Estimating genotyping errors from genotype and reconstructed pedigree data

1. Genotyping errors are rules rather than exceptions in reality, and are found in virtually all but very small datasets. These errors, even when occurring at an extremely low rate, can derail many genetic analyses such as parentage/sibship assignments and linkage/association studies. 2. Nonetheless, few robust and accurate methods are available for estimating the rate of occurrence of genotyping errors and for identifying individual erroneous genotypes at a locus. Methods based on duplicate genotyping are expensive, and estimate genotype inconsistency rather than error rate at a locus. Methods based on Hardy-Weinberg equilibrium tests have low robustness and low power, and apply only to those particular errors that cause excessive homozygosity. Methods based on pedigrees are powerful, robust and accurate. However, they rely on known and complete pedigrees that are unfortunately rarely available from natural populations in the wild. 3. I proposed a maximum likelihood method to reconst...1. 在实际研究中，基因分型错误（genotyping errors）实为常态而非特例，几乎存在于除极小型数据集外的所有数据集当中。即便此类错误的发生概率极低，仍可能严重干扰诸多遗传学分析工作，例如亲权/同胞关系鉴定以及连锁/关联研究。 2. 尽管如此，当前可用于精准估算基因分型错误发生率，并在位点层面识别单个错误基因型的稳健方法仍寥寥无几。基于重复分型的方法成本高昂，且仅能估算基因型不一致性，而非特定位点的错误率。基于哈迪-温伯格平衡（Hardy-Weinberg equilibrium）检验的方法稳健性与统计效力均较低，且仅适用于引发纯合子过剩的特定错误类型。基于系谱（pedigrees）的方法虽具备出色的统计效力、稳健性与准确性，但依赖已知且完整的系谱信息，而野生自然种群往往难以获取此类数据。 3. 本研究提出了一种最大似然法（maximum likelihood method），用于重构……