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. 2015 Apr 15;23(12):1739–1743. doi: 10.1038/ejhg.2015.64

Figure 1.

Figure 1

Coding of regional markers using the Collapsed Haplotype Pattern (CHP) method. Three two-generational autosomal recessive pedigrees display the coding for a regional marker using information from six variant sites. Panel a shows two families segregating the same autosomal recessive disease, which is due to different causal variants. Treating the entire region as a bin to collapse the variants effectively captures transmission of disease variants and allows for linkage information for a region to be summed across families. For regions with more diverse rare variant architecture as displayed in panel b, where for this example disease etiology is caused by compound heterozygotes variants, coding which represents both rare variant haplotypes is used to ensure that all meioses are informative. It should be noted that if coding as is shown in panel a is used in this situation there will be a loss of information because all heterozygous offspring will be uninformative for linkage information, for example, the meioses to offspring II:1 and II:4.

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