Differential pulse-position modulation(DP PM)can achieve a good compromise between power and bandwidth requirements.However,the output sequence has undetectable insertions and deletions.This paper proposes a successiv...Differential pulse-position modulation(DP PM)can achieve a good compromise between power and bandwidth requirements.However,the output sequence has undetectable insertions and deletions.This paper proposes a successive cancellation(SC)decoding scheme based on the weighted levenshtein distance(WLD)of polar codes for correcting insertions/deletions in DPPM systems.In this method,the WLD is used to calculate the transfer probabilities recursively to obtain likelihood ratios,and the low-complexity SC decoding method is built according to the error characteristics to match the DPPM system.Additionally,the proposed SC decoding scheme is extended to list decoding,which can further improve error correction performance.Simulation results show that the proposed scheme can effectively correct insertions/deletions in the DPPM system,which enhances its reliability and performance.展开更多
Objective The present study aimed to estimate the association between susceptibility to migraine and the 12nucleotide insertion/deletion （indel） polymorphism in promoter region ofα 2B -adrenergic receptor gene （AD...Objective The present study aimed to estimate the association between susceptibility to migraine and the 12nucleotide insertion/deletion （indel） polymorphism in promoter region ofα 2B -adrenergic receptor gene （ADRA2B）.Methods A case-control study was carried out in Chinese Han population,including 368 cases of migraine and 517 controls.Genomic DNA was extracted from blood samples,and DNA fragments containing the site of polymorphism were amplified by PCR.Data were adjusted for sex,age,migraine history and family history,and analyzed using a logistic regression model.Results There was no association between indel polymorphism and migraine,at either the allele or the genotype level.Conclusion These findings do not support a functional significance of ADRA2B indel polymorphism at position-4825 relative to the start codon in the far upstream region of the promoter in the present migraine subjects.展开更多
This study investigated the relationship between angiotensin-converting enzyme (ACE) gene insertion/deletion polymorphism and the occurrence, severity, prognosis of HSPN. The polymorphism of ACE gene in 103 HSPN case...This study investigated the relationship between angiotensin-converting enzyme (ACE) gene insertion/deletion polymorphism and the occurrence, severity, prognosis of HSPN. The polymorphism of ACE gene in 103 HSPN cases and 100 healthy children was studied by using the polymerase chain reactions (PCR). Its relation to the clinical manifestation, pathological classification and prognosis of HSPN was analyzed accordingly. The results showed that: (1) there was a significantly higher frequency for DD genotype in HSPN children (P<0.01); (2) DD genotype was more frequently seen in HSPN children with gross hematuria and massive proteinuria (P<0.05), while DI genotype was more common in HSPN children group with renal insufficiency (P<0.05); (3) although mesangial proliferative lesion was most frequently observed in 21 biopsied HSPN children, and DD genotype frequency was still higher in children with severe pathology (Class Ⅲ Ⅳ); (4)II genotype was significantly frequent in HSPN children with complete remission in the follow-up of 32 HSPN children. It was concluded that the deletion allele of ACE gene might play a role, at least to some extent, in the occurrence, deterioration and progression in juvenile HSPN.展开更多
Insertion and deletion(indel) mutations, which can trigger single nucleotide substitutions on the flanking regions of genes, may generate abundant materials for disease defense, reproduction, species survival and evol...Insertion and deletion(indel) mutations, which can trigger single nucleotide substitutions on the flanking regions of genes, may generate abundant materials for disease defense, reproduction, species survival and evolution. However, genetic and evolutionary mechanisms of indels remain elusive. We establish a comparative genome-transcriptome-alignment approach for a large-scale identification of indels in Monopterus population. Over 2000 indels in 1738 indel genes, including 1-21 bp deletions and 1-15 bp insertions, were detected. Each indel gene had ～1.1 deletions/insertions, and 2-4 alleles in population. Frequencies of deletions were prominently higher than those of insertions on both genome and population levels. Most of the indels led to in frame mutations with multiples of three and majorly occurred in non-domain regions, indicating functional constraint or tolerance of the indels. All indel genes showed higher expression levels than non-indel genes during sex reversal. Slide window analysis of global expression levels in gonads showed a significant positive correlation with indel density in the genome. Moreover, indel genes were evolutionarily conserved and evolved slowly compared to nonindel genes. Notably, population genetic structure of indels revealed divergent evolution of Monopterus population, as bottleneck effect of biogeographic isolation by Taiwan Strait, China.展开更多
Objective: The aim of this work is to determine whether the angiotensin converting enzyme(ACE) I/D(insertion/deletion) polymorphism is associated with the susceptibility to congenital heart disease(CHD) in the Qinghai...Objective: The aim of this work is to determine whether the angiotensin converting enzyme(ACE) I/D(insertion/deletion) polymorphism is associated with the susceptibility to congenital heart disease(CHD) in the Qinghai Han Chinese. Methods: This study enrolled 59 CHD patients and 193 CHD controls from Qinghai Cardiovascular Diseases Vocational Hospital. Blood samples were collected from each of the patient and control groups. The ACE-I/D polymorphism was detected by polymerase chain reaction(PCR). Results: The genotype frequencies of ACE-I/D for II, ID, DD in patients and controls were 0.475, 0.441, 0.085 and 0.430, 0.446, 0.124, respectively. The allelic frequencies of I and D were 0.650, 0.350 and 0.695, 0.305, respectively. The OR of ID, DD and D alleles relative to II for CHD was 1.116(0.604-2.060), 1.619(0.564-4.648) and 1.211(0.777-1.889). There was no significant difference of the genotypic and the allelic frequencies in ACE-I/D polymorphism between the patient and control groups. Conclusion: There is no relation between ACE-I/D polymorphism and CHD in current Qinghai Han Chinese.展开更多
Objective To investigate the 23 bp and 12 bp insertion/deletion(indel)mutations within the bovine prion protein(PRNP)gene in Chinese dairy cows,and to detect the associations of two indel mutations with BSE susceptibi...Objective To investigate the 23 bp and 12 bp insertion/deletion(indel)mutations within the bovine prion protein(PRNP)gene in Chinese dairy cows,and to detect the associations of two indel mutations with BSE susceptibility and milk performance.Methods Based on bovine PRNP gene sequence,two pairs of primers for testing the 23 bp and 12 bp indel mutations were designed.The PCR amplification and agarose electrophoresis were carried out to distinguish the different genotypes within the mutations.Moreover,based on previous data from other cattle breeds and present genotypic and allelic frequencies of two indels mutations in this study,the corrections between the two indel mutations and BSE susceptibility were tested,as well as the relationships between the mutations and milk performance traits were analyzed in this study based on the statistical analyses.Results In the analyzed Chinese Holstein population,the frequencies of two"del"alleles in 23 bp and 12 bp indel muations were more frequent.The frequency of haplotype of 23del-12del was higher than those of 23del-12ins and 23ins-12del.From the estimated r2and D’values,two indel polymorphisms were linked strongly in the Holstein population(D’=57.5%,r2=0.257).Compared with the BSE-affected cattle populations from the reported data,the significant differences of genotypic and allelic frequencies were found among present Holstein and some BSE-affected populations(P<0.05 or P<0.01).Similarly,there were significant frequency distribution differences of genotypes and alleles among Chinese Holstein and several previous reported healthy dairy cattle(P<0.05 or P<0.01).Moreover,association of genotype and combined genotypes of two indel polymorphisms with milk performance and resistant mastitis traits were analyzed in Holstein population,but no significant differences were found(P>0.05).Conclusions These observations revealed that the influence of two indel mutations within the bovine PRNP gene on BSE depended on the breed and they did not affect the milk production traits,which layed the foundation for future selection of resistant animals,and for improving health conditions for dairy breeding against BSE in China.展开更多
Despite one SINE retrotransposon insertion polymorphism(sRTIP)in the vertebrae development-associated(VRTN)gene was identified in pigs,the structural variations(SVs)in VRTN gene and its proximal flank regions were lar...Despite one SINE retrotransposon insertion polymorphism(sRTIP)in the vertebrae development-associated(VRTN)gene was identified in pigs,the structural variations(SVs)in VRTN gene and its proximal flank regions were largely unknown.VRTN genic and flanking sequences from 14 breeds were assembled or downloaded from whole genome shotgun contings(WGS)database,and aligned to identify the SVs with Clustalx,and retrotransposons in VRTN gene were annotated by RepeatMasker,the splicing patterns of VRTN gene were predicted by Genescan,and large SVs were evaluated by PCR.A total of 12 small SVs and three large SVs in intron of VRTN,derived from SINE insertion polymorphisms.were identifed,and two of them(VRTN-sRTIP2 and VRTN-sRTIP3)were not reported before.These VRTN-sRTIPs may affect the splicing patterns of VRTN.They displayed polymorphisms in most detected eight breeds.VRTN-sRTIP2 and VRTN-sRTIP3 showed Hardy-Weinberg equilibrium distributions in most populations except the Chinese local Erhualian pigs,while VRTN-sRTIP1 showed genetic equilbrium in Erhualian pigs.Three VRTN-sRTIPs were identified,and displayed polymorphisms in pigs,and two of them were not reported before.These SVs provide a useful molecular markers for genetic analysis in pigs,and offer new information to facilitate the understanding the SVs of VRTN gene and their putative roles in the variation of vertebral number.展开更多
Genotyping by sequencing(GBS) is the recent approach of next-generation sequencing technique for discovering and genotyping single nucleotide polymorphisms(SNPs) in crop species. Genotypic variation studies(SNPs and i...Genotyping by sequencing(GBS) is the recent approach of next-generation sequencing technique for discovering and genotyping single nucleotide polymorphisms(SNPs) in crop species. Genotypic variation studies(SNPs and insertion-deletions/In Dels) were performed using four rice lines based on GBS data by aligning to the reference genome Nipponbare. Local aromatic rice landrace Tulaipanji was crossed with Ranjit, and two distinct lines were identified from the progenies: one line with awns and aroma traits and the other without awns and aroma. Total number of SNPs and In Dels identified were 52 810 and 4 327 at read depth 10, respectively. Out of the total polymorphic SNPs/In Dels, 16 490 were intergeneric, 7 812 were inside gene, and 4 435 were intronic. Phylogenetically, Tulaipanji was closer to the reference genome nipponbare. Based on recurrent parent genome analysis, out of 10 013 alleles, 92.52% was introgressed into progeny-awn from Tulaipanji and 7.48% from Ranjit, whereas progeny-awnless carried 89.19% alleles from Ranjit and only 10.81% alleles from Tulaipanji. In addition, progeny-awn was the highest heterozygous(83.88%) and progeny-awnless was the least(2.24%) at this fifth generation of recombinant inbred lines. These SNP variations may be linked to the phenotypic traits and can be utilized in crop improvement through linkage mapping. These results suggest that adding a high density of SNP markers to a mapping or breeding population through GBS has a great value for numerous applications in rice breeding and genetics research.展开更多
AIM:To investigate the genetic and clinical characteristics of patients with a large heterozygous copy number deletion on 7q31.31-7q31.32.METHODS:A family with familial exudative vitreoretinopathy(FEVR)phenotype was i...AIM:To investigate the genetic and clinical characteristics of patients with a large heterozygous copy number deletion on 7q31.31-7q31.32.METHODS:A family with familial exudative vitreoretinopathy(FEVR)phenotype was included in the study.Whole-exome sequencing(WES)was initially used to locate copy number variations(CNVs)on 7q31.31-31.32,but failed to detect the precise breakpoint.The long-read sequencing,Oxford Nanopore sequencing Technology(ONT)was used to get the accurate breakpoint which is verified by quantitative real-time polymerase chain reaction(QPCR)and Sanger Sequencing.RESULTS:The proband,along with her father and younger brother,were found to have a heterozygous 4.5 Mb CNV deletion located on 7q31.31-31.32,which included the FEVRrelated gene TSPAN12.The specific deletion was confirmed as del(7)(q31.31q31.32)chr7:g.119451239_123956818del.The proband exhibited a phase 2A FEVR phenotype,characterized by a falciform retinal fold,macular dragging,and peripheral neovascularization with leaking of fluorescence.These symptoms led to a significant decrease in visual acuity in both eyes.On the other hand,the affected father and younger brother showed a milder phenotype.CONCLUSION:The heterozygous CNV deletion located on 7q31.31-7q31.32 is associated with the FEVR phenotype.The use of long-read sequencing techniques is essential for accurate molecular diagnosis of genetic disorders.展开更多
Genetic,environmental and demographic factors contribute to the development of essential hypertension.Genetic polymorphism of Rennin-angiotensin-aldosterone system(RAAS)has been extensively studied to determine the ge...Genetic,environmental and demographic factors contribute to the development of essential hypertension.Genetic polymorphism of Rennin-angiotensin-aldosterone system(RAAS)has been extensively studied to determine the genetic susceptibility to hypertension.The insertion/deletion(I/D)angiotensin converting enzyme(ACE)polymorphism has been established as a cardiovascular risk factor in some population,but its association with essential hypertension is controversial.This study sought to determine the association of I/D polymorphism of the ACE gene in south Indian essential hypertensive subjects.A total of 208 clinically diagnosed essential hypertensive patients without any associated diseases and 220 healthy control subjects were included in this study.Distribution and allelic frequency of Insertion(I)and Deletion(D)polymorphism at the 287 base pair Alu repeat sequence in the intron 16 of ACE gene were analyzed.The distribution of II,ID,DD genotypes of ACE gene was 28.3%,32.6%and 38.9%respectively in essential hypertensive patients and to 53.6%,26.3%and 20%in controls.The allele frequency for D allele is 0.58 in essential hypertension as compared to 0.34 of control subjects.The genotype and allele frequency of ACE gene polymorphism is significantly differed in patients when compared to controls.In conclusion,the I/D polymorphism of ACE gene is associated with Indian essential hypertension.展开更多
Background: Several studies have investigated the association of angiotensin-converting enzyme (ACE) gene insertion/deletion (I/D) polymorphism with peripheral vascular disease (PVD); however, the results remain contr...Background: Several studies have investigated the association of angiotensin-converting enzyme (ACE) gene insertion/deletion (I/D) polymorphism with peripheral vascular disease (PVD); however, the results remain controversial. Therefore, we conducted the current meta-analysis to evaluate this relationship in the general population of different ethnicities. Methods: We searched PubMed, Embase, Web of Science, Wanfang Database, and CNKI to identify eligible studies. Random-effect models were applied to estimate the pooled odds ratio (OR) with a 95％ confidence interval (CI), regardless of between-study heterogeneity. Results: A total of 13 studies with 1966 cases and 6129 controls were included in this meta-analysis. The pooled ORs for the association between ACE I/D polymorphism and PVD risk were not statistically significant in the overall population under all genetic models. In further ethnicity-stratified analyses, we found a statistically significant association of ACE I/D polymorphism with PVD susceptibility in Asians under most models. However, the association among Caucasians did not reach statistical significance. Conclusion: ACE I/D polymorphism might be associated with susceptibility to PVD in the Asian population, but there was no clear evidence indicating a similar significant relationship among Caucasians.展开更多
Due to its specific characteristics, such as ma-ternal inheritance and absence of recombination, each mtDNA belongs to certain monophyletic clade in the rooted mtDNA tree (haplogroup) according to the mutations it har...Due to its specific characteristics, such as ma-ternal inheritance and absence of recombination, each mtDNA belongs to certain monophyletic clade in the rooted mtDNA tree (haplogroup) according to the mutations it harbors. Rare mutation (excluding parallel mutation) occur-ring at multiple times in different haplogroups could thus be a potential reading error according to the mtDNA phylogeny. This experience has been widely used in double-checking the credibility of the rare mutations in human mtDNA sequences. However, no test has been performed so far for the feasibility of applying this strategy to the rare insertion/deletion (indel) events in mtDNA sequences. In this study, we attempted to relate the rare indels in mtDNAs to their haplogroup status in a total of 2352 individuals from 50 populations in China. Our results show that the insertion of A at position 16259 is restricted to a subclade of haplogroup C and can be verified. The other indel polymorphisms, which occur in the repeat of the deleted or inserted nucleotide(s), may not be distin-guished from phantom mutations from a phylogenetic point of view. Independently and multiply sequencing the frag-ment with the indel is the best and the most reliable way for confirmation.展开更多
For comprehensive understanding of practical application and evaluation on the power of30 commonly used InDeis(Qiagen Investigator DIPplex®kit),we captured population data from 25 Chinese populations and employed...For comprehensive understanding of practical application and evaluation on the power of30 commonly used InDeis(Qiagen Investigator DIPplex®kit),we captured population data from 25 Chinese populations and employed F-statistics for population genetics analysis.The results indicated that the distributions of allelic frequencies among populations were in different levels.Furthermore,the phylogeny confoiming pairwise FST distances showed that the difierentiation of majority populations were consistent with their geographic locations and historic dispersals.We conduct the comprehensive correlation analysis between FST and heterozygosity of30 InDel loci and provided strong evidence for ongoing InDei loci selection.The Fst values of 30 InDels were calculated within 25 Chinese populations,and then,these loci were characterized definitely based on their roles in population genetics or individual identification.Data indicated that 17 InDels with FST<0.01 could be utilized regarding Chinese individual identification(total discrimination power=0.999985 and cumulative matching probability=0.00000009).We comprehensively reconstructed the population structure and filled the gap of evaluating the ability of InDels in personal as well as population identification.The application of InDel loci in the forensic area would convincingly promote the development matter of forensic population identification and personal discrimination.展开更多
Objective To explore the interaction of angiotensinconverting enzyme (ACE) insertion /deletion(I /D) polymorphism( rs1799752 ) with diabetic kidney disease(DKD) development as well as its interaction with smokingand o...Objective To explore the interaction of angiotensinconverting enzyme (ACE) insertion /deletion(I /D) polymorphism( rs1799752 ) with diabetic kidney disease(DKD) development as well as its interaction with smokingand obesity in Chinese type 2 diabetic mellitus(T2DM) using an improved experiment method. MethodsFrom June 2016 to March 2018,300 T2DM patientswith DKD [DKD( +)]and 300 T2DM patients withoutDKD [DKD ( - )] were selected from China-JapanFriendship Hospital. The improved Triple Primer Methodthat combined PCR with capillary electrophoresis was establishedin this study to detect the ACE genotype. Therelevant clinical data as well as the frequencies of genotypeand allele of ACE gene I /D polymorphism betweenthe two groups were statistically analyzed. Patients werefurther grouped based on smoking status and obesity formultivariate regression.展开更多
基金supported by National Natural Science Foundation of China(No.61801327).
文摘Differential pulse-position modulation(DP PM)can achieve a good compromise between power and bandwidth requirements.However,the output sequence has undetectable insertions and deletions.This paper proposes a successive cancellation(SC)decoding scheme based on the weighted levenshtein distance(WLD)of polar codes for correcting insertions/deletions in DPPM systems.In this method,the WLD is used to calculate the transfer probabilities recursively to obtain likelihood ratios,and the low-complexity SC decoding method is built according to the error characteristics to match the DPPM system.Additionally,the proposed SC decoding scheme is extended to list decoding,which can further improve error correction performance.Simulation results show that the proposed scheme can effectively correct insertions/deletions in the DPPM system,which enhances its reliability and performance.
基金supported by the National Natural Science Foundation of China(No.30800621)China Postdoctoral Science Foundation(No.20080431121,200902530)
文摘Objective The present study aimed to estimate the association between susceptibility to migraine and the 12nucleotide insertion/deletion （indel） polymorphism in promoter region ofα 2B -adrenergic receptor gene （ADRA2B）.Methods A case-control study was carried out in Chinese Han population,including 368 cases of migraine and 517 controls.Genomic DNA was extracted from blood samples,and DNA fragments containing the site of polymorphism were amplified by PCR.Data were adjusted for sex,age,migraine history and family history,and analyzed using a logistic regression model.Results There was no association between indel polymorphism and migraine,at either the allele or the genotype level.Conclusion These findings do not support a functional significance of ADRA2B indel polymorphism at position-4825 relative to the start codon in the far upstream region of the promoter in the present migraine subjects.
文摘This study investigated the relationship between angiotensin-converting enzyme (ACE) gene insertion/deletion polymorphism and the occurrence, severity, prognosis of HSPN. The polymorphism of ACE gene in 103 HSPN cases and 100 healthy children was studied by using the polymerase chain reactions (PCR). Its relation to the clinical manifestation, pathological classification and prognosis of HSPN was analyzed accordingly. The results showed that: (1) there was a significantly higher frequency for DD genotype in HSPN children (P<0.01); (2) DD genotype was more frequently seen in HSPN children with gross hematuria and massive proteinuria (P<0.05), while DI genotype was more common in HSPN children group with renal insufficiency (P<0.05); (3) although mesangial proliferative lesion was most frequently observed in 21 biopsied HSPN children, and DD genotype frequency was still higher in children with severe pathology (Class Ⅲ Ⅳ); (4)II genotype was significantly frequent in HSPN children with complete remission in the follow-up of 32 HSPN children. It was concluded that the deletion allele of ACE gene might play a role, at least to some extent, in the occurrence, deterioration and progression in juvenile HSPN.
基金supported by the National Natural Science Foundation of China (31571280 and 31771370)National Key Technologies R&D Program and Hubei Province Science and Technology project
文摘Insertion and deletion(indel) mutations, which can trigger single nucleotide substitutions on the flanking regions of genes, may generate abundant materials for disease defense, reproduction, species survival and evolution. However, genetic and evolutionary mechanisms of indels remain elusive. We establish a comparative genome-transcriptome-alignment approach for a large-scale identification of indels in Monopterus population. Over 2000 indels in 1738 indel genes, including 1-21 bp deletions and 1-15 bp insertions, were detected. Each indel gene had ～1.1 deletions/insertions, and 2-4 alleles in population. Frequencies of deletions were prominently higher than those of insertions on both genome and population levels. Most of the indels led to in frame mutations with multiples of three and majorly occurred in non-domain regions, indicating functional constraint or tolerance of the indels. All indel genes showed higher expression levels than non-indel genes during sex reversal. Slide window analysis of global expression levels in gonads showed a significant positive correlation with indel density in the genome. Moreover, indel genes were evolutionarily conserved and evolved slowly compared to nonindel genes. Notably, population genetic structure of indels revealed divergent evolution of Monopterus population, as bottleneck effect of biogeographic isolation by Taiwan Strait, China.
基金supported by Qinghai Science & Technology Support Program(2015-SF-124)Basic Applied Study Foundation of Qinghai(2016-ZJ-706)
文摘Objective: The aim of this work is to determine whether the angiotensin converting enzyme(ACE) I/D(insertion/deletion) polymorphism is associated with the susceptibility to congenital heart disease(CHD) in the Qinghai Han Chinese. Methods: This study enrolled 59 CHD patients and 193 CHD controls from Qinghai Cardiovascular Diseases Vocational Hospital. Blood samples were collected from each of the patient and control groups. The ACE-I/D polymorphism was detected by polymerase chain reaction(PCR). Results: The genotype frequencies of ACE-I/D for II, ID, DD in patients and controls were 0.475, 0.441, 0.085 and 0.430, 0.446, 0.124, respectively. The allelic frequencies of I and D were 0.650, 0.350 and 0.695, 0.305, respectively. The OR of ID, DD and D alleles relative to II for CHD was 1.116(0.604-2.060), 1.619(0.564-4.648) and 1.211(0.777-1.889). There was no significant difference of the genotypic and the allelic frequencies in ACE-I/D polymorphism between the patient and control groups. Conclusion: There is no relation between ACE-I/D polymorphism and CHD in current Qinghai Han Chinese.
基金supported by the National Natural Science Foundation of China (Grant No. 31272408 30972080)+2 种基金the National 863 Program of China (Grant No. 2013AA102505)the Program of National Beef Cattle and yak Industrial Technology System (CARS-38)the Agricultural Science and Technology Innovation Projects of Shanxi Province (No. 2012NKC01-13).
文摘Objective To investigate the 23 bp and 12 bp insertion/deletion(indel)mutations within the bovine prion protein(PRNP)gene in Chinese dairy cows,and to detect the associations of two indel mutations with BSE susceptibility and milk performance.Methods Based on bovine PRNP gene sequence,two pairs of primers for testing the 23 bp and 12 bp indel mutations were designed.The PCR amplification and agarose electrophoresis were carried out to distinguish the different genotypes within the mutations.Moreover,based on previous data from other cattle breeds and present genotypic and allelic frequencies of two indels mutations in this study,the corrections between the two indel mutations and BSE susceptibility were tested,as well as the relationships between the mutations and milk performance traits were analyzed in this study based on the statistical analyses.Results In the analyzed Chinese Holstein population,the frequencies of two"del"alleles in 23 bp and 12 bp indel muations were more frequent.The frequency of haplotype of 23del-12del was higher than those of 23del-12ins and 23ins-12del.From the estimated r2and D’values,two indel polymorphisms were linked strongly in the Holstein population(D’=57.5%,r2=0.257).Compared with the BSE-affected cattle populations from the reported data,the significant differences of genotypic and allelic frequencies were found among present Holstein and some BSE-affected populations(P<0.05 or P<0.01).Similarly,there were significant frequency distribution differences of genotypes and alleles among Chinese Holstein and several previous reported healthy dairy cattle(P<0.05 or P<0.01).Moreover,association of genotype and combined genotypes of two indel polymorphisms with milk performance and resistant mastitis traits were analyzed in Holstein population,but no significant differences were found(P>0.05).Conclusions These observations revealed that the influence of two indel mutations within the bovine PRNP gene on BSE depended on the breed and they did not affect the milk production traits,which layed the foundation for future selection of resistant animals,and for improving health conditions for dairy breeding against BSE in China.
基金Supported by the National Natural Science Foundation of China(31872977 and 31572364)the Jiangsu Agricultural Science and Technology Innovation Fund(CX(19)2016)the Priority Academic Program Development of Jiangsu Higher Education Institutions,China.
文摘Despite one SINE retrotransposon insertion polymorphism(sRTIP)in the vertebrae development-associated(VRTN)gene was identified in pigs,the structural variations(SVs)in VRTN gene and its proximal flank regions were largely unknown.VRTN genic and flanking sequences from 14 breeds were assembled or downloaded from whole genome shotgun contings(WGS)database,and aligned to identify the SVs with Clustalx,and retrotransposons in VRTN gene were annotated by RepeatMasker,the splicing patterns of VRTN gene were predicted by Genescan,and large SVs were evaluated by PCR.A total of 12 small SVs and three large SVs in intron of VRTN,derived from SINE insertion polymorphisms.were identifed,and two of them(VRTN-sRTIP2 and VRTN-sRTIP3)were not reported before.These VRTN-sRTIPs may affect the splicing patterns of VRTN.They displayed polymorphisms in most detected eight breeds.VRTN-sRTIP2 and VRTN-sRTIP3 showed Hardy-Weinberg equilibrium distributions in most populations except the Chinese local Erhualian pigs,while VRTN-sRTIP1 showed genetic equilbrium in Erhualian pigs.Three VRTN-sRTIPs were identified,and displayed polymorphisms in pigs,and two of them were not reported before.These SVs provide a useful molecular markers for genetic analysis in pigs,and offer new information to facilitate the understanding the SVs of VRTN gene and their putative roles in the variation of vertebral number.
基金the Authority of the University of North Bengal for giving financial assistance and field work facility to carry out this Research Project on Molecular Breeding on Rice(2015–2016)
文摘Genotyping by sequencing(GBS) is the recent approach of next-generation sequencing technique for discovering and genotyping single nucleotide polymorphisms(SNPs) in crop species. Genotypic variation studies(SNPs and insertion-deletions/In Dels) were performed using four rice lines based on GBS data by aligning to the reference genome Nipponbare. Local aromatic rice landrace Tulaipanji was crossed with Ranjit, and two distinct lines were identified from the progenies: one line with awns and aroma traits and the other without awns and aroma. Total number of SNPs and In Dels identified were 52 810 and 4 327 at read depth 10, respectively. Out of the total polymorphic SNPs/In Dels, 16 490 were intergeneric, 7 812 were inside gene, and 4 435 were intronic. Phylogenetically, Tulaipanji was closer to the reference genome nipponbare. Based on recurrent parent genome analysis, out of 10 013 alleles, 92.52% was introgressed into progeny-awn from Tulaipanji and 7.48% from Ranjit, whereas progeny-awnless carried 89.19% alleles from Ranjit and only 10.81% alleles from Tulaipanji. In addition, progeny-awn was the highest heterozygous(83.88%) and progeny-awnless was the least(2.24%) at this fifth generation of recombinant inbred lines. These SNP variations may be linked to the phenotypic traits and can be utilized in crop improvement through linkage mapping. These results suggest that adding a high density of SNP markers to a mapping or breeding population through GBS has a great value for numerous applications in rice breeding and genetics research.
基金Supported by the National Natural Science Foundation of China(No.82060183)Ningxia Natural Science Foundation(No.2022AAC03388)the Key Research and Development Project of Ningxia Hui Autonomous Region(No.2021BEG02045,No.2020BEG03044).
文摘AIM:To investigate the genetic and clinical characteristics of patients with a large heterozygous copy number deletion on 7q31.31-7q31.32.METHODS:A family with familial exudative vitreoretinopathy(FEVR)phenotype was included in the study.Whole-exome sequencing(WES)was initially used to locate copy number variations(CNVs)on 7q31.31-31.32,but failed to detect the precise breakpoint.The long-read sequencing,Oxford Nanopore sequencing Technology(ONT)was used to get the accurate breakpoint which is verified by quantitative real-time polymerase chain reaction(QPCR)and Sanger Sequencing.RESULTS:The proband,along with her father and younger brother,were found to have a heterozygous 4.5 Mb CNV deletion located on 7q31.31-31.32,which included the FEVRrelated gene TSPAN12.The specific deletion was confirmed as del(7)(q31.31q31.32)chr7:g.119451239_123956818del.The proband exhibited a phase 2A FEVR phenotype,characterized by a falciform retinal fold,macular dragging,and peripheral neovascularization with leaking of fluorescence.These symptoms led to a significant decrease in visual acuity in both eyes.On the other hand,the affected father and younger brother showed a milder phenotype.CONCLUSION:The heterozygous CNV deletion located on 7q31.31-7q31.32 is associated with the FEVR phenotype.The use of long-read sequencing techniques is essential for accurate molecular diagnosis of genetic disorders.
文摘Genetic,environmental and demographic factors contribute to the development of essential hypertension.Genetic polymorphism of Rennin-angiotensin-aldosterone system(RAAS)has been extensively studied to determine the genetic susceptibility to hypertension.The insertion/deletion(I/D)angiotensin converting enzyme(ACE)polymorphism has been established as a cardiovascular risk factor in some population,but its association with essential hypertension is controversial.This study sought to determine the association of I/D polymorphism of the ACE gene in south Indian essential hypertensive subjects.A total of 208 clinically diagnosed essential hypertensive patients without any associated diseases and 220 healthy control subjects were included in this study.Distribution and allelic frequency of Insertion(I)and Deletion(D)polymorphism at the 287 base pair Alu repeat sequence in the intron 16 of ACE gene were analyzed.The distribution of II,ID,DD genotypes of ACE gene was 28.3%,32.6%and 38.9%respectively in essential hypertensive patients and to 53.6%,26.3%and 20%in controls.The allele frequency for D allele is 0.58 in essential hypertension as compared to 0.34 of control subjects.The genotype and allele frequency of ACE gene polymorphism is significantly differed in patients when compared to controls.In conclusion,the I/D polymorphism of ACE gene is associated with Indian essential hypertension.
文摘Background: Several studies have investigated the association of angiotensin-converting enzyme (ACE) gene insertion/deletion (I/D) polymorphism with peripheral vascular disease (PVD); however, the results remain controversial. Therefore, we conducted the current meta-analysis to evaluate this relationship in the general population of different ethnicities. Methods: We searched PubMed, Embase, Web of Science, Wanfang Database, and CNKI to identify eligible studies. Random-effect models were applied to estimate the pooled odds ratio (OR) with a 95％ confidence interval (CI), regardless of between-study heterogeneity. Results: A total of 13 studies with 1966 cases and 6129 controls were included in this meta-analysis. The pooled ORs for the association between ACE I/D polymorphism and PVD risk were not statistically significant in the overall population under all genetic models. In further ethnicity-stratified analyses, we found a statistically significant association of ACE I/D polymorphism with PVD susceptibility in Asians under most models. However, the association among Caucasians did not reach statistical significance. Conclusion: ACE I/D polymorphism might be associated with susceptibility to PVD in the Asian population, but there was no clear evidence indicating a similar significant relationship among Caucasians.
文摘Due to its specific characteristics, such as ma-ternal inheritance and absence of recombination, each mtDNA belongs to certain monophyletic clade in the rooted mtDNA tree (haplogroup) according to the mutations it harbors. Rare mutation (excluding parallel mutation) occur-ring at multiple times in different haplogroups could thus be a potential reading error according to the mtDNA phylogeny. This experience has been widely used in double-checking the credibility of the rare mutations in human mtDNA sequences. However, no test has been performed so far for the feasibility of applying this strategy to the rare insertion/deletion (indel) events in mtDNA sequences. In this study, we attempted to relate the rare indels in mtDNAs to their haplogroup status in a total of 2352 individuals from 50 populations in China. Our results show that the insertion of A at position 16259 is restricted to a subclade of haplogroup C and can be verified. The other indel polymorphisms, which occur in the repeat of the deleted or inserted nucleotide(s), may not be distin-guished from phantom mutations from a phylogenetic point of view. Independently and multiply sequencing the frag-ment with the indel is the best and the most reliable way for confirmation.
基金This study was financially supported by The Fundamental Research Funds for the Central Research Institutes with project number“2017JB004.”
文摘For comprehensive understanding of practical application and evaluation on the power of30 commonly used InDeis(Qiagen Investigator DIPplex®kit),we captured population data from 25 Chinese populations and employed F-statistics for population genetics analysis.The results indicated that the distributions of allelic frequencies among populations were in different levels.Furthermore,the phylogeny confoiming pairwise FST distances showed that the difierentiation of majority populations were consistent with their geographic locations and historic dispersals.We conduct the comprehensive correlation analysis between FST and heterozygosity of30 InDel loci and provided strong evidence for ongoing InDei loci selection.The Fst values of 30 InDels were calculated within 25 Chinese populations,and then,these loci were characterized definitely based on their roles in population genetics or individual identification.Data indicated that 17 InDels with FST<0.01 could be utilized regarding Chinese individual identification(total discrimination power=0.999985 and cumulative matching probability=0.00000009).We comprehensively reconstructed the population structure and filled the gap of evaluating the ability of InDels in personal as well as population identification.The application of InDel loci in the forensic area would convincingly promote the development matter of forensic population identification and personal discrimination.
文摘Objective To explore the interaction of angiotensinconverting enzyme (ACE) insertion /deletion(I /D) polymorphism( rs1799752 ) with diabetic kidney disease(DKD) development as well as its interaction with smokingand obesity in Chinese type 2 diabetic mellitus(T2DM) using an improved experiment method. MethodsFrom June 2016 to March 2018,300 T2DM patientswith DKD [DKD( +)]and 300 T2DM patients withoutDKD [DKD ( - )] were selected from China-JapanFriendship Hospital. The improved Triple Primer Methodthat combined PCR with capillary electrophoresis was establishedin this study to detect the ACE genotype. Therelevant clinical data as well as the frequencies of genotypeand allele of ACE gene I /D polymorphism betweenthe two groups were statistically analyzed. Patients werefurther grouped based on smoking status and obesity formultivariate regression.
文摘为了研究主要促进因子超家族成员13A(major facilitator superfamily domain containing 13A,MFSD13A)基因第一内含子区21 bp和第二外显子区19 bp插入/缺失(insertion/deletion,indel)变异对夏南牛生长性状的影响,试验以夏南牛、郏县红牛和南阳牛等12个品种为研究对象,采用PCR、琼脂糖凝胶电泳和实时荧光定量PCR等方法检测MFSD13A基因40 bp indel基因分型及MFSD13A基因组织表达分析,通过牛基因型-组织表达(genotype-issue expression,GTEx)数据分析40 bp indel变异对MFSD13A基因表达的影响。结果表明:MFSD13A基因上游存在完全连锁平衡的21 bp与19 bp两个indel变异;40 bp indel等位基因型频率在12个品种(群体)中I等位基因频率高于D等位基因且属于中度或低度多态,并在夏南牛、郏县红牛、南阳牛、皖东牛、大别山牛和德南牛品种中处于Hardy-Weinberg平衡状态(P>0.05);MFSD13A基因40 bp indel位点与夏南牛和南阳牛的体重、体高和胸围均呈显著相关(P<0.05);肾脏和脂肪组织中MFSD13A基因的相对表达量显著高于其他组织(P<0.05);II基因型个体MFSD13A基因的mRNA表达量显著高于ID和DD基因型(P<0.05)。说明MFSD13A基因突变对夏南牛生长性状有显著影响,可作为夏南牛优良性状选育的候选分子标记。
