Jasmine and Iris: population-scale structural variant comparison and analysis.
Jasmine and Iris: population-scale structural variant comparison and analysis.
复制标题
茉莉花和鸢尾花：群体规模结构变异比较和分析。
DOI：
10.1038/s41592-022-01753-3
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发表时间：
2023-03
期刊：
影响因子：
48
通讯作者：
Schatz, Michael C. C.
中科院分区：
文献类型：
--
作者：
Kirsche, Melanie;Prabhu, Gautam;Sherman, Rachel;Ni, Bohan;Battle, Alexis;Aganezov, Sergey;Schatz, Michael C. C.
长读的可用性正在彻底改变结构变异（SVs）的研究。然而，由于sv因个体而异，并且是通过不精确的读取技术和方法发现的，因此很难对它们进行比较。为了解决这个问题，我们提出了Jasmine和Iris (https://github.com/mkirsche/Jasmine)，用于快速准确的SV细化、比较和种群分析。使用SV接近图，Jasmine优于六种广泛使用的比较方法，包括将三个数据集的孟德尔不一致率降低了五倍以上，并揭示了一组经过多种技术确认的高置信度的从头SV。我们还提出了来自31个不同祖先样本的122,813个sv和82,379个索引的统一调用集。我们在来自1000基因组计划和GTEx的1317个样本中使用DNA和RNA测序数据对这些变异进行了基因分型，并评估了它们对基因表达的广泛影响，包括在医学相关基因中。
The availability of long-reads is revolutionizing studies of structural variants (SVs). However, because SVs vary across individuals and are discovered through imprecise read technologies and methods, they can be difficult to compare. Addressing this, we present Jasmine and Iris (https://github.com/mkirsche/Jasmine), for fast and accurate SV refinement, comparison, and population analysis. Using an SV proximity graph, Jasmine outperforms six widely-used comparison methods, including reducing the rate of Mendelian discordance in trio datasets by more than five-fold, and reveals a set of high-confidence de novo SVs confirmed by multiple technologies. We also present a unified callset of 122,813 SVs and 82,379 indels from 31 samples of diverse ancestry sequenced with long reads. We genotype these variants in 1,317 samples from the 1000 Genomes Project and GTEx with DNA and RNA sequencing data and assess their widespread impact on gene expression, including within medically relevant genes.
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影响因子：
64.8
作者：
Iossifov, Ivan;O'Roak, Brian J.;Sanders, Stephan J.;Ronemus, Michael;Krumm, Niklas;Levy, Dan;Stessman, Holly A.;Witherspoon, Kali T.;Vives, Laura;Patterson, Karynne E.;Smith, Joshua D.;Paeper, Bryan;Nickerson, Deborah A.;Dea, Jeanselle;Dong, Shan;Gonzalez, Luis E.;Mandell, Jeffrey D.;Mane, Shrikant M.;Murtha, Michael T.;Sullivan, Catherine A.;Walker, Michael F.;Waqar, Zainulabedin;Wei, Liping;Willsey, A. Jeremy;Yamrom, Boris;Lee, Yoon-ha;Grabowska, Ewa;Dalkic, Ertugrul;Wang, Zihua;Marks, Steven;Andrews, Peter;Leotta, Anthony;Kendall, Jude;Hakker, Inessa;Rosenbaum, Julie;Ma, Beicong;Rodgers, Linda;Troge, Jennifer;Narzisi, Giuseppe;Yoon, Seungtai;Schatz, Michael C.;Ye, Kenny;McCombie, W. Richard;Shendure, Jay;Eichler, Evan E.;State, Matthew W.;Wigler, Michael
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通讯作者：
Stefansson, Kari
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Abel HJ;Larson DE;Regier AA;Chiang C;Das I;Kanchi KL;Layer RM;Neale BM;Salerno WJ;Reeves C;Buyske S;NHGRI Centers for Common Disease Genomics;Matise TC;Muzny DM;Zody MC;Lander ES;Dutcher SK;Stitziel NO;Hall IM
通讯作者：
Hall IM