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Chunk #12 — Studying Fine-scale Recombination with Increased Sample Size

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Detection of sharing by descent, long-range phasing and haplotype imputation.
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Applying LRP, we were able to phase the mother using her more distant relatives. This phasing information together with the data on the father and C3 alone allowed us to infer the same recombination event that was deduced by also using the data of C1 and C2. As detailed in the figure legend (Fig. 3), having relatives R2 to R4 could actually provide better resolution of the recombination event than having the parents of M genotyped. As noted earlier, a substantial fraction of the heterozygous SNPs in M could remain unphased even with data on parents, but having a large number of surrogate parents and surrogate relatives could have every SNP phased. Also worth noting is that a sibling of M, SM, is genotyped, but because he shares both haplotypes with M he is actually not useful for phasing M at this locus. By contrast, R2 and R4, the key individuals, are separated from M by 7 meioses and hence not close relatives.