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Population genomics of human gene expression

Population genomics of human gene expression. Anders Långberg Carolina Håkanson BIMM53. A study of how different population varies in their gene expression Epstein Barr transformed lymphoblastoid cell lines 4’000’000 SNP’s from 270 individuals from 4 HapMap populations. The aim:.

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Population genomics of human gene expression

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  1. Population genomics of human gene expression Anders Långberg Carolina Håkanson BIMM53

  2. A study of how different population varies in their gene expression • Epstein Barr transformed lymphoblastoid cell lines • 4’000’000 SNP’s from 270 individuals from 4 HapMap populations

  3. The aim: • Insight into variabel gene expression • Cis- and trans acting regulatory elements • Shared functional genetic effects between populations

  4. Abbreveations • CEU – Caucasian European • CHB – Chinese Beijing University • JPT – Japanease from Tokyo • YRI – Yoruba from Ibadan, Nigeria • Pooling of cell lines in different combinations

  5. Methods • Pooling of cell lines • Normalization • Quantile across the four replicates • Median Normalization • To prove the relevance of the following experiments they proformed a heritability estimation for expression phenotypes • After a comparison of the populations gene expression, genes that differ more than 16% were chosen • To verify these results they performed a second array, not related to the first – high correlation was shown

  6. Linear regression model • A way to look at correlation between two sample series • Each series plotted on each axis.

  7. Spearman Rank Correlation • Another way to look at correlation between series • Special case of Pearson

  8. Methods Cis-Assocation between SNP variation and expression variation • SNP’s (HapMap PII) 1Mbp upstream and downstream from probe midpoint • gene expression and SNP’s were regression analysed • Determining the significance of the regression p-value 10’000 permutations were preformed of the data independetly for each gene • Analysed in depth those associations significant at the 0.001 permutation threshold • Single populations as well as pooled population (CEU-CHB-JPT) (CHB-JPT) (CEU-CHB-JPT-YRI)

  9. Significant associated SNP’s to genes show a trend to be positioned close to TSS. • A significant amount of SNP’s found in promoter and coding sequence regions of genes.

  10. Same study as preformed for cis reulated was preformed on trans acting elements • Results not to conclusive? – due to unspecificity of trans-acting elemnts

  11. CEU more divergent –due to old age????

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