Effects of sequence alterations on results from genotypic tropism testing

Backgroundgeno2pheno_[coreceptor] is a bioinformatic method for genotypic tropism determination (GTD) which has been extensively validated.ObjectivesGTD can be affected by sequencing/base-calling variability and unreliable representation of minority populations in Sanger bulk sequencing. This study aims at quantifying the robustness of geno2pheno_[coreceptor] with respect to these issues. GTD with a single amplification or in triplicate (henceforth singleton/triplicate) is considered.Study DesignFrom a dataset containing 67,997HIV-1 V3 nucleotide sequences, two datasets simulating sequencing variability were created. Further two datasets were created to simulate unreliable representation of minority variants. After interpretation of all sequences with geno2pheno_[coreceptor], probabilities of change of predicted tropism were calculated.Resultsgeno2pheno_[coreceptor] tends to report reduced false-positive rates (FPRs) when sequence alterations are present. Triplicate FPRs tend to be lower than singleton FPRs, resulting in a bias towards classifying viruses as X4-capable. Alterations introduced into nucleotide sequences by simulation change singleton predicted tropism with a probability ≤ 2%. Triplicate prediction lowers this probability for predicted X4 tropism, but raises it for predicted R5 tropism ≤ 6%. Simulated limited detection of minority variants in X4 sequences resulted in unchanged predicted tropism with probability above 90% as compared to probability above 98% with triplicate FPRs.Conclusionsgeno2pheno_[coreceptor] proved to be robust when sequence alterations are present and when detectable minorities are missed by bulk sequencing. Changes in tropism prediction due to sequence alterations as well as triplicate prediction are much more likely to result in false X4-capable predictions than in false R5 predictions.     

伊宁市19例HIV-1感染者gag基因序列分型研究

目的：通过扩增伊宁市维吾尔族HIV-1感染者gag基因片段,确定该民族HIV-1感染者流行株的基因亚型。方法：抽提20例新疆伊宁市HIV-1感染者的血浆标本的RNA,用巢式PCR扩增gag基因片段。将所得到的序列与国际标准株进行比较,确定被检标本的亚型。结果：在20例HIV感染者的血浆标本中,共成功扩增19例gag基因片段,扩增率为95％。经BLAST初步判断和构建进化树并与国际标准株比对确认,19例感染者感染的HIV毒株序列中,发现18例为CRF07_BC亚型,1例为C亚型。19例毒株之间的平均基因距离为0．043±0．003,与3例CKF07_BC亚型国际参考株之间的平均基因距离在0．034±0．004-0．039±0．005之间。结论：新疆伊宁市HIV-1感染者以CRF07_BC亚型为主要流行株。19例序列相互之间以及与3株不同来源的国际参考毒株之间表现出高度的同源性。     

Role of line probe assay in detection of extra-pulmonary tuberculosis: Experience from a tertiary care hospital in western Maharashtra

BackgroundDiagnosis of extra pulmonary tuberculosis (EPTB) is challenging due to its atypical clinical presentation and frequently results in a delay or deprivation of treatment. Apart from rapid case detection, early determination of MDR status is imperative in such situations. The commercially available Geno Type MTBDRplus assay version 2.0 (Hain Lifescience, Nehren, Germany) detects both the presence of Mycobacterium tuberculosis (MTB) complex as well as the presence of INH and Rifampcin resistance. We aim to evaluate the role of this test in diagnosis and detection of resistance by comparing its performance against gold standard i.e. culture and against the composite reference standards (CRS) in the diagnosis of EPTB.Material and methodsThe data of 130 EPTB samples processed form January 2014 till May 2017 at Poona Hospital and Research centre were selected for the study. All the samples were processed for Ziehl–Neelsen stain, Geno Type MTBDRplus assay (LPA) and liquid automated culture (BacT/Alert) simultaneously. Geno Type MTBDRplus assay (LPA) was performed directly on the samples. The 24 samples giving positive results on LPA and grown M. tuberculosis on culture were subjected to anti mycobacterial susceptibility testing for 1st line anti-tubercular drugs by BACTEC MGIT 320 system.ResultsOut of 130 samples, 7 samples grew atypical mycobacterium and all the 7 samples turned negative on Line Probe Assay. Direct LPA on processed samples yielded 48/130 (36.9%) positivity. Geno Type MTBDRplus assay was positive for M. tuberculosis in (72.09%) 31/43 culture positive cases and (21%) 17/80 of culture negative cases. Geno Type MTBDRplus assay sensitivity and specificity results were assessed in comparison to CRS made up of culture results and clinical, radiological and histological findings. The overall sensitivity of Geno Type MTBDRplus assay was 45.19% (47/104) and specificity was 94.73 (18/19). Out of 24 samples which were compared for results between LPA and culture, Geno Type MTBDRplus assay accurately identified 3 of 3 of Rifampcin resistant strains and 20 of 21 Rifampcin sensitive strains. Geno Type MTBDRplus assay identified 4 of 4 INH resistant strains and 19 of 20 INH sensitive strains and MDR was obtained for 3 of 3 strains.ConclusionsGeno Type MTBDRplus assay can give early diagnosis and sensitivity for both INH and Rifampcin in extra pulmonary samples. More number of studies is further required to establish Geno Type MTBDRplus assay as an important tool for obtaining diagnosis and resistance to first line drugs in extra pulmonary samples.     

家族性扩张型心肌病分子遗传学研究进展

随着分子生物学技术的发展,对扩张型心肌病(FDCM)的分子遗传学认识不断提高,目前已发现FDCM有19个不同的致病基因,基因型和基因表型关系的研究也在深入,对该分子水平的研究可能引起临床治疗学上的新观点。现对FDCM遗传学研究新进展做一综述。     

鸡胚微量中同型半胱氨酸,叶酸,HCY—2抗体水平和MTHFR基因型检测？…

为建立鸡胚胎尿绒膜一血采集方法和检测胚胎血中同型半胱氨酸（ＨＣＹ）、叶酸、ＨＣＹ－２抗体及亚甲基四氢叶酸还原酶（ＭＴＨＦＲ）基因型变化情况,采用ＨＰＬＣ法测血浆总ＨＣＹ,ＰＣＲ－ＲＦＬＰ法测纸血片ＭＴＨＦＲ,ＳＬＩＳＡ法测血清ＨＣＹ－２抗体和微生物法测纸血片血红蛋白叶酸盐。结果发现连续７ｄ给Ｄ．Ｌ－ＨＣＹ后,鸡胚血浆总ＨＣＹ浓度（１０６．９２μｍｏｌ／Ｌ）显著高于正常对照组（１４．１６μｍｏｌ／Ｌ