HapScope: A Software System for Automated and Visual Analysis of Functionally Annotated Haplotypes

Jinghui Zhang, William L. Rowe, Jeffery P. Struewing, Kenneth H. Buetow
Laboratory of Population Genetics
National Cancer Institute/National Institutes of Health
8424 Helgerman Court, Room 101, MSC 8302
Bethesda, Maryland 20892-8302
U. S. A

Downloads
You can download the HapScope files from the following FTP site:

ftp://ftp1.nci.nih.gov/pub/HapScope/.

Abstract
We have developed a software analysis package, HapScope, which includes a comprehensive analysis pipeline and a sophisticated visualization tool for analyzing functionally annotated haplotypes. The HapScope analysis pipeline supports: a) computational haplotype construction with an EM or Bayesian statistical algorithm; b) SNP classification by protein coding change, homology to model organisms or putative regulatory regions; c) minimum SNP subset selection by either a Brute Force Algorithm or a Greedy Partition Algorithm. The HapScope viewer displays genomic structure with haplotype information in an integrated environment, providing eight alternative views for assessing genetic and functional correlation. It has a user-friendly interface for: a) haplotype block visualization; b) SNP subset selection; c) haplotype consolidation with subset SNP markers; d) incorporation of both experimentally determined haplotypes and computational results; e) data export for additional analysis. Comparison of haplotypes constructed by the statistical algorithms with those determined experimentally shows variation in haplotype prediction accuracies in genomic regions with different levels of nucleotide diversity. We have applied HapScope in analyzing haplotypes for candidate genes and genomic regions with extensive SNP and genotype data. We envision that the systematic approach of integrating functional genomic analysis with population haplotypes, supported by HapScope, will greatly facilitate current genetic disease research.