A reference human genome dataset of the BGISEQ-500 sequencer.

Background: BGISEQ-500 is a new desktop sequencer developed by BGI. Using DNA nanoball and combinational probe anchor synthesis developed from Complete Genomics™ sequencing technologies, it generates short reads at a large scale. Here, we present the first human whole-genome sequencing dataset of BGISEQ-500. The dataset was generated by sequencing the widely used cell line HG001 (NA12878) in two sequencing runs of paired-end 50 bp (PE50) and two sequencing runs of paired-end 100 bp (PE100). We also include examples of the raw images from the sequencer for reference. Finally, we identified variations using this dataset, estimated the accuracy of the variations, and compared to that of the variations identified from similar amounts of publicly available HiSeq2500 data. We found similar single nucleotide polymorphism (SNP) detection accuracy for the BGISEQ-500 PE100 data (false positive rate [FPR] = 0.00020%, sensitivity = 96.20%) compared to the PE150 HiSeq2500 data (FPR = 0.00017%, sensitivity = 96.60%) better SNP detection accuracy than the PE50 data (FPR = 0.0006%, sensitivity = 94.15%). But for insertions and deletions (indels), we found lower accuracy for BGISEQ-500 data (FPR = 0.00069% and 0.00067% for PE100 and PE50 respectively, sensitivity = 88.52% and 70.93%) than the HiSeq2500 data (FPR = 0.00032%, sensitivity = 96.28%). Our dataset can serve as the reference dataset, providing basic information not just for future development, but also for all research and applications based on the new sequencing platform.

[The Quality Analysis of National Supervising Sampling for Rubella Virus IgM Diagnostic Kits in 2014].

OBJECTIVE: To evaluate the quality status of rubella virus IgM diagnostic kits by national supervising sampling. METHODS: Using legal inspection combining with exploratory study, the positive and negative coincidence rate, detection limit and repeatability of kits were verified. RESULTS: The results showed that 15 of 16 batches of kits were qualified using legal inspection, and the passing rate was 93.8%. The unqualified item was negative coincidence rate. In exploratory study, only 11 batches (68.8%) complied with industry standard. The unqualified items were negative coincidence rate, detection limit and repeatability. CONCLUSION: At present, rubella virus IgM diagnostic Kits have some quality problems in the market. It is recommended that we adopt industry standard and national reference panel in the registration inspection for the future, which will prompt enterprises to improve quality.

Sensitive detection of trace amounts of KRAS codon 12 mutations by a fast and novel one-step technique.

OBJECTIVES: The objective of this study is to develop a novel and sensitive method for KRAS codon 12 mutation testing. DESIGN AND METHODS: We developed a sensitive one-step real-time digestion-and-block TaqMan probe PCR (RTDB-PCR) technique that uses a thermostable endonuclease and a minor groove binder (MGB) blocker to detect KRAS codon 12 mutations. Dilution mimic DNA panels were used to assess the sensitivity of this technique. The RTDB-PCR method was performed and compared with three other methods: PCR sequencing, mutant-enriched PCR sequencing and mutant-enriched PCR-MassArray. A total of 100 formalin-fixed paraffin-embedded (FFPE) metastatic colorectal cancer (mCRC) specimens were also tested by all four methods. RESULTS: The RTDB-PCR was sensitive to as little as 0.01% mutant DNA, significantly higher than other methods. Among the 100 FFPE mCRC specimens examined, 45 tested positive for KRAS codon 12 mutations according to RTDB-PCR, 44 tested positive according to mutant-enriched PCR sequencing and mutant-enriched PCR-MassArray, and only 26 samples tested positive according to PCR sequencing. CONCLUSIONS: Compared with mutant-enriched PCR sequencing and mutant-enriched PCR-MassArray, RTDB-PCR is more cost effective, saves time, and is easier to use, making it suitable for the detection of low-level KRAS mutations in the clinic.

A PCR-based microwell-plate hybrid capture assay for high-risk human papillomavirus.

Human papillomavirus (HPV) is associated with cervical cancer. In this study, we developed a high-throughput microwell-plate hybrid capture (MPHC) method for epidemiological studies of high-risk HPV (HRHPV). The results with 1238 cervical specimens from female outpatients showed a concordance rate of 94.3 % between the MPHC and Hybrid Capture II assay. The MPHC assay showed an average HRHPV rate of 29.3 % for high-risk populations in populous cities of China. The established MPHC assay could sensitively and specifically detect 13 types of HRHPV and is suitable for large-scale screening, especially in areas where real-time PCR or fluorescence equipment is unavailable.

[Situation and suggestions on IVD industrial standards].

This paper briefly introduces the working procedure of in vitro diagnostic products (IVD) industrial standards, and elaborates the importance of professional standards for production and supervision. Based on the analysis of working progress during the past 10 years, some problems and countermeasures on project setting, participation, standard material, personnel training, work cycle are put forward, which are helpful for the future development of the IVD.

A sensitive time-resolved fluoroimmunoassay for determination of median levels of pregnancy-associated plasma protein a in pregnant women in China.

Pregnancy-associated plasma protein A (PAPP-A) is an important serum marker for first trimester screening. Its weekly median value varies with ethnicity. A one-step time-resolved fluoroimmunoassay (TRFIA) using two monoclonal antibodies against PAPP-A with Eu(3+) chelates as labels has been developed. Using the assay described here, we evaluated 5,301 normal serum samples from Chinese women at 7-13 weeks of gestation. The detection limit using this assay was 1.2 mIU/L, and the maximum detection range was up to 10,000 mIU/L. The intra-assay and inter-assay coefficients of variation were <3.0% and <5.0%, respectively, and the mean recovery rate was 98.0%. PAPP-A concentrations measured in 516 maternal serum samples correlated well with those obtained by Dissociation-Enhanced Lanthanide Fluorescent Immunoassay (DELFIA) PAPP-A assay (r=0.988, P<0.001). The medians for 7-13 weeks of maternal serum PAPP-A were higher in the women from China compared to reports from other countries. The present assay possesses accuracy and high sensitivity and exhibits great potential for the clinical analysis of PAPP-A. Our investigation on the median concentrations of PAPP-A will help establish reference values that are specific for China and study the importance of ethnic factors in biochemical screening.

A prognostic biomarker for gastric cancer with lymph node metastases.

Gastric cancer is one of the leading causes of tumor-related deaths in China. The tumor, node, metastasis (TNM) classification system is useful for predicting clinical prognosis of patients with gastric cancer. However, determining the presence of lymph node involvement in the early stages of gastric cancer is difficult without biopsy. Therefore, it is necessary to identify novel serum biomarkers for TNM cancer staging and prognostic follow-up. In this study, we have reported fibrinopeptide-A (FPA) with alanine truncation at the N-terminal as a novel biomarker to differentiate gastric cancer with and without lymph node metastases. We analyzed 369 individual serum samples including gastric cancer patients without lymph node metastases (n = 33), gastric cancer patients with lymph node metastases (n = 157; confirmed by pathology), and age- and sex-matched healthy individuals (n = 179). The data showed that 85.4% of patients with lymph node metastases were positive for FPA with alanine truncation at the N-terminal (degAla-FPA, 1,465.63 Da), as determined by tandem mass spectrometry (MS). Using degAla-FPA as the biomarker, the sensitivity was 85.4% for gastric cancer patients with lymph node metastases, and the specificity was 100% for gastric cancer patients without lymph node metastases. The high sensitivity and specificity achieved with serum degAla-FPA levels indicated that MS technology could facilitate the discovery of a novel and quantitative prognostic biomarker for gastric cancer with lymph node involvement.

Restriction endonuclease-mediated real-time digestion-PCR for somatic mutation detection.

PCR is a powerful platform for clinical and diagnostic applications, but challenges remain in detecting somatic mutations, as mutant cells are often mixed with more numerous wild-type cells at the tissue-sample sites. Here, we describe a novel method that couples PCR with restriction endonuclease digestion (designated real-time digestion-PCR, or RTD-PCR) in a one-step reaction tube for detecting somatic mutations from a minority of cells. The PCR mixture contains a thermostable restriction enzyme that digests wild-type alleles during the PCR program, allowing selective amplification of the mutant alleles. To validate this method, we used real-time digestion-PCR for the specific detection of the EGFR (epidermal growth factor receptor) treatment resistance-inducing mutation, T790M, combining with three different platforms: Sanger sequencing, TaqMan probe PCR and Sequenom MassArray. From 78 clinical samples, seven T790M mutations were consistently detected on all three platforms, indicating that RTD-PCR may be a useful clinical tool for analyzing the T790M point mutation.

Effect of non-cell Corynebacterium Parvum on differentiation and maturation of bone marrow-derived dendritic cells.

Corynebacterium parvum (CP), with their potent anti-tumor activities, has been well documented. Non-cell Corynebacterium Parvum (NCPP) is a neotype of biological preparation, which based on manipulating CP with nanotechnology. The present study was designed to investigate the effect of NCPP/CP on bone marrow derived dendritic cells (BMDCs) in tumor-bearing mice, especially focused on the differentiation and maturation of these BMDCs. BM cells from tumor-bearing mice administrated with NCPP/CP were analyzed by flow cytometry, which exhibit enhanced numbers of DCs and macrophages. In the meanwhile, flow cytometry analysis showed mild but significant difference for CD80 expression on these LPS- treated BMDCs between NCPP/CP administrated mice and the control animals. Furthermore, antigen presenting assay for these LPS-treated BMDCs showed significant difference for cytolytic assay of CD8+T cells against B16 melanoma cells, which indicate that NCPP treatments have enhanced the cytolytic rates of CD8+T cells from 47.9%±2.3% to 54.2%±2.4%. The data suggest that NCPP/CP treatment can efficiently facilitate the generation of BMDCs in vivo and enhance the maturation of these BMDCs in vitro.

NCPP treatment alleviates ConA-induced hepatitis via reducing CD4+T activation and NO production.

Corynebacterium parvum (CP), a kind of immunomodulator, has been well documented in many diseases. Non-cell C. parvum product (NCPP) is a newly-found nano-preparation. To investigate the effect of NCPP on Con A-induced murine severe hepatitis, we pretreated mice with NCPP intraperitoneally. After 12 h, ConA (25 µg/g body wt) was injected intravenously to provoke severe hepatitis and the degree of liver injury was evaluated by serum transaminase analysis and heptatic tissue pathology. Results have shown that levels of serum transaminase and degree of liver injury in ConA/NCPP groups had significantly declined than those in ConA/PBS groups. Notably, results of flow cytometry have demonstrated that activation of CD4+T cells in ConA/NCPP groups has been down-regulated, compared with ConA/PBS groups. Further, levels of serum and KC-related nitric oxide (NO) was displayed significantly lower in ConA/NCPP groups than those in ConA/PBS groups. The results indicate that NCPP may alleviate ConA-induced hepatitis by reducing CD4+T activation and NO production.

MGB-based one-step multiplex real-time PCR method for rapid detection of HPV.

AIM: For full-scale analysis of Human Papillomavirus (HPV) status in humans, two minor groove binder (MGB)-based one-step multiplex real-time PCR systems were developed: one to screen 16 high-risk HPV (HR-HPV) types, and one to screen a broader spectrum of HPV types (common HPV or C-HPV). METHODS: Sensitivity and specificity were evaluated using diluted reference plasmids and 20 control human DNA samples. For clinical evaluation, 510 cervical scrape samples were evaluated. RESULTS: The sensitivity assays revealed that the C-HPV detection system could detect 10 ~ 100 plasmid copies/reaction, while the HR-HPV detection system detected 10 ~ 500 copies. The specificity test revealed that the systems did not yield positive signals from the 20 human genomic DNA samples. Performance was tested on 510 usable clinical samples. The HR-HPV results were compared to those from the Hybrid Capture 2 (HC2) test, which assesses 13 HR-HPV types; the concordance level between the two methods was 90.8% with a kappa value of 0.813. CONCLUSIONS: These results showed that our novel MGB-based one-step multiplex real-time PCR method may be used for the diagnosis and mass screening of HPV in clinical and large-scale epidemiological studies.

A comparison of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and surface plasmon resonance for genotyping of high-risk human papillomaviruses.

BACKGROUND: Human papillomavirus (HPV) testing coupled with appropriate clinical management is associated with a significant decline in the rate of advanced cervical cancer and associated death. METHODS: In this present study, we evaluated the performance of 2 new HPV genotyping methods, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) and surface plasmon resonance (SPR) in 30 kinds of HPV control materials and in 129 cases of cervical smears including 79 HPV-positive samples screened from 1,600 abnormal clinical samples and 50 cervical cytology samples. RESULTS: The HPV genotyping accuracy of both MALDI-TOFMS and SPR was 100% for the HPV genotyping of control materials. In the analysis of the 79 HPV-positive samples by MALDI-TOFMS, HPV positivity was 88.6% (70/79). Nine samples were non-high-risk HPV (non-HR-HPV), which were not targets of MALDI-TOFMS. In the analysis of the 50 cervical samples, the agreement of both tests was 84% with a κ value of 0.660. By using consensus results that mean agreement between 2 of 3 methods, the HR-HPV genotyping accuracy was 100% (77/77) by MALDI-TOFMS and 94.8% (73/77) by SPR in the 129 cervical samples. The sensitivity (88.2%; 82/93) and specificity (88.9%; 32/36) of MALDI-TOFMS were similar to those of SPR. CONCLUSION: These results support that MALDI-TOFMS is a sensitive, specific and feasible method for HR-HPV detection in clinical application, compared with the SPR method.

Non-cell Corynebacterium parvum generated by nanotechnology: a promising immunomodulator with less side effects.

Corynebacterium parvum (CP), a kind of immunomodulator, has been well documented in immunotherapy to tumor. However, severe side effects, such as intrahepatic granulomas and scleromas in injected areas, restrict its clinical application. To minimize side effects of CP, a non-cell Corynebacterium parvum product (NCPP) was prepared by disposing CP with Nanotechnology. In present study, we compared effect of NCPP with that of CP and found: (1) NCPP with non-formaldehyde residue was easy to be absorbed without swelling and scleroma in local injected areas; (2) NCPP caused no obvious liver injury in murine and macaques; (3) NCPP maintained powerful anti-tumor activity, increased splenic index, elevated macrophage number, phagocytosis and production of hydrogen peroxide (H(2)O(2)), and nitric oxide (NO); (4) Importantly, unparallel CP, NCPP could stimulate macrophages to produce low level of tumor necrosis factor-alpha(TNF-alpha) but high level of interferon-gamma (IFN-gamma), an inhibitor to fibrosis. Our study has led to the view that NCPP will evolve into a new valuable immunomodulator for clinical application.

Tumor microenvironment: hypoxia and buffer capacity for immunotherapy.

In recent years, significant progress has been made in the study of tumor biology and anti-tumor immunotherapy. However, the cellular and molecular mechanisms of tumor progression still remain obscure. As we know, tumor microenvironment that can directly influence tumor development and prognosis has attracted much attention of large number of immunologists. Accumulated evidence has suggested that tumor microenvironment is in a hypoxic condition, under which immune cells may exhibit distinct functions compared to those under normal oxygen tension. The article we propose here will offer a novel point of view for understanding tumor microenvironment in order to instruct clinical immunotherapy. Just like the pH buffer system in human body, interactions of immune cells in tumor microenvironment may also constitute a buffer system, the balance of which is of great importance during immunotherapy for tumors. However, many protocols for tumor immunotherapy in clinic at present have not taken it into account, so the therapeutic outcome is often disappointing. In the present study, we have demonstrated the effect of Corynebacterium parvum, a well known immune stimulator, on malignant melanoma. Cell ingredients in tumor-infiltrating lymphocytes (TIL) and their anti-tumor effect have been altered when dosage of Corynebacterium parvum is changed. So, to obtain better therapeutic purposes, what we should do first is to detect an index to evaluate immune buffer capacity for the patient during tumor immunotherapy, then to choose appropriate drug doses to augment buffer capacity for their immune buffer system. Taken together, the hypothesis proposed here may help understand the pathogenesis of tumor progression and design more effective strategy for clinical immunotherapy for tumors.