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Pros and cons of HaloPlex enrichment in cancer predisposition genetic diagnosis

机译：HaloPlex富集在癌症易感基因诊断中的利弊

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摘要

Panel sequencing is a practical option in genetic diagnosis. Enrichment and library preparation steps are critical in the diagnostic setting. In order to test the value of HaloPlex technology in diagnosis, we designed a custom oncogenetic panel including 62 genes. The procedure was tested on a training set of 71 controls and then blindly validated on 48 consecutive hereditary breast/ovarian cancer (HBOC) patients tested negative for BRCA1/2 mutation. Libraries were sequenced on HiSeq2500 and data were analysed with our academic bioinformatics pipeline. Point mutations were detected using Varscan2, median size indels were detected using Pindel and large genomic rearrangements (LGR) were detected by DESeq. Proper coverage was obtained. However, highly variable read depth was observed within genes. Excluding pseudogene analysis, all point mutations were detected on the training set. All indels were also detected using Pindel. On the other hand, DESeq allowed LGR detection but with poor specificity, preventing its use in diagnostics. Mutations were detected in 8% of BRCA1/2 -negative HBOC cases. HaloPlex technology appears to be an efficient and promising solution for gene panel diagnostics. Data analysis remains a major challenge and geneticists should enhance their bioinformatics knowledge in order to ensure good quality diagnostic results.
机译：面板测序是遗传诊断中的一种实用选择。富集和文库制备步骤对于诊断设置至关重要。为了测试HaloPlex技术在诊断中的价值，我们设计了一个定制的致癌基因组，包括62个基因。该程序在71名对照组的训练集上进行了测试，然后对BRCA1 / 2突变测试为阴性的48位连续遗传性乳腺癌/卵巢癌（HBOC）患者进行盲法验证。在HiSeq2500上对图书馆进行测序，并使用我们的学术生物信息学管道分析数据。使用Varscan2检测点突变，使用Pindel检测中值大小插入缺失，通过DESeq检测大基因组重排（LGR）。获得了适当的覆盖范围。然而，在基因内观察到高度可变的读取深度。除假基因分析外，在训练组上检测到所有点突变。还使用Pindel检测到所有插入缺失。另一方面，DESeq允许LGR检测，但特异性较差，因此无法将其用于诊断。在8％的BRCA1 / 2阴性HBOC病例中检测到突变。 HaloPlex技术似乎是基因面板诊断的有效且有前途的解决方案。数据分析仍然是一项重大挑战，遗传学家应增强其生物信息学知识，以确保获得高质量的诊断结果。

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