Here we present the first diploid genome sequence of an Asian individual. The genome was sequenced to 36-fold average coverage using massively parallel sequencing technology. We aligned the short reads onto the NCBI human reference genome to 99.97% coverage, and guided by the reference genome, we used uniquely mapped reads to assemble a high-quality consensus sequence for 92% of the Asian individual's genome. We identified approximately 3 million single-nucleotide polymorphisms (SNPs) inside this region, of which 13.6% were not in the dbSNP database. Genotyping analysis showed that SNP identification had high accuracy and consistency, indicating the high sequence quality of this assembly. We also carried out heterozygote phasing and haplotype prediction against HapMap CHB and JPT haplotypes (Chinese and Japanese, respectively), sequence comparison with the two available individual genomes (J. D. Watson and J. C. Venter), and structural variation identification. These variations were considered for their potential biological impact. Our sequence data and analyses demonstrate the potential usefulness of next-generation sequencing technologies for personal genomics.

No abstract

BackgroundGenes related to antigen presentation pathway, which are in the non-classical class-II region of human leukocyte antigen (HLA), play a vital role during the infection of hepatitis C virus (HCV).MethodsThe current study determined the genotypes of 34 tagging-SNPs (single nucleotide polymorphisms) from 9 candidate genes (HLA-DMA, HLA-DMB, HLA-DOA, HLA-DOB, TAP1, TAP2, LMP2, LMP7, and tapasin) in a Chinese population of paid blood donors with high risk of HCV infection. The distributions of those SNPs were compared among the 1207 former paid blood donors with different HCV infection outcomes.ResultsHLA-DMA rs1063478 and HLA-DOA rs2284191 were independent factors of acquiring HCV infection. Carrying three favorable alleles of rs1063478-T and rs2284191-G offered the highest protective effect (odds ratio = 0.46, 95% confidence intervals = 0.27-0.78). HLA-DOB rs7383287 and LMP2 rs17587 were independent factors of infection chronicity. Subjects carrying two favorable alleles of rs7383287-G and rs17587-A had a decreased risk of HCV chronicity (odds ratio = 0.42, 95% confidence intervals = 0.26-0.66). The interaction analysis showed that experience of plasma donation interacted with the combined effects of rs1063478 and rs2284191 for HCV susceptibility, and the experience of whole blood donation interacted with the association of rs7383287 with HCV clearance.ConclusionsOur results suggested that genetic variants in antigen presentation pathway had influence on susceptibility to HCV infection and viral clearance. HLA-DMA rs1063478, HLA-DOA rs2284191, and HLA-DOB rs7383287 were identified as novel loci in Chinese population that were involved in HCV infection.Electronic supplementary materialThe online version of this article (doi:10.1186/s12879-014-0716-8) contains supplementary material, which is available to authorized users.

No abstract

BACKGROUND Iron (Fe)‐containing groundwater treatment residual is a kind of waste from groundwater treatment plants, showing good potential to be reused. Attention has been paid to Fe‐based magnetic water treatment materials for their easy magnetic separation, and in the meantime, kinds of adsorbents were developed to address the severe global dyes pollution. RESULTS Black magnetic material was obtained with using the iron‐containing wastes as iron source without adding other iron chemical reagents by hydrothermal reaction. The X‐ray diffraction (XRD), X‐ray photoelectron spectroscopy (XPS) and Fourier‐transform infrared (FTIR) results show that the product is comprised of crystalline iron(II,III) oxide (Fe3O4) core and amorphous carbon shell (Fe3O4@C), and the core‐shell structure can also been seen clearly in transmission electron microscopy (TEM) images. Vibrating sample magnetometer (VSM) result shows its saturation magnetization is 33.56 emu/g. This sample's sorption experiments for methylene blue (MB) removal were conducted, and the experiment results indicated that this sample could be used in a wide range of pH (5–12) and the adsorption might be a complex chemical diffusion process consisting of boundary layer effect due to kinetic modeling fitting analysis. The maximum sorption amount of MB was 16.33 and 19.13 mg/g, respectively at 298 K and 308 K. This sample after five regeneration cycles still had 72.1% MB removal rate. CONCLUSION The Fe3O4@C particles with good magnetism were synthesized successfully with Fe‐containing water treatment residuals, water treatment waste sludge, via a one‐step hydrothermal reaction, which could be of reasonable analogy for treating other Fe‐containing industrial waste. Furthermore, this sample could be used as adsorbent for MB molecules removal from dyed water with good reusability and easy magnetic separation. © 2019 Society of Chemical Industry