Extended Enrichment for Ultrasensitive Detection of Low-Frequency Mutations by Long Blocker Displacement Amplification

Detecting low-frequency DNA mutations hotspots cluster is critical for cancer diagnosis but remains challenging. Quantitative PCR (qPCR) is constrained by sensitivity, and allele-specific PCR is restricted by throughput. Here we develop a long blocker displacement amplification (LBDA) coupled with qPCR for ultrasensitive and multiplexed variants detection. By designing long blocker oligos to perfectly match wildtype sequences while mispairing with mutants, long blockers enable 14-44 nt enrichment regions which is 2-fold longer than normal BDA in the experiments. For wild template with a specific nucleotide, LBDA can detect different mutation types down to 0.5 % variant allele frequency (VAF) in one reaction, with median enrichment fold of 1,000 on 21 mutant DNA templates compared to the wild type. We applied LBDA-qPCR to detect KRAS and NRAS mutation hotspots, utilizing a single plex assay capable of covering 81 mutations and tested in synthetic templates and colorectal cancer tissue samples. Moreover, the mutation types were verified through Sanger sequencing, demonstrating concordance with results obtained from next generation sequencing. Overall, LBDA-qPCR provides a simple yet ultrasensitive approach for multiplexed detection of low VAF mutations hotspots, presenting a powerful tool for cancer diagnosis and monitoring.

Enhanced Detection of Novel Low-Frequency Gene Fusions via High-Yield Ligation and Multiplexed Enrichment Sequencing

Panel-based methods are commonly employed for the analysis of novel gene fusions in precision diagnostics and new drug development in cancer. However, these methods are constrained by limitations in ligation yield and the enrichment of novel gene fusions with low variant allele frequencies. In this study, we conducted a pioneering investigation into the stability of double-stranded adapter DNA, resulting in improved ligation yield and enhanced conversion efficiency. Additionally, we implemented blocker displacement amplification, achieving a remarkable 7-fold enrichment of novel gene fusions. Leveraging the pre-enrichment achieved with this approach, we successfully applied it to Nanopore sequencing, enabling ultra-fast analysis of novel gene fusions within one hour with high sensitivity. This method offers a robust and remarkably sensitive mean of analyzing novel gene fusions, promising the discovery of pivotal biomarkers that can significantly improve cancer diagnostics and the development of new therapeutic strategies.

Microsatellite Instability Detection in Cancer: A Multiplex qPCR Approach that Obviates the Need for Matching Normal Samples

BACKGROUND

Microsatellite instability (MSI) indicates DNA mismatch repair deficiency in certain types of cancer, such as colorectal cancer. The current gold standard technique, PCR-capillary electrophoresis (CE), requires matching normal samples and specialized instrumentation. We developed VarTrace, a rapid and low-cost quantitative PCR (qPCR) assay, to evaluate MSI using solely the tumor sample DNA, obviating the requirement for matching normal samples.

METHODS

One hundred and one formalin-fixed paraffin-embedded (FFPE) tumor samples were tested using VarTrace and compared with the Promega OncoMate assay utilizing PCR-CE. Tumor percentage limit of detection was evaluated on contrived samples derived from clinical high MSI (MSI-H) samples. Analytical sensitivity, specificity, limit of detection, and input requirements were assessed using synthetic commercial reference standards.

RESULTS

VarTrace successfully analyzed all 101 clinical FFPE samples, demonstrating 100% sensitivity and 98% specificity compared to OncoMate. It detected MSI-H with 97% accuracy down to 10% tumor. Analytical studies using synthetic samples showed a limit of detection of 5% variant allele frequency and a limit of input of 0.5 ng.

CONCLUSIONS

This study validates VarTrace as a swift, accurate, and economical assay for MSI detection in samples with low tumor percentages without the need for matching normal DNA. VarTrace's capacity for highly sensitive MSI analysis holds potential for enhancing the efficiency of clinical work flows and broadening the availability of this test.

Rapid, tunable, and multiplexed detection of RNA using convective array PCR

Detection of RNA targets is typically achieved through RT-qPCR or RNAseq. RT-qPCR is rapid but limited in number and complexity of targets detected, while RNAseq is high-throughput but takes multiple days. We demonstrate simultaneous amplification and detection of 28 distinct RNA targets from a single unsplit purified RNA sample in under 40 minutes using our convective array PCR (caPCR) technology. We integrate tunable strand displacement probes into caPCR to allow detection of RNA species with programmable sequence selectivity for either a single, perfectly matched target sequence or for targets with up to 2 single-nucleotide variants within the probe-binding regions. Tunable probes allow for robust detection of desired RNA species against high homology background sequences and robust detection of RNA species with significant sequence diversity due to community-acquired mutations. As a proof-of-concept, we experimentally demonstrated detection of 7 human coronaviruses and 7 key variants of concern of SARS-CoV-2 in a single assay.

Screening hydrogels for antifibrotic properties by implanting cellularly barcoded alginates in mice and a non-human primate

Screening implantable biomaterials for antifibrotic properties is constrained by the need for in vivo testing. Here we show that the throughput of in vivo screening can be increased by cellularly barcoding a chemically modified combinatorial library of hydrogel formulations. The method involves the implantation of a mixture of alginate formulations, each barcoded with human umbilical vein endothelial cells from different donors, and the association of the identity and performance of each formulation by genotyping single nucleotide polymorphisms of the cells via next-generation sequencing. We used the method to screen 20 alginate formulations in a single mouse and 100 alginate formulations in a single non-human primate, and identified three lead hydrogel formulations with antifibrotic properties. Encapsulating human islets with one of the formulations led to long-term glycaemic control in a mouse model of diabetes, and coating medical-grade catheters with the other two formulations prevented fibrotic overgrowth. High-throughput screening of barcoded biomaterials in vivo may help identify formulations that enhance the long-term performance of medical devices and of biomaterial-encapsulated therapeutic cells.

[Correlation between BRAFV600E mutation and aggressive biological behavior of papillary thyroid carcinoma]

The current study analyzed the mutation rate of BRAF^V600E in papillary thyroid carcinoma patients and the correlation between BRAF^V600E mutation and aggressive biological behavior of papillary thyroid carcinoma. A total of 160 patients with papillary thyroid carcinoma who underwent surgical treatment in the Affiliated Cancer Hospital of Zhengzhou University from October 2020 to November 2021 were retrospectively included. All patients underwent BRAF^V600E gene detection. There were 37 males and 123 females, with a mean age of (46.5±11.1) years. The mutation rate of BRAF^V600E was 86.3% (138/160). There was no significant correlation between the mutation of BRAF^V600E and aggressive factors such as age (P=0.917), single focal/multifocal tumor (P=0.673), tumor size (P=0.360), tumor invasion (P=0.150) and regional lymph node metastasis (P=0.406). Therefore, for papillary thyroid cancer, mutations in a single gene like BRAF^V600E fail to determine more active diagnosis and treatment.

Highly Sensitive Blocker Displacement Amplification for Detection of Low-Level JAK2V617F Variant

BACKGROUND

Key criteria in the diagnostic workup and risk stratification for myeloproliferative neoplasms (MPN) include molecular testing for JAK2V617F and other mutant alleles. Multiple methods for quantitatively detecting nucleotide sequence changes exist, but the lower limit of detection can limit identification of the low-level allele fraction of a variant. We evaluated a recently developed blocker displacement amplification (BDA)-based quantitative PCR platform for detection and quantitation of JAK2V617F variant allele fraction (VAF).

METHODS

Clinical samples were tested using BDA, next-generation sequencing (NGS), and droplet digital PCR (ddPCR) in a head-to-head comparison of sensitivity and specificity in detecting the JAK2V617F variant. In total, 112 human genomic DNA specimens previously tested for JAK2V617F gene mutation status with NGS were analyzed, including 12 samples with low-level variants with VAF ≤2%, 6 samples with VAF >2%, and 94 samples with no variant previously identified by NGS.

RESULTS

BDA and ddPCR results correlated well across a range of VAFs, with both methods identifying the JAK2V617F variant down to at least 0.05% VAF. NGS of routine sequencing depth was less sensitive, identifying JAK2V617F only at 0.6% VAF.

CONCLUSIONS

BDA can provide a cost-effective alternative means to identify low-level variants using instrumentation commonly found in laboratories.

[Inter-laboratory comparison analysis of noise measurement in 91 occupational hygiene technical service organizations]

Objective: To understand the comparability of noise measurement results of various occupational hygiene technical service organizations in Guangdong Province by conducting inter-laboratory comparison of measuring instruments and personnel operation. Methods: In October 2020, the instrument comparison and personnel comparison among 91 occupational hygiene technical service organizations engaged in noise measurement in Guangdong Province were carried out in the form of fixed-point measurement and simulated workplace measurement, and the results were analyzed and evaluated by using the robust z-ratio score. Results: In the instrument comparison, 6 organizations had 1 or 2 outliers in their z-ratio scores, 2 organizations had 2 problematic values in their z-ratio scores, and a total of 8 organizations (accounting for 8.8%) were judged as unqualified; A total of 83 organizations (accounting for 91.2%) with satisfactory z-ratio scores or only one problematic value were judged as qualified. In the personnel comparison, there were 11 organizations with 1 or 2 outliers in the z-ratio score, and 1 organization with 2 problematic values in the z-ratio score. A total of 12 organizations (13.2%) were judged as unqualified and 79 organizations (accounting for 86.8%) with satisfactory z-ratio scores or only one problematic value were judged as qualified. Through comprehensive judgment, 20 organizations (22.0%) were judged as unqualified, and 71 organizations (78.0%) were judged as qualified. There was no statistically significant difference in the qualified rates of instrument comparison results, personnel comparison results and comprehensive evaluation results of non-private organizations and private organizations (P>0.05). There was no significant difference in the qualified rates of instrument comparison results and comprehensive evaluation results of qualified organizations and unqualified organizations (P>0.05), there was significant difference in the qualified rate of personnel comparison results (P<0.05) . Conclusion: The noise measurement results of some occupational health technical service organizations in Guangdong Province are generally comparable. To carry out inter-laboratory comparison of noise instrument performance and personnel operation ability of occupational hygiene technical service organizations, can comprehensively evaluate the testing process of each organization and find out the problems existing in each organization.

Direct capture and sequencing reveal ultra-short single-stranded DNA in biofluids

Cell-free DNA (cfDNA) has become the predominant analyte of liquid biopsy; however, recent studies suggest the presence of subnucleosomal-sized DNA fragments in circulation that are likely single-stranded. Here, we report a method called direct capture and sequencing (DCS) tailored to recover such fragments from biofluids by directly capturing them using short degenerate probes followed by single strand-based library preparation and next-generation sequencing. DCS revealed a new DNA population in biofluids, named ultrashort single-stranded DNA (ussDNA). Evaluation of the size distribution and abundance of ussDNA manifested generality of its presence in humans, animal species, and plants. In humans, red blood cells were found to contain abundant ussDNA; plasma-derived ussDNA exhibited modal size at 50 nt. This work reports the presence of an understudied DNA population in circulation, and yet more work is awaiting to study its generation mechanism, tissue of origin, disease implications, etc.

[Analysis of epidemiological characteristics of pulmonary tuberculosis patients in Fengtai District, Beijing City from 2011 to 2021]

Objective: To analyze the epidemiological characteristics of pulmonary tuberculosis (PTB) in Fengtai District from 2011 to 2021. Methods: A retrospective study was conducted, the data of PTB patients in Fengtai District from 2011 to 2021 were collected in Chinese disease prevention and Control Information System, which included etiological classification, gender, age, occupation, onset time, demographic information etc. the epidemiological characteristics of reported PTB patients was analysis. Results: A total of 10 342 cases of PTB were reported from 2011 to 2021 in Fengtai District, with an average annual reported incidence rate of 42.87/ 100 000. The incidence rate was the highest in 2012(75.89/100 000), and significantly declined from 2013, which declined to 29.70/100 000 in 2017. It showed a slow rise from 2018 to 2021. The difference was statistically significant (χ²=1 471.77,P<0.001).There were 2 975 cases of etiologic positive PTB from 2011 to 2021, and 76 cases of Rifampicin-resistant PTB from 2017 to 2021. The ratio of male cases to female was 1.75, the average annual incidence rate of male (53.94/100 000) was higher, than female(31.57/100 000).(χ²=704.01,P<0.001). Among all age groups, 25-29 years group, 20-24 years group and 30-34 years group had the highest proportion, which were 1 506 cases (14.56%) , 1 292 cases (12.49%) and 1 024 cases (9.90%) respectively. The average annual incidence rate was the lowest in the group less than 10 years old (1.43/100 000), and the highest in the group 85 years old and over (195.20/100 000), the difference was statistically significant(χ²=3164.24, P<0.001). The top occupations from high to low were housework and unemployment (2 917 cases, 28.21%), retirees (2 308 cases, 22.32%), workers (1 047 cases, 10.12%), cadres and staff (950 cases, 9.19%), farmers (860 cases, 8.32%), business services (698 cases, 6.75%), teachers and students (455 cases, 4.40%). Conclusion: From 2011 to 2021, the incidence rate of PTB was decreased from 2012 to 2017, and slowly increased lately in Fengtai District. The epidemiological characteristics of PTB vary in different age and gender.

Hairpin Structure Facilitates Multiplex High-Fidelity DNA Amplification in Real-Time Polymerase Chain Reaction

Clinically and biologically, it is essential to detect rare DNA-sequence variants for early cancer diagnosis or drug-resistance mutation identification. Some of the common quantitative polymerase chain reaction (qPCR)-based variant detection methods are restricted in the limit of detection (LoD) because the DNA polymerases used for these methods have a high polymerase misincorporation rate; thus, the detection sensitivity is sometimes unsatisfactory. With the proofreading activity, high-fidelity (HiFi) DNA polymerases have a 50- to 250-fold higher fidelity. However, there are currently no proper probe-based designs functioning as the fluorescence indicator allowing multiplexed HiFi qPCR reactions, thus restricting the application of HiFi DNA polymerases like the variant detection. We presented the occlusion system, composed of a 5'-overhanged primer with a fluorophore modification and a probe with a short-stem hairpin and a 3' quencher modification. We demonstrated that the occlusion system allowed multiplexing HiFi qPCR reaction, and it was compatible with the current variant-enrichment method to improve the LoD up to 10-fold. Thus, the occlusion system satisfactorily functioned as an efficient fluorescence indicator in HiFi qPCR reactions and allowed the application of HiFi DNA polymerases in variant detection methods to improve detection sensitivity.

High-Throughput Variant Detection Using a Color-Mixing Strategy

Many diseases are related to multiple genetic alterations along a single gene. Probing for highly multiple (>10) variants in a single quantitative PCR tube is not possible because of a limited number of fluorescence channels and one variant per channel, so many more tubes are needed. Herein, a novel color-mixing strategy that uses fluorescence combinations as digital color codes to probe multiple variants simultaneously was experimentally validated. The color-mixing strategy relies on a simple intratube assay that can probe for 15 variants as part of an intertube assay that can probe for an exponentially increased number of variants. This strategy is achieved by using multiplex double-stranded toehold probes modified with fluorophores and quenchers; the probes are designed to be quenched or luminous after binding to wild-type or variant templates. The color-mixing strategy was used to probe for 21 pathogenic variants in thalassemia and to distinguish between heterozygous and homozygous variants in six tubes, with a specificity of 99% and a sensitivity of 94%. To support tuberculosis diagnosis, the same strategy was applied to simultaneously probe in Mycobacterium tuberculosis for rifampicin-resistance mutations occurring within one 81-bp region and one 48-bp region in the rpoB gene, plus five isoniazid-resistance mutations in the inhA and katG genes.

Cost-Efficient Sequence-Based Nonextensible Oligonucleotide in Real-Time PCR and High-Throughput Sequencing

Molecular detection of disease-associated mutations, especially those with low abundance, is essential for academic research and clinical diagnosis. Certain variant detection methods reach satisfactory sensitivity and specificity in detecting rare mutations based on the introduction of blocking oligos to prevent the amplification of wild-type or unwanted templates, thus selectively amplifying and enriching the mutations. These blocking oligos usually suppress PCR amplification through the 3' chemical modifications, with high price, slow synthesis, and reduced purity. Herein, we introduce chemistry-free designs to block enzymatic extension during PCR by the steric hindrance from the secondary structures attached to the 3' end of the oligos (nonextensible oligonucleotide, NEO). We demonstrated that NEO efficiently prohibited the extension of both Taq and high-fidelity DNA polymerases. By further applying NEO as blockers in blocker displacement amplification (BDA) qPCR, multiplex BDA (mBDA) NGS, and quantitative BDA (QBDA) NGS methods, we showed that NEO blockers had performance comparable with previously validated chemical modifications. Comparison experiments using QBDA with NEO blockers and droplet digital PCR (ddPCR) on clinical formalin-fixed paraffin-embedded (FFPE) samples exhibited 100% concordance. Lastly, the ability of NEO to adjust plex uniformity through changes of PCR amplification efficiency was demonstrated in an 80-plex NGS panel.

Limitations and opportunities of technologies for the analysis of cell-free DNA in cancer diagnostics

Cell-free DNA (cfDNA) in the circulating blood plasma of patients with cancer contains tumour-derived DNA sequences that can serve as biomarkers for guiding therapy, for the monitoring of drug resistance, and for the early detection of cancers. However, the analysis of cfDNA for clinical diagnostic applications remains challenging because of the low concentrations of cfDNA, and because cfDNA is fragmented into short lengths and is susceptible to chemical damage. Barcodes of unique molecular identifiers have been implemented to overcome the intrinsic errors of next-generation sequencing, which is the prevailing method for highly multiplexed cfDNA analysis. However, a number of methodological and pre-analytical factors limit the clinical sensitivity of the cfDNA-based detection of cancers from liquid biopsies. In this Review, we describe the state-of-the-art technologies for cfDNA analysis, with emphasis on multiplexing strategies, and discuss outstanding biological and technical challenges that, if addressed, would substantially improve cancer diagnostics and patient care.

[Analysis on prevalence and epidemic risk of animal plague in different ecological plague foci in Inner Mongolia Autonomous Region]

The risk of plague epidemics and relapse of various types of plague foci persists in Inner Mongolia Autonomous Region. For Marmota sibirica plague foci, the animal plague has not been found but antibody has been detected positive. Nowadays, Marmota sibirica has been increasing in population and distribution in China. In bordering countries Mongolia and Russia, the animal plague has been continuously prevalent. For Spermophilus dauricus plague foci, the animal plague has been taken place now and then. Compared to the above foci, the animal plague is most prevalent in Meriones unguiculatus plague foci and frequently spread to humans. Due to higher strain virulence and historical disaster in Marmota sibirica plague foci and Spermophilus dauricus plague foci, plague prevention and control should be strengthened on these foci. In addition to routine surveillance, epidemic dynamics need to be further monitored in these two foci, in order to prevent their relapse and spread to humans.

[Clinical analysis of ureteral endometriosis complicated with hydronephrosis:92 cases series]

Objective: To investigate the diagnosis, treatment and prognosis of ureteral endometriosis with hydronephrosis. Methods: A retrospective study was performed of 92 cases diagnosed as ureteral endometriosis with surgery confirmed in Peking University First Hospital from January 2000 to January 2021. Results: The incidence of ureteral endometriosis was 0.9% (92/10 222), with an average age of (40.0±6.0) years. Among 92 cases, urological symptoms and pelvic pain including dysmenorrheal, periodic abdominal pain were the main forms of clinical characteristics, while 11 patients (12%, 11/92) were asymptomatic. All patients with ureteral endometriosis had hydronephrosis and hydroureter before surgery, hydronephrosis were left sided in 48 (52%, 48/92) patients, right sided in 39 (42%, 39/92) patients, both sided in 5 (5%,5/92) patients. The distal and middle sections of ureteral obstructions existed in 73 (79%, 73/92) patients and 19 (21%, 19/92) patients, respectively. Out of the 92 ureteral lesions 71 (77%, 71/92) patients were extrinsic lesions, 21 (23%, 21/92) patients presented intrinsic lesions. Of the 38 cases who took preoperative radionuclide renal dynamic imaging examination, there were 6 (16%, 6/38) cases of mildly damaged, 7 (18%, 7/38) cases of moderately dameged, 14 (37%, 14/38) cases of severely damaged, and 11 (29%, 11/38) cases of normal renal function. Laparotomy was decided in 25 (27%, 25/92) patients, and laparoscopic surgery in 67 (73%, 67/92) patients. In cases of ureteral surgery, ureterolysis, partial ureteral resection and ureterocystoneostomy, partial ureteral resection and end-to-end ureteral anastomosis and nephroureterectomy were undertaken in 52 (57%, 52/92), 20 (22%, 20/92), 12 (13%, 12/92) and 8 (9%, 8/92) patients separately. The median follow up was 108 months (range: 6 to 240 months). During the follow-up period, 68 (87%, 68/78) patients took urinary ultrasound after surgery, and 60 (88%, 60/68) cases of hydronephrosis disappeared, and 8 (12%, 8/68) cases were better than before. Conclusion: Most of the patients with ureteral endometriosis are impaired with renal function, and early surgical treatment could effectively relieve urinary obstruction and promote the recovery of renal function.

Single-Tube qPCR Detection and Quantitation of Hotspot Mutations Down to 0.01% Variant Allele Fraction

Clinically and biologically, rare DNA sequence variants are significant and informative. However, existing common detection technologies are either complex and time-consuming in workflow, or restricted in the limit of detection (LoD), or do not allow for multiplexing. Blocker displacement amplification (BDA) method can stably and effectively detect and enrich multiple rare variants with LoD around 0.1% variant allele fraction (VAF). Nonetheless, the detailed mutation information has to be identified by additional sequencing technologies. Here, we present allele-specific BDA (As-BDA), a method combining BDA with allele-specific TaqMan (As-TaqMan) probes for effective variant enrichment and simultaneous single nucleotide variant or small insertions and deletions (INDELs) profiling. We demonstrated that As-BDA could detect mutations down to 0.01% VAF. Further, As-BDA could detect up to four mutations with low to 0.1% VAF per reaction using only 15 ng DNA input. The median error of As-BDA in VAF determination is approximately 9.1%. Comparison experiments using As-BDA and droplet digital PCR on peripheral blood mononuclear cell clinical samples showed 100% concordance for samples with mutations at ≥ 0.1% VAF. Hence, we have shown that As-BDA can achieve simultaneous enrichment and identification of multiple targeted mutations within the same reaction with high clinical sensitivity and specificity, thus helpful for clinical diagnosis.

Calibration-free NGS quantitation of mutations below 0.01% VAF

Quantitation of rare somatic mutations is essential for basic research and translational clinical applications including minimal residual disease (MRD) detection. Though unique molecular identifier (UMI) has suppressed errors for rare mutation detection, the sequencing depth requirement is high. Here, we present Quantitative Blocker Displacement Amplification (QBDA) which integrates sequence-selective variant enrichment into UMI quantitation for accurate quantitation of mutations below 0.01% VAF at only 23,000X depth. Using a panel of 20 genes recurrently altered in acute myeloid leukemia, we demonstrate quantitation of various mutations including single base substitutions and indels down to 0.001% VAF at a single locus with less than 4 million sequencing reads, allowing sensitive MRD detection in patients during complete remission. In a pan-cancer panel and a melanoma hotspot panel, we detect mutations down to 0.1% VAF using only 1 million reads. QBDA provides a convenient and versatile method for sensitive mutation quantitation using low-depth sequencing.

Oncogene Concatenated Enriched Amplicon Nanopore Sequencing for rapid, accurate, and affordable somatic mutation detection

We develop the Oncogene Concatenated Enriched Amplicon Nanopore Sequencing (OCEANS) method, in which variants with low variant allele frequency (VAFs) are amplified and subsequently concatenated for Nanopore Sequencing. OCEANS allows accurate detection of somatic mutations with VAF limits of detection between 0.05 and 1%. We construct 4 distinct multi-gene OCEANS panels targeting recurrent mutations in acute myeloid leukemia, melanoma, non-small- cell lung cancer, and hepatocellular carcinoma and validate them on clinical samples. By demonstrating detection of low VAF single nucleotide variant mutations using Nanopore Sequencing, OCEANS is poised to enable same-day clinical sequencing panels.

Predicting stability of DNA bulge at mononucleotide microsatellite

Mononucleotide microsatellites are clinically and forensically crucial DNA sequences due to their high mutability and abundance in the human genome. As a mutagenic intermediate of an indel in a microsatellite and a consequence of probe hybridization after such mutagenesis, a bulge with structural degeneracy sliding within a microsatellite is formed. Stability of such dynamic bulges, however, is still poorly understood despite their critical role in cancer genomics and neurological disease studies. In this paper, we have built a model that predicts the thermodynamics of a sliding bulge at a microsatellite. We first identified 40 common bulge states that can be assembled into any sliding bulges, and then characterized them with toehold exchange energy measurement and the partition function. Our model, which is the first to predict the free energy of sliding bulges with more than three repeats, can infer the stability penalty of a sliding bulge of any sequence and length with a median prediction error of 0.22 kcal/mol. Patterns from the prediction clearly explain landscapes of microsatellites observed in the literature, such as higher mutation rates of longer microsatellites and C/G microsatellites.

A deep learning model for predicting next-generation sequencing depth from DNA sequence

Targeted high-throughput DNA sequencing is a primary approach for genomics and molecular diagnostics, and more recently as a readout for DNA information storage. Oligonucleotide probes used to enrich gene loci of interest have different hybridization kinetics, resulting in non-uniform coverage that increases sequencing costs and decreases sequencing sensitivities. Here, we present a deep learning model (DLM) for predicting Next-Generation Sequencing (NGS) depth from DNA probe sequences. Our DLM includes a bidirectional recurrent neural network that takes as input both DNA nucleotide identities as well as the calculated probability of the nucleotide being unpaired. We apply our DLM to three different NGS panels: a 39,145-plex panel for human single nucleotide polymorphisms (SNP), a 2000-plex panel for human long non-coding RNA (lncRNA), and a 7373-plex panel targeting non-human sequences for DNA information storage. In cross-validation, our DLM predicts sequencing depth to within a factor of 3 with 93% accuracy for the SNP panel, and 99% accuracy for the non-human panel. In independent testing, the DLM predicts the lncRNA panel with 89% accuracy when trained on the SNP panel. The same model is also effective at predicting the measured single-plex kinetic rate constants of DNA hybridization and strand displacement.

DNA probes used in next generation sequencing (NGS) have variable hybridisation kinetics, resulting in non-uniform coverage. Here, the authors develop a deep learning model to predict NGS depth using DNA probe sequences and apply to human and non-human sequencing panels.

Highly multiplexed rapid DNA detection with single-nucleotide specificity via convective PCR in a portable device

Assays for the molecular detection of nucleic acids are typically constrained by the level of multiplexing (this is the case for the quantitative polymerase chain reaction (qPCR) and for isothermal amplification), turnaround times (as with microarrays and next-generation sequencing), quantification accuracy (isothermal amplification, microarrays and nanopore sequencing) or specificity for single-nucleotide differences (microarrays and nanopore sequencing). Here we show that a portable and battery-powered PCR assay performed in a toroidal convection chamber housing a microarray of fluorescently quenched oligonucleotide probes allows for the rapid and sensitive quantification of multiple DNA targets with single-nucleotide discrimination. The assay offers a limit of detection of 10 DNA copies within 30 min of turnaround time and a dynamic range spanning 4 orders of magnitude of DNA concentration, and we show its performance by detecting 20 genomic loci and 30 single-nucleotide polymorphisms in human genomic DNA samples, and 15 bacterial species in clinical isolates. Portable devices for the fast and highly multiplexed detection of nucleic acids may offer advantages in point-of-care diagnostics.

Selective multiplexed enrichment for the detection and quantitation of low-fraction DNA variants via low-depth sequencing

DNA sequence variants with allele fractions below 1% are difficult to detect and quantify by sequencing owing to intrinsic errors in sequencing-by-synthesis methods. Although molecular-identifier barcodes can detect mutations with a variant-allele frequency (VAF) as low as 0.1% using next-generation sequencing (NGS), sequencing depths of over 25,000× are required, thus hampering the detection of mutations at high sensitivity in patient samples and in most samples used in research. Here we show that low-frequency DNA variants can be detected via low-depth multiplexed NGS after their amplification, by a median of 300-fold, using polymerase chain reaction and rationally designed 'blocker' oligonucleotides that bind to the variants. Using an 80-plex NGS panel and a sequencing depth of 250×, we detected single nucleotide polymorphisms with a VAF of 0.019% and contamination in human cell lines at a VAF as low as 0.07%. With a 16-plex NGS panel covering 145 mutations across 9 genes involved in melanoma, we detected low-VAF mutations (0.2-5%) in 7 out of the 19 samples of freshly frozen tumour biopsies, suggesting that tumour heterogeneity could be notably higher than previously recognized.

Confirming putative variants at ≤ 5% allele frequency using allele enrichment and Sanger sequencing

Whole exome sequencing (WES) is used to identify mutations in a patient's tumor DNA that are predictive of tumor behavior, including the likelihood of response or resistance to cancer therapy. WES has a mutation limit of detection (LoD) at variant allele frequencies (VAF) of 5%. Putative mutations called at ≤ 5% VAF are frequently due to sequencing errors, therefore reporting these subclonal mutations incurs risk of significant false positives. Here we performed ~ 1000 × WES on fresh-frozen and formalin-fixed paraffin-embedded (FFPE) tissue biopsy samples from a non-small cell lung cancer patient, and identified 226 putative mutations at between 0.5 and 5% VAF. Each variant was then tested using NuProbe NGSure, to confirm the original WES calls. NGSure utilizes Blocker Displacement Amplification to first enrich the allelic fraction of the mutation and then uses Sanger sequencing to determine mutation identity. Results showed that 52% of the 226 (117) putative variants were disconfirmed, among which 2% (5) putative variants were found to be misidentified in WES. In the 66 cancer-related variants, the disconfirmed rate was 82% (54/66). This data demonstrates Blocker Displacement Amplification allelic enrichment coupled with Sanger sequencing can be used to confirm putative mutations ≤ 5% VAF. By implementing this method, next-generation sequencing can reliably report low-level variants at a high sensitivity, without the cost of high sequencing depth.

[PD-1/PD-L1 expression and its interaction with interferon-γ in Toxoplasma gondii-infected mice at middle and late pregnancy]

OBJECTIVE

To explore the dynamic expression of programmed cell death-1 (PD-1) and its ligand PD-L1 at the maternal-fetal interface of mice post-infection with Toxoplasma gondii at early pregnancy and examine its interaction with interferon-γ (IFN-γ).

METHODS

A total of 20 mice at day 0 of pregnancy were randomly assigned into 4 groups, including the 12-day pregnancy control group (12 dpn group), 12-day pregnancy and infection group (12 dpi group), 18-day pregnancy control group (18 dpn group) and 18-day pregnancy and infection group (18 dpi group), respectively. On the 6th day of the pregnancy, mice in the 12 dpi and 18 dpi groups were injected intraperitoneally with 150 tachyzoites of the T. gondii PRU strain, while mice in the 12 dpn and 18 dpn groups were injected with the same volume of PBS. All mice in the four groups were sacrificed on 12th and 18^th day of the pregnancy, and the number of placenta and fetus was counted and the weight of placenta and fetus was measured. Then, the placental and uterine tissues of the pregnant mice in each group were sampled for pathological examinations. The mRNA expression of PD-1, PD-L1, T. gondii surface antigen SAG-1 and IFN-γ genes was quantified using a quantitative real-time PCR (qPCR) assay, and the correlation between PD-1 and IFN-γ expression was examined. In addition, the 12 dpn group, 12 dpi group, 18 dpn group, 18 dpi group, PBS negative control of the 12 pdi group and PBS negative control of the 18 dpi group were assigned, and the PD-1 expression was determined in the uterine and placenta tissues of the pregnant mice.

RESULTS

Adverse pregnant outcomes were seen in mice in the 12 dpi and 18 dpi groups, including placental dysplasia and fetal maldevelopment, and the placental weights and fetal body weights were significantly lower in mice in the 12 dpi and 18 dpi groups than those in the 12 dpn and 18 dpn groups (t = 5.52, 11.44, 12.63 and 11.67, all P < 0.01). The histopathological examinations showed that the decidua and junctional regions of the placental tissues were loosely connected in the 12 dpi and 18 dpi groups, and a large number of inflammatory cells infiltration and congestion were seen in the placental and uterine tissues. qPCR assay detected significant differences in PD-1, PD-L1, IFN-γ and SAG-1 expression in the placental and uterine tissues among the 12 dpn, 12 dpi, 18 dpn and 18 dpi groups (F = 22.48, 51.23, 9.61, 47.49, 16.08, 21.52, 28.66 and 238.90, all P < 0.05), and the PD-1, PD - L1, IFN - γ and SAG - 1 expression was all significantly higher in the placental and uterine tissues of mice in the 12 dpi group than in the 12 dpn group (all P values < 0.05). The PD-1 and PD-L1 expression was significantly lower in the placental tissues of mice in the 18 dpi group than in the 18 dpn group (all P values < 0.05), and the IFN-γ and SAG-1 expression was significantly higher in the placental and uterine tissues of mice in the 18 dpi group than in the 18 dpn group (all P values < 0.05), while the PD-1 and PD-L1 expression was significantly lower in the placental and uterine tissues of mice in the 18 dpi group than in the 12 dpi group (all P values < 0.05). Immunohistochemical staining showed PD-1 expression in the inflammatory cells of the placental tissues of mice in the 12 dpi group, and no apparent PD-1 expression in the 18 dpi group, while strongly positive PD-1 expression was found in the uterine epithelium of mice in the 12 dpi group, and mildly strong expression was in the 18 dpi group. In addition, the IFN-γ mRNA expression was positively correlated with the PD-1 mRNA expression in placental (r_s = 0.99, P < 0.01) and uterine tissues of mice in the 12 dpi group (r_s = 0.97, P < 0.01) and in placental (r_s = 0.82, P < 0.01) and uterine tissues of mice in the 18 dpi group (r_s = 0.81, P < 0.01).

CONCLUSIONS

Following T. gondii infection at early pregnancy, the PD-1 and PD-L1 expression shows a remarkable rise at middle pregnancy and a reduction at late pregnancy in placental and uterine tissues of mice, which appears the same tendency with IFN-γ expression during the same time period, and PD-1 expression positively correlates with IFN-γ expression. The dynamic expression of PD-1 and PD-L1 on the maternal-fetal interface of mice may be mutually mediated by IFN-γ induced by T. gondii infection.

High sensitivity sanger sequencing detection of BRAF mutations in metastatic melanoma FFPE tissue specimens

Mutations in the BRAF gene at or near the p. V600 locus are informative for therapy selection, but current methods for analyzing FFPE tissue DNA generally have a limit of detection of 5% variant allele frequency (VAF), or are limited to the single variant (V600E). These can result in false negatives for samples with low VAFs due to low tumor content or subclonal heterogeneity, or harbor non-V600 mutations. Here, we show that Sanger sequencing using the NuProbe VarTrace BRAF assay, based on the Blocker Displacement Amplification (BDA) technology, is capable of detecting BRAF V600 mutations down to 0.20% VAF from FFPE lymph node tissue samples. Comparison experiments on adjacent tissue sections using BDA Sanger, immunohistochemistry (IHC), digital droplet PCR (ddPCR), and NGS showed 100% concordance among all 4 methods for samples with BRAF mutations at ≥ 1% VAF, though ddPCR did not distinguish the V600K mutation from the V600E mutation. BDA Sanger, ddPCR, and NGS (with orthogonal confirmation) were also pairwise concordant for lower VAF mutations down to 0.26% VAF, but IHC produced a false negative. Thus, we have shown that Sanger sequencing can be effective for rapid detection and quantitation of multiple low VAF BRAF mutations from FFPE samples. BDA Sanger method also enabled detection and quantitation of less frequent, potentially actionable non-V600 mutations as demonstrated by synthetic samples.

[Expression of hypoxia-inducible factor-1 in mice infected with Toxoplasma gondii during pregnancy]

OBJECTIVE

To investigate the expression and possible role of hypoxia-inducible factor-1 (HIF-1) at the maternal-fetal interface following Toxoplasma gondii infection during early pregnancy.

METHODS

Twenty pregnant C57BL/6 mice, each weighing 16 to 20 g, were randomly divided into 4 groups, including the 12-d control group, 12-d infection group, 18-d control group and 18-d infection group. Mice in the 12-d and 18-d infection groups were injected intraperitoneally with 150 tachyzoites of the T. gondii PRU strain on day 6 of pregnancy, while mice in the 12-d control and 18-d control groups were injected with the same volume of phosphate buffered saline (PBS). Mice in the control and infection groups were sacrificed on days 12 and 18 of pregnancy, and the placental and uterine specimens of the pregnant mice in each group were sampled for pathological examinations. The mRNA expression of HIF-1α, HIF-1β and vascular endothelial growth factor (VEGF) was quantified using quantitative fluorescent real-time PCR (qPCR) assay in the placental and uterine specimens, and the correlation between HIF-1α and VEGF mRNA expression was examined. In addition, and the HIF-1α expression was detected using immunohistochemical staining in the placental and uterine specimens of pregnant mice.

RESULTS

Compared with the 12-d and 18-d control groups, adverse pregnant outcomes were observed in mice in 12-d and 18-d infection groups, such as teratism and placental dysplasia. HE staining showed swelling and blood stasis of cells, sinusoid reduction and inflammatory cell infiltration in the labyrinth area of the placenta specimens of mice in 12-d and 18-d infection groups relative to 12-d and 18-d control groups, and columnar epithelial cell injury and inflammatory cell infiltration were seen in the mouse uterine specimens in both infection groups. qPCR assay detected significantly higher HIF-1α (F = 132.6, P < 0.05) and HIF-1β mRNA expression (F = 286.9, P < 0.05) in the placental specimens and lower HIF-1α (F = 111.5, P < 0.05) and HIF-1β mRNA expression (F = 55.2, P < 0.05) in the uterine specimens in the 12-d infection group than in the 12-day control group, and significantly lower HIF-1α and HIF-1β mRNA expression was detected in the placental and uterine specimens in the 18-d infection group than in the 18-day control group (F = 215.8, 418.9, 156.8 and 200.1; all P values < 0.05). Significantly lower VEGF-A (F = 426.2, P < 0.05), VEGF-B (F = 104.6, P < 0.05) and VEGF-C mRNA expression (F = 566.9, P < 0.05) in the placental specimens and higher VEGF-A (F = 426.2, P < 0.05), VEGF-B (F = 104.6, P < 0.05) and VEGF-C mRNA expression (F = 566.9, P < 0.05) in the uterine specimens were detected in the 12-d infection group than in the 12-d control group, and higher VEGF-A, VEGF-B and VEGF-C mRNA expression was found in the placental and uterine specimens in the 18-d infection group than in the 18-d control group (F = 521.9, 100.6, 275.9, 224.6, 108.2 and 333.4; all P values < 0.05). Immunohistochemical staining showed strongly and mildly positive HIF-1α expression in the mouse placental labyrinth area in the 12-d and 18-d infection groups relative to 12-d and 18-d control groups, while no HIF-1α expression was detected in mouse uterine specimens.

CONCLUSIONS

HIF-1α expression appears a tendency towards a rise in the second trimester and a reduction in the third trimester in mice following T. gondii infection during early pregnancy, which is contrary to the changing tendency of VEGF-A, VEGF-B, and VEGF-C expression. It is hypothesized that HIF-1α inhibits placental angiogenesis in mice during pregnancy through suppressing VEGF expression, resulting in adverse pregnant outcomes.

[Research progress of neural precursor cells-expressed developmentally down-regulated protein-8 in liver diseases]

Neural precursor cells-expressed developmentally down-regulated protein-8 (NEDD8) is one of the important members of the ubiquitin family, which plays an important role in maintaining cell stability, cell cycle regulation, signal transduction, transcription, and translation, DNA repair, and tumorigenesis through covalently bound substrates (also known as neddylation modification). In recent years, studies have found that the dysfunction of NEDD8 and its related enzymes is common in liver diseases, and is widely involved in the biological processes of hepatitis, liver fibrosis, proliferation, invasion, apoptosis and autophagy of liver cancer cells. This article focuses on the research progress of NEDD8 in liver diseases.

Characterization of the rumen microbiota and its relationship with residual feed intake in sheep

Feed efficiency is a highly important economic trait in sheep production and has a significant impact on the economic benefits of sheep farming. Microbial fermentation of the rumen has a vital role in the host's nutrition; the rumen microbiota might affect host feed efficiency. However, the relationship between the rumen microbiota and feed efficiency in sheep is unclear. In the present study, the microbiota of 195 Hu sheep was investigated and their residual feed intake (RFI), a commonly used measure of feed efficiency, was determined. From birth, all sheep were subjected to the same management practices. At slaughter, samples of liquid rumen contents were collected and subjected to amplicon sequencing for the 16S rDNA gene on the IonS5™XL platform. To identify the bacterial taxa differentially represented at the genus or higher taxonomy levels, we used linear discriminant analysis coupled with effect size and curve fitting. In the sheep rumen, the four most abundant phyla were Firmicutes, Bacteroidetes, Fibrobacteres, and Proteobacteria; and the dominant genera were unidentified Prevotellaceae, Fibrobacter, unidentified Lachnospiraceae, Saccharofermentans, and Succinivibrio. Pathway analysis of the 16S rDNA sequencing data from the rumen microbiota identified that carbohydrate metabolism was enriched. Using α-diversity analysis, we further identified that Observed species, ACE, Good's coverage, and Chao1 are more abundant (P < 0.01) in the low-RFI (L-RFI) group compared to the high-RFI (H-RFI) group. High-RFI sheep had a higher abundance of three bacterial taxa (Prevotellaceae, Negativicutes, and Selenomonadales), and one taxa was overrepresented in the L-RFI sheep (Succinivibrio), respectively. Furthermore, model fitting showed that Veillonellaceae, Sphaerochaeta, Negativibacillus, Saccharofermentans, and members of the Tenericutes, Kiritimatiellaeota, Deltaproteobacteria, and Campylobacterales were correlated with the sheep RFI classification and thus were indicative of a role in animal efficiency. Tax4Fun analysis revealed that metabolic pathways such as "energy metabolism," "metabolism of cofactors and vitamins," "poorly characterized," and "replication recombination and repair proteins" were enriched in the rumen from H-RFI sheep, and "genetic information processing" and "lipopolysaccharide biosynthesis" were overrepresented in L-RFI sheep rumen. In addition, six Kyoto Encyclopedia of Genes and Genomes orthology pathways were identified as different between H-RFI and L-RFI groups. In conclusion, the low RFI phenotype (efficient animals) consistently (or characteristically) exhibited a more abundant and diverse microbiome in sheep.

Transcriptome analysis of long noncoding RNAs ribonucleic acids from the livers of Hu sheep with different residual feed intake

Long noncoding RNAs (LncRNAs), as key regulators, have vital functions in various biological activities. However, in sheep, little has been reported concerning the genetic mechanism of LncRNA regulation of feed efficiency. In the present study, we explored the genome-wide expression of LncRNAs and transcripts of uncertain coding potential (TUCPs) in the livers of sheep with extreme residual feed intake (RFI) using RNA sequencing. We identified 1 523 TUCPs and 1 996 LncRNAs, among which 10 LncRNAs and 16 TUCPs were identified as being differentially expressed between the High-RFI and Low-RFI groups. Co-expression and co-localization methods were used to search for LncRNA and TUCP target genes, which identified 970/1 538 and 23/27 genes, respectively. Ontology and pathways analysis revealed that the LncRNAs/TUCPs that were highly expressed in the Low-RFI group are mostly concentrated in energy metabolism pathways. For example, LNC_000890 and TUCP_000582 might regulate liver tissue metabolic efficiency. The LncRNAs/TUCPs that were highly expressed in the High-RFI group are mostly enriched in immune function pathways. For example, TUCP_000832 might regulate animal health, thereby affecting feed efficiency. Subsequently, a co-expression network was established by applying the expression information of both the differentially expressed LncRNAs and TUCPs and their target mRNAs. The network indicated that differentially expressed genes targeted by the upregulated LncRNAs and TUCPs were mainly related to energy metabolism, while those genes targeted by the downregulated LncRNAs and TUCPs were mainly related to immune response. These results provide the basis for further study of LncRNA/TUCP-mediated regulation of feed efficiency.

High-throughput methods for measuring DNA thermodynamics

Understanding the thermodynamics of DNA motifs is important for prediction and design of probes and primers, but melt curve analyses are low-throughput and produce inaccurate results for motifs such as bulges and mismatches. Here, we developed a new, accurate and high-throughput method for measuring DNA motif thermodynamics called TEEM (Toehold Exchange Energy Measurement). It is a refined framework of comparing two toehold exchange reactions, which are competitive strand displacement between oligonucleotides. In a single experiment, TEEM can measure over 1000 ΔG° values with standard error of roughly 0.05 kcal/mol.

Nucleic Acid Quantitation with Log-Linear Response Hybridization Probe Sets

Concentrations of different nucleic acid species in biological samples span many orders of magnitude. A real-time polymerase chain reaction maps the concentration of a target nucleic acid sequence log-linearly into cycle threshold to enable quantitation with a wide dynamic range but suffers from enzymatic biases. Here, we present a general design for constructing hybridization probe sets with highly log-linear response curves to enable accurate enzyme-free quantitation across large ranges (more than 6 logs) of target DNA concentrations. The sensitivity of each component probe is accurately adjusted via formulation stoichiometry to reduce the standard error of target quantitation down to 7%. As a proof of concept, we show multiplexed quantitation of three microRNA species in total RNA of the human brain and liver.

Encoding multiple digital DNA signals in a single analog channel

For many analytic and biomedical applications, the presence of an analyte above or below a critical concentration is more informative for decision making than the actual concentration value. Straightforward analog-to-digital signal conversion does not take full advantage of the precision and dynamic range of modern sensors. Here, we present and experimentally demonstrate an analog-to-multiple-digital signal conversion, reporting digital signals that indicate whether the concentrations of specific DNA sequences exceed respective threshold values. These threshold values can be individually programmed for each target sequence. Experimentally, we showed representation of four DNA targets’ information in a single fluorescence channel.

[Prevalence of cataract among the population aged 50 years and over at different altitudes in Gansu Province]

Objective: To assess the prevalence and influence factors of cataract at different altitudes in Gansu Province. Methods: A total of 7 560 permanent residents aged 50 years and over in seven regions of Gansu Province (altitude, 900 meters to 3 500 meters) were selected as subjects, including 2 402 males and 5 158 females, with an average age of 62.04 years. The cluster random sampling method was used to conduct the survey at village or township health service centers. The investigation procedure included questionnaire survey, pre-investigation, visual acuity examination, intraocular pressure measurement, slit lamp microscopy and fundus examination. The diagnostic criterion for cataract was typical opacity of the lens or no other eye diseases that led to visual impairment but with visual acuity less than 0.7. The prevalence of cataract was calculated according to factors such as altitude, age and sex. The Chi-square test and two-element unconditional logistic regression were used for statistical analyses. Results: A total of 7 560 people were surveyed. The prevalence rate of cataract was 39.7%, and the age-standardized prevalence was 37.7%. The prevalence of cataract increased with age (χ(2)=2 107.19, P<0.01). It was 14.1% in the group of 50-59 years, 42.9% in the group of 60-69 years and 79.2% in the group of over 70 years. The prevalence of cataract also increased with altitude (χ(2)=33.66, P<0.01). It was 36.9% in the group of altitude less than 1 000 meters, 39.0% in the group of altitude between 1 000 meters and 1 999 meters, 45.9% in the group of altitude between 2 000 meters and 2 999 meters, and 51.5% in the group of altitude more than 3 000 meters. With age stratification, the prevalence of cataract at high altitude was higher than that at low altitude (χ(2)=26.74, 16.06, P<0.01). Multivariate regression analysis showed that the risk of cataract was higher in subjects at altitude of 2 000-2 999 meters than those below 1 000 meters (OR=1.42, 95%CI 1.11-1.82), and even higher in those at altitude of 3 000 meters (OR=1.76, 95%CI 1.01-3.06). Conclusions: High altitude and old age are important risk factors for cataract, and high altitude is an independent risk factor for cataract. It is necessary for local health institutions to take measures to reduce the prevalence of blindness and low vision, especially the blindness caused by cataract. (Chin J Ophthalmol, 2019, 55:589-594).

[Comparison of safety and efficacy between proximal gastrectomy and total gastrectomy for upper third gastric cancer: a Meta-analysis]

Objective: To compare the safety and efficacy between proximal gastrectomy and total gastrectomy and to ascertain the optimized procedure for patients with upper third gastric cancer through meta-analysis. Methods: The English literatures about proximal gastrectomy and total gastrectomy for upper third gastric cancer were searched from PubMed, EMBASE, the Cochrane Library and the Web of Science database and then collected. The quality of enrolled studies was independently assessed by two researchers according to the Newcastle-Ottawa Scale for retrospective studies and Jadad scale for RCT studies. The basic information of the literature and related clinical indicators were extracted. The primary endpoints were 5-year overall survival rate and recurrence rate. The secondary endpoints were operative time, intraoperative blood loss, morbidity of postoperative complication, incidence of anastomotic stenosis and incidence of reflux esophagitis. Considering the influence of tumor staging on postoperative clinicopathological features and prognosis, a subgroup analysis was performed on the literatures including cases of early gastric cancer and those including cases of tumor stage I to IV. Statistical analyses were carried out by the "metafor" and "meta" software packages from RevMan 5.3 software and R software (V3.2.4). Results: Twenty-five literatures involving 3667 patients (proximal gastrectomy for 1483, total gastrectomy for 2184) were finally enrolled for analysis, including 24 retrospective studies with ≥ 5 points and 1 RCT with 3 points, and all the literatures were of high quality. A total of 2516 cases of early gastric cancer were enrolled in 18 articles, including 1027 with proximal gastrectomy and 1489 with total gastrectomy. A total of 1151 cases with stage I to IV were enrolled in 7 articles, including 456 in proximal gastrectomy group and 695 in total gastrectomy group. Five-year survival rate was not significantly different for patients with early gastric cancer between the proximal gastrectomy group and total gastrectomy group (OR=1.16, 95% CI: 0.72 to 1.86, P=0.54). Similarly, there was no significant difference for patients with stage I to IV between the proximal gastrectomy group and the total gastrectomy group (OR=1.19, 95% CI: 0.92 to 1.53, P=0.18). Recurrence rate of early gastric cancer patients was not significantly different between the proximal gastrectomy group and the total gastrectomy group (OR=0.40, 95% CI: 0.05 to 3.16, P=0.39).However, the recurrence rate of the proximal gastrectomy group was higher than that of the total gastrectomy group in patients with stage I to IV (OR=1.55, 95% CI: 1.09 to 2.19, P<0.01), whose difference was statistically significant. There was no significant differences in postoperative complication between the groups, both in patients with early gastric cancer, and in those with stage I to IV (both P>0.05). The incidences of postoperative anastomotic stenosis (OR=3.57, 95% CI: 1.82 to 6.99, P<0.01) and reflux esophagitis (OR=2.83, 95% CI: 1.23 to 6.54, P=0.01) in the proximal gastrectomy group were significantly higher than those in the total gastrectomy group in patients with early gastric cancer. Conclusions: There is no significant difference in long-term survival outcomes between total gastrectomy and proximal gastrectomy for upper gastric tumors. However,incidence of anastomotic stenosis and reflux esophagitis, and tumor recurrence rate after total gastrectomy are significantly lower. The total gastrectomy is recommended as the first choice for advanced upper gastric tumor.

[Effects of preoperative percutaneous transhepatic biliary drainage on surgical treatment of type Ⅲ and Ⅳ hilar cholangiocarcinoma]

Objective: To investigate the effects of preoperative percutaneous transhepatic biliary drainage on surgical treatment of type Ⅲ and Ⅳ hilar cholangiocarcinoma. Methods: Clinical data of 72 patients with hilar cholangiocarcinoma of the Bismuth-Corlette type Ⅲ and Ⅳ treated at Department of General Surgery,First Affiliated Hospital of Bengbu Medical College from January 2010 to December 2017 were analyzed retrospectively.Patients were divided into two groups based on whether PTBD was performed:a drained group and an undrained group.In the drained group,there were 31 patients,20 males and 11 females,aged (59.9±9.7)years (range: 39-73 years).Among them,14 patients underwent hepatectomy with half or more than half of the liver removed (extended hepatectomy)and 17 patients underwent non-anatomical hepatectomy in the hilar region (limited hepatectomy).In the undrained group,there were 41 patients, 26 males and 15 females, aged (60.8±7.8)years(range: 45-75 years).Among them, 17 patients underwent hepatectomy with half or more than half of the liver removed (extended hepatectomy)and 24 patients underwent non-anatomical hepatectomy in the hilar region (limited hepatectomy).Percutaneous transhepatic biliary drainage(PTBD)was used in the drained group.Under the guidance of ultrasound,one or more hepatobiliary ducts could be sufficiently drained,which had good effect and was not restricted by the obstruction location of hilar cholangiocarcinoma.The analysis of the measurement data was performed using t test,and the analysis of the count data was performed using χ(2) test,and the survival curve was plotted using Kaplan-meier method. Results: In total, 72 jaundiced patients with hilar cholangiocarcinoma underwent surgical treatment: 31 had PTBD prior to operation while 41 did not had PTBD.There were significant differences in ALT((93.2±21.4)U/L vs.(207.4±65.1)U/L),AST((87.6±18.1)U/L vs.(188.9±56.6)U/L)and total bilirubin((68.8±12.6)μmol/L vs.(227.5±87.7)μmol/L)between the patients after treatment and those before treatment(t=10.958, P=0.000; t=10.845, P=0.000; t=10.386, P=0.000).Compared with those in the undrained group, the operation time was shorter, the amount of intraoperative bleeding and the incidence of complications were lower in the drained group(t=-2.840, P=0.006; t=-3.698, P=0.000; χ(2)=4.108, P=0.043).There were no perioperative death cases in drained group and 2 perioperative death cases in undrained group.There was no significant difference in R0 resection rate between the two groups(χ(2)=0.778,P=0.378).The 1-,3-,5-year survival rate of patients in the drained group and the undrained group was 72.7%,34.2%, 13.7% and 72.8%, 31.5%, 11.8%, respectively.The difference was not statistically significant(all P>0.05). Conclusions: The preoperative percutaneous transhepatic biliary drainage in patients with hilar cholangiocarcinoma of Bismuth-Corlette type Ⅲ and Ⅳ could effectively shorten operative time, reduce amount of intraoperative bleeding and incidence of postoperative complications,but have no significant effect on the R0 resection rate and survival rate.

[Clinical efficacy of ultrasound-guided subacromial drug injection in the treatment of subacromial impingement syndrome]

Objective: To evaluate the clinical effects of ultrasound-guided subacromial injection of two drugs in treatment of subacromial impingement syndrome. Methods: This was a randomized controlled trial study, prospective collection of patients' data who were diagnosed as subacromial impingement syndrome at Orthopedic of Tianjin Fifth Central Hospital from January 2015 to August 2017. To ensure the randomness of the study, patients were randomized into two groups using a random number table. Pain(visual analogue scale(VAS)) and shoulder function (University of California Shoulder Score System(UCLA) and shoulder abduction) were performed before and after each injection.For continuous endings with multiple points in time, firstly, the normality, the homogeneity of variance, and the sphericity test of Mauchly were performed. After the condition was satisfied, the variance analysis of the two-factor repeated measurement data was performed. Results: Fifty-two patients completed the injection within 5 minutes and 41 patients got the final follow-up. Twenty-two patients in the corticosteroid group, 14 males and 8 females, aged (44.7±9.5) years old(range: 35-68 years old). The lesion involved 13 cases of superior shoulder, more than 1 time injection in 4 cases. There were 19 patients in the NSAID group, 7 males and 12 females, aged (37.2±10.1) years old(range: 27-63 years old), 10 cases with lesions involving superior shoulders, and 1 case with more than one injection. (1)VAS score: compared with pre-injection(Corticosteroid group 5.0(4.0-6.0)and NSAIDS group 5.0(4.0-6.0)), both groups showed significant pain relief at 60 minutes(1.0(1.0-2.0)and 1.0(1.0-2.0)) and 6 weeks(1.5(1.0-2.0)and 1.0(1.0-2.0)) after injection(χ²=47.293, 41.173, 45.174, 40.113; P<0.01). (2)UCLA score: compared with pre-injection(30.2±2.5 and 30.5±3.0), UCLA scores improved significantly in both groups at the 6-week after injection(Corticosteroid group: MD=9.727, t=19.218, P<0.001; NSAID Group: MD=9.579, t=11.467, P<0.01). The UCLA score improvement between the two groups was no statistical difference(all P>0.05). (3)shoulder abduction degree: compared with pre-injection(92.7±9.4 and 93.2±11.6), the abduction degree was significantly improved in both groups at 60 minutes(131.8±9.6 and 127.4±16.6) and 6 weeks(115.9±9. 1 and 127.9±14.4) after the injection, but the improvement in each time point has no statistical correlation(MD=4.450, t=1.069, P=0.292). NSAID group had better improvement of shoulder abduction degree than corticosteroid group at the 6 weeks after the injection(MD=-11.986, t=-3.238, P=0.002). Conclusions: Ultrasound-guided subacromial injection can reduce pain in patients with subacromial impingement syndrome.The effect of injection of NSAID drugs is the same as corticosteroid drugs, it can avoid hormone-induced complications and reduce the repeat of the punctures.

[Correlation between severity of gastroesophageal reflux cough and degree of gastroesophageal reflux disease]

Objective: To explore the correlation between the severity of gastroesophageal reflux cough and degree of gastroesophageal reflux. Methods: A cross-sectional investigation was carried out. Data of 174 cases of chronic cough were collected in Children's Hospital of Fuzhou from March 2009 to December 2016. The esophageal 24 hours pH value dynamic monitoring was used to detect gastric acid reflux index. Cases with abnomal results were divided into mild, moderate and severe groups according to severity of reflux and that of day and night cough symptoms, respectively. They were also divided into infant (1-3 years old), preschool (4-6 years old), and school age (>7 years old) groups according to age. Comparative analysis between groups by chi-square test and rank sum test were performed. Correlation analysis was used to analyze the correlation between cough severity and gastroesophageal reflux index. Results: A total of 174 patients with chronic cough, including 115 males and 59 females, aged from 1 to 15 years with an average age of (8.5±2.3) years, and (1.6±0.8) years of disease duration were enrolled. Among them, 129 cases (74.1%) were positive for esophageal reflux test and 45 cases (25.9%) with no obvious pathological gastroesophageal reflux. Patients with positive esophageal reflux test were divided into severe (n=37, 28.7%), moderate (n=23, 17.8%), and mild (n=69, 53.5%). There was no significant difference in the distribution of gastroesophageal reflux in each age group. (The proportions of mild, moderate and severe reflux in infants were 45.0% (9/20), 25.0% (5/20), and 30.0% (6/20), respectively. The proportions of mild, moderate and severe reflux in preschool children were 53.3% (32/60), 16.7% (10/60), 30.0% (18/60), respectively. The proportions of mild, moderate and severe reflux in school age children were 57.1% (28/49), 16.3% (8/49), 26.5% (13/49), respectively χ(2)=1.204, P=0.877). There was no correlation between age group and gastroesophageal reflux (r=-0.065, P=0.489).The severity of nighttime cough was positively correlated with percentages of distal esophagus pH≤4 in time, recumbent pH≤4 in time, and DeMeester score<14.72 (r=0.689, 0.621, and 0.707 respectively, all P<0.05). There was no statistically significant correlation between the severity of nighttime cough symptoms and percentage of standing pH≤4 in time (r=0.113, P>0.05). There were no statistically significant correlation between the severity of daytime cough and all gastroesophageal reflux markers (all P>0.05). Conclusion: The severity of nocturnal symptoms of gastroesophageal reflux cough is related to the degree of gastroesophageal reflux, to which clinical pediatricians should pay attention.

[DeSUMOylation of protein kinase B1 inhibits cell proliferation and metastasis of hepatocellular carcinoma]

Objective: To investigate the effect of AKT1 deSUMOylation induced by Ubc9 silencing on the proliferation and metastasis of hepatocellular carcinoma (HCC) cells. Methods: The Ubc9 gene was silenced using RNA interference, and the expression levels of Ubc9, SUMO1 and AKT1 protein were detected by Western blot. Cell proliferation and cell cycle was analyzed by MTT and flow cytometry. Wound healing and transwell assays were used to detect the cell migration ability. Furthermore, the xenograft model was established, and tumor growth curves were drawn. The in situ apoptotic rates was measured using TUNEL Apoptosis Assay. The expression of proliferating cell nuclear antigen (PCNA), matrix metalloproteinase (MMP)-2 and MMP-9 were evaluated by immunohistochemical staining. Results: Knockdown of Ubc9 gene significantly decreased the protein expression levels of Ubc9, conjugated SUMO1, free SUMO1 and AKT1 in HCC cells (P<0.05 for all). In control, siR-neg and siR-Ubc9 groups, the cell proliferation indexes were 53.19%, 54.25% and 39.17%, respectively. Moreover, cell migration distance and migrating cells per low power field for all these three groups were (59.47±4.66) μm and 89.44±8.36, (56.56±5.37) μm and 93.84±8.79, as well as (34.57±6.61) μm and 41.67±5.39, respectively. In the xenograft model, the weights of subcutaneous tumors for these three groups were (3.78±0.69) g, (3.72±0.72) g and (2.09±0.61) g, respectively. The corresponding apoptotic cell rates were (7.79±2.21)%, (6.45±2.48)% and (33.59±5.44)%, respectively. The expression levels of PCNA, MMP-2 and MMP-9 protein were significantly decreased in siR-Ubc9 group (P<0.05). Conclusions: Ubc9 silencing in HCC cells induces AKT1 deSUMOylation, and then inhibits the proliferation and metastasis. These results provide a new therapeutic strategy for liver cancer in the future.

Predicting DNA hybridization kinetics from sequence

Hybridization is a key molecular process in biology and biotechnology, but so far there is no predictive model for accurately determining hybridization rate constants based on sequence information. Here, we report a weighted neighbour voting (WNV) prediction algorithm, in which the hybridization rate constant of an unknown sequence is predicted based on similarity reactions with known rate constants. To construct this algorithm we first performed 210 fluorescence kinetics experiments to observe the hybridization kinetics of 100 different DNA target and probe pairs (36 nt sub-sequences of the CYCS and VEGF genes) at temperatures ranging from 28 to 55 °C. Automated feature selection and weighting optimization resulted in a final six-feature WNV model, which can predict hybridization rate constants of new sequences to within a factor of 3 with ∼91% accuracy, based on leave-one-out cross-validation. Accurate prediction of hybridization kinetics allows the design of efficient probe sequences for genomics research.