Study plan - MartenKlaesson/Research_training GitHub Wiki

Title:

Genome-wide scan on signs of Selection among ethnic groups of Philippines

Brief Background:

The population structure of Islands Southeast Asia is predominantly defined by two-layered ancestry of Australasian and East Asian-related genetic clusters. The former is best characterized by Philippine Negrito hunter-gatherers and the latter by Cordilleran highland agriculturalists. More than 90% of Philippine ethnic groups exhibit an ancestry profile that is an admixture, in varying degree, between Negritos and Cordillerans. It is these admixed populations that offer us a unique opportunity to investigate signs of selection. Using recent bioinformatic tools, we can examine the distribution of Cordilleran-related vs Negrito- related ancestries among admixed populations, and test the hypothesis whether genetic adaptation in some groups have occurred. If there is no selection, it is expected that the ancestry associated with each parental group of an admixed population to be randomly distributed evenly across the genome; while a significant departure from this expected distribution present as a potential signal for selection. 

Aim:

To identify signs of selection in Philippine ethnic groups.

Methods:

General population genetic analysis: Processing of genotyped data with PLINK v1.9; Principal component analysis and calculation of between population FST using EIGENSOFT v7.1; Clustering analysis to analyze population structure with ADMIXTURE v1.3, CLUMMP, and Pong v1.4; Outgroup f3 statistics and formal tests of admixture with qp3Pop and qpDstat of AdmixTools v5.0 package; Inferring local ancestries in populations with RFMix. Selection scans: Detection of local deviations in FST; LD-based methods such as extended haplotype homozygosity (EHH) metric and integrated haplotype score (iHS) test.

Schedule:

Week 1 – Literature Review, Introduction to Human Population Genetics Week 2 – General Population Genetic Analysis Week 3-5 – Selection Analysis, Selection Analysis Part 1 Week 6-8 – Midterm Review, Selection Analysis Part 2 Week 9 – Finalizing Analysis, Draft for Written Report Week 10 – Examination, Oral presentation, Submission of Final Report