Multi-factor data normalization enables the detection of copy number aberrations in amplicon sequencing data.
Multi-factor data normalization enables the detection of copy number aberrations in amplicon sequencing data.
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DOI：
10.1093/bioinformatics/btu436
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发表时间：
2014-12-15
期刊：
影响因子：
--
通讯作者：
Laes JF
中科院分区：
文献类型：
--
作者：
Boeva V;Popova T;Lienard M;Toffoli S;Kamal M;Le Tourneau C;Gentien D;Servant N;Gestraud P;Rio Frio T;Hupé P;Barillot E;Laes JF
动机：由于其低成本，扩增子测序，也被称为超深度靶向测序，现在正被广泛应用于肿瘤学，用于检测可操作的突变，即影响细胞对靶向治疗敏感性的突变。扩增子测序是基于感兴趣区域的聚合酶链式反应扩增，这一过程严重扭曲了最初存在于肿瘤DNA中的拷贝数的信息。因此，额外的实验，如单核苷酸多态(SNP)或比较基因组杂交(CGH)阵列，经常补充临床上的扩增序列，以确定其扩增或缺失对特定癌症治疗的疗效有直接影响的基因的拷贝数状态。到目前为止，还没有被证实的方法来提取关于基因拷贝数偏差的信息，仅基于扩增子序列。结果：在这里，我们介绍了ONCOCNV，一种包括多因子归一化和注释技术的方法，能够从扩增子测序数据中检测大量拷贝数的变化。我们在高和低扩增子密度数据集上验证了我们的方法，并证明了ONCOCNV在检测拷贝数像差方面可以达到与阵列CGH技术相当的精度。因此，ONCOCNV应用于扩增子测序数据将使使用额外的阵列CGH或SNP阵列实验变得不必要。供应和实施：http://oncocnv.curie.fr/联系人：valentina.boeva@curie.fr补充信息：补充数据可在生物信息学在线上获得。
Motivation: Because of its low cost, amplicon sequencing, also known as ultra-deep targeted sequencing, is now becoming widely used in oncology for detection of actionable mutations, i.e. mutations influencing cell sensitivity to targeted therapies. Amplicon sequencing is based on the polymerase chain reaction amplification of the regions of interest, a process that considerably distorts the information on copy numbers initially present in the tumor DNA. Therefore, additional experiments such as single nucleotide polymorphism (SNP) or comparative genomic hybridization (CGH) arrays often complement amplicon sequencing in clinics to identify copy number status of genes whose amplification or deletion has direct consequences on the efficacy of a particular cancer treatment. So far, there has been no proven method to extract the information on gene copy number aberrations based solely on amplicon sequencing. Results: Here we present ONCOCNV, a method that includes a multifactor normalization and annotation technique enabling the detection of large copy number changes from amplicon sequencing data. We validated our approach on high and low amplicon density datasets and demonstrated that ONCOCNV can achieve a precision comparable with that of array CGH techniques in detecting copy number aberrations. Thus, ONCOCNV applied on amplicon sequencing data would make the use of additional array CGH or SNP array experiments unnecessary. Availability and implementation: http://oncocnv.curie.fr/ Contact: valentina.boeva@curie.fr Supplementary information: Supplementary data are available at Bioinformatics online.
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影响因子：
5.8
作者：
Sathirapongsasuti, Jarupon Fah;Lee, Hane;Nelson, Stanley F.
通讯作者：
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影响因子：
3
作者：
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DOI：
10.1093/bioinformatics/btr670
发表时间：
2012-02-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Boeva V;Popova T;Bleakley K;Chiche P;Cappo J;Schleiermacher G;Janoueix-Lerosey I;Delattre O;Barillot E
通讯作者：
Barillot E
影响因子：
7.8
作者：
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通讯作者：
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影响因子：
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作者：
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通讯作者：
PARZEN, E