A resampling-based approach to share reference panels

IF 12 Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS Nature computational science Pub Date : 2024-05-14 DOI:10.1038/s43588-024-00630-7
Théo Cavinato, Simone Rubinacci, Anna-Sapfo Malaspinas, Olivier Delaneau
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Abstract

For many genome-wide association studies, imputing genotypes from a haplotype reference panel is a necessary step. Over the past 15 years, reference panels have become larger and more diverse, leading to improvements in imputation accuracy. However, the latest generation of reference panels is subject to restrictions on data sharing due to concerns about privacy, limiting their usefulness for genotype imputation. In this context, here we propose RESHAPE, a method that employs a recombination Poisson process on a reference panel to simulate the genomes of hypothetical descendants after multiple generations. This data transformation helps to protect against re-identification threats and preserves data attributes, such as linkage disequilibrium patterns and, to some degree, identity-by-descent sharing, allowing for genotype imputation. Our experiments on gold-standard datasets show that simulated descendants up to eight generations can serve as reference panels without substantially reducing genotype imputation accuracy. The authors develop the tool RESHAPE to share reference panels in a safer way. The genome–phenome links in reference panels can generate re-identification threats and RESHAPE breaks these links by shuffling haplotypes while preserving imputation accuracy.

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基于重采样的共享参考面板方法。
对于许多全基因组关联研究来说,从单倍型参考面板推算基因型是一个必要的步骤。在过去的 15 年中,参考面板的规模越来越大,种类也越来越多,从而提高了归因的准确性。然而,由于对隐私的担忧,最新一代的参考面板在数据共享方面受到了限制,从而限制了它们在基因型推算方面的作用。在这种情况下,我们在这里提出了 RESHAPE,一种在参考面板上采用重组泊松过程来模拟多代后假设后代基因组的方法。这种数据转换有助于防止再识别威胁,并保留数据属性,如连锁不平衡模式,以及一定程度上的后代身份共享,从而实现基因型估算。我们在黄金标准数据集上的实验表明,长达八代的模拟后代可以作为参考面板,而不会大大降低基因型估算的准确性。
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