A Streamlined Approach to Antibody Novel Germline Allele Prediction and Validation.
A Streamlined Approach to Antibody Novel Germline Allele Prediction and Validation.
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DOI：
10.3389/fimmu.2017.01072
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发表时间：
2017
影响因子：
7.3
通讯作者：
Jiang N
中科院分区：
文献类型：
--
作者：
Wendel BS;He C;Crompton PD;Pierce SK;Jiang N
高通量测序和基于分子标识符的纠错技术的进步为单突变精确抗体库测序打开了大门，增加了免疫反应表征的广度和深度。然而，测序技术的改进不能解决抗体库测序准确性的一个关键方面：未记录的新型种系等位基因的可能性。体细胞超突变（Somatic hypermutation， SHM）召唤需要参考种系序列，IMGT数据库收集的抗体可变区基因等位基因虽然数量众多，但并不全面。由单核苷酸多态性或其他遗传变异导致的真实种系序列与最接近的IMGT等位基因之间的不匹配会导致SHM计数增加，导致抗体库分析不准确。在这里，我们开发了一种简化的方法来预测和验证新的等位基因，使用大量PBMC抗体库测序数据和靶向基因组DNA扩增和测序，使用仅来自4 ml血液的PBMC，以快速有效地提高抗体库分析的保真度。该方法建立了一种利用少量血液样本全面注释新等位基因的框架，这对研究幼儿免疫系统非常有用。
Advancements in high-throughput sequencing and molecular identifier-based error correction have opened the door to antibody repertoire sequencing with single mutation precision, increasing both the breadth and depth of immune response characterization. However, improvements in sequencing technology cannot resolve one key aspect of antibody repertoire sequencing accuracy: the possibility of undocumented novel germline alleles. Somatic hypermutation (SHM) calling requires a reference germline sequence, and the antibody variable region gene alleles collected by the IMGT database, although large in number, are not comprehensive. Mismatches, resulted from single nucleotide polymorphisms or other genetic variation, between the true germline sequence and the closest IMGT allele can inflate SHM counts, leading to inaccurate antibody repertoire analysis. Here, we developed a streamlined approach to novel allele prediction and validation using bulk PBMC antibody repertoire sequencing data and targeted genomic DNA amplification and sequencing using PBMCs from only 4 ml of blood to quickly and effectively improve the fidelity of antibody repertoire analysis. This approach establishes a framework for comprehensively annotating novel alleles using a small amount of blood sample, which is extremely useful in studying young children’s immune systems.
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影响因子：
14.9
作者：
Yaari G;Uduman M;Kleinstein SH
通讯作者：
Kleinstein SH
DOI：
10.1073/pnas.1417683112
发表时间：
2015-02-24
影响因子：
11.1
作者：
Gadala-Maria, Daniel;Yaari, Gur;Kleinstein, Steven H.
通讯作者：
Kleinstein, Steven H.
影响因子：
48
作者：
Shugay, Mikhail;Britanova, Olga V.;Chudakov, Dmitriy M.
通讯作者：
Chudakov, Dmitriy M.
DOI：
10.1073/pnas.1219320110
发表时间：
2013-04-16
影响因子：
11.1
作者：
Zhu, Jiang;Ofek, Gilad;Kwong, Peter D.
通讯作者：
Kwong, Peter D.
DOI：
10.1038/nri3804
发表时间：
2015-03
期刊：
Nature reviews. Immunology
影响因子：
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作者：
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