Center for Human Genetics and Genomics, New York University Grossman School of Medicine, New York, New York 10016, USA.
Department of Pediatrics, Department of Neuroscience & Physiology, Institute for Systems Genetics, Perlmutter Cancer Center, and Neuroscience Institute, New York University Grossman School of Medicine, New York, New York 10016, USA.
Genome Res. 2024 Aug 20;34(7):1008-1026. doi: 10.1101/gr.278785.123.
Microsatellites are highly mutable sequences that can serve as markers for relationships among individuals or cells within a population. The accuracy and resolution of reconstructing these relationships depends on the fidelity of microsatellite profiling and the number of microsatellites profiled. However, current methods for targeted profiling of microsatellites incur significant "stutter" artifacts that interfere with accurate genotyping, and sequencing costs preclude whole-genome microsatellite profiling of a large number of samples. We developed a novel method for accurate and cost-effective targeted profiling of a panel of more than 150,000 microsatellites per sample, along with a computational tool for designing large-scale microsatellite panels. Our method addresses the greatest challenge for microsatellite profiling-"stutter" artifacts-with a low-temperature hybridization capture that significantly reduces these artifacts. We also developed a computational tool for accurate genotyping of the resulting microsatellite sequencing data that uses an ensemble approach integrating three microsatellite genotyping tools, which we optimize by analysis of de novo microsatellite mutations in human trios. Altogether, our suite of experimental and computational tools enables high-fidelity, large-scale profiling of microsatellites, which may find utility in diverse applications such as lineage tracing, population genetics, ecology, and forensics.
微卫星是高度易变的序列，可以作为个体或群体内细胞之间关系的标记。重建这些关系的准确性和分辨率取决于微卫星分析的保真度和分析的微卫星数量。然而，目前用于靶向微卫星分析的方法会产生显著的“拖尾”伪影，干扰准确的基因分型，而测序成本则排除了对大量样本进行全基因组微卫星分析的可能性。我们开发了一种新的方法，可以针对每个样本进行超过 150,000 个微卫星的准确且具有成本效益的靶向分析，并开发了一种用于设计大规模微卫星面板的计算工具。我们的方法解决了微卫星分析中最大的挑战——“拖尾”伪影——通过低温杂交捕获，显著减少了这些伪影。我们还开发了一种用于准确基因分型的计算工具，该工具使用集成了三种微卫星基因分型工具的集成方法，我们通过分析人类三体型中的从头微卫星突变对其进行了优化。总的来说，我们的实验和计算工具套件实现了微卫星的高保真度、大规模分析，这在谱系追踪、群体遗传学、生态学和法医学等多种应用中可能具有实用价值。
