Quantifying Hematopoietic Stem Cell Clonal Diversity by Selecting Informative Amplicon Barcodes.
Quantifying Hematopoietic Stem Cell Clonal Diversity by Selecting Informative Amplicon Barcodes.
复制标题
通过选择信息丰富的扩增子条形码来量化造血干细胞克隆多样性。
DOI：
10.1038/s41598-020-59119-8
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发表时间：
2020
影响因子：
4.6
通讯作者：
Blaser,BradleyW
中科院分区：
文献类型：
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作者：
Teets,EmilyM;Gregory,Charles;Shaffer,Jami;Blachly,JamesS;Blaser,BradleyW
造血干细胞（HSC）在功能和遗传上是多样的，这种多样性随着年龄和疾病而减少。已经开发了许多系统来通过遗传条形码量化HSC多样性，但是还没有建立框架来凭经验验证条形码序列。在这里，我们开发了一个分析框架，从实验重复中选择信息性扩增子条形码（SABER），该框架可识别大量实验重复中唯一的条形码。扩增子条形码从56条成年斑马鱼的血液中测序，分成训练组和验证组。鉴定信息性条形码，并通过自举法选择具有高分数信息性条形码的样品。在训练集中每个样品有4.2 ± 1.8个条形码化HSC克隆，在验证集中有3.5 ± 2.1个（p = 0.3）。SABER可重复量化功能性HSC，并可适应各种实验组规模。未来旨在了解HSC克隆进化机制的大规模研究将受益于这种识别信息扩增子条形码的新方法。
Hematopoietic stem cells (HSCs) are functionally and genetically diverse and this diversity decreases with age and disease. Numerous systems have been developed to quantify HSC diversity by genetic barcoding, but no framework has been established to empirically validate barcode sequences. Here we have developed an analytical framework, Selection of informative Amplicon Barcodes from Experimental Replicates (SABER), that identifies barcodes that are unique among a large set of experimental replicates. Amplicon barcodes were sequenced from the blood of 56 adult zebrafish divided into training and validation sets. Informative barcodes were identified and samples with a high fraction of informative barcodes were chosen by bootstrapping. There were 4.2 ± 1.8 barcoded HSC clones per sample in the training set and 3.5 ± 2.1 in the validation set (p = 0.3). SABER reproducibly quantifies functional HSCs and can accommodate a wide range of experimental group sizes. Future large-scale studies aiming to understand the mechanisms of HSC clonal evolution will benefit from this new approach to identifying informative amplicon barcodes.