Development and validation of the AmpFℓSTR® Identifiler® Direct PCR Amplification Kit: a multiplex assay for the direct amplification of single-source samples

Abstract: The AmpF?STR^® Identifiler^® Direct PCR Amplification Kit is a new short tandem repeat multiplex assay optimized to allow the direct amplification of single‐source blood and buccal samples on FTA^® card without the need for sample purification and quantification. This multiplex assay has been validated according to the FBI/National Standards and SWGDAM guidelines. Validation results revealed that slight variations in primer concentration, master mix component concentration, and thermal cycling parameters did not affect the performance of the chemistry. The assay’s sensitivity was demonstrated by amplifying known amounts of white blood cells spotted onto FTA^® cards, and the assay’s specificity was verified by establishing minimal cross‐reactivity with nonhuman DNA. No effect on the age of the sample stored on the FTA^® substrate was observed and full concordance was established in the population study. These findings of the validation study support the use of the Identifiler^® Direct Kit for forensic standards and database samples genotyping.     

322例慢性乙型肝炎患者肝脏病理与病毒学指标的相关性研究

目的 研究慢性乙型肝炎患者肝脏病理与肝组织中及血清病毒标志物等因素的相关性。方法 回顾322例HBsAg阳性超过6个月并行肝穿刺活组织检查患者的临床资料,分析肝脏病理与肝组织中病毒标志物、血清HBeAg状态、血清HBV DNA水平及血清丙氨酸氨基转移酶（alanine aminotransferase,ALT）水平的相关性。结果 322例患者中,肝组织炎症分级（G）＞1且纤维化分期（S）＞1者314例,G≥3者44例,S≥3者40例。G与S呈明显正相关 (r=0.594,P<0.05)。 肝组织HBsAg、HBcAg不同表达状态患者,不同血清HBeAg状态患者,不同血清HBV DNA水平患者的肝脏炎症分级及其肝脏纤维化分期比较,差异均无统计学意义（P>0.05）。不同血清ALT水平患者的肝脏炎症分级比较,差异具有统计学意义（P<0.05）,血清ALT水平与肝脏炎症分级呈正相关（r=0.322,P<0.05）,而与肝脏纤维化分期的相关性无统计学意义(r=0.267,P>0.05)。结论 慢性乙型肝炎患者的肝脏炎症及纤维化程度与肝组织中病毒标志物、血清HBeAg状态、血清HBV DNA水平并无明显相关性,其炎症分级与血清ALT水平呈明显正相关。     

复方苦参注射液生物碱类成分及血中移行成分的分析

目的 利用超高效液相色谱—电喷雾离子化—四极杆飞行时间质谱（ultra-high-performance liquid chromatography-electrospray ionization-quadrupole time-of-flight mass spectrometry,UHPLC-ESI-QTOF/MS）结合UNIFI构建靶向筛查策略分析复方苦参注射液（Compound Kushen Injection,CKI）的生物碱类成分及血中移行成分。方法 首先,采用ESI-QTOF/MS的全信息串联质谱技术采集经UHPLC分离的CKI样品及其空白样品、CKI给药后的大鼠血浆样品及空白血浆样品的信息;然后,建立CKI生物碱化学成分数据库,与MSE数据一同导入UNIFI进行靶向筛查;依据母离子、碎片离子的精确质量对筛查出的化合物进行识别;最后,使用MassLynx 4.1工作站对UNIFI输出的结果进行核实。结果 本实验共分离、鉴定了20种CKI生物碱,其中17种生物碱能在大鼠血浆中被检出。结论 该方法能够快速分析CKI生物碱类成分及其血中移行成分,可为CKI的质量控制及药效物质研究提供参考。     

Sequencing of human identification markers in an Uyghur population using the MiSeq FGxTM Forensic Genomics System

Massively parallel sequencing (MPS) offers a useful alternative to capillary electrophoresis (CE) based analysis of human identification markers in forensic genetics. By sequencing short tandem repeats (STRs) instead of determining the fragment lengths by CE, the sequence variation within the repeat region and the flanking regions may be identified. In this study, we typed 264 Uyghur individuals using the MiSeq FGx™ Forensic Genomics System and Primer Mix A of the ForenSeq™ DNA Signature Prep Kit that amplifies 27 autosomal STRs, 25 Y-STRs, seven X-STRs, and 94 HID-SNPs. STRinNGS v.1.0 and GATK 3.6 were used to analyse the STR regions and HID-SNPs, respectively. Increased allelic diversity was observed for 33 STRs with the PCR-MPS assay. The largest increases were found in DYS389II and D12S391, where the numbers of sequenced alleles were 3–4 times larger than those of alleles determined by repeat length alone. A relatively large number of flanking region variants (28 SNPs and three InDels) were observed in the Uyghur population. Seventeen of the flanking region SNPs were rare, and 12 of these SNPs had no accession number in dbSNP. The combined mean match probability and typical paternity index based on 26 sequenced autosomal STRs were 3.85E−36 and 1.49E + 16, respectively. This was 10 000 times lower and 1 000 times higher, respectively, than the same parameters calculated from STR repeat lengths.

Key Points

• Sequencing data on STRs and SNPs used for human identification are presented for the Uyghur population.
• STRinNGS v.1.0 was used to analyse the flanking regions of STRs.
• The concordance between PCR-CE and PCR-MPS results was 99.86%.
• Detection of sequence variation in STRs and their flanking regions increased the allelic diversity.