Summary: We present a program to improve haplotype reconstruction by incorporating information from paired-end reads, and demonstrate its utility on simulated data. We find that given a fixed coverage, longer reads (implying fewer of them) are preferable. Availability: The executable and user manual can be freely downloaded from ftp://ftp.sanger.ac.uk/pub/zn1/HI.

Although high-throughput genotyping arrays have made whole-genome association studies (WGAS) feasible, only a small proportion of SNPs in the human genome are actually surveyed in such studies. In addition, various SNP arrays assay different sets of SNPs, which leads to challenges in comparing results and merging data for meta-analyses. Genome-wide imputation of untyped markers allows us to address these issues in a direct fashion.

how to correct for the ascertainment bias caused by SNP finding protocols. In the preliminary phase of projects like Hapmap, HGDP, seattle, etc.. a set of snps is chosen to be genotyped, trying to select the snps which are more representative to the genome. Usually this is done by analyzing a smaller set of individuals or looking at existent databases (e.g. dbsnp). During this phase, errors may occur, caused by the smaller number of individuals analyzed. This paper explain how this ascertainment biasis can be reduced.

Open access guide to accessing HapMap data.

Recent studies of the HapMap lymphoblastoid cell lines have identified large numbers of quantitative trait loci for gene expression (eQTLs). Reanalyzing these data using a novel Bayesian hierarchical model, we were able to create a surprisingly high-resolution map of the typical locations of sites that affect mRNA levels in cis. Strikingly, we found a strong enrichment of eQTLs in the 250 bp just upstream of the transcription end site (TES), in addition to an enrichment around the transcription start site (TSS). Most eQTLs lie either within genes or close to genes; for example, we estimate that only 5% of eQTLs lie more than 20 kb upstream of the TSS. After controlling for position effects, SNPs in exons are ~2-fold more likely than SNPs in introns to be eQTLs. Our results suggest an important role for mRNA stability in determining steady-state mRNA levels, and highlight the potential of eQTL mapping as a high-resolution tool for studying the determinants of gene regulation.