Mutation detection and fast identification of switching system based on data-driven method

In the engineering field,switching systems have been extensively studied,where sudden changes of parameter value and structural form have a significant impact on the operational performance of the system.Therefore,it is important to predict the behavior of the switching system,which includes the accurate detection of mutation points and rapid reidentification of the model.However,few efforts have been contributed to accurately locating the mutation points.In this paper,we propose a new measure of mutation detection—the threshold-based switching index by analogy with the Lyapunov exponent.We give the algorithm for selecting the optimal threshold,which greatly reduces the additional data collection and the relative error of mutation detection.In the system identification part,considering the small data amount available and noise in the data,the abrupt sparse Bayesian regression(abrupt-SBR)method is proposed.This method captures the model changes by updating the previously identified model,which requires less data and is more robust to noise than identifying the new model from scratch.With two representative dynamical systems,we illustrate the application and effectiveness of the proposed methods.Our research contributes to the accurate prediction and possible control of switching system behavior.

APPLICATION OF GENETIC DEAFNESS GENE CHIP FOR DETECTION OF GENE MUTATION OF DEAFNESS IN PREGNANT WOMEN

Objective The study is to identify the carrier rate of common deafness mutation in Chinese pregnant women via detecting deafness gene mutations with gene chip. Methods The pregnant women in obstetric clinic without hearing impairment and hearing disorders family history were selected. The informed consent was signed. Peripheral blood was taken to extract genom- ic DNA. Application of genetic deafness gene chip for detecting 9 mutational hot spot of the most common 4 Chinese deafness genes, namely GJB2 （35delG, 176del16bp, 235delC, 299delAT）, GJB3 （C538T） ,SLC26A4 （ IVS72A〉G, A2168G） and mito- chondrial DNA 12S rRNA （A1555G, C1494T） . Further genetic testing were provided to the spouses and newborns of the screened carriers. Results Peripheral blood of 430 pregnant women were detected, detection of deafness gene mutation carri- ers in 24 cases（4.2%）, including 13 cases of the GJB2 heterozygous mutation, 3 cases of SLC26A4 heterozygous mutation, 1 cases of GJB3 heterozygous mutation, and 1 case of mitochondrial 12S rRNA mutation. 18 spouses and 17 newborns took further genetic tests, and 6 newborns inherited the mutation from their mother. Conclusion The common deafness genes muta- tion has a high carrier rate in pregnant women group, 235delC and IVS7-2A〉G heterozygous mutations are common.

Highly sensitive ECL-PCR method for detection of K-ras point mutation

A highly sensitive electrochemiluminescence-polymerase chain reaction (ECL-PCR) method for K-ras point mutation detection is developed. Briefly, K-ras oncogene was amplified by a Ru(bpy)3(2+) (TBR)-labeled forward and a biotin-labeled reverse primer, and followed by digestion with MvaI restriction enzyme, which only cut the wild-type amplicon containing its cutting site. The digested product was then adsorbed to the streptavidin-coated microbead through the biotin label and detected by ECL assay. The experiment results showed that the different genotypes can be clearly discriminated by ECL-PCR method. It is useful in point mutation detection, due to its sensitivity, safety, and simplicity.

Thermodynamics-guided two-way interlocking DNA cascade system for universal multiplexed mutation detection

Detection of point mutations in driver genes is of great significance for the early diagnosis,treatment,and prognostic evaluation of cancer.However,current detection methods do not offer versatility,specificity,and rapid performance simultaneously.Thus,multiple mutation detection processes are necessary,which results in long processing times and high costs.In this study,we developed a thermodynamics-guided two-way interlocking DNA cascade system for universal multiplexed mutation detection(TTI-CS).This strategy is based on the DNA probe,which changes the thermodynamic balance of the DNA cascade by the designed bubble structure,thereby achieving a good distinction between mutant and wild-type DNA.The designed method greatly shortens the detection time through two-way intrusion.In addition,this method only changes two inexpensive trigger and bridge sequences,which replace the specific and expensive nucleic acid probes used in analyses based on traditional DNA probe methods,thereby enabling multiple detections.We performed the detection of synthetic single-stranded DNA for the five mutation points and successfully detected in endometrial cancer specimens.The detection limit of this method is0.1%,which better meets the needs of clinical low-abundance multiple mutation detection.Overall,TTI-CS is currently one of the best methods for detecting multiple mutation detections.

DETECTION OF p53 GENE MUTATION OF BRONCHOSCOPIC SAMPLIES IN THE PATIENTS SUSPECTED TO LUNG CANCER

Objective: To determine the feasibility of detecting p53 gene mutations for early diagnosis of lung cancer using the samples from bronchoscopic examination. Methods: Point mutations of the exon 5-8 of p53 gene were detected in 85 bronchoscopic samples of 35 patients suspected to be lung cancer using silver staining PCR-SSCP. Results: p53 gene mutations were founded in 10 of 35 patients(28.6%). The incidence of p53 gene mutations (14.9%) was obviously higher than the cytological positive incidence(2.9%) in samples of sputum, bronchoalveolar lavage and brush, especially for the sputum(27.7%). In the bronchoscopic biopsy specimens, the incidence of p53 gene mutations (12.5%) was lower than that of pathologic positive result (50.0%). However, in view of all the bronchoscopic samples, there was no statistically difference between cytopathologic positive results (11.8%) and the incidence of p53 gene mutations (14.1%). Although the p53 mutations were most common in the samples from the patients bronchoscopically manifested as neoplasm compared with other manifestations, there was no statistical difference. It is valuable to notice that 3 patients with p53 gene mutation merely presented as bronchial inflammation in bronchoscope. Conclusion: Results indicated that the value of detecting p53 gene mutation for the diagnosis of lung cancer using the bronchoscopic samples was more superior to cytological examination and detection of p53 gene mutations in post-bronchoscopic sputum was easy and effective, may be used as a valuable method for early diagnosis of lung cancer.

Comparison of diagnostic value of TIRADS,BSRTC,BRAF^(V600E) mutation detection and their combined use in differentiating thyroid nodules

Objective To compare the diagnostic efficiency of the thyroid imaging reporting and data system(TIRADS),the Bethesda system for reporting thyroid cytopathology(BSRTC)and BRAFV600Edetection,and their combined use in the differentiation between benign and malignant thyroid nodules.Methods One hundred

DETECTION OF GENE MUTATION IN SPUTUM OF LUNG CANCER PATIENT

Lungcancerisacommonmalignanttumor,whichhasahighincidenceandmortalityrate.Therefore,itisnecessarytoseekanewmethodforthediagnosis,especiallytheearlydiagnosisoflungcancer.Thedevelopmentofmolecularbiologymakesthegenediagnosisoflungcancerpossible.PCR-SSCP...

Clinicopathological features and prognosis assessment of extranodal follicular dendritic cell sarcoma

AIM: To establish a model for prognosis assessment of extranodal follicular dendritic cell (FDC) sarcoma.METHODS: Nine lesions were examined by routine and molecular approaches.Clinicopathological factors from the new cases and 97 reported cases were analyzed for their prognostic values.RESULTS: The current lesions were found in f ive male and four female patients,located mainly in the head and neck area and averaging 7.2 cm in size.Six patients had recurrence or metastasis and three remained free of disease.The 106 patients (male/female ratio,1.1:1) were aged from 9 to 82 years (median,44 years).The tumor sizes ranged from 1.5 to 21 cm (mean,7.4 cm).Abdominal/pelvic region was affected most frequently (43%).Surgical resection was performed in 100 patients,followed by radiation and/or chemotherapy in 35 of them.Follow-up data were available in 91 cases,covering a period of 3-324 mo (mean,27 mo;median,19 mo).Of the informative cases,38 (42%) had recurrence or metastasis,and 12 (13%) died of the disease.These tumors were classif ied histologically into lowand high-grade lesions.A size ≥ 5 cm (P = 0.003),highgrade histology (P = 0.046) and a mitotic count ≥ 5/10 HPF (P = 0.013) were associated with tumor recurrence.The lesions were def ined as low-,intermediateand high-risk tumors,and their recurrence rates were 16%,46% and 73%,and their mortality rates 0%,4% and 45%,respectively.CONCLUSION: Extranodal FDC tumors behave like soft tissue sarcomas.Their clinical outcomes are variable and can be evaluated according to their sizes and grades.

Development and validation of a novel PCR-RFLP based method for the detection of 3 primary mitochondrial mutations in Leber's hereditary optic neuropathy patients

Background:Leber’s Hereditary Optic Neuropathy(LHON;MIM 535000)is one of the most commonly inherited optic neuropathies and it results in significant visual morbidity among young adults with a peak age of onset between the ages of 15–30.The worldwide incidence of LHON is approximately 1 in 31,000.95%of LHON patients will have one of 3 primary mitochondrial mutations,G3460A(A52T of ND1),G11778A(R340H of ND4)and T14484C(M64V of ND6).There is incomplete penetrance and a marked gender bias in the development of visual morbidity with approximately 50%of male carriers and 10%of female carriers developing optic neuropathy.Visual recovery can occur but is dependent on the mutation present with the highest level of visual recovery seen in patients who have the T14484C mutation.The 3 primary mutations are typically identified by individual end-point PCR-restriction fragment length polymorphism(RFLP)or individual targeted bi-directional Sanger sequencing reactions.The purpose of this study was to design a simple multiplex PCR-RFLP that could detect these 3 primary LHON mutations in one assay.Methods:PCR primers were designed to incorporate a MaeIII restriction site in the presence of 3460A and 14484C mutations with the 11778A mutation naturally incorporating a MaeIII site.A multiplex PCR-RFLP assay was developed to detect the 3 common mutations in a single assay.Synthetic LHON controls based on the mitochondrial genome harbouring the 3 common mutations were synthesized and cloned into plasmids to act as reliable assay controls.DNA from previously tested patients and the synthetic LHON controls were subjected to the multiplex PCR-RFLP assay.The RFLP products were detected by agarose gel electrophoresis.Results:The novel PCR-RFLP assay accurately detects the 3 primary mutations both in patient DNA and in synthesized DNA control samples with a simple visual mutation detection procedure.The synthesized DNA was demonstrated to be a robust control for the detection of LHON Mutations.Conclusion:In this paper,we describe a novel,robust and simple PCR-RFLP based method for the detection of mutations causing LHON,and report the generation of a series of LHON DNA controls suitable for all currently published assays.

Variation Characteristics and Trends of Temperature and Evaporation in Huanren County in Recent 60 Years

Based on the data of daily average temperature and evaporation in Huanren County from 1953 to 2012, the changing characteristics and trends of temperature and evaporation were analyzed by using climatic tendency rate and sliding Ttest method. The results showed that annual av- erage temperature in Huanren County showed a significant increasing trend in recent 60 years, and its linear tendency rate was 0.26 ℃/10 a. Tem- perature increase was in other seasons except for summer. There was a sudden change in annual average temperature in 1987, and winter average temperature changed suddenly in 1969 and 1985, while there were no sudden changes in average temperature in other seasons. Annual average evaporation also decreased, and its linear trend rate was -8.19 mm/10 a; average evaporation tended to decrease in spring and summer and in- creased in autumn and winter. In a word, the climate tended to be warm and dry in Huanren County.

Detection of p53 gene mutations in skeletal muscle cell of patients with chronic heart failure

Progressive deterioration of physical work capacity in congestive heart failure (CHF) is often attributed to ongoing skeletal muscle atrophy and abnormalities in muscle metabolism. The purpose of the present study was to investigate if mutations in the p53 gene thought to be a promotor of apoptosis are involved in intrinsic apoptotic abnormalities in skeletal muscle of patients (pts) with CHF. Percutaneous needle biopsy from the m. vastus lateralis were obtained from 19 pts with CHF (LV EF 25%±10%). Single strand confirmation polymorphism analysis of polymerase chain reation products (PCR SSCP analysis) was used for detection of mutations in exon 5 8 of the p53 gene in skeletal Heart Center, University Leipzig, Germany (Yu JT, Adams V, Fiehn E, Schuler G and Hambrecht R) Institut of Pathology, University Freiburg, Germany (Ye J and Riede U)muscle cells. Four of 19 muscle specimens (21%) showed mobility shifts. To characterize the nuleotide sequence alterations specimens were examined further by direct sequence analysis of PCR product. Two of four specimens showing a band shift in the SSCP analysis exhibited a mutated p53 sequence. Sequence analysis revealed that these alteratons were point mutation exon 8 (14482, G→A) and deletion in exon 5 (13143 13157). A high frequency of p53 mutations was detected in skeletal muscle cells of patients with chronic heart failure. These findings suggest a role for apoptosis in the progression of intrinsic skeletal muscle abnormalities and consequently of exercise intolerance in chronic heart failure.

Genetic Analysis of the PKHD1 Gene with Long-rang PCR Sequencing

PKHD1 gene mutations are found responsible for autosomal recessive polycystic kidney disease（ARPKD）. However, it is inconvenient to detect the mutations by common polymerase chain reaction（PCR） because the open reading frame of PKHD1 is very long. Recently, long-range（LR） PCR is demonstrated to be a more sensitive mutation screening method for PKHD1 by directly sequencing. In this study, the entire PKHD1 coding region was amplified by 29 reactions to avoid the specific PCR amplification of individual exons, which generated the size of 1 to 7 kb products by LR PCR. This method was compared to the screening method with standard direct sequencing of each individual exon of the gene by a reference laboratory in 15 patients with ARPKD. The results showed that a total of 37 genetic changes were detected with LR PCR sequencing, which included 33 variations identified by the reference laboratory with standard direct sequencing. LR PCR sequencing had 100% sensitivity, 96% specificity, and 97.0% accuracy, which were higher than those with standard direct sequencing method. In conclusion, LR PCR sequencing is a reliable method with high sensitivity, specificity and accuracy for detecting genetic variations. It also has more intronic coverage and lower cost, and is an applicable clinical method for complex genetic analyses.

Whole-genome sequencing to detect mutations associated with resistance to insecticides and Bt proteins in Spodoptera frugiperda

The fall armyworm(FAW),Spodoptera frugiperda,is a major pest native to the Americas that has recently invaded the Old World.Point mutations in the target-site proteins acetylcholinesterase-1(ace-1),voltage-gated sodium channel(VGSC)and ryanodine receptor(RyR)have been identified in S.frugiperda as major resistance mechanisms to organophosphate,pyrethroid and diamide insecticides respectively.Mutations in the adenosine triphosphate-binding cassette transporter C2 gene(ABCC2)have also been identified to confer resistance to Cry IF protein.In this study,we applied a whole-genome sequencing(WGS)approach to identify point mutations in the target-site genes in 150 FAW individuals collected from China,Malawi,Uganda and Brazil.This approach revealed three amino acid substitutions(A201S,G227A and F290V)of S.frugiperda ace-1,which are known to be associated with organophosphate resistance.The Brazilian population had all three ace-1 point mutations and the 227A allele(mean frequency=0.54)was the most common.Populations from China,Malawi and Uganda harbored two of the three ace-1 point mutations(A201S and F290V)with the 290V allele(0.47-0.58)as the dominant allele.Point mutations in VGSC(T929I,L932F and L1014F)and RyR(I4790M and G4946E)were not detected in any of the 150 individuals.A novel 12-bp insertion mutation in exon 15 of the ABCC2 gene was identified in some of the Brazilian individuals but absent in the invasive populations.Our results not only demonstrate robustness of the WGS-based genomic approach for detection of resistance mutations,but also provide insights for improvement of resistance management tactics in S.frugiperda.

Identification of a mutation hotspot in exon 8 of Wilson disease gene by cycle sequencing

Objective To screen for mutation hotspot of Wilson disease (WD) gene in Chinese population Methods Cycle sequencing was used to detect mutation in exon 8 of WD gene in 30 patients with Wilson disease Results The same missense mutation, Arg779Leu, was identified in 14 WD patients, four of whom were homozygous and the other heterozygous for this mutation The frequency of this mutation in Chinese patients was 30% Conclusion The codon 779 (CCG→CTG) of exon 8 of WD gene was one of mutation hotspots in Chinese

Autozygosity Mapping by Genome-wide Single Nucleotide Polymorphism Array Identifies a Novel Homozygous HR Mutation in a Consanguineous Family with Universal Hereditary Hair Loss

Objective:Isolated hereditary hypotrichosis is caused by mutations in as many as 11 different genes.The conventional mutation detection strategy consists of sequencing of individual candidate genes separately,a time consuming and costly approach.In this study,we perform genome-wide single nucleotide polymorphism(SNP)array to identify candidate genes of hereditary hypotrichosis.Methods:A consanguineous family with two patients with hereditary hypotrichosis was enrolled,and autozygosity mapping by genome-wide SNP array was utilized to identify candidate genes.Results:Autozygosity mapping delineated runs of homozygosity,and alignment of the 11 genes identified the hairless(HR)gene as the candidate gene.Nucleotide sequencing revealed a novel homozygous mutation c.381delT,p.Ser127ArgfsTer40.Conclusion:This study illustrates how autozygosity mapping by a high-density SNP array streamlines mutation detection in heritable skin diseases.

Progress in TILLING as a tool for functional genomics and improvement of crops

Food security is a global concern and substantial yield increases in crops are required to feed the growing world population. Mutagenesis is an important tool in crop improvement and is free of the regulatory restrictions imposed on genetically modified organisms. Targeting Induced Local Lesions in Genomes（TILLING）, which combines traditional chemical mutagenesis with high‐throughput genome‐wide screening for point mutations in desired genes, offers a powerful way to create novel mutant alleles for both functional genomics and improvement of crops. TILLING is generally applicable to genomes whether small or large, diploid or evenallohexaploid, and shows great potential to address the major challenge of linking sequence information to the function of genes and to modulate key traits for plant breeding. TILLING has been successfully applied in many crop species and recent progress in TILLING is summarized below, especially on the developments in mutation detection technology, application of TILLING in gene functional studies and crop breeding. The potential of TILLING/EcoTILLING for functional genetics and crop improvement is also discussed. Furthermore, a small‐scale forward strategy including backcross and selfing was conducted to release the potential mutant phenotypes masked in M2（or M3） plants.

Genetic characterization of Stargardt clinical phenotype in South Indian patients using sanger and targeted sequencing

Background:Stargardt disease 1(STGD1;MIM 248200)is a monogenic form of autosomal recessive genetic disease caused by mutation in ABCA4.This gene has a major role in hydrolyzing N-retinylidene-phosphatidylethanolamine to all-trans-retinal and phosphatidylethanolamine.The purpose of this study is to identify the frequency of putative disease-causing mutations associated with Stargardt disease in a South Indian population.Methods:A total of 28 clinically diagnosed Stargardt-like phenotype patients were recruited from south India.Ophthalmic examination of all patients was carefully carried out by a retina specialist based on the stages of fundus imaging and ERG grouping.Genetic analysis of ABCA4 was performed for all patients using Sanger sequencing and clinical exome sequencing.Results:This study identified disease-causing mutations in ABCA4 in 75%(21/28)of patients,7%(2/28)exhibited benign variants and 18%(5/28)were negative for the disease-causing mutation.Conclusion:This is the first study describing the genetic association of ABCA4 disease-causing mutation in South Indian Stargardt 1 patients(STGD1).Our findings highlighted the presence of two novel missense mutations and an(in/del,single base pair deletion&splice variant)in ABCA4.However,genetic heterogeneity in ABCA4 mutants requires a larger sample size to establish a true correlation with clinical phenotype.

Programmable endonuclease combined with isothermal polymerase amplification to selectively enrich for rare mutant allele fractions

Liquid biopsy is a highly promising method for non-invasive detection of tumor-associated nucleic acid fragments in body fluids but is challenged by the low abundance of nucleic acids of clinical interest and their sequence homology with the vast background of nucleic acids from healthy cells.Recently,programmable endonucleases such as clustered regularly interspaced short palindromic repeats(CRISPR)associated protein(Cas)and prokaryotic Argonautes have been successfully used to remove background nucleic acids and enrich mutant allele fractions,enabling their detection with deep next generation sequencing(NGS).However,the enrichment level achievable with these assays is limited by futile binding events and off-target cleavage.To overcome these shortcomings,we conceived a new assay(Programmable Enzyme-Assisted Selective Exponential Amplification,PASEA)that combines the cleavage of wild type alleles with concurrent polymerase amplification.While PASEA increases the numbers of both wild type and mutant alleles,the numbers of mutant alleles increase at much greater rates,allowing PASEA to achieve an unprecedented level of selective enrichment of targeted alleles.By combining CRISPR-Cas9 based cleavage with recombinase polymerase amplification,we converted samples with0.01%somatic mutant allele fractions(MAFs)to products with 70%MAFs in a single step within 20 min,enabling inexpensive,rapid genotyping with such as Sanger sequencers.Furthermore,PASEA's extraordinary efficiency facilitates sensitive real-time detection of somatic mutant alleles at the point of care with custom designed Exo-RPA probes.Real-time PASEA'performance was proved equivalent to clinical amplification refractory mutation system(ARMS)-PCR and NGS when testing over hundred cancer patients'samples.This strategy has the potential to reduce the cost and time of cancer screening and genotyping,and to enable targeted therapies in resource-limited settings.

In-depth cDNA Library Sequencing Provides Quantitative Gene Expression Profiling in Cancer Biomarker Discovery

Quantitative gene expression analysis plays an important role in identifying differentially expressed genes in various pathological states, gene expression regulation and co-regulation, shedding light on gene functions. Although microarray is widely used as a powerful tool in this regard, it is suboptimal quantitatively and unable to detect unknown gene variants. Here we demonstrated effective detection of differential expression and co-regulation of certain genes by expressed sequence tag analysis using a selected subset of cDNA libraries. We discussed the issues of sequencing depth and library preparation, and propose that increased sequencing depth and improved preparation procedures may allow detection of many expression features for less abundant gene variants. With the reduction of sequencing cost and the emerging of new generation sequencing technology, in-depth sequencing of cDNA pools or libraries may represent a better and powerful tool in gene expression profiling and cancer biomarker detection. We also propose using sequence-specific subtraction to remove hundreds of the most abundant housekeeping genes to increase sequencing depth without affecting relative expression ratio of other genes, as transcripts from as few as 300 most abundantly expressed genes constitute about 20% of the total transcriptome. In-depth sequencing also represents a unique advantage of detecting unknown forms of transcripts, such as alternative splicing variants, fusion genes, and regulatory RNAs, as well as detecting mutations and polymorphisms that may play important roles in disease pathogenesis.