美国纽约基因组中心Michael C. Zody、Marta Byrska-Bishop等研究人员合作完成拓展的千人基因组计划的高覆盖率全基因组测序。2022年9月1日，国际知名学术期刊《细胞》发表了这一成果。
研究人员提出了一个高覆盖率的3202个样本的全基因组测序（WGS）千人基因组计划（1kGP）资源，其中包括602个完整的trios，使用Illumina测序，深度为30X。研究人员进行了单核苷酸变异（SNV）和短时插入和缺失（INDEL）的发现，并通过机器学习模型整合多种分析方法生成了一套全面的结构变异（SV）。结果显示，与第三阶段相比，变异调用的敏感性和精确性有所提高，特别是在罕见的SNV以及INDEL和SV的跨频谱中。研究人员还产生了一个改进的参考归因数据，使该研究发现的变体可用于关联研究。
据悉，1kGP是最大的WGS数据的完全开放资源，同意公开发布，没有访问或使用限制。1kGP第三阶段的最终版本包括来自26个种群的2504个无关联样本，主要基于低覆盖率的WGS。
附：英文原文
Title: High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios
Author: Marta Byrska-Bishop, Uday S. Evani, Xuefang Zhao, Anna O. Basile, Haley J. Abel, Allison A. Regier, André Corvelo, Wayne E. Clarke, Rajeeva Musunuri, Kshithija Nagulapalli, Susan Fairley, Alexi Runnels, Lara Winterkorn, Ernesto Lowy, Evan E. Eichler, Jan O. Korbel, Charles Lee, Tobias Marschall, Scott E. Devine, William T. Harvey, Weichen Zhou, Ryan E. Mills, Tobias Rausch, Sushant Kumar, Can Alkan, Fereydoun Hormozdiari, Zechen Chong, Yu Chen, Xiaofei Yang, Jiadong Lin, Mark B. Gerstein, Ye Kai, Qihui Zhu, Feyza Yilmaz, Chunlin Xiao, Paul Flicek, Soren Germer, Harrison Brand, Ira M. Hall, Michael E. Talkowski, Giuseppe Narzisi, Michael C. Zody
Issue&Volume: 2022/09/01
Abstract: The 1000 Genomes Project (1kGP) is the largest fully open resource of whole-genome sequencing (WGS) data consented for public distribution without access or use restrictions. The final, phase 3 release of the 1kGP included 2,504 unrelated samples from 26 populations and was based primarily on low-coverage WGS. Here, we present a high-coverage 3,202-sample WGS 1kGP resource, which now includes 602 complete trios, sequenced to a depth of 30X using Illumina. We performed single-nucleotide variant (SNV) and short insertion and deletion (INDEL) discovery and generated a comprehensive set of structural variants (SVs) by integrating multiple analytic methods through a machine learning model. We show gains in sensitivity and precision of variant calls compared to phase 3, especially among rare SNVs as well as INDELs and SVs spanning frequency spectrum. We also generated an improved reference imputation panel, making variants discovered here accessible for association studies.
DOI: 10.1016/j.cell.2022.08.004
Source: https://www.cell.com/cell/fulltext/S0092-8674(22)00991-6