Single molecule sequencing of the M13 virus genome without amplification

Zhao, Lei; Deng, Liwei; Li, Gailing; Huan, Jianya; Cai, Jinsen; Shang, Huan; Li, Yán; Wu, Haomin; Xu, Weibin; Zeng, Lidong; Zhang, Renli; Zhao, Huan; Wu, Ping; Zhou, Zhongwu; Zheng, Jiao; Ezanno, Pierre; Yang, Andrew X.; Yan, Qin; Deem, Michael W.; He, Jiankui

doi:10.1371/journal.pone.0188181

Cited by 12 publications

(5 citation statements)

References 31 publications

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“…Third-generation sequencing was performed on the single-molecule sequencer GenoCare at the GeneMind Biosciences Company Limited, Guangzhou, China. GenoCare sequencing was performed according to a previously disclosed protocol [ 11 ]. We found that the two patients’ deletions were identical; both were 6.0 Mb, with breakpoints at 44850001 bp and 50,850,001 bp (GRCh37/hg19).…”

Section: Case Presentationmentioning

confidence: 99%

Fraternal twins with Phelan-McDermid syndrome not involving the SHANK3 gene: case report and literature review

Liu

et al. 2020

BMC Med Genomics

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Background Phelan-McDermid syndrome (PMS, OMIM#606232), or 22q13 deletion syndrome, is a rare genetic disorder caused by deletion of the distal long arm of chromosome 22 with a variety of clinical features that display considerably heterogeneous degrees of severity. The SHANK3 gene is understood to be the critical gene for the neurological features of this syndrome. Case presentation We describe one pair of boy-girl twins with a 22q13 deletion not involving the SHANK3 gene. Interestingly, the clinical and molecular findings of the two patients were identical, likely resulting from germline mosaicism in a parent. The boy-girl twins showed intellectual disability, speech absence, facial dysmorphism, cyanosis, large fleshy hands and feet, dysplastic fingernails and abnormal behaviors, and third-generation sequencing showed an identical de novo interstitial deletion of 6.0 Mb in the 22q13.31-q13.33 region. Conclusions Our case suggests that prenatal diagnosis is essential for normal parents with affected children due to the theoretical possibility of parental germline mosaicism. Our results also indicated that other genes located in the 22q13 region may have a role in explaining symptoms in individuals with PMS. In particular, we propose that four candidate genes, CELSR1, ATXN10, FBLN1 and WNT7B, may also be involved in the etiology of the clinical features of PMS. However, more studies of smaller interstitial deletions with 22q13 are needed to corroborate our hypothesis and better define the genotype-phenotype correlation. Our findings contribute to a more comprehensive understanding of PMS.

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Section: Case Presentationmentioning

confidence: 99%

Fraternal twins with Phelan-McDermid syndrome not involving the SHANK3 gene: case report and literature review

Liu

et al. 2020

BMC Med Genomics

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“…Recently, GeneMind Biosciences Company Limited (GeneMind), launched a new sequencing instrument (GenoLab M™) based on their previous work on Geno-Care™ single molecule sequencer [16]. An overview of the mechanism of GenoLab M DNA sequencer is outlined in Fig.…”

Section: Introductionmentioning

confidence: 99%

Comparative performance of the GenoLab M and NovaSeq 6000 sequencing platforms for transcriptome and LncRNA analysis

et al. 2021

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Background GenoLab M is a recently established next-generation sequencing platform from GeneMind Biosciences. Presently, Illumina sequencers are the globally leading sequencing platform in the next-generation sequencing market. Here, we present the first report to compare the transcriptome and LncRNA sequencing data of the GenoLab M sequencer to NovaSeq 6000 platform in various types of analysis. Results We tested 16 libraries in three species using various library kits from different companies. We compared the data quality, genes expression, alternatively spliced (AS) events, single nucleotide polymorphism (SNP), and insertions–deletions (InDel) between two sequencing platforms. The data suggested that platforms have comparable sensitivity and accuracy in terms of quantification of gene expression levels with technical compatibility. Conclusions Genolab M is a promising next-generation sequencing platform for transcriptomics and LncRNA studies with high performance at low costs.

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“…The samples were sequenced on Genemind Bioscience's single-molecule sequencer GenoCare and Illumina's HiseqX10 sequencer, yielding more than 4% genome coverage for each sample. GenoCare sequencing was performed according to the previously disclosed protocol [11]. For each sample, 25% of the area of each flowcell channel was imaged, and 72 cycles of sequencing data were collected, yielding more than 4 million reads.…”

Section: Sequencing and Data Analysismentioning

confidence: 99%

Accurate CNV identification from only a few cells with low GC bias in a single-molecule sequencing platform

Lin²,

Xie

et al. 2020

Preprint

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A technical problem of characterizing copy number variation of several cells with next-generation sequencing is the whole genome amplification induced bias. The result of CNVs and mosaicism detection is affected by the GC bias. Here, we report a rapid non-WGA sample preparation strategy for a single-molecule sequencing platform GenoCare1600. This approach, combined with a single-molecule sequencing platform that avoids the use of WGA and bridge PCR processes, can provide higher reliability with its lower GC bias. By combining our optimized Tn5-based transposon insertion approach with GenoCare, we successfully detected CNVs as small as 1.29M and mosaicism as small as 20%, which is consistent with next-generation sequencing (NGS) data. Moreover, our GenoCare-TTI protocol showed less GC bias and less Mad of Diff. These results suggest that the optimized TTI approach, together with the GenoCare1600 sequencing platform, is a promising option for CNV characterization from maybe one single cell.

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Single molecule sequencing of the M13 virus genome without amplification

Cited by 12 publications

References 31 publications

Fraternal twins with Phelan-McDermid syndrome not involving the SHANK3 gene: case report and literature review

Fraternal twins with Phelan-McDermid syndrome not involving the SHANK3 gene: case report and literature review

Comparative performance of the GenoLab M and NovaSeq 6000 sequencing platforms for transcriptome and LncRNA analysis

Accurate CNV identification from only a few cells with low GC bias in a single-molecule sequencing platform

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