Detection and removal of barcode swapping in single-cell RNA-seq data.
Detection and removal of barcode swapping in single-cell RNA-seq data.
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DOI：
10.1038/s41467-018-05083-x
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发表时间：
2018-07-10
影响因子：
16.6
通讯作者：
Marioni JC
中科院分区：
文献类型：
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作者：
Griffiths JA;Richard AC;Bach K;Lun ATL;Marioni JC
条形码交换导致在图案化的流动细胞Illumina测序机上的多路样品之间错误地标记测序读数。这可能会损害众多基因组分析的有效性；然而，条形码交换的严重性和后果仍然知之甚少。我们使用了两种统计方法来稳健地量化两个平板单细胞RNA测序数据集中的交换读数的比例。我们发现，在HiSeq 4000上，大约2.5%的读数在样本之间被错误标记，这一数字低于之前的报告。我们没有观察到读数的交换分数和跨平板的自由条形码浓度之间的相关性。此外，我们已经证明，在基于液滴的单细胞RNA测序研究中，条形码交换可能会产生复杂但人为的细胞库。为了消除这些假象，我们开发了一种算法，在10倍基因组学实验中排除在样本之间交换的单个分子，从而允许继续使用尖端测序机进行这些分析。DNA条形码交换会导致多路传输样本之间的测序读数标记错误。在这里，作者调查了单细胞RNA-seq数据条形码交换的严重性和后果，并开发了一种计算方法来排除交换的读取。
Barcode swapping results in the mislabelling of sequencing reads between multiplexed samples on patterned flow-cell Illumina sequencing machines. This may compromise the validity of numerous genomic assays; however, the severity and consequences of barcode swapping remain poorly understood. We have used two statistical approaches to robustly quantify the fraction of swapped reads in two plate-based single-cell RNA-sequencing datasets. We found that approximately 2.5% of reads were mislabelled between samples on the HiSeq 4000, which is lower than previous reports. We observed no correlation between the swapped fraction of reads and the concentration of free barcode across plates. Furthermore, we have demonstrated that barcode swapping may generate complex but artefactual cell libraries in droplet-based single-cell RNA-sequencing studies. To eliminate these artefacts, we have developed an algorithm to exclude individual molecules that have swapped between samples in 10x Genomics experiments, allowing the continued use of cutting-edge sequencing machines for these assays. DNA barcode swapping results in mislabelling of sequencing reads between multiplexed samples. Here, the authors investigate the severity and consequences of barcode swapping for single-cell RNA-seq data, and develop a computational method to exclude swapped reads.
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DOI：
10.1126/science.1247651
发表时间：
2014-02-14
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Jaitin DA;Kenigsberg E;Keren-Shaul H;Elefant N;Paul F;Zaretsky I;Mildner A;Cohen N;Jung S;Tanay A;Amit I
通讯作者：
Amit I
影响因子：
16.6
作者：
Zheng GX;Terry JM;Belgrader P;Ryvkin P;Bent ZW;Wilson R;Ziraldo SB;Wheeler TD;McDermott GP;Zhu J;Gregory MT;Shuga J;Montesclaros L;Underwood JG;Masquelier DA;Nishimura SY;Schnall-Levin M;Wyatt PW;Hindson CM;Bharadwaj R;Wong A;Ness KD;Beppu LW;Deeg HJ;McFarland C;Loeb KR;Valente WJ;Ericson NG;Stevens EA;Radich JP;Mikkelsen TS;Hindson BJ;Bielas JH
通讯作者：
Bielas JH
影响因子：
64.5
作者：
Dixit, Atray;Pamas, Oren;Li, Biyu;Chen, Jenny;Fulco, Charles P.;Jerby-Amon, Livnat;Marjanovic, Nemanja D.;Dionne, Danielle;Burks, Tyler;Raychowdhury, Raktima;Adamson, Britt;Norman, Thomas M.;Lander, Eric S.;Weissman, Jonathan S.;Friedman, Nir;Regev, Aviv
通讯作者：
Regev, Aviv
影响因子：
20.3
作者：
Nestorowa, Sonia;Hamey, Fiona K.;Gottgens, Berthold
通讯作者：
Gottgens, Berthold
使用纳米液液滴对单个细胞的高度平行基因组表达分析。
影响因子：
64.5
作者：
Macosko EZ;Basu A;Satija R;Nemesh J;Shekhar K;Goldman M;Tirosh I;Bialas AR;Kamitaki N;Martersteck EM;Trombetta JJ;Weitz DA;Sanes JR;Shalek AK;Regev A;McCarroll SA
通讯作者：
McCarroll SA