetic diversity and local adaptation using New Generation Sequencing technology which extends the success of the previous SNP project covering ~2,000 Asian samples from 71 ethnic groups, which was published in Science in Dec. 2009.
The initial project revealed the scale of Asian diversity and the single major migration route from Africa to East Asia. PASNP 2.0 was met with much enthusiasm and serious debate on how to drive forward the initiative that now involves hundreds of scientists with diverse cultural backgrounds.
The session speakers and participants from Asian, Arabic, Middle Eastern, and American countries agreed, in principle, upon establishing a coalition among H3Africa (the African genome project, headed by Charles Rotimi), Arabic genome project, and the Pan Asian genome project. If it is launched on a full scale, it will be the largest genome project ever to date.

Challenge

The challenge is how to synchronize heterogeneous data production and analyze using a working genome handling protocol.  
 
Collaborations among Asian scientists are just not as strong as those they share with scientists in the West. Why?
 

History

HUGO PAPGI (Population Genomics Initiative) is a version 2.0 of PASNP (Pan Asian Single Nucleotide Polymorphism). The previous PASNP consortium was benefited by strong bioinformatics researchers from China, India, Japan, Korea, Singapore, and Thailand. In addition, the combined strengths from Indonesia, Malaysia, Philippines, and Taiwan assured unprecedented access human biodiversity from many additional ethnicities which further enriched the project.
The second phase will receive assistance from Saudi Arabia. Tim Ravashi, a KAUST bioinformatist, expressed willingness to contribute both in data and number crunching. Fahd Al-Mulla, a molecular pathologist will be contributing data from Kuwait and United Arab Emirates as well as utilizing the Biodiscovery platform for analysis. As happened in PASNP 1.0, PASNP 2.0 will be an interesting test-bed on how far science can go in merging diverse data, people, and cultures.

Participating Organizations

PAPGI is an open project.

It welcomes any researcher to join the consortium.

To join the consortium, please contact Maude Phipps, maudephipps@yahoo.co.uk,  Jong Bhak, jongbhak@yahoo.comLai Poh Sanpoh_san_lai@nuhs.edu.sg, Vinod Scaria, or any member that you know. 

Technology

Whole-genome sequencing, whole-exome sequencing, targeted genomic capture sequencing, and high density SNP/CNV chips will be used.

Task Force

Task force is a group of people who contribute substantially to maintain and to manage the web sites, FTP sites, conferences, meetings, and data analysis.

Mailing List

PAPGI has a mailing list: papgi@biomaillist.com

Useful Web Sites

Publications

  • Ngamphiw C, Assawamakin A, Xu S, Shaw PJ, Yang JO, Ghang H, Bhak J, Liu E, Tongsima S and the HUGO Pan-Asian SNP Consortium. PanSNPdb: The Pan-Asian SNP Genotyping Database. PLoS One. 2011 June 23, 6(6): e21451.
  • Hatin WI, Nur-Shafawati AR, Zahri MK, Xu S, Jin L, Tan SG, Rizman-Idid M, Zilfalil BA; HUGO Pan-Asian SNP Consortium. Population genetic structure of peninsular Malaysia Malay sub-ethnic groups. PLoS One. 2011 Apr 5;6(4):e18312.
  • Xu S, Kangwanpong D, Seielstad M, Srikummool M, Kampuansai J, Jin L; HUGO Pan-Asian SNP Consortium. Genetic evidence supports linguistic affinity of Mlabri--a hunter-gatherer group in Thailand. BMC Genet. 2010 Mar 19;11:18.
  • HUGO Pan-Asian SNP Consortium, Abdulla MA, Ahmed I, Assawamakin A, Bhak J, Brahmachari SK, Calacal GC, Chaurasia A, Chen CH, Chen J, Chen YT, Chu J, Cutiongco-de la Paz EM, De Ungria MC, Delfin FC, Edo J, Fuchareon S, Ghang H, Gojobori T, Han J, Ho SF, Hoh BP, Huang W, Inoko H, Jha P, Jinam TA, Jin L, Jung J, Kangwanpong D, Kampuansai J, Kennedy GC, Khurana P, Kim HL, Kim K, Kim S, Kim WY, Kimm K, Kimura R, Koike T, Kulawonganunchai S, Kumar V, Lai PS, Lee JY, Lee S, Liu ET, Majumder PP, Mandapati KK, Marzuki S, Mitchell W, Mukerji M, Naritomi K, Ngamphiw C, Niikawa N, Nishida N, Oh B, Oh S, Ohashi J, Oka A, Ong R, Padilla CD, Palittapongarnpim P, Perdigon HB, Phipps ME, Png E, Sakaki Y, Salvador JM, Sandraling Y, Scaria V, Seielstad M, Sidek MR, Sinha A, Srikummool M, Sudoyo H, Sugano S, Suryadi H, Suzuki Y, Tabbada KA, Tan A, Tokunaga K, Tongsima S, Villamor LP, Wang E, Wang Y, Wang H, Wu JY, Xiao H, Xu S, Yang JO, Shugart YY, Yoo HS, Yuan W, Zhao G, Zilfalil BA; Indian Genome Variation Consortium. Mapping Human Genetic Diversity in Asia. Science 326, 1541 (2009).
Personal tools