推断的 APOE 基因型在一系列基因分型阵列和 imputation 参考面板中的准确性。
Accuracy of Inferred APOE Genotypes for a Range of Genotyping Arrays and Imputation Reference Panels.
机构信息
QIMR Berghofer Medical Research Institute, Brisbane, Australia.
University of Western Australia Centre for Ophthalmology and Visual Science, Lions Eye Institute, Perth, Australia.
出版信息
J Alzheimers Dis. 2018;64(1):49-54. doi: 10.3233/JAD-171104.
Cohort studies investigating aging and dementia require APOE genotyping. We compared directly measured APOE genotypes to 'hard-call' genotypes derived from imputing genome-wide genotyping data from a range of platforms using several imputation panels. Older GWAS arrays imputed to 1000 Genomes Project (1KGP) phases and the Haplotype Reference Consortium (HRC) reference panels were able to achieve concordance rates of over 98% with stringent quality control (hard-call-threshold 0.8). However, this resulted in high levels of missingness (>12% with 1KGP and 5% with HRC). With recent GWAS arrays, concordance of 99% could be obtained with relatively lenient QC, resulting in no missingness.
队列研究调查衰老和痴呆需要 APOE 基因分型。我们将直接测量的 APOE 基因型与通过使用多个 imputation 面板从一系列平台的全基因组基因分型数据推断得出的“硬call”基因型进行了比较。在严格的质量控制（硬call 阈值 0.8）下，使用 1000 基因组计划（1KGP）阶段和单倍型参考联盟（HRC）参考面板直接测量的较老的 GWAS 阵列可以实现超过 98%的一致性率。然而，这导致了高水平的缺失率（1KGP 中超过 12%，HRC 中 5%）。对于最近的 GWAS 阵列，可以通过相对宽松的 QC 获得 99%的一致性，从而没有缺失。
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