Genome Technology Center

Haplotype and linkage block structure in human genome

Peidong Shen
Dennis Wall
Marc Feldman
Peter Oefner (PI)

This project extends the previous project of DNA sequence variation in human genome. More than 30 human genes were screened in 94 global individuals for more than 100kb sequences and nearly 1000 SNPs were discovered in both coding and non coding regions of genome from previous study. SNPs with minor allele frequency of 0.15 or greater are constructed into haplotypes and used for linkage analysis in current study. In order to increase resolution of the SNPs map to construct the haplotype block we are including available SNPs in the public domain. For each highly conserved linkage block region, a phylogenetic network can be obtained, and then the phylogeny of different genes can be compared.

We will explore a possible connection between the phylogenetic patterns and the evidence for selective forces operating on a gene. For better understanding the evaluation of various important human disease genes, we are also sequencing 24 chimpanzee and macaque chromosomes to compare their linkage patterns with that of human’s. Completed denaturing HPLC is used for SNP genotyping which offers the cheapest genotyping tool so far. Nielson’s and Yang’s likelihood ratio test is used to detect selection forces along the human and primates lineage.


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