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Whole genome amplification with SurePlex results in better copy number alteration detection using sequencing data compared to the MALBAC method

机译:与maLBaC方法相比,使用测序数据,使用sureplex进行全基因组扩增导致更好的拷贝数改变检测

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摘要

Current whole genome amplification (WGA) methods lead to amplification bias resulting in over-and under-represented regions in the genome. Nevertheless, certain WGA methods, such as SurePlex and subsequent arrayCGH analysis, make it possible to detect copy number alterations (CNAs) at a 10 Mb resolution. A more uniform WGA combined with massive parallel sequencing (MPS), however, could allow detection at higher resolution and lower cost. Recently, MALBAC, a new WGA method, claims unparalleled performance. Here, we compared the well-established SurePlex and MALBAC WGA for their ability to detect CNAs in MPS generated data and, in addition, compared PCR-free MPS library preparation with the standard enrichment PCR library preparation. Results showed that SurePlex amplification led to more uniformity across the genome, allowing for a better CNA detection with less false positives compared to MALBAC amplified samples. An even more uniform coverage was observed in samples following a PCR-free library preparation. In general, the combination of SurePlex and MPS led to the same chromosomal profile compared to a reference arrayCGH from unamplified genomic DNA, underlining the large potential of MPS techniques in CNA detection from a limited number of DNA material.
机译:当前的全基因组扩增(WGA)方法会导致扩增偏倚,从而导致基因组中的代表区域过多和不足。但是,某些WGA方法(例如SurePlex和随后的arrayCGH分析)使检测10 Mb分辨率的拷贝数变化(CNA)成为可能。但是,更统一的WGA与大规模并行测序(MPS)相结合,可以实现更高分辨率和更低成本的检测。最近,一种新的WGA方法MALBAC声称具有无与伦比的性能。在这里,我们比较了完善的SurePlex和MALBAC WGA在MPS生成的数据中检测CNA的能力,此外,还比较了无PCR的MPS文库制备与标准富集PCR文库制备。结果表明,与MALBAC扩增的样品相比,SurePlex扩增导致整个基因组的一致性更高,从而可以实现更好的CNA检测,假阳性更少。无需PCR的文库制备后,样品中的覆盖率甚至更加均匀。通常,与未扩增的基因组DNA的参考arrayCGH相比,SurePlex和MPS的组合可产生相同的染色体谱,这突显了MPS技术在从有限数量的DNA材料中检测CNA的巨大潜力。

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