Assessment of the cPAS-based BGISEQ-500 platform for metagenomic sequencing.
Assessment of the cPAS-based BGISEQ-500 platform for metagenomic sequencing.
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DOI：
10.1093/gigascience/gix133
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发表时间：
2018-03-01
期刊：
影响因子：
9.2
通讯作者：
Li J
中科院分区：
文献类型：
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作者：
Fang C;Zhong H;Lin Y;Chen B;Han M;Ren H;Lu H;Luber JM;Xia M;Li W;Stein S;Xu X;Zhang W;Drmanac R;Wang J;Yang H;Hammarström L;Kostic AD;Kristiansen K;Li J
宏基因组鸟枪测序在微生物组研究中的更广泛使用依赖于高通量、成本效益高的测序的发展。在这里，我们提出了一个新的高通量测序平台BGISEQ-500的宏基因组鸟枪测序的性能进行全面评估，并比较其性能与2 Illumina平台。使用来自20个健康个体的粪便样品，我们在包括8个文库重复和8个测序重复的设置中评估了BGISEQ-500平台上宏基因组测序的平台内再现性。通过比较BGISEQ-500平台与Illumina HiSeq 2000平台和Illumina HiSeq 4000平台上的20个成对重复来评估跨平台一致性。此外，我们还比较了两个Illumina平台的性能。通过新开发的整体准确性质量控制方法，使用BGISEQ-500平台，每个样本平均获得8245万个高质量读数（原始读数的96.06%），其中90.56%的碱基得分为Q30及以上。定量分析显示BGISEQ-500平台内重复检测之间的重现性极高。跨平台重复的差异略大于平台内重复，但观察到高度一致性。与BGISEQ-500和HiSeq平台相比，只有低百分比（2.02%-3.25%）的基因表现出相对丰度的显著差异，偏向于具有较高GC含量的基因在HiSeq平台上富集。我们的研究提供了使用BGISEQ-500的人类肠道宏基因组测序数据的第一组性能指标。高准确性和技术再现性证实了新平台对宏基因组研究的适用性，尽管在组合来自不同平台的宏基因组数据时仍需谨慎。
More extensive use of metagenomic shotgun sequencing in microbiome research relies on the development of high-throughput, cost-effective sequencing. Here we present a comprehensive evaluation of the performance of the new high-throughput sequencing platform BGISEQ-500 for metagenomic shotgun sequencing and compare its performance with that of 2 Illumina platforms. Using fecal samples from 20 healthy individuals, we evaluated the intra-platform reproducibility for metagenomic sequencing on the BGISEQ-500 platform in a setup comprising 8 library replicates and 8 sequencing replicates. Cross-platform consistency was evaluated by comparing 20 pairwise replicates on the BGISEQ-500 platform vs the Illumina HiSeq 2000 platform and the Illumina HiSeq 4000 platform. In addition, we compared the performance of the 2 Illumina platforms against each other. By a newly developed overall accuracy quality control method, an average of 82.45 million high-quality reads (96.06% of raw reads) per sample, with 90.56% of bases scoring Q30 and above, was obtained using the BGISEQ-500 platform. Quantitative analyses revealed extremely high reproducibility between BGISEQ-500 intra-platform replicates. Cross-platform replicates differed slightly more than intra-platform replicates, yet a high consistency was observed. Only a low percentage (2.02%–3.25%) of genes exhibited significant differences in relative abundance comparing the BGISEQ-500 and HiSeq platforms, with a bias toward genes with higher GC content being enriched on the HiSeq platforms. Our study provides the first set of performance metrics for human gut metagenomic sequencing data using BGISEQ-500. The high accuracy and technical reproducibility confirm the applicability of the new platform for metagenomic studies, though caution is still warranted when combining metagenomic data from different platforms.