High sensitivity multiplex short tandem repeat loci analyses with massively parallel sequencing

STR typing in forensic genetics has been performed traditionally using capillary electrophoresis (CE). However, CE-based method has some limitations: a small number of STR loci can be used; stutter products, dye artifacts and low level alleles. Massively parallel sequencing (MPS) has been considered a viable technology in recent years allowing high-throughput coverage at a relatively affordable price. Some of the CE-based limitations may be overcome with the application of MPS. In this study, a prototype multiplex STR System (Promega) was amplified and prepared using the TruSeq DNA LT Sample Preparation Kit (Illumina) in 24 samples. Results showed that the MinElute PCR Purification Kit (Qiagen) was a better size selection method compared with recommended diluted bead mixtures. The library input sensitivity study showed that a wide range of amplicon product (6–200 ng) could be used for library preparation without apparent differences in the STR profile. PCR sensitivity study indicated that 62 pg may be minimum input amount for generating complete profiles. Reliability study results on 24 different individuals showed that high depth of coverage (DoC) and balanced heterozygote allele coverage ratios (ACRs) could be obtained with 250 pg of input DNA, and 62 pg could generate complete or nearly complete profiles. These studies indicate that this STR multiplex system and the Illumina MiSeq can generate reliable STR profiles at a sensitivity level that competes with current widely used CE-based method.     

肝癌患者肠道微生态结构变化的特点分析

目的探讨原发性肝癌患者肠道菌群结构的变化。方法选择2017年9月至2018年12月广东省第二人民医院诊疗的原发性肝癌患者87例,另取健康体检者80名作为健康对照。制备微生物基因组DNA后Illumina平台进行高通量测序。结果原发性肝癌组和健康对照组间α多样性差异无统计学意义(P>0.05)。肝癌组拟杆菌门和变形菌门所占百分比为(56.41±4.63)%和(9.26±1.82)%,显著高于健康对照组的(53.32±4.22)%和(7.42±1.16)%(均P<0.05)。肝癌组厚壁菌门和放线菌门所占百分比为(32.62±3.75)%和(0.34±0.05)%,显著低于健康对照组的(37.25±4.13)%和(0.62±0.11)%(均P<0.05)。肝癌组拟杆菌属和大肠杆菌螺旋杆菌属所占百分比为(50.83±4.15)%和(11.35±1.87)%,显著高于健康对照组的(42.45±3.84)%和(8.52±1.71)%(均P<0.01)。肝癌组双歧杆菌属和梭菌属所占百分比为(21.13±3.64)%和(10.44±1.25)%,显著低于健康对照组的(28.54±4.13)%和(14.28±1.52)%(均P<0.01)。结论肝癌患者肠道微生态系统中拟杆菌以及其隶属的拟杆菌门,大肠杆菌螺旋杆菌属属以及其隶属的变形菌门所占比例明显著高于对照组,双歧杆菌属以及其隶属的放线菌门和梭菌属以及其隶属的厚壁菌门所占比例明显著低于对照组。     

Common epigenetic variation in a European population of mentally healthy young adults

DNA methylation represents an important link between structural genetic variation and complex phenotypes. The study of genome-wide CpG methylation and its relation to traits relevant to psychiatry has become increasingly important. Here, we analyzed quality metrics of 394,043 CpG sites in two samples of 568 and 319 mentally healthy young adults. For 25% of all CpGs we observed medium to large common epigenetic variation. These CpGs were overrepresented in open sea and shore regions, as well as in intergenic regions. They also showed a strong enrichment of significant hits in association analyses. Furthermore, a significant proportion of common DNA methylation is at least partially genetically driven and thus may be observed similarly across tissues. These findings could be of particular relevance for studies of complex neuropsychiatric traits, which often rely on proxy tissues.     

Advances in DNA sequencing technologies for high resolution HLA typing

This communication describes our experience in large-scale G group-level high resolution HLA typing using three different DNA sequencing platforms – ABI 3730 xl, Illumina MiSeq and PacBio RS II. Recent advances in DNA sequencing technologies, so-called next generation sequencing (NGS), have brought breakthroughs in deciphering the genetic information in all living species at a large scale and at an affordable level. The NGS DNA indexing system allows sequencing multiple genes for large number of individuals in a single run. Our laboratory has adopted and used these technologies for HLA molecular testing services. We found that each sequencing technology has its own strengths and weaknesses, and their sequencing performances complement each other. HLA genes are highly complex and genotyping them is quite challenging. Using these three sequencing platforms, we were able to meet all requirements for G group-level high resolution and high volume HLA typing.     

唐氏综合征胎儿全基因组miRNA表达谱特征及其染色体分布

目的研究唐氏综合征(DS)胎儿全基因组miRNA表达谱及其编码基因的染色体分布特征。方法采用Illumina深度测序技术对6例DS胎儿(DS组)和6例正常胎儿脐带血(对照组)单个核细胞小RNA测序比对分析,确定DS全基因组miRNA表达谱及其编码基因的染色体分布特征。结果两组共检测到395种miRNA,编码于316个miRNA基因。其中149种miRNA在两组中的表达具有显著性差异(DS组中6种上调,143种下调),有51种miRNA特异性表达于对照组。21号染色体编码的14个miRNA基因在DS组中有1个(miR-802)高表达,4个(let-7c、miR-99a、miR-125b和miR-155)低表达,余下9个在两组样本中均未表达。两组样本miRNA基因表达的染色体分布趋于一致,但miRNA基因表达丰度的分布却不尽相同:DS组主要分布于8、16、17和21号染色体,对照组主要分布于3、8、14、16、17和22号染色体。结论 DS胎儿脐带血单个核细胞具有其特定的miRNA表达谱和染色体分布特征,表达丰度差异分布的染色体编码miRNA可能在DS各临床性状的形成过程中具有重要作用。     

Colonic In Vitro Model Assessment of the Prebiotic Potential of Bread Fortified with Polyphenols Rich Olive Fiber

The use of olive pomace could represent an innovative and low-cost strategy to formulate healthier and value-added foods, and bakery products are good candidates for enrichment. In this work, we explored the prebiotic potential of bread enriched with Polyphenol Rich Fiber (PRF), a defatted olive pomace byproduct previously studied in the European Project H2020 EcoProlive. To this aim, after in vitro digestion, the PRF-enriched bread, its standard control, and fructo-oligosaccharides (FOS) underwent distal colonic fermentation using the in vitro colon model MICODE (multi-unit colon gut model). Sampling was done prior, over and after 24 h of fermentation, then metabolomic analysis by Solid Phase Micro Extraction Gas Chromatography Mass Spectrometry (SPME GCMS), 16S-rDNA genomic sequencing of colonic microbiota by MiSeq, and absolute quantification of main bacterial species by qPCR were performed. The results indicated that PRF-enriched bread generated positive effects on the host gut model: (i) surge in eubiosis; (ii) increased abundance of beneficial bacterial groups, such as Bifidobacteriaceae and Lactobacillales; (iii) production of certain bioactive metabolites, such as low organic fatty acids; (iv) reduction in detrimental compounds, such as skatole. Our study not only evidenced the prebiotic role of PRF-enriched bread, thereby paving the road for further use of olive by-products, but also highlighted the potential of the in vitro gut model MICODE in the critical evaluation of functionality of food prototypes as modulators of the gut microbiota.