A new massively parallel nanoball sequencing platform for whole exome research

Xu, Yu; Zhe, Liu; Tang, Chong; Tang, Y. Tom; Cai, Yuchen; Huang, Zhong; Wang, Xuebin; Zhang, Wenwei; Xu, Chongjun; Wang, Jingjing; Wang, Jian; Yang, Huanming; Yang, L.; Gao, Qiang

doi:10.1186/s12859-019-2751-3

Cited by 63 publications

(46 citation statements)

References 17 publications

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“…For example, the MGISEQ-2000 currently generates 1.44 TB of sequence data in a single run with a running cost of 10 USD/GB. Several recent studies have compared the performance of BGI sequencers with Illumina’s sequencers and showed that the BGI sequencers produced high-quality sequence data at lower or similar prices in studies of whole-exome [2,3], whole-genome [4][1], transcriptome [5,6], single-cell transcriptome [2,78], metagenome [9], and small RNA sequencing [10].…”

Section: Introductionmentioning

confidence: 99%

Comparison of the MGISEQ-2000 and Illumina HiSeq 4000 sequencing platforms for RNA sequencing

et al. 2019

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Currently, Illumina sequencers are the globally leading sequencing platform in the next-generation sequencing market. Recently, MGI Tech launched a series of new sequencers, including the MGISEQ-2000, which promise to deliver high-quality sequencing data faster and at lower prices than Illumina's sequencers. In this study, we compared the performance of two major sequencers (MGISEQ-2000 and HiSeq 4000) to test whether the MGISEQ-2000 sequencer delivers high-quality sequence data as suggested. We performed RNA sequencing of four human colon cancer samples with the two platforms, and compared the sequencing quality and expression values. The data produced from the MGIS-EQ-2000 and HiSeq 4000 showed high concordance, with Pearson correlation coefficients ranging from 0.98 to 0.99. Various quality control (QC) analyses showed that the MGIS-EQ-2000 data fulfilled the required QC measures. Our study suggests that the performance of the MGISEQ-2000 is comparable to that of the HiSeq 4000 and that the MGISEQ-2000 can be a useful platform for sequencing.

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Section: Introductionmentioning

confidence: 99%

Comparison of the MGISEQ-2000 and Illumina HiSeq 4000 sequencing platforms for RNA sequencing

et al. 2019

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“…This includes rolling circle replication and a novel DNA nanoball (DNB™) technology that leads to less CG bias compared to PCR assays and assures high signal to noise ratio (SNR) imaging for accurate base calling. BGISEQ is a reliable sequencing platform as recently reported by Xu and colleagues who compared BGISEQ to HiSEQ4000 platform and BGISEQ demonstrated similarly high reproducibility as HiSeq for variation detection [20]. In addition, Mak and colleagues reported a comparative performance of the BGISEQ-500 versus Illumina HiSeq2500 for WGS of ancient DNA [21].…”

Section: Discussionmentioning

confidence: 94%

Prospect and challenge of detecting dynamic gene copy number increases in stem cells by whole genome sequencing

et al. 2019

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Gene amplification is an evolutionarily well-conserved and highly efficient mechanism to increase the amount of specific proteins. In humans, gene amplification is a hallmark of cancer and has recently been found during stem cell differentiation. Amplifications in stem cells are restricted to specific tissue areas and time windows, rendering their detection difficult. Here, we report on the performance of deep WGS sequencing (average 82-fold depth of coverage) on the BGISEQ with nanoball technology to detect amplifications in human mesenchymal and neural stem cells. As reference technology, we applied array-based comparative genomic hybridization (aCGH), fluorescence in situ hybridization (FISH), and qPCR. Using different in silico strategies for amplification detection, we analyzed the potential of WGS for amplification detection. Our results provide evidence that WGS accurately identifies changes of the copy number profiles in human stem cell differentiation. However, the identified changes are not in all cases consistent between WGS and aCGH. The results between WGS and the validation by qPCR were concordant in 83.3% of all tested 36 cases. In sum, both genome-wide techniques, aCGH and WGS, have unique advantages and specific challenges, calling for locus-specific confirmation by the low-throughput approaches qPCR or FISH. Key messages WGS allows for the identification of dynamic copy number changes in human stem cells. Less stringent threshold setting is crucial for detection of copy number increase. Broad knowledge of dynamic copy number is pivotal to estimate stem cell capabilities. Electronic supplementary material The online version of this article (10.1007/s00109-019-01792-y) contains supplementary material, which is available to authorized users.

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“…Revolutionary NGS technologies have decreased the cost of genome sequencing, and they provide several hundred millions or billions of short DNA sequences on the surface of a flow cell for the study of protein-DNA interactions. In addition to Illumina's HiSeq, NextSeq, and NovaSeq platforms, Beijing Genomics Institute (BGI's) BGISEQ-500 and MGISEQ-2000 sequencing platforms have been extensively used in applications such as exon sequencing (12), single-cell RNA sequencing (13), small noncoding RNA analysis (14), and noninvasive prenatal testing (NIPT) (15). The technology underlying BGISEQ-500 or MGISEQ-2000 combines DNA nanoball (DNB) nanoarrays (16) with polymerase-based stepwise sequencing (DNBSEQ).…”

Section: Introductionmentioning

confidence: 99%

DNB-based on-chip motif finding: A high-throughput method to profile different types of protein-DNA interactions

Wang

et al. 2020

Sci. Adv.

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Here, we report a sensitive DocMF system that uses next-generation sequencing chips to profile protein-DNA interactions. Using DocMF, we successfully identified a variety of endonuclease recognition sites and the protospacer adjacent motif (PAM) sequences of different CRISPR systems. DocMF can simultaneously screen both 5′ and 3′ PAMs with high coverage. For SpCas9, we found noncanonical 5′-NAG-3′ (~5%) and 5′-NGA-3′ (~1.6%), in addition to its common PAMs, 5′-NGG-3′ (~89.9%). More relaxed PAM sequences of two uncharacterized Cas endonucleases, VeCas9 and BvCas12a, were extensively characterized using DocMF. Moreover, we observed that dCas9, a DNA binding protein lacking endonuclease activity, preferably bound to the previously reported 5′-NGG-3′ sequence. In summary, our studies demonstrate that DocMF is the first tool with the capacity to exhaustively assay both the binding and the cutting properties of different DNA binding proteins.

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A new massively parallel nanoball sequencing platform for whole exome research

Cited by 63 publications

References 17 publications

Comparison of the MGISEQ-2000 and Illumina HiSeq 4000 sequencing platforms for RNA sequencing

Comparison of the MGISEQ-2000 and Illumina HiSeq 4000 sequencing platforms for RNA sequencing

Prospect and challenge of detecting dynamic gene copy number increases in stem cells by whole genome sequencing

DNB-based on-chip motif finding: A high-throughput method to profile different types of protein-DNA interactions

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