Novel Metrics for Mutation Analysis

A measure of the“goodness”or efficiency of the test suite is used to determine the proficiency of a test suite.The appropriateness of the test suite is determined through mutation analysis.Several Finite State Machine(FSM)mutants are produced in mutation analysis by injecting errors against hypotheses.These mutants serve as test subjects for the test suite(TS).The effectiveness of the test suite is proportional to the number of eliminated mutants.The most effective test suite is the one that removes the most significant number of mutants at the optimal time.It is difficult to determine the fault detection ratio of the system.Because it is difficult to identify the system’s potential flaws precisely.In mutation testing,the Fault Detection Ratio(FDR)metric is currently used to express the adequacy of a test suite.However,there are some issues with this metric.If both test suites have the same defect detection rate,the smaller of the two tests is preferred.The test case(TC)is affected by the same issue.The smaller two test cases with identical performance are assumed to have superior performance.Another difficulty involves time.The performance of numerous vehicles claiming to have a perfect mutant capture time is problematic.Our study developed three metrics to address these issues:FDR/|TS|,FDR/|TC|,and FDR/|Time|;In this context,most used test generation tools were examined and tested using the developed metrics.Thanks to the metrics we have developed,the research contributes to eliminating the problems related to performance measurement by integrating the missing parameters into the system.

Temperature Variation and Mutation Analysis over the Past 59 Years in Shenyang

In this paper,based on the observation data of air temperature during 1951-2009 in Shenyang,the interannual and interdecadal variation of annual average temperature,maximum and minimum temperature in Shenyang were conducted the statistical analysis by means of linear trend estimation and mutation detection by using Mann-Kendall method.As was demonstrated in the results,the annual average temperature,maximum and minimum temperature in Shenyang showed an upward trend,whose linear tendency rate was 0.231,0.181 and 0.218 respectively.The increment trend of annual average temperature,maximum and minimum temperature was extremely clear.The increase in minimum temperature was more significant than that in mean temperature and maximum temperature.The abrupt change point of annual mean temperature in Shenyang appeared in 1981;the abrupt change point of annual mean maximum temperature appeared in 1994;the annual mean minimum temperature underwent mutation in 1978.

Mutation Analysis of IgVH Gene in B-Cell Chronic Lymphocytic Leukemia

Summary: The variable heavy chain region (VH) genes of 3 untreated patients with B cell chronic lymphocytic leukemia (B CLL) were cloned and analyzed. The VH family used was VH3 11, VH3 72 and VH3 33. More than 2 % difference from the corresponding germline gene was detected in all the 3 obtained potential functional genes (average 16.7). Mutation pattern analysis indicated evidence of antigen selective pressure observed in 1 of 3 cases. Our findings suggested that the tumor cells originate from post GC cells.

RET proto-oncogene mutation analysis in a pedigree with multiple endocrine neoplasia 2A

Objective To discuss clinical diagnosis and treatment of multiple endocrine neoplasia ( MEN) 2A,and report the mutation of RET proto-oncogene in a pedigree of three patients with MEN 2A. Methods Bilateral adrenalectomy was performed on two of the three

Partial Fusion (F) Gene Analysis of Newcastle Disease Virus Detected in Pakistan during 2021-2022

Newcastle disease (ND) virus is a leading threat to commercial and domestic poultry in Pakistan. The virus infects and constitutes irreversible impairment to the nervous system, damages the respiratory system, and marks severe gastrointestinal lesions leading to heavy mortality in short-living birds and substantial losses in layers and breeders. The continuous emergence and evolution of the virus made it inclined to evade the humoral response and indirectly the circumvention of artificial active immunization. Newcastle disease is caused by the orthoavula genus of the paramyxoviridae family and has shown high genetic diversity even in their genotypes while information regarding enzootic trends of the virus is scanty in Pakistan. A total of 40 tracheal samples of NDV were collected from different commercial broiler farms and 11 isolates of NDV were identified. In the current study, we determined the genetic diversity of the Newcastle disease virus based on the partial sequencing of the fusion protein gene available in the NCBI database. Genetic analysis showed that seven isolates belonged to class I genotype VII and four belonged to class II genotype II. Interestingly, two isolates had epidemiological connections with vaccine-like class II genotype II. Our findings, concerning the recent outbreaks of class I genotype VII and class II genotype II of NDV in vaccinated commercial flocks, suggest possible potential partial mutations in the fusion protein gene. Genetic diversity and formation of the new cleavage site in an important neutralizing protein of wild strain are linked with the potency of artificial active immunization and a major cause of vaccine failure.

Mutation analysis of PAX6 gene in a large Chinese family with aniridia

Background Mutations in PAX6 gene have been shown to be the genetic cause of aniridia, which is a severe panocular eye disease characterised by iris hypoplasia. However, there is no study to do genetic analysis of aniridia, although there are several case reports in China. Here, we describe a mutation analysis of PAX6 in a large Chinese family with aniridia. Methods Genomic DNA from venous blood samples was prepared. Haplotype analysis was performed with two genetic markers ( D11S904 and D11S935). Fourteen exons of the PAX6 gene were amplified from genomic DNA. Polymerase chain reaction ( PCR) products of each exon were analysed by single strand conformational polymorphism (SSCP). The PCR products having an abnormal pattern were sequenced to confirm the mutation. Results Significant evidence for allele sharing in affected patients was detected suggesting that PAX6 mutation links to aniridia in this family. An extra band corresponding to exon 9 in PAX6 was found by single strand conformational polymorphism analysis in all the aniridia patients in this family, but not detected in the unaffected members. A mutation of C to T was detected by sequencing at the nucleotide 1080 that converts the Arg codon (CGA) to the termination codon (TGA). Conclusions Aniridia is caused by a nonsense mutation of PAX6 gene in the large Chinese kindred. Genetic test is important to prevent the transmission of aniridia to their offsprings in the kindred by prenatal diagnosis.

Clinical classification and gene mutation of Chinese probands with Charcot-Marie-Tooth disease Analysis of 57 cases

Charcot-Marie-Tooth （CMT） disease is the most common inherited peripheral neuropathic disorder. CMT is clinically and genetically heterogeneous. To date, 27 genes associated with the disease have been cloned. The present study carried out clinical classification according to clinical, electrophysiological and pathological features, conducted inheritance classification according to inheritance patterns, and performed mutation analysis of 13 CMT disease genes （PMP22, CX32, HSPB1, MNF2, MPZ, HSPB8, GDAP1, NFL, EGR2, SIMPLE, RAB7, LMNA, MTMR2） in 57 Chinese probands with CMT. Five cases of AD-CMT1 and 13 cases of sporadic CMT1 were diagnosed as CMT1A; five cases of X-CMT1, one case of X-CMT2 and one case of sporadic CMT1 were diagnosed as CMTXl; four cases of AD-CMT2 were diagnosed as CMT2F; one case of AD-CMT2 and one case of sporadic CMT2 were diagnosed as CMT2A2; one case of AD-CMT2 was diagnosed as CMT2L; one case of AD-CMT2 was diagnosed as CMT2J; one case of AR-CMT1 was diagnosed as CMT4A. Among the 57 CMT probands, seven genotypes were determined among 34 patients, with a detection rate of 59.6%. The results indicated that the clinical classification and inheritance classification are indispensable for selecting potential disease genes for mutation detection, and for efficient molecular diagnosis.

Performance of K-ras mutation analysis plus endoscopic ultrasound- guided fine-needle aspiration for differentiating diagnosis of pancreatic solid mass： a meta-analysis

Background Difficulties persist in differentiating pancreatic ductal adenocarcinomas （PDAC） from pancreatic inflammatory masses （PIM）. Auxiliary diagnostic techniques which enhance the endoscopic ultrasound-guided fine-needle aspiration （EUS-FNA） diagnostic yield have been attempted, for example, K-ras mutation analysis. We aimed to evaluate the accuracy of K-ras mutation analysis combined with EUS-FNA for the differential diagnosis of PDAC and PIM by pooling data of existing trials. Methods We systematically searched the Medline, PubMed, Web of Science, Embase, and Cochrane Central Trials databases for relevant published studies. Meta-analysis was performed. Pooling was conducted in fixed-effect model or random-effect model. Results In total eight studies, with 696 cases of PDAC and 138 cases of PIM, met our inclusion criteria. The pooled sensitivity, specificity, positive likely ratio and negative likely ratio of K-ras mutation analysis combined with cytopathology for diagnosis of PDAC versus PIM were 90%, 95%, 13.45, and 0.13, respectively. Especially, among total 123 patients whose EUS-FNA results were inconclusive or negative, fifty-nine had K-ras mutations and were finally diagnosed with PDAC （48%, 59/123）. Publication bias was not present. Conclusions Combining K-ras mutation analysis with routine cytology moderately improves the ability of EUS-FNA to differentially diagnose between PDAC and PIM, especially for patients with suspected PDAC yet inconclusive EUS-FNA findings, and may prove to be a valuable supplemental method to EUS-FNA.

Investigation of Single and Multiple Mutations Prediction Using Binary Classification Approach

The mutation is a critical element in determining the proteins’stability,becoming a core element in portraying the effects of a drug in the pharmaceutical industry.Doing wet laboratory tests to provide a better perspective on protein mutations is expensive and time-intensive since there are so many potential muta-tions,computational approaches that can reliably anticipate the consequences of amino acid mutations are critical.This work presents a robust methodology to analyze and identify the effects of mutation on a single protein structure.Initially,the context in a collection of words is determined using a knowledge graph for feature selection purposes.The proposed prediction is based on an easier and sim-pler logistic regression inferred binary classification technique.This approach can able to obtain a classification accuracy(AUC)Area Under the Curve of 87%when randomly validated against experimental energy changes.Moreover,for each cross-fold validation,the precision,recall,and F-Score are presented.These results support the validity of our strategy since it performs the vast majority of prior studies in this domain.

Comparative analysis of dideoxy sequencing,the KRAS StripAssay and pyrosequencing for detection of KRAS mutation

AIM:To compare the differences between dideoxy sequencing/KRAS StripAssay/pyrosequencing for detection of KRAS mutation in Chinese colorectal cancer (CRC) patients.METHODS:Formalin-f ixed, paraff in-embedded (FFPE) samples with tumor cells ≥ 50% were collected from 100 Chinese CRC patients at Beijing Cancer Hospital. After the extraction of genome DNA from FFPE samples, fragments contained codons 12 and 13 of KRAS exon 2 were amplified by polymerase chain reaction and analyzed by dideoxy sequencing, the KRAS Strip Assay and pyrosequencing. In addition, the sensitivities of the 3 methods were compared on serial dilutions (contents of mutant DNA: 100%,50%,20%, 5%,10%, 5%,1%,0%) of A549 cell line DNA (carrying the codon 12 Gly>Ser mutation) into wild-type DNA (human normal intestinal mucosa). The results of dideoxy sequencing,the KRAS StripAssay and pyrosequencing were analyzed by Chromas Software, Collector forKRAS Strip Assay and the pyrosequencing PyroMarkTM Q24 system, respectively.RESULTS: Among 100 patients, KRAS mutations were identif ied in 34%, 37% and 37% of patients by dideoxy sequencing, the KRAS StripAssay and pyrosequencing, respectively. The sensitivity was highest with the KRAS Strip Assay (1%), followed by pyrosequencing (5%), and dideoxy sequencing was lowest (15%). Six different mutation types were found in this study with 3 main mutations Gly12 Asp (GGT>GAT), Gly12 Val (GGT>GTT) and Gly13 Asp (GGC>GAC). Thirty-three patients were identifi ed to have KRAS mutations by the 3 methods, and a total of 8 patients had conflicting results between 3 methods: 4 mutations not detected by dideoxy sequencing and the KRAS StripAssay were identified by pyrosequencing; 3 mutations not detected by dideoxy sequencing and pyrosequencing were identif ied by the KRAS StripAssay; and 1 mutation not detected by pyrosequencing was conf irmed by dideoxy sequencing and the KRAS StripAssay. Among these discordant results, the results identif ied by dideoxy sequencing were consistent either with the KRAS StripAssay or with pyrosequencing, which indicated that the accuracy of dideoxy sequencing was high. CONCLUSION: Taking a worldwide view of reports and our results,dideoxy sequencing remains the most popular method because of its low cost and high accuracy.

Epidemiology and Mutational Analysis of Global Strains of Crimean-Congo Haemorrhagic Fever Virus

Crimean-Congo hemorrhagic fever (CCHF) is a severe illness with high fatality.Cases are reported in several countries in Africa,Europe,the Middle East,and Asia.Phylogenetic analyses based on the virus S (nucleocapsid),M (glycoprotein),and L (polymerase) genome segments sequences indicate distinct geographic lineages exist but their specific genetic characteristics require elucidation.In this work we collected all full length S segment sequences and generated a phylogenetic tree based on the alignment of these 62 samples.We then analyzed the alignment using entries from AAIndex,the Amino Acid Index database,to identify amino acid mutations that performed significant changes in charge,pka,hydropathy and side chain volume.Finally,we mapped these changes back to the tree and alignment to identify correlated mutations or sites that characterized a specific lineage.Based on this analysis we are able to propose a number of sites that appear to be important for virus function and which would be good candidates for experimental mutational analysis studies.

Analysis of the human Atox 1 homologue in Wilson patients

AIM: To analyze the metallochaperone antioxidant-1 (Atox1) gene sequence in Wilson disease patients. METHODS: Mutation analysis of the four exons of the Atox1 gene including the intron- exon boundaries was performed in 63 Wilson disease patients by direct sequencing. RESULTS: From 63 selected patients no mutations were identified after the entire coding region including the intron- exon boundaries of Atox1 were sequenced. One known polymorphism within the Atox1 gene (5’UTR -99 T>C) in 31 (49%) of the Wilson patients as well as one previously undescribed variation (5’UTR -68 C>T) in 2 of the Wilson patients could be detected. Statistical analyses revealed that the existence of a variation within the Atox1- gene showed a tendency towards an earlier onset of the disease. CONCLUSION: Based on the data of this study, no major role can be attributed to Atox1 in the pathophysiology or clinical variation of Wilson disease.

Identification of speckle-type POZ protein somatic mutations in African American prostate cancer

The speckle-type POZ protein （SPOP） is a tumor suppressor in prostate cancer （PCa）. SPOP somatic mutations have been reported in up to 15% of PCa of those of European descent. However, the genetic roles of SPOP in African American （AA）-PCa are currently unknown. We sequenced the SPOP gene to identify somatic mutations in 49 AA prostate tumors and identified three missense mutations （p.Y87C, p.F102S, and p.G111E） in five AA prostate tumors （10%） and one synonymous variant （p.11061） in one tumor. Intriguingly, all of mutations and variants clustered in exon six, and all of the mutations altered conserved amino acids. Moreover, two mutations （p.F102S and p.G111E） have only been identified in AA-PCa to date. Quantitative real-time polymerase chain reaction analysis showed a lower level of SPOP expression in tumors carrying SPOP mutations than their matched normal prostate tissues. In addition, SPOP mutations and novel variants were detected in 5 of 27 aggressive PCa and one of 22 less aggressive PCa （P 〈 0.05）. Further studies with increased sample size are needed to validate the clinicopathological significance of these SPOP mutations in AA-PCa.

Novel mutations and sequence variants in exons 3-9 of human T Cell Factor-4 gene in sporadic rectal cancer patients stratified by microsatellite instability

AIM： To establish the role of human T Cell Factor-4 （hTCF-4） gene exons 3-9 mutation status in association with sporadic rectal cancer with microsatellite instability （MSI）. METHODS： Microsatellite markers were genotyped in 93 sporadic rectal cancer patients. Eleven cases were found to be high-frequency MSI （MSI-H）. Sequence analysis of the coding region of the exons 3-9 of hTCF-4 gene was carried out for the 11 MSI-H cases and 10 controls （5 microsatellite stability （MSS） cases and 5 cases with normal mucosa）. The sequencing and MSI identification were used. RESULTS： Several novel mutations and variants were revealed. In exon 4, one is a 4-position continuous alteration which caused amino acid change from Q131T and S132I （391insA, 392 G 〉 A, 393 A 〉 G and 395delC） and another nucleotide deletion （395delC） is present in MSI-H cases （5/10 and 4/10, respectively） but completely absent in the controls.CONCLUSION： Novel mutations in exon 4 of hTCF-4 gene were revealed in this study, which might be of importance in the pathogenesis of sporadic rectal cancer patients with MSI-H.

Identifying Driver Genes Mutations with Clinical Significance in Thyroid Cancer

Advances in technology are enabling gene mutations in papillary thyroid carcinoma(PTC)to be analyzed and clinical outcomes,such as recurrence,to be predicted.To date,the most common genetic mutation in PTC is in BRAF kinase(BRAF).However,whether mutations in other genes coincide with those in BRAF remains to be clarified.The aim of this study was to find mutations in other genes that co-exist with mutated BRAF,and to analyze their frequency and clinical relevance in PTC.Clinical and genetic data were collected from 213 PTC patients with a total of 36,572 mutation sites in 735 genes.After matching with genes from PTC entries in a global database(NCBI Gene),69 genes with mutations in coding regions were chosen for further study.Through frequency-based analysis,we identified commonly mutated genes co-existing with mutated BRAF and,using the mutation count correlation matrix(MCCM)method,analyzed their incidence according to age and gender.We designed Chord diagrams to reveal gene relationships concerning age and gender,and found that mutations in ALK,ATM,COL1A1,MSTIR,PRKCA,and WNK1 most commonly coincide with mutated BRAF,followed by APC,AURKA,and AURKB.These findings provide further insight into the genetic profile of PTC.

Analysis on the Variation of Rainfall Data from Guilin Weather Station during 1957-2007

[Objective] The research aimed to study the variation of rainfall data from Guilin Weather Station during 1957-2007.[Method] Based on the daily rainfall data in Guilin during 1957-2007,the trend,period and mutation of precipitation in Guilin in 51 years were analyzed by using the trend analysis,wavelet analysis and Mann-Kendall non-parameter statistics test method.[Result] The rainfall in Guilin in 51 years presented the rising trend.The rainfall variation was same in the first,second and third quarters of most years,except in the individual year.The rainfall in the fourth quarter had the decrease trend,and the variation was obvious in each year.It illustrated that the rainfall variation in winter was very unstable and had the decrease trend in recent years.But as a whole,the variation of total rainfall in Guilin wasn’t obvious and had the rise trend.It illustrated that the climate variation in Guilin in 51 years wasn’t obvious.The wavelet analysis showed that the rainfall variation in Guilin had 15-year big period and the small period of 2-3 years.Mann-Kendall non-parameter statistics test showed that the mutation situation of total rainfall in Guilin in 51 years wasn’t obvious.But the mutation situations in the second and third quarters were more.The variation in recent 10 years was the most obvious.Maybe it was affected by the global climate variation.[Conclusion] The research provided the theory basis for analyzing the climate variation in Guilin.

Analysis on Changing Trends of Temperature and Precipitation in Huanren County over the Past 58Years

Based on data of temperature and precipitation in Huanren County from 1953 to 2010, linear trend analysis and mutation detection of temperature and precipitation sequence were carried out using linear trend, Mann-Kendall detection and dryness of the de Martonne method. The results showed that during 1953-2010, annual average temperature, annual average maximum and minimum temperature in Huanren County showed an increasing trend; annual precipitation showed a decreasing trend; there was a downward trend in annual dryness. The mutation of annu- al average temperature, annual average maximum and minimum temperature appeared in 1978, 1987 and 1982 respectively; there was no mutation of annual precipitation and dryness. On the whole, the climate of Huanren County tended to be warm and dry over the past 58 years.

NOVEL SPLICING MUTATION OF COL1A1 GENE CAUSING OSTEOGENESIS IMPERFECTA TYPE I IN CHINESE PEDIGREE

Objective To detect the peculiar mutation in a Chinese family with osteogenesis imperfecta, COL1A1 and COL1A2 being analysed. Methods A genome screen was undertaken covering COL1A1 at 17q21- 22 and COLIA2 at 7q22.1. The Linkage （ Version 5. 1 ） was used for 2-point analysis. DNA sequencing was used to screen and identify the mutation. Results A linkage to the markers on chromosome 17q21-22 was observed. Se- quence analysis of COLIA1 revealed a splicing mutation （IVSS-2A 〉 G） that converted the 3＇ end of intron 8 from AG to GG. Conclusion This mutation （ IVS 8-2A 〉 G） is novel, and has not yet been registered in the Human Type I and Type Ⅲ Collagen Mutations Database.

APC and K-ras gene mutation in aberrant crypt foci of human colon

AIM:To study the genetic alteration in ACF and to define the possibility that ACF may be a very early morphological lesion with molecular changes,and to explore the relationship between ACF and colorectal adenoma even carcinoma. METHODS: DNA from 35 CRC, 15 adenomas, 34 ACF and 10 normal mucus was isolated by means of microdissection. Direct gene sequencing of K-ras gene including codon 12, 13 and 61 as well as the mutation cluster region (MCR) of APC gene was performed. RESULTS: K-ras gene mutation frequency in ACF, adenoma and carcinoma was 17.6% (6/34), 13.3% (2/15), and 14.3% (5/35) respectively, showing no difference (P 】 0.05) in K-ras gene mutation among three pathologic procedures. The K-ras gene mutation in adenoma, carcinoma and 4 ACF restricted in codon 12 (GGT GAT), but the other 2 mutations from ACF located in codon 13 (GGC GAC). K-ras gene mutation was found more frequently in older patients and patients with polypoid cancer. No mutation in codon 61 was found in the three tissue types. Mutation rate of APC gene in adenoma and carcinoma was 22.9% (8/35) and 26.7% (4/15), which was higher than ACF (2.9%) (P 【0.05). APC gene mutation in carcinoma was not correlated with age of patients, location, size and differentiation of tumor. CONCLUSION: ACF might be a very early morphological lesion in the tumorogenesis of colorectal tumor. The morphological feature and gene mutation status was different in ACF and adenoma. ACF is possibly putative microadenoma that might be the precursor of adenoma. In addition, the development of a subgroup of colorectal carcinomas might undergo a way of normal epithelium ACF carcinomas .

Characteristics of the dynamic changes in active accumulated temperature in Sichuan,China in the last 51 years against the background of climate change

It is of utmost necessity to understand the dynamics of regional active accumulated temperature(AAT)to cope with the negative impacts of global warming on agroforestry development and food security and to provide a real-time and effective reference basis for regional agroforestry planning.The daily temperature data from 30 meteorological stations in Sichuan Province from 1970 to 2020,and sea surface temperature(SST)index data from the Atlantic Multiphase Oscillation(AMO)and Pacific Decadal Oscillation(PDO)were used for the study.Sichuan Province was divided into the western region(WS)and the eastern region(ES),considering 1000 m above sea level as the boundary.The spatiotemporal characteristics of≥0℃ and≥10℃ active accumulated temperature(AAT0,AAT10)in WS and ES were analyzed comprehensively using 5-day average sliding,empirical orthogonal function(EOF),ensemble empirical mode decomposition(EEMD),and multiple mutation tests.The results show that(1)AAT0 and AAT10 of WS ranged from 3034℃ to 3586℃ and 1971℃ to 2636℃,respectively,while the AAT0 and AAT10 of ES ranged from 5863℃ to 6513℃ and 4847℃ to 5875℃,respectively.The period around 1997 was a significant abrupt change,and the AAT in the province generally increased during the subsequent time period(2)AAT in the study area is mainly driven by the fluctuations of AMO,as reflected by the low-to-high variation of AAT coinciding with the jump of the cold-to-warm phase of AMO.Considering different time scale fluctuations in the past 51 years,the major cycle for both AAT0 and AAT10 in WS is 3.40 a,while the major cycles in ES are 3.64 a and 3.19 a,respectively with a sub-cycle of 7.29 a.AAT fluctuation has an insignificant periodic characteristic of 25.50 a on the interdecadal scale(3)The spatial heterogeneity of AAT in WS is prominent and is mainly reflected by the significantly warm conditions in the south of the WS region and relatively slight warm conditions in the north,as well as by the isolated cooling area in the form of"freezing point",i.e.,Xiaojin county.In contrast,the spatial variability of AAT in ES is more or less consistent,with the warming areas concentrated in the foothills of the western edge of the basin and a slight increase in AAT observed in the central part of the basin.