Epidemiological characteristics of hand, foot, and mouth disease in China: A meta-analysis.

BACKGROUND: To study the epidemic features of hand-foot-mouth disease (HFMD) in mainland China through systematic review and meta-analysis so as to provide evidence for the future prevention and control of HFMD. METHODS: Articles on the epidemic features of HFMD in mainland China, written in English or Chinese and released between January 1, 2015 and January 1, 2020, were searched from English literature databases including Embase, Web of Science, PubMed, Cochrane library, Google academic, and Chinese literature databases including China national knowledge infrastructure (CNKI), Wanfang, and China Biology Medicine (CBM). Papers were selected according to the inclusion and exclusion criteria, and quality scoring was performed. Meta-analysis, sensitivity analysis, and identification of publication bias were finished through STATA version 12.0 software. RESULTS: A total of 23 articles were included in this study, the total number of cases was 377,083, of which the total number of male cases was 231,798 and the total number of female cases was 145,285, the sex ratio was about 1.6:1, and the incidence of HFMD in China was 1.61‰ (95% confidence interval [CI]: 1.21‰-1.94‰). The results of the subgroup analysis showed that the incidence of HFMD in mainland China was the highest in South China, in 2014, in 1-year-old group and in other types of enteroviruses, respectively, with the rate of 3.48‰ (95% CI: 1.22‰-5.73‰), 1.81‰ (95% CI: 1.06‰-2.57‰), 15.20‰ (95% CI: 5.00‰-25.30‰), and 1.83‰ (95% CI: 1.32‰-2.33‰), respectively. The differences among the above 4 subgroups were statistically significant (P < .05). There were no publication bias in this study, and the sensitivity analysis results suggested that the meta-analysis results were robust. CONCLUSION: There were differences in the distribution of region, time, population, and etiology of HFMD in mainland China. Health departments should adopt key strategies and measures for key populations in key areas to prevent and control the development of HFMD, and improve the ability of pathogen detection and typing in laboratories.

Combination of Proactive Molecular Risk Classifier for Endometrial cancer (ProMisE) with sonographic and demographic characteristics in preoperative prediction of recurrence or progression of endometrial cancer.

OBJECTIVE: To evaluate the ability of demographic and sonographic variables and the Proactive Molecular Risk Classifier for Endometrial cancer (ProMisE) classification to predict preoperatively tumor recurrence or progression in women with endometrial cancer. METHODS: The study included 339 women with histologically confirmed endometrial cancer who underwent expert transvaginal ultrasound in a single center before surgery as part of the prospective International Endometrial Tumor Analysis 4 study or who were evaluated using the same protocol. The tumors were classified according to histotype, FIGO (International Federation of Gynecology and Obstetrics) grade and FIGO stage. In addition, molecular analysis was performed for classification into the four ProMisE subtypes: polymerase-ϵ exonuclease domain mutations (POLE EDM), mismatch repair proteins deficiency (MMR-D), protein 53 wild type (p53 wt) and protein 53 abnormal (p53 abn). Demographic and preoperative sonographic characteristics, tumor recurrence or progression and survival were compared between the ProMisE subgroups. Cox regression analysis was used to identify prognostic factors associated with recurrence or progression, using univariable models to study crude associations and multivariable models to study adjusted associations. Logistic regression and receiver-operating-characteristics (ROC)-curve analysis were used to assess the predictive ability of the preoperative prognostic factors regarding recurrence or progression of cancer within 3 years after surgery, and to compare their predictive ability to that of the European Society for Medical Oncology (ESMO) preoperative (based on depth of myometrial invasion, histotype and grade) and postoperative (based on histotype, grade, surgical stage and lymphovascular space invasion) risk classifications. In a separate subanalysis, cases were stratified according to ProMisE p53 abn status (present vs absent) and sonographic tumor size (anteroposterior (AP) diameter < 2 cm vs ≥ 2 cm). RESULTS: Median follow-up time from surgery was 58 months (interquartile range, 48-71 months; range, 0-102 months). Recurrence or progression of cancer occurred in 51/339 (15%) women, comprising 14% of those with MMR-D, 8% of those with POLE EDM, 9% of those with p53 wt and 45% of those with p53 abn ProMisE subtype. On multivariable analysis, age, waist circumference, ProMisE subtype and tumor extension and AP diameter on ultrasound were associated with tumor recurrence or progression. A multivariable model comprising ProMisE subtype, age, waist circumference and sonographic tumor extension and size (area under the ROC curve (AUC), 0.89 (95% CI, 0.85-0.93)) had comparable ability to predict tumor recurrence/progression to that of a multivariable model comprising histotype, grade, age, waist circumference and sonographic tumor extension and size (AUC, 0.88 (95% CI, 0.83-0.92)), and better predictive ability than both the preoperative (AUC, 0.74 (95% CI, 0.67-0.82); P < 0.01) and postoperative (AUC, 0.79 (95% CI, 0.72-0.86); P < 0.01) ESMO risk classifications. Women with a combination of non-p53 abn subtype and tumor size < 2 cm (164/339 (48%)) had a very low risk (1.8%) of tumor recurrence or progression. CONCLUSIONS: The combination of demographic characteristics, sonographic findings and ProMisE subtype had better preoperative predictive ability for tumor recurrence or progression than did the ESMO classification, supporting their use in the preoperative risk stratification of women with endometrial cancer. The combination of p53 status with ultrasound tumor size has the potential to identify preoperatively a large group of women with a very low risk of recurrence or progression. © 2020 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology. - Legal Statement: This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Frequency of Hepatitis C Virus Genotypes in Patients Who Had Hepatocellular Carcinoma in Gastroenterological Hospitals of Tabriz.

BACKGROUND: Generally, hepatitis C has been identified as one of the major health issues that about 3% of the world's population have been threatened and affected by it (about 170 million people), and also, it can be considered a factor in acute and chronic hepatitis. METHODS: The aim of this study is to determine the prevalence of HCV genotypes in Azerbaijan patients. In this study, sampling was done on the referred patients to the hospitals (Mahallati and Behbud Hospital). RNA was extracted after isolation of plasma, and then, after the synthesizing of cDNA, the sample was carried out to the laboratory for performing the real-time PCR in order to determine the genotypes. RESULTS: The evaluation of HCV genotypes in positive plasma samples showed that dominant subsets were remarkable and the mean age of the patients was 37/3 ± 11/8 (in the age range of 2-63). Among the 235 patients,139 of them (59%) were male. Statistically, the average number of women was more than men (T test, P < 0/05). 1b genotype was reported 70% in the patients above 40 years old, and also, it was reported as 71/6% in the patients under 40 years old that was not statistically significant. The incidence of serotype 3a was higher among the patients younger than 40 years old (3a was 18.1% vs. 15%), and this serotype was prevalent among men (3a was 18.7% vs. 14.6%), which was statistically significant. CONCLUSION: The findings indicate that among Azerbaijan's patients with chronic hepatitis C, genotypes 1b (71.1%) and 3a (17%) were dominant.

The impact analysis of a multiplex PCR respiratory panel for hospitalized pediatric respiratory infections in Japan.

BACKGROUND: Rapid molecular diagnosis of infections has contributed to timely treatments and antimicrobial stewardship. However, the benefit and cost-effectiveness vary in each country or community because they have different standard practices and health care systems. In Japan, rapid antigen tests (RATs) have been frequently used for pediatric respiratory infections. We investigated the impact and cost-effectiveness of a multiplex PCR (mPCR) respiratory panel for pediatric respiratory infections in a Japanese community hospital. METHODS: We replaced RATs with an mPCR respiratory panel (FilmArray®) for admitted pediatric respiratory infections on March 26, 2018. We compared the days of antimicrobial therapy (DOT) and length of stay (LOS) during the mPCR period (March 2018 to April 2019) with those of the RAT period (March 2012 to March 2018). RESULTS: During the RAT and mPCR periods, 1132 and 149 patients were analyzed. The DOT/case was 12.82 vs 8.56 (p < 0.001), and the LOS was 8.18 vs 6.83 days (p = 0.032) in the RAT and mPCR groups, respectively. The total costs during admissions were ∖258,824 ($2331.7) and ∖243,841 ($2196.8)/case, respectively. Pathogen detection rates were 30.2% vs 87.2% (p < 0.001). CONCLUSION: Compared to conventional RATs, the mPCR test contributed to a reduction in the DOT and LOS in a Japanese community hospital for admission-requiring pediatric respiratory infections. However, a proper stewardship program is essential to further reduce the unnecessary usage of antimicrobials.

The Clinical and Epidemiological Study of Children with Hand, Foot, and Mouth Disease in Hunan, China from 2013 to 2017.

Hand, foot, and mouth disease (HFMD) is endemic in the Pacific region, especially in mainland China. The case-fatality ratio of HFMD is increasing steadily. Knowledge of the changing epidemiology of HFMD in different regions is necessary for implementing appropriate intervention strategies. In this study, we describe the clinical and epidemiological characteristics of HFMD in Hunan Children's Hospital between 2013 and 2017. A total of 7203 patients with HFMD were admitted, with complication and mortality rates of 35.62% and 0.78%, respectively. The total number of children with HFMD, proportion of severely ill children, and HFMD mortality rate were the highest in 2014. The number of cases caused by EV-A71 and CV-A16 decreased continuously, while the number of cases caused by 'other enteroviruses' increased yearly since 2014, suggesting that other enteric viruses will gradually replace EV-A71 and CV-A16 as the main pathogenic HFMD agents. Furthermore, EV-A71 and mixed infections accounted for the high case fatality rates in children with severe HFMD, among whom EV-A71 infection resulted in the highest complication and mortality rates; the mild form of the disease was dominated by 'other enteroviruses'. In conclusion, the changing etiological pattern highlights the need to improve pathogen surveillance and vaccine strategies for HFMD control.

A Clinical TB Detection Method Based on Molecular Typing Technique with Quality Control.

The gold standard for diagnosing pulmonary Mycobacterium tuberculosis (TB) is the detection of tubercle bacillus in patient sputum samples. However, current methods either require long waiting times to culture the bacteria or have a risk of getting false-positive results due to cross-contamination. In this study, a method to detect tubercle bacillus based on the molecular typing technique is presented. This method can detect genetic units, variable number of tandem repeat (VNTR), which are the characteristic of tuberculosis (TB), and performs quality control using a mathematical model, ensuring the reliability of the results. Compared to other methods, the proposed method was able to process and diagnose a large volume of samples in a run time of six hours, with high sensitivity and specificity. Our method is also in the pipeline for implementation in clinical testing. Reliable and confirmed results are stored into a database, and these data are used to further refine the model. As the volume of data processed from reliable samples increases, the diagnostic power of the model improves. In addition to improving the quality control scheme, the collected data can be also used to support other TB research, such as that regarding the evolution of the tubercle bacillus.

Influence of GeneXpert MRSA/SA test implementation on clinical outcomes of Staphylococcus aureus bacteremia - a before-after retrospective study.

Use of GeneXpert MRSA/SA in diagnostic algorithms of Staphylococcus aureus bacteremia may influence both patients' clinical outcomes and antibiotic stewardship. We evaluated these outcomes in a retrospective cohort before (1/6/2015-31/5/2016) and after (1/6/2016-31/8/2017) the introduction of the test in adult patients with Gram-positive cocci in clusters in blood cultures. We included 254 patients (125 preintervention, 129 postintervention). No significant difference in 30-day mortality or clinical success was demonstrated between periods. Appropriate antibiotic therapy rates were significantly higher in the postintervention group, and vancomycin use was significantly reduced (80.6% vs 53.6%, P < 0.01; 2.3±0.38 vs 2.98±1.02 defined daily doses/100 patient days, P = 0.026, respectively). Appropriate beta-lactam use was also significantly higher (56.7% postintervention vs 23.1% preintervention, P < 0.01). Use of GeneXpert MRSA/SA test has a positive effect on antibiotic stewardship measures, though it has no significant effect on clinical outcomes including mortality in this fatal infection.

The rapid diagnosis of viral respiratory tract infections and its impact on antimicrobial stewardship programs.

We aimed to describe the potential benefit of new rapid molecular respiratory tests (MRT) in decreasing inappropriate antibiotic use among the inpatients presenting with influenza-like illness (ILI). We included patients from inpatient and outpatient departments who had ILI and performed MRT between 1 January 2015 and 31 December 2016 in a 265-bed private hospital in Istanbul. At the end of 2015, we implemented antimicrobial stewardship including systematic use of MRT. Then, we compared our observations between the year 2015 and the year 2016. We designed the study according to the STrengthening the Reporting of OBservational studies in Epidemiology (STROBE) tool. A U.S. Food and Drug Administration (FDA)-cleared multiplexed polymerase chain reaction (PCR) system (BioFire FilmArray, Idaho Technology, Salt Lake City, UT) which detects 17 viruses and three bacteria was used for diagnosis. In total, 1317 patients were included; 630 (48%) were inpatients and 569 (43%) were older than 16 years of age. At least one virus was detected in 747 (57%) patients. Rhinovirus/enterovirus, influenza virus, and adenovirus were the most commonly detected. Among hospitalized patients, in children, a significant decrease in antibiotic use (44.5% in 2015 and 28.8% in 2016, p = 0.009) was observed, but in adults, the decrease was not statistically significant (72% in 2015 and 63% in 2016, p = 0.36). The duration of antibiotic use after the detection of virus was significantly decreased in both children and adults (p < 0.001 and p = 0.007, respectively). By using MRT, inappropriate antibiotic use and, also, duration of inappropriate antibiotic use after the detection of virus was significantly decreased. It is time to increase the awareness about the viral etiology in respiratory tract infections (RTIs) and implement MRT in clinical practice.

Application of molecular, microbiological, and immunological tests for the diagnosis of bone and joint tuberculosis.

BACKGROUND: To evaluate the application of interferon gamma release assay (IGRA), rifampicin resistant real-time fluorescence quantitative PCR technique Xpert Mycobacterium tuberculosis/rifampicin (Xpert MTB/RIF), and the levels of TNF-α and TGF-ß in the diagnosis of bone and joint tuberculosis. METHODS: Eighty-six patients with bone and joint tuberculosis, diagnosed by pathology or microbiology, were examined by Xpert MTB/RIF and IGRA (T-SPOT. TB) for Mycobacterium tuberculosis infection, and the TNF-α and TGF-ß levels of the patients were measured. RESULTS: The sensitivity of IGRA in diagnosing bone and joint tuberculosis was 81.4%; Xpert MTB/RIF's sensitivity was 70.9%. The combined sensitivity of the two methods was 91.9%. The combined detection sensitivity of the two methods was higher than individual IGRA or Xpert MTB/RIF detection sensitivity. The TNF-α and TGF-ß levels in bone and joint tuberculosis patients were higher than those in the control group. CONCLUSION: Xpert MTB/RIF, IGRA, TNF-α, and TGF-ßs expression have value in the rapid diagnosis of bone and joint tuberculosis, and the sensitivity and accuracy of bone and joint tuberculosis diagnosis by combining them can improve it.

Should We Be Testing for Baseline Integrase Resistance in Patients Newly Diagnosed With Human Immunodeficiency Virus?

Background: Current guidelines recommend genotype resistance testing at diagnosis to guide initial selection of antiretroviral therapy (ART). Many standard resistance genotypes exclude testing for resistance to integrase inhibitors ("IR testing"), although this class of drugs is a component of most recommended first-line regimens. Methods: We compared the 96-week clinical outcomes and cost-effectiveness of 2 strategies: no IR testing vs IR testing performed at human immunodeficiency virus (HIV) diagnosis. The base case prevalence of transmitted integrase strand transfer inhibitor (INSTI)-resistant (INSTI-R) virus is estimated at 0.1%. With no IR testing, all patients start dolutegravir (DTG)-based ART after genotype; 12-week suppression rates are 90% (INSTI-susceptible [INSTI-S] virus) and 35% (INSTI-R virus). Those not suppressed at 12 weeks undergo IR testing; if diagnosed with INSTI-R virus, they change to ritonavir-boosted darunavir (DRV/r)-based ART. With IR testing, all patients are diagnosed with INSTI-S/INSTI-R virus prior to ART initiation and start DTG- or DRV/r-based regimens, respectively. Costs include IR tests (175 US dollars [USD]) and ART (41100-44900 USD/year). We examined the impact of key parameters in sensitivity analyses. Results: IR testing resulted in worse clinical outcomes compared to no IR testing and increased costs by 200 USD/person/year. Prevalence of transmitted INSTI-R virus did not affect the favored strategy. No IR testing remained clinically preferred unless DTG suppression of INSTI-R virus was <20% or 96-week DRV/r suppression was >92%. If quality of life was worse with DRV/r- than DTG-based ART, no IR testing was clinically preferred over an even broader range of parameters. Conclusions: In patients with newly diagnosed HIV, IR testing is projected to result in worse outcomes and is not cost-effective. Pretreatment assessment for INSTI resistance should not be recommended in treatment guidelines.

The added value of hepatitis E diagnostics in determining causes of hepatitis in routine diagnostic settings in the Netherlands.

OBJECTIVES: Hepatitis E virus (HEV) genotype 3 is endemic in Europe and an underdiagnosed and emerging (public) health issue. In recent years commercial enzyme immunoassays (EIAs) that detect antibodies to HEV more adequately, became available. We investigated the added value of this HEV serology in the diagnostic work flow to detect viral causes of recent hepatitis. METHODS: During a 2-year period (May 2013 to May 2015), HEV serology was added to the hepatitis work flow, consisting of serological detection of hepatitis viruses A, B and C (HAV, HBV, HCV), Epstein-Barr virus (EBV) and cytomegalovirus (CMV). Samples positive for HEV IgM were also analysed using PCR to detect HEV RNA. If positive, HEV sequencing was performed for genotyping purposes. RESULTS: In 235 out of 2521 patients (9.3%), a viral cause for hepatitis was found. Recent HAV, HBV, HCV, EBV or CMV infections were serologically diagnosed in 3, 34, 10, 69 and 42 patients, respectively. Seventy-eight patients (3.1%) had a recent HEV infection. In 49 of them, sufficient HEV RNA was present for genotyping. All patients were infected with HEV genotype 3. CONCLUSIONS: In our region, an HEV infection is the most frequently diagnosed viral cause for recent hepatitis. These results indicate that, in a country where HEV is endemic, serological HEV diagnostics should be added to the standard work-up for viral hepatitis.

Improvement of infection control management by routine molecular evaluation of pathogen clusters.

BACKGROUND: Undetected pathogen clusters can often be a source of spreading in-hospital infections. Unfortunately, detection of clusters can be problematic because epidemiological connection is not always easily established. Infection prevention and control (IPC) measures, however, are most effective when applied at the earliest possible stage. AIM: The goal of our study was to evaluate the benefits of routine use of molecular typing techniques for IPC management in a large University teaching hospital. METHODS: We implemented daily routine molecular typing of pathogen clusters using cost-effective standard methods such as random amplified polymorphic DNA PCR, multiple-locus variable number tandem repeat analysis, and spa-typing over a 4-year study period (2012-2015). FINDINGS: Four pathogen clusters were evaluated: (I) 14 cases of Clostridium difficile in a peripheral ward, (II) 17 cases of methicillin-resistant Staphylococcus aureus (MRSA) in two intensive-care units (ICUs), (III) 21 cases of multidrug-resistant Klebsiella pneumoniae within one department, and (IV) 6 cases of vancomycin-resistant Enterococcus faecium in an interdisciplinary ICU. Typing revealed that cluster I was not caused by an outbreak strain but was likely due to different endogenous infections. Clusters III and IV showed a classical space-time clustering of point source outbreaks. Cluster II represented a prolonged temporal cluster, which would have gone undetected without molecular typing because of large intercase intervals. CONCLUSION: Implementing daily routine molecular typing is effective for detecting and analyzing pathogen clusters. Falsely suspected outbreaks can be quickly resolved, whereas actual outbreaks can be identified faster, so that targeted IPC measures can be applied earlier.

Syndrome Evaluation System (SES) versus Blood Culture (BACTEC) in the Diagnosis and Management of Neonatal Sepsis--A Randomized Controlled Trial.

OBJECTIVE: To compare the clinical outcome of a multiplex polymerase chain reaction (PCR) based molecular diagnostic method -- Syndrome Evaluation System (SES) directed treatment strategy vs. standard of care (blood culture) directed treatment strategy for neonatal sepsis. METHODS: This randomized controlled trial (RCT) included 385 neonates with sepsis who were randomized into two groups -- SES and control (BACTEC). Both tests were performed for all the neonates. However, in the SES group, the results of SES test were revealed to the treating clinicians, while in the control group, SES results were withheld. Two ml of blood was drawn from each baby. One aliquot was sent for blood culture, whereas the remaining aliquot was sent for SES. Babies were then administered empirical IV antibiotics and given supportive care. Further antibiotic changes, if required were done in SES and control groups based on their respective reports. The microbiological profile, immediate outcome, duration of hospital stay, number of antibiotics used and readmission within a month in both groups were compared. RESULTS: SES was better than BACTEC in identifying the causative organism in both the groups (68 % vs. 18 % in SES group and 72 % vs. 18 % in control group). SES had 100 % concordance with blood culture by BACTEC. Detection of bacteria and fungi were four and ten-fold higher respectively with SES when compared to BACTEC culture. Microbiological diagnosis was rapid with SES compared to BACTEC (7 h vs. 72 h). Treatment based on SES resulted in significantly less mortality (3 % vs. 18 %). Readmission rate, duration of hospital stay and change in antibiotics were also significantly less in SES group. CONCLUSIONS: This new molecular based diagnostic system (SES) helps in rapid and accurate diagnosis of neonatal sepsis and reduces mortality and morbidity in affected neonates.

Barriers to using molecularly typed minority red blood cell donors in support of chronically transfused adult patients with sickle cell disease.

BACKGROUND: Much effort and resources have been devoted to programs that provide transfusion support for patients with sickle cell disease (SCD). The focus of many donor programs is to prevent alloimmunization by recruiting racially matched African American donors to limit the red blood cell (RBC) antigenic differences that exist between Caucasian donors and patients with SCD. STUDY DESIGN AND METHODS: In this study, we evaluated the RBC antigen characteristics of both the recipient population with SCD and the African American donor population from 2010 to 2013. We evaluated the genotype-derived predicted antigen frequencies of the donors and compared these frequencies with those of the population supported by these units. Specific attention was given to the alloimmunization rate over the 3 years and the number of D- units provided to D+ patients. RESULTS: We recruited 6066 African American donors during the 3-year study period with 77.3% of these donors donating no more than twice. The observed genotype-derived predicted antigen frequencies were similar to the expected frequencies, and the antigen frequencies of a cohort of 54 adult patients with SCD (p > 0.05). Twelve patients (22.2%) with SCD had alloantibodies and five of these patients developed these antibodies while receiving Rh and K antigen-matched blood during the study interval. Finally, we found that 607 (37.1%) D- units were diverted to D+ patients. CONCLUSIONS: New recruitment and prevention strategies are needed to increase the pool of available antigen-matched RBCs and decrease alloimmunization risk for this patient population.

Enterovirus infections in England and Wales, 2000-2011: the impact of increased molecular diagnostics.

There have recently been significant changes in diagnostic practices for detecting enterovirus (EV) infections across England and Wales. Reports of laboratory-confirmed EV infections submitted by National Health Service (NHS) hospital laboratories to Public Health England (PHE) over a 12-year period (2000-2011) were analysed. Additionally, the PHE Virus Reference Department (VRD) electronic database containing molecular typing data from 2004 onwards was interrogated. Of the 13,901 reports, there was a decline from a peak of 2254 in 2001 to 589 in 2006, and then an increase year-on-year to 1634 in 2011. This increase coincided with increasing PCR-based laboratory diagnosis, which accounted for 36% of reported cases in 2000 and 92% in 2011. The estimated annual incidence in 2011 was 3.9/100,000 overall and 238/100,000 in those aged <3 months, who accounted for almost one-quarter of reported cases (n = 2993, 23%). During 2004-2011, 2770 strains were submitted for molecular typing to the VRD, who found no evidence for a predominance of any particular strain. Thus, the recent increase in reported cases closely reflects the increase in PCR testing by NHS hospitals, but is associated with a lower proportion of samples being submitted for molecular typing. The high EV rate in young infants merits further investigation to inform evidence-based management guidance.

Gene chip technology used in the detection of HPV infection in esophageal cancer of Kazakh Chinese in Xinjiang Province.

This study was aimed to screen human papillomavirus (HPV) types associated with esophageal squamous cell carcinoma of Kazakh in Xinjiang using the gene chip technique and study the clinical significance of this application. The DNAs were collected from esophageal squamous cell carcinoma tissues and healthy esophageal mucosa of Kazakh adults in Xinjiang, and amplified firstly using HPV MY09/11 and then using HPV G5+/6+ to screen positive HPV specimens. These positive specimens were further detected by the gene chip technique to screen highly pathogenic HPV types. After determination with nested PCR amplification with HPV MY09/11 and G5+/6+, the infection rate of HPV was 66.67% in the esophageal squamous cell carcinoma group and 12.12% in the healthy control group. By testing the positive HPV specimens from the esophageal squamous cell carcinoma group, the infection rate of HPV16 was 97.72% and the co-infection rate of HPV16 and HPV18 was 2.27%. HPV16 infection may be involved in the development of esophageal squamous cell carcinoma in Xinjiang Hazakh adults.

On the design of clone-based haplotyping.

BACKGROUND: Haplotypes are important for assessing genealogy and disease susceptibility of individual genomes,but are difficult to obtain with routine sequencing approaches. Experimental haplotype reconstruction based on assembling fragments of individual chromosomes is promising, but with variable yields due to incompletely understood parameter choices. RESULTS: We parameterize the clone-based haplotyping problem in order to provide theoretical and empirical assessments of the impact of different parameters on haplotype assembly. We confirm the intuition that long clones help link together heterozygous variants and thus improve haplotype length. Furthermore, given the length of the clones, we address how to choose the other parameters, including number of pools, clone coverage and sequencing coverage, so as to maximize haplotype length. We model the problem theoretically and show empirically the benefits of using larger clones with moderate number of pools and sequencing coverage. In particular, using 140 kb BAC clones, we construct haplotypes for a personal genome and assemble haplotypes with N50 values greater than 2.6 Mb. These assembled haplotypes are longer and at least as accurate as haplotypes of existing clone-based strategies, whether in vivo or in vitro. CONCLUSIONS: Our results provide practical guidelines for the development and design of clone-based methods to achieve long range, high-resolution and accurate haplotypes.