The Long-Range Haplotype (LRH), integrated Haplotype Score (iHS) and Cross Population EHH (XP-EHH) tests detect alleles that have risen to high frequency rapidly enough that long-range association with nearby polymorphisms—the long-range haplotype—has not been eroded by recombination; haplotype length is measured by the EHH8 (link),9 (link). The first two tests detect partial selective sweeps, whereas XP-EHH detects selected alleles that have risen to near fixation in one but not all populations. To evaluate the tests, we simulated genomic data for each HapMap population in a range of demographic scenarios—under neutral evolution and twenty scenarios of positive selection—developing the program Sweep (www.broad.mit.edu/mpg/sweep ) for analysis. For our top candidates by the three tests, we tested for haplotype-specific recombination rates and copy-number polymorphisms, possible confounders.
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Evaluating Rapid Allele Selection Tests
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Other organizations : Broad Institute, Harvard University, IIT@MIT
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Variable analysis
independent variables
- Positive selection scenarios
- EHH (Extended Haplotype Homozygosity) test results
- LRH (Long-Range Haplotype) test results
- IHS (integrated Haplotype Score) test results
- XP-EHH (Cross Population EHH) test results
- Haplotype-specific recombination rates
- Copy-number polymorphisms
- Neutral evolution scenario
- Positive control: Positive selection scenarios
- Negative control: Neutral evolution scenario
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