Subclonal phylogenetic structures in cancer revealed by ultra-deep sequencing
Subclonal phylogenetic structures in cancer revealed by ultra-deep sequencing
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DOI：
10.1073/pnas.0801523105
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发表时间：
2008-09-02
影响因子：
11.1
通讯作者：
Stratton, Michael R.
中科院分区：
文献类型：
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作者：
Campbell, Peter J.;Pleasance, Erin D.;Stratton, Michael R.
在癌症从具有起始致癌突变的祖细胞克隆性扩增到有症状的肿瘤过程中，体细胞突变（包括驱动突变和乘客突变）的发生可用于追踪肿瘤的持续演变。癌症内的所有亚克隆在系统发育上是相关的，每个亚克隆的流行程度由其进化适应性以及相对于其他亚克隆的起源时间决定。最近开发的大规模平行测序平台有望在无需事先了解所涉及突变的情况下检测罕见的基因变异亚克隆。我们使用超深度焦磷酸测序研究了22例B细胞慢性淋巴细胞白血病患者的Ig重链基因座的克隆内多样化。对一个非多态性对照基因座的分析揭示了由测序错误导致的人为插入和缺失，以及在PCR扩增过程中聚合酶错误掺入引起的碱基替换。我们开发了一种算法，将体细胞超突变的真实单倍型与这类假象区分开来。这被证明能够检测频率低至5000个拷贝中有1个的多个罕见亚克隆，并能够描述每个患者内亚克隆之间的系统发育相互关系。这项研究证明了超深度重测序在重现癌细胞群体克隆进化动态方面的潜力。
During the clonal expansion of cancer from an ancestral cell with an initiating oncogenic mutation to symptomatic neoplasm, the occurrence of somatic mutations (both driver and passenger) can be used to track the on-going evolution of the neoplasm. All subclones within a cancer are phylogenetically related, with the prevalence of each subclone determined by its evolutionary fitness and the timing of its origin relative to other subclones. Recently developed massively parallel sequencing platforms promise the ability to detect rare subclones of genetic variants without a priori knowledge of the mutations involved. We used ultra-deep pyro-sequencing to investigate intraclonal diversification at the Ig heavy chain locus in 22 patients with B-cell chronic lymphocytic leukemia. Analysis of a non-polymorphic control locus revealed artifactual insertions and deletions resulting from sequencing errors and base substitutions caused by polymerase misincorporation during PCR amplification. We developed an algorithm to differentiate genuine haplotypes of somatic hypermutations from such artifacts. This proved capable of detecting multiple rare subclones with frequencies as low as 1 in 5000 copies and allowed the characterization of phylogenetic interrelationships among subclones within each patient. This study demonstrates the potential for ultra-deep resequencing to recapitulate the dynamics of clonal evolution in cancer cell populations.