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Proposal PAPGI as PASNP 2.0 P an A sia P ersonal G enomics I nitiative

Proposal PAPGI as PASNP 2.0 P an A sia P ersonal G enomics I nitiative. PASNPi consortium Presented by Jong Bhak on behalf of the consortium March 2011. Dubai UAE Theragen BiO Institute TheragenEtex & Personal Genomics Institute, Genome Research Foundation. B i o Acknowledgement.

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Proposal PAPGI as PASNP 2.0 P an A sia P ersonal G enomics I nitiative

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  1. ProposalPAPGI as PASNP 2.0Pan Asia Personal Genomics Initiative PASNPi consortium Presented by Jong Bhak on behalf of the consortium March 2011. Dubai UAE TheragenBiO Institute TheragenEtex& Personal Genomics Institute, Genome Research Foundation

  2. BioAcknowledgement Scientists who shaped the world as we know by being factual, rational, honest, and free-thinking. Tax payers who support researchers Jong’sformer and present colleagues in MRC, Harvard Med., EBI, KAIST, KOBIC, TBI, & PGI from whom I learned so much. TheragenEtex for generous financial support All the PASNP consortium members:

  3. PASNP 1.0: • Genetic diversity in Pan Asia • A model project for Asian Genomics • PASNP consortium • http://pasnpi.org • Science Dec. 12th, 2009 6 billion people

  4. PASNP 1.0 project (2004 – 2009) • An international consortium project for Pan Asia led by Ed Liu of HUGO and GIS. • Researches with Asian populations : • 1. Population diversity mapping (Phylogenic study) • 2. Functional annotation study • 3. CNV study • 4. Migration mapping • Results • 1. SNP data repository and basic information services via web for Pan Asians • http://pasnpi.org

  5. Genotyped 126 ethnic groups over 10 countries

  6. 1. Sample number: ~20002. Ethnic group: 713. Country: 104. SNP marker number: 58,960 (Affymetrix 56K Xba SNP genotyping chip) Sampling from Pan Asia 10 countries

  7. Genotyped 71 ethnic groups over 10 countries

  8. 6 large ethnic groups Maximum likelihood tree of 29 populations. The tree is based on data from 19,934 SNPs. Bootstrap values based on 100 replicates

  9. Phylogentic and population structure analysis results Finding 1: Genetic ancestry is strongly correlated with linguistic affiliations as well as geography Finding 2: Most populations show relatedness within ethnic/linguistic groups despite prevalent gene flow amongst populations Phylogenic tree: Maximum Likelihood tree Population stratification : STRUCTURE

  10. Peopling of Asia: one-wave VS. two-wave hypothesis • Two-wave hypothesisCavalli-Sforza et al (Nat Genet, 2003) suggested a hypothesis of peopling of Asia that anatomically modern humans (also called Homo sapiens sapiens) spread into Asia through two routes. • One-wave hypothesis • All modern East Asian and Southeast Asian populations was derived from a single initial entry of modern humans into the subcontinent. • Which model can be a better explanation for our observation? Our current observation is expressed in right figures.

  11. Results and Conclusion: Forward time simulation Peopling of Asia: one-wave versus two-wave hypothesis Negrito: The Semang people of the Malay Peninsula Thailand people

  12. Finding 3: Haplotypediversity was strongly correlated with latitude with diversity decreasing from South to North Haplotype diversity versus latitudes • Haplotype diversity was strongly correlated with latitude (R2 = 0.91, P < 0.0001), with diversity decreasing from South to North. • This is consistent with a loss of diversity as the populations moved to higher latitudes. ① Indonesian; ② Malay; ③ Philippine; ④ Thai; ⑤ South Chinese minorities; ⑥ Southern Han Chinese; ⑦ Japanese & Korean; ⑧ Northern Han Chinese; ⑨ Northern Chinese Minorities; ⑩ Yakut.

  13. Finding 4: Southeast Asian has the most of the Asian gene pools Group private haplotype sharing analysis (Frequency was not considered (type only)) • HSa :CSA private • HSb : EA private • HSc : sharing by all groups • HSd: SE private * YKT: Yakut; N-CM: Northern Chinese minorities; N-HAN: Northern Han Chinese; JP-KR: Japanese and Korean; S-HAN: Southern Han Chinese; S-CM: Southern Chinese minorities; EA: East Asian

  14. PASNP 1.0 was done by SNP chips. The main result was anthropological:  human migration

  15. Sequencing gets cheap

  16. Ome and Omics Graph $3,000,000,000 $10,000 per person To analyze Cost $ 0 2016 2003 Year Ome and Omics Balance point 2010 - 2011 Jong Bhak, under BioLicense (public domain)

  17. The Genomics T-Backbone7 billion x 7 billion 6 billion people 50,000 Bases for PASNP Jong Bhak, under BioLicense (public domain)

  18. Genomics Y axis: becomes personal

  19. Ethnic diversity in genomes is significant Not represented in dbSNP

  20. Future: Personalized Medicine • A big hype  Many problems. • Political, • Administrative • Medical/healthcare • Social / ethical • Still, that is the way • Mapping Personal Genomes of Pan Asia • Foundation for personalized medicine in Asia

  21. Sequencing as big biology tool Envirome 1,000,000 epigenetic variation 1,000,000 microbes 7billion persons 1,000,000 Phenotypes 1,000,000 RNA expression 7billion Bases

  22. PASNP 2 proposal: Sequencing PGP(personal genome project) 1. Well established protocol 2. good philosophy 3. international support * Apply PGP experience to PAPGI

  23. Target: minimum 500 samples • from all the major Asian ethnic groups • (Yin: How many groups, 10?) • openfree data project (PGP style) • Consortium project. • Full genome data and analyses. • Members pay for their own sequencing • Biomedical Data analysis by the consortium • Minimum two sample per ethnic group • Uses already available genomes (1000 genomes, PGP, and other genome projects)

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