LRP was performed in two rounds of three steps each. At Round 1, Step 1 identified putative surrogate parents for each proband. To minimize the impact of III described above, only those individuals who had IBS ≥ 1 for all 2187 SNPs in the extended 14Mb (10 cM) region were selected. This increased the chance that a putative surrogate parent actually shares a haplotype IBD with the proband for the entire 10 Mb target region. Missing genotypes were treated as wild cards and considered to be consistent with sharing. Even though we plan to do that in the future, imputation was not attempted. At Step 2, for each proband, surrogate parents were first checked for incompatibilities. A proband was phased at this step only if no incompatibilities were observed for any of the SNPs. Because genotypes phased at this step would contribute to the next phasing step, this ensured that only very high quality results would be carried over. Note that at Step 2, data of surrogate parents entered the processing of a proband as unphased. But every surrogate parent
