Zongze Wu:
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In the first study, we research the genetic variation in North Asian populations. Genetic variation in North Asian populations is being sampled. By sequencing 175 Mongols from 6 tribes, we established a new genetic variation reference group. A classificatory change on the panels indicates a significant level of stratification among these tribes, which is likely related to historically different demographic histories in the region. Using data from the 1000 Genome Project, we determined that derived alleles are common to both Finns and Mongolians / Siberians, indicating gene flow across the two populations in the past significantly. Additionally, this study emphasizes that the relationship between populations in North, East, and South-East Asia is stronger than between those populations in South Asia and Oceania.
In the second study, as crucial predators in the ecosystem, spiders have complex venom and extraordinarily tough silk, allowing for the catch of large prey. Representing two main taxonomic categories of spiders, we present the completed genome of the velvet spider and the draft assembly of the tarantula genome. Featured in short exons and long introns, the spider genomes have similarities with mammalian genomes. The phylogenetic analysis indicates that spiders and ticks have a sister group relationship that supports their polyphyly. Multiple sets of silk and venom genes have also been identified. According to our research, venom developed through sequential replication and was likely activated by proteases within the venom. Serine kinase (SDS) encodes a protein whose function is related to silk. S-type cilia play an important role in the formation of silk fibers. In addition, filamentase is involved in the synthesis of sericin. New silk genes and proteins are identified in this series of silk genes, as well as new uses for needle-like silk. It is hoped that these insights will lead to new possibilities for venom-based medicines and the use of silk as a biomaterial.
In the third study, whole-genome sequencing of human genomes has been widely applied in research and started to be applied in clinical applications, thus comprehensive comparisons of sequencing data of different platforms are important, especially for new sequencing platforms. Here, we sequenced a cell line in the whole genome using four major second-generation sequencing platforms, including Illumina Hiseq, Life Ion Proton, Complete Genomics BlackBird and BGISEQ-500. We sequenced DNA from a cell line using these platforms and compared the sequencing quality, coverage, and variation calling results. Under the basis of ~30× genome data, ~1.28 million SNPs were concordant among all the platforms, while each platform had 80~500 thousand specific SNPs. A similar concordant rate was also found for insertions and deletions. Our results included analysis of data from new sequencing platforms thus providing novel insights for the data quality, accuracy, and completeness of second-generation sequencing platforms.
In the fourth study, the extraction kit for cell-free DNA from serum/plasma in this study includes: (1) magnetic bead lysis binding buffer, (2) first washing buffer, (3) second washing buffers, and (4) elution buffers. Cell-free DNA in plasma can be extracted quickly and easily by using the extraction kit, which only takes half an hour to complete the batch extraction without centrifugation. The quality of the extracted DNA is stable, and the results for subsequent sequencing and detection are accurate and reliable. It is completely applicable to the current non-invasive prenatal genetic testing technology and has important significance in scientific research and clinical testing.
In the fifth study, the DNA purification buffers included Tris-HCl, NaCl, NaN3, and polyethylene glycol. The final concentration of Tris-HCl is 100mmol/L-1mol/L, the final concentration of NaCl is 1mol/L-5mol/L, the final concentration of NaN3 is 0.02%w/v-1.00%w/v, and the final concentration of polyethylene glycol is 1%v/v-30%v/v. In this study, the DNA purification buffer was optimized for the composition and ratio of several reagents, so that the buffer can be used well in magnetic beads to purify DNA and improve the quality of magnetic beads. Based on the buffer in this study, it can completely replace expensive imported kits, while ensuring the quality of DNA purification, greatly reducing the cost of DNA purification research.