China’s bid to be a DNA superpower

Cyranoski, David

doi:10.1038/534462a

Cited by 15 publications

(7 citation statements)

References 3 publications

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“…Through these initiatives, China has become a major force in the field of DNA sequencing, and since the turn of the 21st century, research in genetics has advanced considerably in this country [54]. In 2010, the BGI became a global leader in DNA sequencing, collaborating with researchers around the world, and in 2016, it not only increased the velocity of its sequencing, but also reduced costs [55]. Between 2006 and 2010, China was the country with the second largest number of papers published in a number of different fields of research [56], and the findings of the present study corroborated this general tendency in the specific case of the papers that report on research in genetic diversity based on chloroplast markers.…”

Section: Discussionmentioning

confidence: 99%

Recent Trends in Research on the Genetic Diversity of Plants: Implications for Conservation

et al. 2019

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Genetic diversity and its distribution, both within and between populations, may be determined by micro-evolutionary processes, such as the demographic history of populations, natural selection, and gene flow. In plants, indices of genetic diversity (e.g., k, h and π) and structure (e.g., FST) are typically inferred from sequences of chloroplast markers. Given the recent advances and popularization of molecular techniques for research in population genetics, phylogenetics, phylogeography, and ecology, we adopted a scientometric approach to compile evidence on the recent trends in the use of cpDNA sequences as markers for the analysis of genetic diversity in botanical studies, over the years. We also used phylogenetic modeling to assess the relative contribution of relatedness or ecological and reproductive characters to the genetic diversity of plants. We postulated that genetic diversity could be defined not only by microevolutionary factors and life history traits, but also by relatedness, so that species more closely related phylogenetically would have similar genetic diversities. We found a clear tendency for an increase in the number of studies over time, confirming the hypothesis that the advances in the area of molecular genetics have supported the accumulation of data on the genetic diversity of plants. However, we found that the vast majority of these data have been produced by Chinese authors, and refer specifically to populations of Chinese plants. Most of the data on genetic diversity have been obtained for species in the International Union for Conservation of Nature (IUCN) category NE (Not Evaluated), which indicates a relative lack of attention on threatened species. In general, we observed very high FST values in the groups analyzed and, as we focused primarily on species that have not been evaluated by the IUCN, the number of plant species that are threatened with extinction may be much greater than that indicated by the listing of this organization. We also found that the number of haplotypes (k) was influenced by the type of geographic distribution of the plant, while haplotype diversity (h) was affected by the type of flower, and the fixation index (FST), by the type of habitat. The plant species most closely-related phylogenetically have similar levels of genetic diversity. Overall, then, it will important to consider phylogenetic dependence in future studies that evaluate the effects of life-history traits on plant genetic diversity.

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Section: Discussionmentioning

confidence: 99%

Recent Trends in Research on the Genetic Diversity of Plants: Implications for Conservation

et al. 2019

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“…Many initial studies have been carried out in populations of European descent, and it is still a challenge to extend the studies to other populations, especially to populations of Asian and African descent 4. Compared with other populations, genetic studies on IAs have rarely been carried out in Chinese populations, which is ill-matched with the increasing rate of sequencing in China 5. Two genetic variations in the Sox17 gene, rs1072737 (NC_000008.11: g.54501764T>G) and rs9298506 (NC_000008.10:g.55437524A>G), have been shown to be risk factors for IA 6–8.…”

Section: Introductionmentioning

confidence: 99%

<p>Genetic polymorphisms in <em>Sox17</em> associated with intracranial aneurysm in Chinese Han people: a genotype-phenotype study</p>

Wang

Zhang

et al. 2019

NDT

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Purpose Genetic factors play a vital role in intracranial aneurysm (IA) onset and development. Studying the relationship between IA and the Sox17 polymorphisms in diverse populations is essential for establishing credibility. Patients and methods We collected blood samples derived from a total of 596 sporadic IA patients and 600 individual controls in several medical institutes in China. We used the Sequenom MassArray system for single nucleotide polymorphisms (SNPs) genotyping after DNA extraction. The SNPs data was tested and analyzed in PLINK (version 1.9). Multiple-testing was performed in PLINK to make the statistics more rigorous and accurate. Results We found that the allelic G of rs1072737 (OR=1.303, genomic-control corrected P -value =0.001032) is a risk allele, while the allelic G of rs9298506 (OR=0.7253, genomic-control corrected P -value =0.01559) is a protective allele in Chinese Han people. Conclusion The allelic G of rs1072737 is a risk factor for IA, while the allelic G of rs9298506 serves as a protective factor for IA in Chinese Han people.

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“…Such high-throughput sequencing technologies generate millions to billions of reads in a matter of days and generate large datasets [6] -it has enabled a number of large-scale sequencing projects. These include the 100,000 genomes project in the UK [7,8], the NIH (National Institute of Health) 23,2020 Precision Medicine 1 million genomes project in the US [9], and a 1 million genome project by the BGI (Beijing Genome Institute) in China [10] to name just a few. Global collaboration, such as that of the International Cancer Genome Consortium (ICGC), which coordinates cancer genomics research across different nations [11] is now possible thanks to the availability of Next-generation sequencing technology.…”

Section: Introductionmentioning

confidence: 99%

Intra-exon motif correlations as a proxy measure for mean per-tile sequence quality data in RNA-Seq

Alnasir

Shanahan

2020

Preprint

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Given the wide variability in the quality of NGS data submitted to public repositories, it is essential to identify methods that can perform quality control on these datasets when additional quality control data, such as mean tile data, is missing. This is particularly important because such datasets are routinely deposited in public archives that now store data at an unprecedented scale. In this paper, we show that correlating counts of reads corresponding to pairs of motifs separated over specific distances on individual exons corresponds to mean tile data in the datasets we analysed, and can therefore be used when mean tile data is not available.As test datasets we use the H. sapiens IVT (in-vitro transcribed) dataset of Lahens et al., and a D. melanogaster dataset comprising wild and mutant types from Aerts et al.The intra-exon motif correlations as a function of both GC content parameters are much higher in the IVT-Plasmids mRNA selection free RNA-Seq sample (control) than in the other RNA-Seq samples that did undergo mRNA selection: both ribosomal depletion (IVT-Only) and PolyA selection (IVT-polyA, wild-type, and mutant). There is considerable degradation of similar correlations in the mutant samples from the D. melanogaster dataset. This matches with the available mean tile data that has been gathered for these datasets. We observe that extremely low correlations are indicative of bias of technical origin, such as flowcell errors.

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China’s bid to be a DNA superpower

Cited by 15 publications

References 3 publications

Recent Trends in Research on the Genetic Diversity of Plants: Implications for Conservation

Recent Trends in Research on the Genetic Diversity of Plants: Implications for Conservation

<p>Genetic polymorphisms in <em>Sox17</em> associated with intracranial aneurysm in Chinese Han people: a genotype-phenotype study</p>

Intra-exon motif correlations as a proxy measure for mean per-tile sequence quality data in RNA-Seq

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