High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios.
High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios.
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包含602个三联体家庭的千人基因组计划扩展队列的高覆盖度全基因组测序。
DOI：
10.1016/j.cell.2022.08.004
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发表时间：
2022-09-01
期刊：
影响因子：
64.5
通讯作者：
Zody, Michael C.
中科院分区：
文献类型：
--
作者：
Byrska-Bishop, Marta;Evani, Uday S.;Zhao, Xuefang;Basile, Anna O.;Abel, Haley J.;Regier, Allison A.;Corvelo, Andre;Clarke, Wayne E.;Musunuri, Rajeeva;Nagulapalli, Kshithija;Fairley, Susan;Runnels, Alexi;Winterkorn, Lara;Lowy, Ernesto;Flicek, Paul;Germer, Soren;Brand, Harrison;Hall, Ira M.;Talkowski, Michael E.;Narzisi, Giuseppe;Zody, Michael C.
千人基因组计划（1kGP）是全基因组测序（WGS）数据的最大完全开放资源，同意公开分发，没有访问或使用限制。1kGP的最终3期发布包括来自26个种群的2，504个无关样本，主要基于低覆盖率的WGS。在这里，我们展示了一个高覆盖率的3，202个样本WGS 1kGP资源，现在包括602个完整的trios，使用Illumina进行了30倍深度的测序。我们进行了单核苷酸变异（SNV）和短插入和缺失（INDEL）发现，并通过机器学习模型整合多种分析方法，生成了一组全面的结构变异（SV）。与第3阶段相比，我们显示了变异调用的灵敏度和精确度的提高，特别是在罕见的SNV以及INDEL和跨越频谱的SV中。我们还生成了一个改进的参考插补面板，使这里发现的变异可用于关联研究。扩大千人基因组计划（1kGP）资源以包括602个trios对扩大的1kGP队列进行高覆盖率全基因组测序在整个频谱中发现更罕见的SNV以及INDEL和SV生成改进的和可访问的参考插补面板对扩大的千人基因组计划（1kGP）进行高覆盖率全基因组测序（WGS）包括602个trios的队列导致发现了额外的罕见非编码单核苷酸变体（SNV），以及与主要基于低覆盖率WGS的原始1kGP资源相比，跨越等位基因频谱的编码和非编码短插入和缺失（INDEL）和结构变体（SV）。
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. Expansion of the 1000 Genomes Project (1kGP) resource to include 602 trios High-coverage whole-genome sequencing of the expanded 1kGP cohort Discovery of more rare SNVs as well as INDELs and SVs across the frequency spectrum Generation of an improved and accessible reference imputation panel High-coverage whole-genome sequencing (WGS) of the expanded 1000 Genomes Project (1kGP) cohort including 602 trios led to the discovery of additional rare non-coding single-nucleotide variants (SNVs), as well as coding and non-coding short insertions and deletions (INDELs) and structural variants (SVs) spanning the allele frequency spectrum compared to the original 1kGP resource based primarily on low-coverage WGS.
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影响因子：
7
作者：
Gardner EJ;Lam VK;Harris DN;Chuang NT;Scott EC;Pittard WS;Mills RE;1000 Genomes Project Consortium;Devine SE
通讯作者：
Devine SE
影响因子：
3.5
作者：
Almeida R;Ricaño-Ponce I;Kumar V;Deelen P;Szperl A;Trynka G;Gutierrez-Achury J;Kanterakis A;Westra HJ;Franke L;Swertz MA;Platteel M;Bilbao JR;Barisani D;Greco L;Mearin L;Wolters VM;Mulder C;Mazzilli MC;Sood A;Cukrowska B;Núñez C;Pratesi R;Withoff S;Wijmenga C
通讯作者：
Wijmenga C
影响因子：
9.2
作者：
Chang CC;Chow CC;Tellier LC;Vattikuti S;Purcell SM;Lee JJ
通讯作者：
Lee JJ
影响因子：
7
作者：
Eberle, Michael A.;Fritzilas, Epameinondas;Bentley, David R.
通讯作者：
Bentley, David R.
影响因子：
14.9
作者：
Fairley, Susan;Lowy-Gallego, Ernesto;Flicek, Paul
通讯作者：
Flicek, Paul