Immune Repertoire Sequencing Using Molecular Identifiers Enables Accurate Clonality Discovery and Clone Size Quantification.
Immune Repertoire Sequencing Using Molecular Identifiers Enables Accurate Clonality Discovery and Clone Size Quantification.
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使用分子标识符进行免疫组库测序可实现准确的克隆性发现和克隆大小定量
DOI：
10.3389/fimmu.2018.00033
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发表时间：
2018
影响因子：
7.3
通讯作者：
Jiang N
中科院分区：
文献类型：
--
作者：
Ma KY;He C;Wendel BS;Williams CM;Xiao J;Yang H;Jiang N
独特的分子标识符（MIDs）已被证明可以有效地提高免疫库测序（IR-seq）的准确性，特别是在抗体库测序中识别体细胞超突变。然而，由于缺乏对T细胞受体（TCR） RNA分子拷贝数的了解和从TCR RNA分子定量估计T细胞克隆大小的通用方法，在IR-seq中评估检测稀有T细胞的敏感性和克隆扩增程度一直很困难。这限制了TCR库测序（TCR-seq）在临床环境中的应用，例如检测淋巴细胞恶性肿瘤治疗后的最小残留疾病，评估疫苗接种的有效性和评估感染程度。在这里，我们描述了使用基于MID聚类的IR-Seq （MIDCIRS）方法定量研究T细胞中TCR RNA分子拷贝数和克隆性。首先，我们证明了执行MID子聚类来消除错误序列的必要性。此外，我们发现，MIDCIRS能够在多达一百万个naïve T细胞中灵敏地检测单个细胞，并准确地估计T细胞克隆表达的程度。MIDCIRS TCR-seq的准确性、灵敏度和宽动态范围为未来在基础研究和临床环境中的应用奠定了基础。
Unique molecular identifiers (MIDs) have been demonstrated to effectively improve immune repertoire sequencing (IR-seq) accuracy, especially to identify somatic hypermutations in antibody repertoire sequencing. However, evaluating the sensitivity to detect rare T cells and the degree of clonal expansion in IR-seq has been difficult due to the lack of knowledge of T cell receptor (TCR) RNA molecule copy number and a generalized approach to estimate T cell clone size from TCR RNA molecule quantification. This limited the application of TCR repertoire sequencing (TCR-seq) in clinical settings, such as detecting minimal residual disease in lymphoid malignancies after treatment, evaluating effectiveness of vaccination and assessing degree of infection. Here, we describe using an MID Clustering-based IR-Seq (MIDCIRS) method to quantitatively study TCR RNA molecule copy number and clonality in T cells. First, we demonstrated the necessity of performing MID sub-clustering to eliminate erroneous sequences. Further, we showed that MIDCIRS enables a sensitive detection of a single cell in as many as one million naïve T cells and an accurate estimation of the degree of T cell clonal expression. The demonstrated accuracy, sensitivity, and wide dynamic range of MIDCIRS TCR-seq provide foundations for future applications in both basic research and clinical settings.
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影响因子：
7.4
作者：
Fu, Glenn K.;Wilhelmy, Julie;Stern, David;Fan, H. Christina;Fodor, Stephen P. A.
通讯作者：
Fodor, Stephen P. A.
影响因子：
17.1
作者：
Jiang N;He J;Weinstein JA;Penland L;Sasaki S;He XS;Dekker CL;Zheng NY;Huang M;Sullivan M;Wilson PC;Greenberg HB;Davis MM;Fisher DS;Quake SR
通讯作者：
Quake SR
影响因子：
30.8
作者：
Li, Bo;Li, Taiwen;Liu, X. Shirley
通讯作者：
Liu, X. Shirley
DOI：
10.1073/pnas.1503587112
发表时间：
2015-04-07
影响因子：
11.1
作者：
Blachly, James S.;Ruppert, Amy S.;Byrd, John C.
通讯作者：
Byrd, John C.
影响因子：
17.1
作者：
Robins HS;Ericson NG;Guenthoer J;O'Briant KC;Tewari M;Drescher CW;Bielas JH
通讯作者：
Bielas JH