Non‐random expression of ribosomal DNA units in a grasshopper showing high intragenomic variation for the ITS2 region

We analyse intragenomic variation of the ITS2 internal transcribed spacer of ribosomal DNA (rDNA) in the grasshopper Eyprepocnemis plorans, by means of tagged PCR 454 amplicon sequencing performed on both genomic DNA (gDNA) and RNA‐derived complementary DNA (cDNA), using part of the ITS2 flanking coding regions (5.8S and 28S rDNA) as an internal control for sequencing errors. Six different ITS2 haplotypes (i.e. variants for at least one nucleotide in the complete ITS2 sequence) were found in a single population, one of them (Hap4) being specific to a supernumerary (B) chromosome. The analysis of both gDNA and cDNA from the same individuals provided an estimate of the expression efficiency of the different haplotypes. We found random expression (i.e. about similar recovery in gDNA and cDNA) for three haplotypes (Hap1, Hap2 and Hap5), but significant underexpression for three others (Hap3, Hap4 and Hap6). Hap4 was the most extremely underexpressed and, remarkably, it showed the lowest sequence conservation for the flanking 5.8‐28S coding regions in the gDNA reads but the highest conservation (100%) in the cDNA ones, suggesting the preferential expression of mutation‐free rDNA units carrying this ITS2 haplotype. These results indicate that the ITS2 region of rDNA is far from complete homogenization in this species, and that the different rDNA units are not expressed at random, with some of them being severely downregulated.     

胚胎植入前非整倍体遗传学检测在中国东北地区高龄复发性流产患者中的应用价值

目的探讨胚胎植入前非整倍体遗传学检测(PGT-A)在高龄复发性流产(RSA)患者中的临床应用价值。方法收集2017年5月-2019年2月在沈阳市妇婴医院生殖中心行PGT-A助孕的RSA患者,根据年龄将患者分为A组(年龄>35岁)、Y组(年龄≤35岁)、A-SET组(行单囊胚解冻移植且未行PGT-A助孕的年龄>35岁的患者)及Y-SET组(行单囊胚解冻移植且未行PGT-A助孕的年龄≤35岁的患者)。分析行PGT-A患者胚胎的染色体非整倍性情况及各组患者胚胎移植后的临床结局。结果A组256枚胚胎扩增成功,染色体异常率为67.2%;Y组162枚胚胎扩增成功,染色体异常率为46.9%,两组差异有统计学意义(P<0.05)。A组h CG阳性率(66.7%vs.42.3%)、临床妊娠率(66.7%vs.34.9%)及活产率(63.3%vs.33.3%)与A-SET组比较,差异均有统计学意义(均P<0.05);A组h CG阳性率(66.7%vs.60.6%)、临床妊娠率(66.7%vs.53.1%)及活产率(63.3%vs.51.2%)与Y-SET组比较,差异均无统计学意义(均P>0.05)。结论为获得整倍体胚胎和良好的临床结局,建议高龄女性在行体外受精-胚胎移植时结合PGT-A。     

Clarification of undiagnosed ataxia using whole-exome sequencing with clinical implications

BackgroundHereditary cerebellar ataxias exhibit heterogeneous phenotypes and genotypes. To date, advancement of next-generation sequencing technologies have identified many causative genes for ataxia in various population. In this study, whole-exome sequencing (WES) was utilized to explore the genetic cause of ataxia among Korean patients who remained undiagnosed following routine investigation.MethodsPatients with ataxia were enrolled in this study. We excluded patients with acquired, degenerative, and trinucleotide repeat ataxias, such as spinocerebellar ataxia 1 (SCA1), SCA2, SCA3, SCA6, SCA7, SCA8, SCA17, Dentatorubral-pallidoluysian atrophy, and Friedreich ataxia. WES was performed. After basic filtering based on population databases, we then performed primary filtering to screen for known ataxia-associated genes, followed by expanded filtering customized for individual patients.ResultsWe enrolled 77 ataxia patients from 68 families. Eighteen families had pathogenic or likely pathogenic variants in 14 different genes, including NEU1, APTX, SPG7, HTRA1, POLG2, SYNE1, CACNA1G, CACNA1A, ITPR1, AHI1, SPG11, ANO10, ATM, and C5orf42, resulting in a diagnostic yield of 26.5%. Hereditary spastic paraplegia was the most common diagnosis. Adult-onset ataxias and those without family history were frequently encountered. Variants of unknown significance were found in 14 (20.6%) families, some of which were highly probable from the clinical perspective.ConclusionUsing WES, we explored the molecular etiology of ataxia in patients whom were not diagnosed through routine clinical investigation. This study revealed unexpected rare disorders as well as the known ataxia-associated genes in a Korean population.     

Microbiological diagnosis in cardiac implantable electronic device infections detected by sonication and next-generation sequencing

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Tracking myeloma tumor DNA in peripheral blood

Over the past years, the emergence of liquid biopsy technologies has dramatically expanded our ability to assess multiple myeloma without the need for invasive sampling. Interrogation of cell-free DNA from the peripheral blood recapitulates the mutational landscape at excellent concordance with matching bone marrow aspirates. It can quantify disease burden and identify previously undetected resistance mechanisms which may inform clinical management in real-time. The convenience of sample acquisition and storage provides strong procedural benefits over currently available testing. Further investigations will have to define the role of cell-free DNA as a diagnostic measure by determining clinically relevant tumor thresholds in comparison to existing routine parameters. This review presents an overview of currently available assays and discusses the clinical value, potential and limitations of cell-free DNA technologies for the assessment of this challenging disease.     

多组学联用在中药作用机制研究中的应用

组学技术的运用主要基于高通量分析检测技术,包括转录组学、蛋白质组学和代谢组学等。生物信息学的飞速发展,为探索中药治疗疾病的机制提供新的思路和方法。在过去的数十年间,组学技术广泛应用于中药作用机制的研究当中。中药具有多成分、多靶点的特点,单一通路研究难以诠释中药"整体观念"的治疗思想,而多组学联用研究与这一观点不谋而合。查阅近年文献,对转录组学、蛋白质组学、代谢组学及16S rRNA测序等联用在中药治疗疾病中发挥的作用进行综述。