Comparison between MGI and Illumina sequencing platforms for whole genome sequencing

Jeon, Sol A; Park, Jong‐Lyul; Park, Seung-Jin; Kim, Jeong Hwan; Goh, Sung‐Ho; Han, Ji‐Youn; Kim, Seon‐Young

doi:10.1007/s13258-021-01096-x

Cited by 57 publications

(34 citation statements)

References 17 publications

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“…By using the same amplicon pools of ~313-bp COI marker gene fragment for platform-specific library preparation and sequence data generation on DNBSEQ-G400RS and NovaSeq 6000 platforms, we demonstrate strongly correlating community and richness profiles. The overall similarities between two short-read sequencing platforms corroborate earlier studies on metabarcoding of bacteria (Sun et al, 2021) and genomics of various organisms (Jeon et al, 2021;Kim et al, 2021).…”

Section: Discussionsupporting

confidence: 83%

“…(e.g., MiSeq and NovaSeq) using sequencing-by-synthesis technology are dominating the market as they offer viable solutions for both ultra-high sequencing depth and paired-end sequencing of short-and mid-sized amplicons (up to 500-600 bases; Kumar, Cowley & Davis, 2019). By utilizing recent advances in DNA nanoball sequencing technology (Drmanac et al, 2010;Li et al, 2019), MGI-Tech, Inc. has produced several DNBSEQ (MGISEQ) platforms with similar throughput and quality profiles compared with Illumina sequencing (Jeon et al, 2021;Kumar, Cowley & Davis, 2019). The results from Illumina and MGI-Tech sequencing platforms are highly comparable and may be used interchangeably for RNA sequencing and whole genome sequencing (Jeon et al, 2019;Kim et al, 2021;Korostin et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

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Highly comparable metabarcoding results from MGI-Tech and Illumina sequencing platforms

Anslan

Mikryukov

Armolaitis

et al. 2021

PeerJ

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With the developments in DNA nanoball sequencing technologies and the emergence of new platforms, there is an increasing interest in their performance in comparison with the widely used sequencing-by-synthesis methods. Here, we test the consistency of metabarcoding results from DNBSEQ-G400RS (DNA nanoball sequencing platform by MGI-Tech) and NovaSeq 6000 (sequencing-by-synthesis platform by Illumina) platforms using technical replicates of DNA libraries that consist of COI gene amplicons from 120 soil DNA samples. By subjecting raw sequencing data from both platforms to a uniform bioinformatics processing, we found that the proportion of high-quality reads passing through the filtering steps was similar in both datasets. Per-sample operational taxonomic unit (OTU) and amplicon sequence variant (ASV) richness patterns were highly correlated, but sequencing data from DNBSEQ-G400RS harbored a higher number of OTUs. This may be related to the lower dominance of most common OTUs in DNBSEQ data set (thus revealing higher richness by detecting rare taxa) and/or to a lower effective read quality leading to generation of spurious OTUs. However, there was no statistical difference in the ASV and post-clustered ASV richness between platforms, suggesting that additional denoising step in the ASV workflow had effectively removed the ‘noisy’ reads. Both OTU-based and ASV-based composition were strongly correlated between the sequencing platforms, with essentially interchangeable results. Therefore, we conclude that DNBSEQ-G400RS and NovaSeq 6000 are both equally efficient high-throughput sequencing platforms to be utilized in studies aiming to apply the metabarcoding approach, but the main benefit of the former is related to lower sequencing cost.

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Section: Discussionsupporting

confidence: 83%

Section: Introductionmentioning

confidence: 99%

Highly comparable metabarcoding results from MGI-Tech and Illumina sequencing platforms

Anslan

Mikryukov

Armolaitis

et al. 2021

PeerJ

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“…Gene+Seq2000 utilizes a state-of-the-art core technology called DNBSEQ. It has the same mechanism as MGI sequencing platforms, which has a comparable performance to Illumina NovaSeq 6000 [ 19 ]. Gene+Seq2000 has high accuracy with 99.69% on human genomic sequencing.…”

Section: Methodsmentioning

confidence: 99%

Genetic and treatment profiles of patients with concurrent Epidermal Growth Factor Receptor (EGFR) and Anaplastic Lymphoma Kinase (ALK) mutations

Yang

Zhong

et al. 2021

BMC Cancer

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Background EGFR and ALK alternations often contribute to human malignancies, including lung cancer. EGFR and ALK mutations are usually sensitive to EGFR-tyrosine kinase inhibitors (TKIs) and ALK-TKIs. Although generally mutually exclusive, these mutations do co-exist in rare cases. This study investigated the frequencies, clinical characteristics, therapeutic efficacies, and genetic profiles of lung cancer patients with EGFR and ALK co-mutations. Methods Patients with concurrent EGFR and ALK mutations were included in this study, which analyzed mutation profiles and treatment histories. SPSS20.0 were used for survival analysis. Results Among 271 ALK-positive (ALK-pos) and 2975 EGFR-positive (EGFR-pos) patients in our database, nine (2.6% of ALK-pos and 0.2% of EGFR-pos) patients had concurrent EGFR and ALK mutations (including three exon19 Indel + EML4-ALK, two exon19 Indel + STRN-ALK, two L858R + L1152R, one L858R + EML4-ALK, and one G719C + S768I + STRN-ALK). Eight patients had at least one type of EGFR-TKIs treatment. The median progression free survival (PFS) of these patients on first-generation EGFR-TKIs was 14.5 months (95% CI: 11 - NR). Of these eight patients, one who progressed on Gefitinib and subsequently on Osimertinib had a T790M + C797G. The other seven EGFR-TKIs resistance patients had no known resistance mutations. No patients had ALK mutations before treatment, so ALK mutations may have developed as resistance mechanisms during EGFR-TKIs therapies. EGFR-TKIs-treated patients with EGFR/ALK L1152R mutations generally had a shorter PFS than patients with other mutation combinations. Conclusions ALK and EGFR mutations coincide at a relatively low frequency in lung cancer patients. ALK mutations developed either synchronously or heterochronously with EGFR mutations. Two ALK mutations (L1152R and STRN-ALK) may co-exist with EGFR mutations at a higher frequency than others. Most EGFR/ALK co-alteration patients (other than the EGFR/ALK L1152R type) can benefit from first line EGFR-TKIs.

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“…This technology offers a range of platforms, including HiSeq 2500, HiSeq 2000, Genome Analyzer IIx, and MiSeq platform genome, NextSeq 550 series, Iseq 100, and MiniSeq ( Table 1 ), with HiSeq 2500 being most powerful and delivering up to 600 Gb of data at up to six billion reads per run (at approximately 2 × 100 bp read length) ( Jeon et al., 2021 ; Modi et al., 2021 ). The Illumina sequencers would have shorter reads with a much higher throughput, which makes them more fit for gene expression studies.…”

Section: Molecular Tools To Evaluate Soil Microbial Communitiesmentioning

confidence: 99%

High-throughput molecular technologies for unraveling the mystery of soil microbial community: challenges and future prospects

Lahlali

Ibrahim

Belabess

et al. 2021

Heliyon

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Soil microbial communities play a crucial role in soil fertility, sustainability, and plant health. However, intensive agriculture with increasing chemical inputs and changing environments have influenced native soil microbial communities. Approaches have been developed to study the structure, diversity, and activity of soil microbes to better understand the biology and plant-microbe interactions in soils. Unfortunately, a good understanding of soil microbial community remains a challenge due to the complexity of community composition, interactions of the soil environment, and limitations of technologies, especially related to the functionality of some taxa rarely detected using conventional techniques. Culture-based methods have been shown unable and sometimes are biased for assessing soil microbial communities. To gain further knowledge, culture-independent methods relying on direct analysis of nucleic acids, proteins, and lipids are worth exploring. In recent years, metagenomics, metaproteomics, metatranscriptomics, and proteogenomics have been increasingly used in studying microbial ecology. In this review, we examined the importance of microbial community to soil quality, the mystery of rhizosphere and plant-microbe interactions, and the biodiversity and multi-trophic interactions that influence the soil structure and functionality. The impact of the cropping system and climate change on the soil microbial community was also explored. Importantly, progresses in molecular biology, especially in the development of high-throughput biotechnological tools, were extensively assessed for potential uses to decipher the diversity and dynamics of soil microbial communities, with the highlighted advantages/limitations.

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Comparison between MGI and Illumina sequencing platforms for whole genome sequencing

Cited by 57 publications

References 17 publications

Highly comparable metabarcoding results from MGI-Tech and Illumina sequencing platforms

Highly comparable metabarcoding results from MGI-Tech and Illumina sequencing platforms

Genetic and treatment profiles of patients with concurrent Epidermal Growth Factor Receptor (EGFR) and Anaplastic Lymphoma Kinase (ALK) mutations

High-throughput molecular technologies for unraveling the mystery of soil microbial community: challenges and future prospects

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