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eBook details

• Title: On the Challenges of the Hapmap Resource (Views & Challenges)
• Author : Bioinformation
• Release Date : January 01, 2008
• Genre: Medical,Books,Professional & Technical,
• Pages : * pages
• Size : 57 KB

Description

Background: The goal of the International HapMap Project [1] is to develop a haplotype map of the human genome, the HapMap, to describe the common patterns of human DNA sequence variation. Four populations were selected for inclusion in the HapMap: 30 trios from Ibadan, Nigeria (YRI), 30 trios of U.S. residents of northern and western European ancestry (CEU), 45 unrelated individuals from Tokyo, Japan (JPT) and 45 unrelated Han Chinese individuals from Beijing, China (CHB). Epstein Barr virus (EBV)-transformed lymphoblastoid cell lines (LCLs) were derived from these individuals. The HapMap resource is comprised of genotypic data on ~4 million single nucleotide polymorphisms (SNPs), gene expression data using various microarray platforms, other phenotypic data such as drug response as well as structural variation data (copy number changes) [2]. In addition, there is data available regarding cellular sensitivity to various chemotherapeutic agents at PharmGKB [3]. Thus, investigators can utilize extensive genotype, gene expression and other phenotypic data on the 270 HapMap samples to perform various genome-wide scans for studies that do not require a priori knowledge or experimentation to generate new hypothesis. Because the HapMap samples provide samples from major world populations, investigations into inter-ethnic variation in genotype, gene expression and phenotype are possible. Recently, using the HapMap resource, some exciting progress has been made in the areas of gene expression variation studies and pharmacogenomics [2]. Albeit the successes, there are some limitations of the HapMap resource [2]. For example, LCLs represent just one human tissue type and gene expression levels vary considerably among tissues. For pharmacologic studies, LCLs may not reflect tumor response or sensitivity of target tissue of known toxicity. Also, studies have suggested that EBV transformation may affect the expression of some genes and certain biological processes in LCLs [4, 5]. Therefore, interpretation of results using these cell lines may be biased by this effect. In this paper, we will not delve into these "intrinsic" limitations of the HapMap resource. Instead, we will discuss some of the technical challenges when utilizing the HapMap resource.

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