Comparative analysis of 7 short-read sequencing platforms using the Korean Reference Genome: MGI and Illumina sequencing benchmark for whole-genome sequencing.
Comparative analysis of 7 short-read sequencing platforms using the Korean Reference Genome: MGI and Illumina sequencing benchmark for whole-genome sequencing.
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使用韩国参考基因组：MGI和Illumina测序基准对7个短读测序平台进行全基因组测序的比较分析。
DOI：
10.1093/gigascience/giab014
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发表时间：
2021-03-12
期刊：
影响因子：
9.2
通讯作者：
Bhak J
中科院分区：
文献类型：
--
作者：
Kim HM;Jeon S;Chung O;Jun JH;Kim HS;Blazyte A;Lee HY;Yu Y;Cho YS;Bolser DM;Bhak J
DNBSEQ-T7是Complete Genomics和华大智造联合开发的一款新型全基因组测序仪，采用DNA纳米球和组合探针锚定合成技术，可大规模生成短读长——每天最多60个人类基因组。然而，它尚未与 Illumina 短读长测序仪进行客观、系统的比较。通过使用相同的KOREF样本，即韩国参考基因组，我们比较了BGISEQ-500、DNBSEQ-T7、HiSeq2000、HiSeq2500、HiSeq4000、HiSeqX10和NovaSeq6000等7个测序平台。我们通过比较 7 个测序平台的测序统计数据（碱基质量、重复率和随机错误率）、作图统计数据（作图率、深度分布和 GC 覆盖百分比）和变异统计数据（转换/颠换比率、dbSNP 注释率以及与单核苷酸多态性 [SNP] 基因分型芯片的一致性率）来测量测序质量。我们发现华大智造平台的SNP基因分型一致性率高于HiSeq2000和HiSeq4000。变异调用的相似性矩阵证实了两个MGI平台与HiSeq2500平台具有最相似的特征。总体而言，MGI 和 Illumina 测序平台在测序质量、覆盖均匀性、GC 覆盖百分比和变异准确性方面表现出相当的水平；因此我们得出的结论是，MGI 平台可以比 Illumina 平台以更低的成本用于广泛的基因组学研究领域。
DNBSEQ-T7 is a new whole-genome sequencer developed by Complete Genomics and MGI using DNA nanoball and combinatorial probe anchor synthesis technologies to generate short reads at a very large scale—up to 60 human genomes per day. However, it has not been objectively and systematically compared against Illumina short-read sequencers. By using the same KOREF sample, the Korean Reference Genome, we have compared 7 sequencing platforms including BGISEQ-500, DNBSEQ-T7, HiSeq2000, HiSeq2500, HiSeq4000, HiSeqX10, and NovaSeq6000. We measured sequencing quality by comparing sequencing statistics (base quality, duplication rate, and random error rate), mapping statistics (mapping rate, depth distribution, and percent GC coverage), and variant statistics (transition/transversion ratio, dbSNP annotation rate, and concordance rate with single-nucleotide polymorphism [SNP] genotyping chip) across the 7 sequencing platforms. We found that MGI platforms showed a higher concordance rate for SNP genotyping than HiSeq2000 and HiSeq4000. The similarity matrix of variant calls confirmed that the 2 MGI platforms have the most similar characteristics to the HiSeq2500 platform. Overall, MGI and Illumina sequencing platforms showed comparable levels of sequencing quality, uniformity of coverage, percent GC coverage, and variant accuracy; thus we conclude that the MGI platforms can be used for a wide range of genomics research fields at a lower cost than the Illumina platforms.
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影响因子：
7
作者：
Huddleston J;Chaisson MJP;Steinberg KM;Warren W;Hoekzema K;Gordon D;Graves-Lindsay TA;Munson KM;Kronenberg ZN;Vives L;Peluso P;Boitano M;Chin CS;Korlach J;Wilson RK;Eichler EE
通讯作者：
Eichler EE
影响因子：
4.4
作者：
Oyola SO;Otto TD;Gu Y;Maslen G;Manske M;Campino S;Turner DJ;Macinnis B;Kwiatkowski DP;Swerdlow HP;Quail MA
通讯作者：
Quail MA
使用下一代 DNA 测序数据进行变异发现和基因分型的框架。
影响因子：
30.8
作者：
通讯作者：
--
影响因子：
3.7
作者：
Rhodes J;Beale MA;Fisher MC
通讯作者：
Fisher MC
影响因子：
9.2
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
通讯作者：
Li J