Genotyping by target sequencing(GBTS)integrates the advantages of silicon-based technology(high stability and reliability)and genotyping by sequencing(high flexibility and cost-effectiveness).However,GBTS panels are n...Genotyping by target sequencing(GBTS)integrates the advantages of silicon-based technology(high stability and reliability)and genotyping by sequencing(high flexibility and cost-effectiveness).However,GBTS panels are not currently available in pigs.In this study,based on GBTS technology,we first developed a 50K panel,including 52,000 single-nucleotide polymorphisms(SNPs),in pigs,designated GBTS50K.A total of 6,032 individuals of Large White,Landrace,and Duroc pigs from 10 breeding farms were used to assess the newly developed GBTS50K.Our results showed that GBTS50K obtained a high genotyping ability,the SNP and individual call rates of GBTS50K were 0.997–0.998,and the average consistency rate and genotyping correlation coefficient were 0.997 and 0.993,respectively,in replicate samples.We also evaluated the efficiencies of GBTS50K in the application of population genetic structure analysis,selection signature detection,genome-wide association studies(GWAS),genotyped imputation,genetic selection(GS),etc.The results indicate that GBTS50K is plausible and powerful in genetic analysis and molecular breeding.For example,GBTS50K could gain higher accuracies than the current popular GGP-Porcine bead chip in genomic selection on 2 important traits of backfat thickness at 100 kg and days to 100 kg in pigs.Particularly,due to the multiple SNPs(mSNPs),GBTS50K generated 100K qualified SNPs without increasing genotyping cost,and our results showed that the haplotype-based method can further improve the accuracies of genomic selection on growth and reproduction traits by 2 to 6%.Our study showed that GBTS50K could be a powerful tool for underlying genetic architecture and molecular breeding in pigs,and it is also helpful for developing SNP panels for other farm animals.展开更多
Asian rice comprises two major subspecies:Xian(X)and Geng(G),and the diverged resistance genes(R)have provided a foundation for breeding improved cultivars to control rice blast disease.After conducting two-phase alle...Asian rice comprises two major subspecies:Xian(X)and Geng(G),and the diverged resistance genes(R)have provided a foundation for breeding improved cultivars to control rice blast disease.After conducting two-phase allele mining using six updated FNP marker systems,the functional haplotypes at Pit,Pib,and Pi63 strictly diverged into the X-populations and were defined as X-R loci,while those at Pi54,Pi37,and Pi36 into the G-populations as G-R loci.The genic diversity at the three X-R loci(16 alleles)was twofold higher than that at the three G-R loci(8 alleles),and the allelic diversity in the Southern region(21 alleles)was nearly double that in the Northeastern region(11 alleles).Both observations reflect a significant difference in genetic diversity between X-and G-populations,and indicate that the effective R-genes mainly originated from X-subspecies.Based on the allelic structures characterized by a set of 10 parameters,8 and 16 alleles were respectively recognized as favorable and promising ones for the regional breeding programs.The genotypic structures of the two regional populations were almost different,indicating that the diverged alleles have been further assembled into two series of regional genotypes through long-term breeding programs,despite the presence of one-third of region-common alleles.The genotypic diversity in the Southern region(55 genotypes)was nearly twice as high as that in the Northeastern region(28),which perfectly reflects the aforementioned differences in both genic and allelic diversities.After analyzing the genotypic structures using a set of 13 parameters,4 and 23 genotypes,respectively,can be recommended as the favorable and promising ones for the regional breeding programs.The case study serves as a concrete sample of how to identify the favorable and promising alleles and genotypes,and beneficial parents based their comprehensive population structures for gene-designed breeding.展开更多
Cervical cancer is the fourth most common cancer worldwide, accounting for 6.8% of new cancer cases and 8.1% of cancer-related deaths. About 85% of these deaths occurred in low- and middle-income countries. The aim of...Cervical cancer is the fourth most common cancer worldwide, accounting for 6.8% of new cancer cases and 8.1% of cancer-related deaths. About 85% of these deaths occurred in low- and middle-income countries. The aim of this study was to assess the frequency and distribution of the human papillomavirus (HPV) genotypes in women showing cytological abnormalities of the cervix at the Sourô SANOU University Hospital (CHUSS) in Bobo-Dioulasso, Burkina Faso. This is a descriptive study of women recruited at the CHUSS. The cervico-uterine smear examination was carried out at the CHUSS Anatomy and Pathology Department for cervical cancer screening. The data were collected from women with atypical cells on their cervico-uterine smear. Cervicovaginal samples were taken from consenting women and HPV genotyping was performed using the HPV Direct FLOW CHIP kit at CERBA. We obtained approval from the ethics committee. The data were analyzed using the SPSS 26 software. The results of the study showed that 67.79% of the participants were aged between 50 and 65, a group that is particularly vulnerable to persistent infection with high-risk oncogenic HPV genotypes. Of the women screened, 40.7% were HPV positive and 29.2% had multiple infections. The most common genotypes were HPV 35, followed by HPV 18, 52, 58 and 66. These data highlight the need for increased surveillance and targeted prevention strategies among this female population.展开更多
Hypertrophic cardiomyopathy(HCM)is the most common genetic cardiovascular disease,mostly inherited in an autosomal dominant manner.It is a global heart disease with complex clinical phenotypes and gene expression.The ...Hypertrophic cardiomyopathy(HCM)is the most common genetic cardiovascular disease,mostly inherited in an autosomal dominant manner.It is a global heart disease with complex clinical phenotypes and gene expression.The prevalence rate in the population is 1:500-1:200.This article mainly introduces the diagnostic criteria,pathological manifestations,and genetic basis of HCM,which is the leading cause of sudden death in adolescents and athletes due to exercise,with 60%-70%showing familial clustering.It also discusses the latest progress in the relationship between different genotypes and clinical phenotypes of HCM pa-tients.展开更多
Background:Human papillomavirus(HPV)infection is a major risk factor of cervical cancer.This study assessed the prevalence and distribution of HPV genotypes in women with cervical or vaginal lesions in Jiangsu Provinc...Background:Human papillomavirus(HPV)infection is a major risk factor of cervical cancer.This study assessed the prevalence and distribution of HPV genotypes in women with cervical or vaginal lesions in Jiangsu Province,China.Methods:A total of 2120 healthy women aged 18–45 years were screened between 2012 and 2013 and 6171 healthy women aged18–45 years were screened between 2020 and 2021 in Jiangsu Province.Cervical specimens collected from each woman were first tested using the HPV DNA enzyme immunoassay method,and positive samples were further tested using the reverse hybridization line probe assay.Differences in HPV prevalence and genotype distribution were compared between women with cervical and vaginal lesions identified during 2 rounds of cross-sectional screening.To account for differences in age composition between the 2 studies,the standardized prevalence of HPV positivity was calculated using the sum of the total number of women diagnosed with cervical or vaginal lesions during both periods as the standard group.Results:Overall,40 women(1.89%)were diagnosed with cervical or vaginal lesions through biopsy during 2012–2013,and 110(1.78%)were diagnosed during 2020–2021.Among women with lesions,the standardized HPV positivity rates were 98.41%in 2012–2013 and99.24%in 2020–2021.Most cases were caused by high-risk HPV,which accounted for 87.18%of the total infections during 2012–2013and 89.91%of those in 2020–2021,with standardized positivity rates of 86.44%and 88.75%,respectively.The standardized positivity rates for single infections were 62.35%in 2012–2013 and 74.95%in 2020–2021.The top 5 high-risk HPV genotypes were HPV type 16(HPV16;29.01%),52(20.63%),18(14.28%),58(13.71%),and 33(12.12%)in 2012–2013,and HPV16(36.95%),58(22.18%),52(13.25%),31(7.63%),and 51(6.81%)in 2020–2021.The standardized positivity rate for HPV18 decreased from 14.28%in2012–2013 to 1.15%in 2020–2021.Among women with cervical or vaginal lesions,the highest proportion was observed in the 36-to 45-year group during 2012–2013,reaching 52.50%,and in the 26-to 35-year group during 2020–2021,peaking at 59.10%.Conclusions:In Jiangsu Province,no significant changes in HPV prevalence among women with cervical or vaginal lesions were observed during 2012–2013 and 2020–2021;however,the distribution of HPV genotypes had changed.展开更多
Dear editor,As of 2023,the domestic cat population in China reached 65 million,surpassing dogs to become the most numerous companion animal in the country.Feline calicivirus(FCV)infection,one of the three most prevale...Dear editor,As of 2023,the domestic cat population in China reached 65 million,surpassing dogs to become the most numerous companion animal in the country.Feline calicivirus(FCV)infection,one of the three most prevalent infectious diseases in cats,poses a severe threat to feline health.FCV,classified under the Caliciviridae family(genus Vesivirus).展开更多
Salt stress is a critical factor affecting the growth and yield of rice.Egypt,the largest rice producer in North Africa and the Middle East,is facing contrasting challenges related to salinity in its agroecosystems.In...Salt stress is a critical factor affecting the growth and yield of rice.Egypt,the largest rice producer in North Africa and the Middle East,is facing contrasting challenges related to salinity in its agroecosystems.In this study,we compared the salt-induced responses among three rice varieties:Giza 176(Egyptian variety),Kaituodao(Chinese variety),and Pokkali(Sri Lanka variety,used as control)under normal and saline stress(100 mmol/L NaCl)conditions at two seedling stages through RNA-seq expression analysis.Giza 176 displayed a salt tolerance score of 7 on the SES(Standard Evaluation Score).Its transcriptome showed dynamic changes,with the number of upregulated genes increasing from 180 to 735,and downregulated genes increasing from 918 to 2930 from the one-week to two-week stress stages,with activated pathways in ion transport,reactive oxygen species(ROS)scavenging,and protein biosynthesis.展开更多
Acute respiratory tract infections(ARTIs)are among the leading causes of morbidity and mortality in children worldwide.Human adenovirus(HAdV)infections are estimated to account for at least 5%of pediatric ARTIs.The ci...Acute respiratory tract infections(ARTIs)are among the leading causes of morbidity and mortality in children worldwide.Human adenovirus(HAdV)infections are estimated to account for at least 5%of pediatric ARTIs.The circulated genotypes of HAdV and the correlation between genotype and clinical manifestations in Wuhan,China,before and after the complete relaxation of nonpharmaceutical interventions against severe acute respiratory syndrome coronavirus 2,remain unknown.Here,101 HAdV strains were isolated from throat swab samples collected from hospitalized children with ARTIs who tested positive for HAdV nucleic acid.Of these,sixty-six strains from 2022 to twenty-three strains from 2023 were successfully genotyped and subjected to phylogenetic analysis based on the hexon,penton base,and fiber genes.Six genotypes,B3,C1,C2,C5,C104,and C108 were identified.HAdV-B3(84.85%)was the most prevalent type in 2022,while HAdV-C(86.96%),including C1,C2,C108,and C104,was the most prevalent in 2023.These strains were phylogenetically related to strains from Japan,China,and the United States in recent years.When comparing clinical characteristics,pediatric patients infected with B3,C1,C2,C5,C104,or C108 exhibited similar clinical manifestations,primarily fever and cough,but varying interleukin(IL)-10 levels.In conclusion,from June 2022 to September 2023,the circulated genotypes of HAdV in Wuhan included B3,C1,C2,C108,C5,and C104.The endemic pattern of HAdV in Wuhan,China,shifted from species B as the dominant type in 2022 to species C in 2023.展开更多
Background:In 2021,the American College of Medical Genetics and Genomics(ACMG)recommended reporting actionable genotypes in 73 genes associated with diseases for which preventive or therapeutic measures are available....Background:In 2021,the American College of Medical Genetics and Genomics(ACMG)recommended reporting actionable genotypes in 73 genes associated with diseases for which preventive or therapeutic measures are available.Evaluations of the association of actionable genotypes in these genes with life span are currently lacking.Methods:We assessed the prevalence of coding and splice variants in genes on the ACMG Secondary Findings,version 3.0(ACMG SF v3.0),list in the genomes of 57,933 Icelanders.We assigned pathogenicity to all reviewed variants using reported evidence in the ClinVar database,the frequency of variants,and their associations with disease to create a manually curated set of actionable genotypes(variants).We assessed the relationship between these genotypes and life span and further examined the specific causes of death among carriers.展开更多
Chinese Kun Ming （KM） mouse, an outbreed strain of laboratory animal, has been widely utilized in related pharmaceutical and genetic studies throughout China. However, the value of KM mice to the research community ...Chinese Kun Ming （KM） mouse, an outbreed strain of laboratory animal, has been widely utilized in related pharmaceutical and genetic studies throughout China. However, the value of KM mice to the research community has been severely limited, partially due to the fact that well-characterized inbred strain of KM mice is not available. Several expected inbred strains from KM mice have been bred, but their genetic purity remains uncertain. In this study, four expected inbred strains of KM mice （A1, T2, N2, and N4） were chosen and their inbred degree were compared with two classical inbred mouse lines （BALB/c and C57BL/6） by analyzing the genotypes of about 30 microsatellite markers. In the four strains, A1 and N4 were homozygous at all genotyped loci, but N2 and T2 were only heterozygous at locus D15Mit16. These results indicate that the level of genetic purity/homozygousity of A1, N4, N2, and T2 inbred line is comparable to those of BALB/c and C57BL/6. This study provided the first and solid evidence for genetic purity of four expected inbred strains of KM mice. These 4 inbred mice strains should be well maintained for further characterization and utilization in genetic studies.展开更多
Two microsateUite DNA loci were used to trace the pedigree structure of six families in the shrimp Fenneropenaeus chinensis. Four of the families were natural mating, and the others were mated by artificial inseminati...Two microsateUite DNA loci were used to trace the pedigree structure of six families in the shrimp Fenneropenaeus chinensis. Four of the families were natural mating, and the others were mated by artificial insemination. Eleven alleles were acquired at two microsatellite DNA loci （locus RS0622 and locus EN0033 ） by investigating 145 offsprings and 11 parents. Five alleles were acquired from locus RS0622 and six from locus EN0033. As analyzed, the gene frequencies were between 0. 024 1 and 0. 493 1, the heterozygosity was 0.652 2 and 0.688 8, and the polymorphism information content （PIC） was 0.585 7 and 0.652 9 for the locus RS0622 and the locus EN0033, respectively. Twenty-three genotypes were detected and the genotypes of the losing parents were also inferred. The pedigrees of three F1 and three F2 generations were determined by matching the genotype at each locus.展开更多
AIM:To evaluate the impact of mass vaccination against the hepatitis B virus (HBV) in Egypt,and to search for vaccinee asymptomatic breakthrough HBV infection and its genotype.METHODS:Seven hundred serum samples from ...AIM:To evaluate the impact of mass vaccination against the hepatitis B virus (HBV) in Egypt,and to search for vaccinee asymptomatic breakthrough HBV infection and its genotype.METHODS:Seven hundred serum samples from vaccinated children and adults (aged 2-47 years) were used for quantitative and qualitative detection of HBsAb by ELISA.Three hundred and sixty serum samples representing undetectable or low or high HBsAb were screened for markers of active HBV infection (HBsAg,HBcAb (IgG) and HBeAb by ELISA,plus HBsAg by AxSYM) and HBV-DNA genotyping by nested multiplex PCR and by DNA sequencing.RESULTS:It was found that 65% of children aged 2-4 years,and 20.5% aged 4-13 years,as well as 45% adults were good responders to HBV vaccination mounting protective level HBsAb.Poor responders were 28%,59.5% and 34%,and non-responders were 7%,20% and 21% respectively,in the three studied groups.Markers of asymptomatic HBV infections were HBsAg detected by ELISA in 2.5% vs 11.39% by AxSYM.Other markers were HBcAb (IgG) in 1.38%,HBeAb in 0.83%,and HBV-DNA in 7.8%.All had HBV genotype E infection.CONCLUSION:It is concluded that HBV vaccine is efficient in controlling HBV infection among children and adults.The vaccine breakthrough infection was by HBV genotype E.A booster dose of vaccine is recommended,probably four years after initial vaccination.展开更多
An improved allele-specific PCR（AS-PCR） approach was applied to investigating -55C/T polymorphism in promoter region of the uncoupling protein 3（UCP3）gene. AS-PCR is a competitive PCR method which is based on posi...An improved allele-specific PCR（AS-PCR） approach was applied to investigating -55C/T polymorphism in promoter region of the uncoupling protein 3（UCP3）gene. AS-PCR is a competitive PCR method which is based on positioning the 3＇ base of a PCR primer to match one single nucleotide polymorphism（SNP） allele and accurately extend only the correctly matched primer. But it is limited in use because of its poor specificity. In this study, we improved the specificity of AS-PCR by introducing additional mismatch at the penultimate base of 3＇ end of AS-PCR primer in combination with decreasing the level of dNTP in the reaction mixture. Sensitivity, specificity and reliability of this method were assessed for both simple plasmid model and complex human genomic SNP targets. The -55C/T（rs1800849） polymorphisrn of the UCP3 gene was analyzed via this AS-PCR and restriction fragment length polymorphism（RFLP）, the latter was used as a gold standard. The results suggest that the increase in AS-PCR discrimination with this method should facilitate the use of this simple, rapid, and inexpensive technique for SNP genotyping application.展开更多
Oculocutaneous albinism（OCA） is an autosomal recessive disorder characterized by hypopigmentation in eyes,hair and skin,accompanied with vision loss.Currently,six genes have been identified as causative genes for no...Oculocutaneous albinism（OCA） is an autosomal recessive disorder characterized by hypopigmentation in eyes,hair and skin,accompanied with vision loss.Currently,six genes have been identified as causative genes for non-syndromic OCA（OCA-1w4,6,7）,and ten genes for syndromic OCA（HPS-1e9,CHS-1）.Genetic counseling of 51 Chinese OCA families（39 OCA-1 with mutations in the TYR gene,6 OCA-2 with mutations in the OCA2 gene,4 OCA-4 with mutations in the SLC45A2 gene,1 HPS-1（Hermanskye Pudlak syndrome-1） with mutation in the HPS1 gene,and 1 mixed OCA-1 and OCA-4） led us to perform the prenatal genetic testing of OCA using amniotic fluid cells through the implementation of our optimized strategy.In our cohort,eleven previously unidentified alleles（PUAs）（5 in TYR,2 in OCA2,and 4 in SLC45A2） were found.Three missense PUAs（p.C112 R,p.H363 R and p.G379 V of TYR） and one in-frame deletional PUA（p.S222 del of SLC24A5） led to fetuses with OCA when co-inherited with other disease causative alleles.Three PUAs（p.P152 H and p.W272 X of TYR,p.A486 T of SLC24A5） identified in the OCA probands did not co-transmit with known pathological alleles and thus gave rise to unaffected fetuses.Four PUAs（p.Q83 X and p.A658 T of TYR,p.G161 R and p.G366 R of SLC24A5） did not transmit to the unaffected fetuses.In addition,the in vitro transfection assays showed that the p.S192 Y variant of TYR produced less pigment compared to the wild-type allele.A fetus with a digenic carrier of OCA-1 and OCA-4 was unaffected.In combination with functional assays,the family inheritance pattern is useful for the evaluation of pathogenicity of PUAs and genetic counseling of OCA.展开更多
We have developed a novel dual enzyme chemistry called rhAmp®SNP genotyping based on RNase H2-dependent PCR (rhPCR) that provides high signal and specificity for SNP analysis. rhAmp SNP genotyping combines a u...We have developed a novel dual enzyme chemistry called rhAmp®SNP genotyping based on RNase H2-dependent PCR (rhPCR) that provides high signal and specificity for SNP analysis. rhAmp SNP genotyping combines a unique two-enzyme system with 3’ end blocked DNA-RNA hybrid primers to interrogate SNP loci. Activation of the blocked primers occurs upon hybridization to its perfectly matched target, which eliminates or greatly reduces primer dimers. A thermostable hot-start RNase H2 cleaves the primer immediately 5’ of the ribose sugar, releasing the blocking group and allowing primer extension. PCR specificity is further improved with the use of a mutant Taq DNA polymerase, resulting in improved allelic discrimination. Signal generation is obtained using a universal reporter system which requires only two reporter probes for any bi-allelic SNP. 1000 randomly selected SNPs were chosen to validate the 95% design rate of the design pipeline. A subsampling of 130 human SNP targets was tested and achieved a 98% call rate, and 99% call accuracy. rhAmp SNP genotyping assays are compatible with various qPCR instruments including QuantStudioTM 7 Flex, CFX384TM, IntelliQube®, and Biomark HDTM. In comparison to TaqMan®, rhAmp SNP genotyping assays show higher signal (Rn) and greater cluster separation, resulting in more reliable SNP genotyping performance. The rhAmp SNP genotyping solution is suited for high-throughput SNP genotyping applications in humans and plants.展开更多
Background:Genotyping by sequencing(GBS)is a robust method to genotype markers.Many factors can influence the genotyping quality.One is that heterozygous genotypes could be wrongly genotyped as homozygotes,dependent o...Background:Genotyping by sequencing(GBS)is a robust method to genotype markers.Many factors can influence the genotyping quality.One is that heterozygous genotypes could be wrongly genotyped as homozygotes,dependent on the genotyping depths.In this study,a method correcting this type of genotyping error was demonstrated.The efficiency of this correction method and its effect on genomic prediction were assessed using simulated data of livestock populations.Results:Chip array(Chip)and four depths of GBS data was simulated.After quality control(call rate≥0.8 and MAF≥0.01),the remaining number of Chip and GBS SNPs were both approximately 7,000,averaged over 10 replicates.GBS genotypes were corrected with the proposed method.The reliability of genomic prediction was calculated using GBS,corrected GBS(GBSc),true genotypes for the GBS loci(GBSr)and Chip data.The results showed that GBSc had higher rates of correct genotype calls and higher correlations with true genotypes than GBS.For genomic prediction,using Chip data resulted in the highest reliability.As the depth increased to 10,the prediction reliabilities using GBS and GBSc data approached those using true GBS data.The reliabilities of genomic prediction using GBSc data were 0.604,0.672,0.684 and 0.704 after genomic correction,with the improved values of 0.013,0.009,0.006 and 0.001 at depth=2,4,5 and 10,respectively.Conclusions:The current study showed that a correction method for GBS data increased the genotype accuracies and,consequently,improved genomic predictions.These results suggest that a correction of GBS genotype is necessary,especially for the GBS data with low depths.展开更多
Anchovy （Engraulis aponicus）, a small pelagic fish and food of other economic fishes, is a key species in the Yellow Sea ecosystem. Understanding the mechanisms of its recruitment and biomass variation is important ...Anchovy （Engraulis aponicus）, a small pelagic fish and food of other economic fishes, is a key species in the Yellow Sea ecosystem. Understanding the mechanisms of its recruitment and biomass variation is important for the prediction and management of fishery resources. Coupled with a hydrodynamic model （POM） and a lower trophic level ecosystem model （NEMURO）, an individual-based model of anchovy is developed to study the influence of physical environment on anchovy＇s biomass variation, Seasonal variations of circulation, water temperature and mix-layer depth from POM are used as external forcing for NEMURO and the anchovy model. Biomasses of large zooplankton and predatory zooplankton which anchovy feeds on are output from NEMURO and are controlled by the consumption of anchovy on them. Survival fitness theory related to temperature and food is used to determine the swimming action of anchovy in the model. The simulation results agree well with observations and elucidate the influence of temperature in over-wintering migration and food in feeding migration.展开更多
Common variants explain little of the variance of most common disease, prompting large-scale sequencing studies to understand the contribution of rare variants to these diseases. Imputation of rare variants from genom...Common variants explain little of the variance of most common disease, prompting large-scale sequencing studies to understand the contribution of rare variants to these diseases. Imputation of rare variants from genome-wide genotypic arrays offers a cost-efficient strategy to achieve necessary sample sizes required for adequate statistical power. To estimate the performance of imputation of rare variants, we imputed 153 individuals, each of whom was genotyped on 3 different genotype arrays including 317k, 610k and 1 million single nucleotide polymorphisms （SNPs）, to two different reference panels： HapMap2 and 1000 Genomes pilot March 2010 release （1KGpilot） by using IMPUTE version 2. We found that more than 94% and 84% of all SNPs yield acceptable accuracy （info 〉 0.4） in HapMap2 and 1KGpilot-based imputation, respectively. For rare variants （minor allele frequency （MAF） 〈5%）, the proportion of well- imputed SNPs increased as the MAF increased from 0.3% to 5% across all 3 genome-wide association study （GWAS） datasets. The proportion of well-imputed SNPs was 69%, 60% and 49% for SNPs with a MAF from 0.3% to 5% for 1M, 610k and 317k, respectively. None of the very rare variants （MAF 〈 0.3%） were well imputed. We conclude that the imputation accuracy of rare variants increases with higher density of genome-wide genotyping arrays when the size of the reference panel is small. Variants with lower MAF are more difficult to impute. These findings have important implications in the design and replication of large-scale sequencing studies.展开更多
The Genome Analysis Toolkit(GATK) is a popular set of programs for discovering and genotyping variants from next-generation sequencing data.The current GATK recommendation for RNA sequencing(RNA-seq) is to perform var...The Genome Analysis Toolkit(GATK) is a popular set of programs for discovering and genotyping variants from next-generation sequencing data.The current GATK recommendation for RNA sequencing(RNA-seq) is to perform variant calling from individual samples,with the drawback that only variable positions are reported.Versions 3.0 and above of GATK offer the possibility of calling DNA variants on cohorts of samples using the HaplotypeCaller algorithm in Genomic Variant Call Format(GVCF) mode.Using this approach,variants are called individually on each sample,generating one GVCF file per sample that lists genotype likelihoods and their genome annotations.In a second step,variants are called from the GVCF files through a joint genotyping analysis.This strategy is more flexible and reduces computational challenges in comparison to the traditional joint discovery workflow.Using a GVCF workflow for mining SNP in RNA-seq data provides substantial advantages,including reporting homozygous genotypes for the reference allele as well as missing data.Taking advantage of RNA-seq data derived from primary macrophages isolated from 50 cows,the GATK joint genotyping method for calling variants on RNA-seq data was validated by comparing this approach to a so-called "per-sample" method.In addition,pair-wise comparisons of the two methods were performed to evaluate their respective sensitivity,precision and accuracy using DNA genotypes from a companion study including the same 50 cows genotyped using either genotyping-by-sequencing or with the Bovine SNP50 Beadchip(imputed to the Bovine high density).Results indicate that both approaches are very close in their capacity of detecting reference variants and that the joint genotyping method is more sensitive than the per-sample method.Given that the joint genotyping method is more flexible and technically easier,we recommend this approach for variant calling in RNA-seq experiments.展开更多
Objective To evaluate four candidate variable number tandem repeat （VNTR） loci for genotyping Mycobacterium tuberculosis complex strains. Methods Genomic sequences for two M. tuberculosis strains （CCDC5079 and CCDC...Objective To evaluate four candidate variable number tandem repeat （VNTR） loci for genotyping Mycobacterium tuberculosis complex strains. Methods Genomic sequences for two M. tuberculosis strains （CCDC5079 and CCDC5180） were generated, and using published sequence data, four candidate VNTR loci were identified. The VNTRs were used to genotype 225 Chinese clinical M. tuberculosis complex strains. The discriminatory power of the VNTRs was evaluated using BioNumerics 5.0 software. Results The Hunter-Gaston Index （HGI） for BJ1, BJ2, BJ3, and BJ4 loci was 0.634, 0.917, 0.697, and 0.910, respectively. Combining all four loci gave an HGI value of 0.995, thus confirming that the genotyping had good discriminatory power. The HGI values for BJ1, BJ2, BJ3, and BJ4, obtained from Beijing family strain genotyping, were 0.447, 0.878, 0.315, and 0.850, respectively. Combining all four loci produced an HGI value of 0.988 for genotyping the Beijing family strains. We observed unique patterns for M. boris and M. africanum strains from the four loci. Conclusion We have shown that the four VNTR loci can be successfully used for genotyping M. tuberculosis complex strains. Notably, these new loci may provide additional information about Chinese M. tuberculosis isolates than that currently afforded by established VNTR loci typing.展开更多
基金supported by the grants from the Key R&D Program of Shandong Province,China(2022LZGC003)the China Agriculture Research System of MOF and MARA(CARS-35)+1 种基金the National Key Research and Development Project of China(2019YFE0106800)the 2115 Talent Development Program of China Agricultural University。
文摘Genotyping by target sequencing(GBTS)integrates the advantages of silicon-based technology(high stability and reliability)and genotyping by sequencing(high flexibility and cost-effectiveness).However,GBTS panels are not currently available in pigs.In this study,based on GBTS technology,we first developed a 50K panel,including 52,000 single-nucleotide polymorphisms(SNPs),in pigs,designated GBTS50K.A total of 6,032 individuals of Large White,Landrace,and Duroc pigs from 10 breeding farms were used to assess the newly developed GBTS50K.Our results showed that GBTS50K obtained a high genotyping ability,the SNP and individual call rates of GBTS50K were 0.997–0.998,and the average consistency rate and genotyping correlation coefficient were 0.997 and 0.993,respectively,in replicate samples.We also evaluated the efficiencies of GBTS50K in the application of population genetic structure analysis,selection signature detection,genome-wide association studies(GWAS),genotyped imputation,genetic selection(GS),etc.The results indicate that GBTS50K is plausible and powerful in genetic analysis and molecular breeding.For example,GBTS50K could gain higher accuracies than the current popular GGP-Porcine bead chip in genomic selection on 2 important traits of backfat thickness at 100 kg and days to 100 kg in pigs.Particularly,due to the multiple SNPs(mSNPs),GBTS50K generated 100K qualified SNPs without increasing genotyping cost,and our results showed that the haplotype-based method can further improve the accuracies of genomic selection on growth and reproduction traits by 2 to 6%.Our study showed that GBTS50K could be a powerful tool for underlying genetic architecture and molecular breeding in pigs,and it is also helpful for developing SNP panels for other farm animals.
基金funded by grants from the National Key R&D Project(2023YFD1400201-02,2023YFD1400203-02)the National Natural Science Foundation of China(31870137)+1 种基金the National Transgenic Research Project(2015ZX08001-002)the Key R&D Project of Guangdong Province(2022B0202060005).
文摘Asian rice comprises two major subspecies:Xian(X)and Geng(G),and the diverged resistance genes(R)have provided a foundation for breeding improved cultivars to control rice blast disease.After conducting two-phase allele mining using six updated FNP marker systems,the functional haplotypes at Pit,Pib,and Pi63 strictly diverged into the X-populations and were defined as X-R loci,while those at Pi54,Pi37,and Pi36 into the G-populations as G-R loci.The genic diversity at the three X-R loci(16 alleles)was twofold higher than that at the three G-R loci(8 alleles),and the allelic diversity in the Southern region(21 alleles)was nearly double that in the Northeastern region(11 alleles).Both observations reflect a significant difference in genetic diversity between X-and G-populations,and indicate that the effective R-genes mainly originated from X-subspecies.Based on the allelic structures characterized by a set of 10 parameters,8 and 16 alleles were respectively recognized as favorable and promising ones for the regional breeding programs.The genotypic structures of the two regional populations were almost different,indicating that the diverged alleles have been further assembled into two series of regional genotypes through long-term breeding programs,despite the presence of one-third of region-common alleles.The genotypic diversity in the Southern region(55 genotypes)was nearly twice as high as that in the Northeastern region(28),which perfectly reflects the aforementioned differences in both genic and allelic diversities.After analyzing the genotypic structures using a set of 13 parameters,4 and 23 genotypes,respectively,can be recommended as the favorable and promising ones for the regional breeding programs.The case study serves as a concrete sample of how to identify the favorable and promising alleles and genotypes,and beneficial parents based their comprehensive population structures for gene-designed breeding.
文摘Cervical cancer is the fourth most common cancer worldwide, accounting for 6.8% of new cancer cases and 8.1% of cancer-related deaths. About 85% of these deaths occurred in low- and middle-income countries. The aim of this study was to assess the frequency and distribution of the human papillomavirus (HPV) genotypes in women showing cytological abnormalities of the cervix at the Sourô SANOU University Hospital (CHUSS) in Bobo-Dioulasso, Burkina Faso. This is a descriptive study of women recruited at the CHUSS. The cervico-uterine smear examination was carried out at the CHUSS Anatomy and Pathology Department for cervical cancer screening. The data were collected from women with atypical cells on their cervico-uterine smear. Cervicovaginal samples were taken from consenting women and HPV genotyping was performed using the HPV Direct FLOW CHIP kit at CERBA. We obtained approval from the ethics committee. The data were analyzed using the SPSS 26 software. The results of the study showed that 67.79% of the participants were aged between 50 and 65, a group that is particularly vulnerable to persistent infection with high-risk oncogenic HPV genotypes. Of the women screened, 40.7% were HPV positive and 29.2% had multiple infections. The most common genotypes were HPV 35, followed by HPV 18, 52, 58 and 66. These data highlight the need for increased surveillance and targeted prevention strategies among this female population.
基金Supported by National Natural Science Foundation of China,No.82230065,No.82371974 and No.82272009.
文摘Hypertrophic cardiomyopathy(HCM)is the most common genetic cardiovascular disease,mostly inherited in an autosomal dominant manner.It is a global heart disease with complex clinical phenotypes and gene expression.The prevalence rate in the population is 1:500-1:200.This article mainly introduces the diagnostic criteria,pathological manifestations,and genetic basis of HCM,which is the leading cause of sudden death in adolescents and athletes due to exercise,with 60%-70%showing familial clustering.It also discusses the latest progress in the relationship between different genotypes and clinical phenotypes of HCM pa-tients.
基金supported by Xiamen University,which played a key role in the collection and analysis of the datafunded by National Natural Science Foundation of China(grants 82341031,82173584,and 82222062)+2 种基金Major Research Plan of the National Natural Science Foundation of China(grant 92269205)Science Fund for Distinguished Young Scholars of Jiangsu Province(grant BK20220064)Jiangsu Provincial Key Project of Science and Technology Plan(grants BE2021738 and BE2023601)。
文摘Background:Human papillomavirus(HPV)infection is a major risk factor of cervical cancer.This study assessed the prevalence and distribution of HPV genotypes in women with cervical or vaginal lesions in Jiangsu Province,China.Methods:A total of 2120 healthy women aged 18–45 years were screened between 2012 and 2013 and 6171 healthy women aged18–45 years were screened between 2020 and 2021 in Jiangsu Province.Cervical specimens collected from each woman were first tested using the HPV DNA enzyme immunoassay method,and positive samples were further tested using the reverse hybridization line probe assay.Differences in HPV prevalence and genotype distribution were compared between women with cervical and vaginal lesions identified during 2 rounds of cross-sectional screening.To account for differences in age composition between the 2 studies,the standardized prevalence of HPV positivity was calculated using the sum of the total number of women diagnosed with cervical or vaginal lesions during both periods as the standard group.Results:Overall,40 women(1.89%)were diagnosed with cervical or vaginal lesions through biopsy during 2012–2013,and 110(1.78%)were diagnosed during 2020–2021.Among women with lesions,the standardized HPV positivity rates were 98.41%in 2012–2013 and99.24%in 2020–2021.Most cases were caused by high-risk HPV,which accounted for 87.18%of the total infections during 2012–2013and 89.91%of those in 2020–2021,with standardized positivity rates of 86.44%and 88.75%,respectively.The standardized positivity rates for single infections were 62.35%in 2012–2013 and 74.95%in 2020–2021.The top 5 high-risk HPV genotypes were HPV type 16(HPV16;29.01%),52(20.63%),18(14.28%),58(13.71%),and 33(12.12%)in 2012–2013,and HPV16(36.95%),58(22.18%),52(13.25%),31(7.63%),and 51(6.81%)in 2020–2021.The standardized positivity rate for HPV18 decreased from 14.28%in2012–2013 to 1.15%in 2020–2021.Among women with cervical or vaginal lesions,the highest proportion was observed in the 36-to 45-year group during 2012–2013,reaching 52.50%,and in the 26-to 35-year group during 2020–2021,peaking at 59.10%.Conclusions:In Jiangsu Province,no significant changes in HPV prevalence among women with cervical or vaginal lesions were observed during 2012–2013 and 2020–2021;however,the distribution of HPV genotypes had changed.
基金supported by grants from the National Key Research and Development Program of China(Grant No.2022YFD1800100)National Natural Science Foundation of China(Grant No.32272982)Natural Science Foundation of Shanghai(Grant No.23ZR1477100).
文摘Dear editor,As of 2023,the domestic cat population in China reached 65 million,surpassing dogs to become the most numerous companion animal in the country.Feline calicivirus(FCV)infection,one of the three most prevalent infectious diseases in cats,poses a severe threat to feline health.FCV,classified under the Caliciviridae family(genus Vesivirus).
基金funded by the National Key R&D Program of China(Grant No.2022YFE0139400)the Egyptian-Chinese Research Fund,and Science,Technology&Innovation Funding Authority Egypt(Grant No.46512)the National Natural Science Foundation of China(Grant No.261143470).
文摘Salt stress is a critical factor affecting the growth and yield of rice.Egypt,the largest rice producer in North Africa and the Middle East,is facing contrasting challenges related to salinity in its agroecosystems.In this study,we compared the salt-induced responses among three rice varieties:Giza 176(Egyptian variety),Kaituodao(Chinese variety),and Pokkali(Sri Lanka variety,used as control)under normal and saline stress(100 mmol/L NaCl)conditions at two seedling stages through RNA-seq expression analysis.Giza 176 displayed a salt tolerance score of 7 on the SES(Standard Evaluation Score).Its transcriptome showed dynamic changes,with the number of upregulated genes increasing from 180 to 735,and downregulated genes increasing from 918 to 2930 from the one-week to two-week stress stages,with activated pathways in ion transport,reactive oxygen species(ROS)scavenging,and protein biosynthesis.
基金supported by the projects of National Virus Resource Center(NVRC-PY-03,E1YZ020501)Natural Science Foundation of Hubei Province(2022CFB564)+4 种基金Foundation of Hubei Provincial Health Commission(WJ2023M108)National Basic Science Data Sharing Platform(no.2018ZX10101004)National Basic Science Data Sharing Service Platform(no.NBSDC-DB-13)the International Cooperation Base of Hubei Province for Infection and Immunitysupported by Outstanding Medical Young Scholars of Hubei Province and Wuhan Young and Middle-aged Medical Backbone Talent Program.
文摘Acute respiratory tract infections(ARTIs)are among the leading causes of morbidity and mortality in children worldwide.Human adenovirus(HAdV)infections are estimated to account for at least 5%of pediatric ARTIs.The circulated genotypes of HAdV and the correlation between genotype and clinical manifestations in Wuhan,China,before and after the complete relaxation of nonpharmaceutical interventions against severe acute respiratory syndrome coronavirus 2,remain unknown.Here,101 HAdV strains were isolated from throat swab samples collected from hospitalized children with ARTIs who tested positive for HAdV nucleic acid.Of these,sixty-six strains from 2022 to twenty-three strains from 2023 were successfully genotyped and subjected to phylogenetic analysis based on the hexon,penton base,and fiber genes.Six genotypes,B3,C1,C2,C5,C104,and C108 were identified.HAdV-B3(84.85%)was the most prevalent type in 2022,while HAdV-C(86.96%),including C1,C2,C108,and C104,was the most prevalent in 2023.These strains were phylogenetically related to strains from Japan,China,and the United States in recent years.When comparing clinical characteristics,pediatric patients infected with B3,C1,C2,C5,C104,or C108 exhibited similar clinical manifestations,primarily fever and cough,but varying interleukin(IL)-10 levels.In conclusion,from June 2022 to September 2023,the circulated genotypes of HAdV in Wuhan included B3,C1,C2,C108,C5,and C104.The endemic pattern of HAdV in Wuhan,China,shifted from species B as the dominant type in 2022 to species C in 2023.
文摘Background:In 2021,the American College of Medical Genetics and Genomics(ACMG)recommended reporting actionable genotypes in 73 genes associated with diseases for which preventive or therapeutic measures are available.Evaluations of the association of actionable genotypes in these genes with life span are currently lacking.Methods:We assessed the prevalence of coding and splice variants in genes on the ACMG Secondary Findings,version 3.0(ACMG SF v3.0),list in the genomes of 57,933 Icelanders.We assigned pathogenicity to all reviewed variants using reported evidence in the ClinVar database,the frequency of variants,and their associations with disease to create a manually curated set of actionable genotypes(variants).We assessed the relationship between these genotypes and life span and further examined the specific causes of death among carriers.
基金This work was supported by the National Natural Science Foundation of China (No. 03114121).
文摘Chinese Kun Ming （KM） mouse, an outbreed strain of laboratory animal, has been widely utilized in related pharmaceutical and genetic studies throughout China. However, the value of KM mice to the research community has been severely limited, partially due to the fact that well-characterized inbred strain of KM mice is not available. Several expected inbred strains from KM mice have been bred, but their genetic purity remains uncertain. In this study, four expected inbred strains of KM mice （A1, T2, N2, and N4） were chosen and their inbred degree were compared with two classical inbred mouse lines （BALB/c and C57BL/6） by analyzing the genotypes of about 30 microsatellite markers. In the four strains, A1 and N4 were homozygous at all genotyped loci, but N2 and T2 were only heterozygous at locus D15Mit16. These results indicate that the level of genetic purity/homozygousity of A1, N4, N2, and T2 inbred line is comparable to those of BALB/c and C57BL/6. This study provided the first and solid evidence for genetic purity of four expected inbred strains of KM mice. These 4 inbred mice strains should be well maintained for further characterization and utilization in genetic studies.
基金the National High Technology Development Project of China under contract No. 2005AA603210 the National Natural Science Foundation of China under contract No. 30500378.
文摘Two microsateUite DNA loci were used to trace the pedigree structure of six families in the shrimp Fenneropenaeus chinensis. Four of the families were natural mating, and the others were mated by artificial insemination. Eleven alleles were acquired at two microsatellite DNA loci （locus RS0622 and locus EN0033 ） by investigating 145 offsprings and 11 parents. Five alleles were acquired from locus RS0622 and six from locus EN0033. As analyzed, the gene frequencies were between 0. 024 1 and 0. 493 1, the heterozygosity was 0.652 2 and 0.688 8, and the polymorphism information content （PIC） was 0.585 7 and 0.652 9 for the locus RS0622 and the locus EN0033, respectively. Twenty-three genotypes were detected and the genotypes of the losing parents were also inferred. The pedigrees of three F1 and three F2 generations were determined by matching the genotype at each locus.
基金Biotechnology and Genetic Engineering National Strategy- Academy for Science,Research and Biotechnology for their financial support to this project
文摘AIM:To evaluate the impact of mass vaccination against the hepatitis B virus (HBV) in Egypt,and to search for vaccinee asymptomatic breakthrough HBV infection and its genotype.METHODS:Seven hundred serum samples from vaccinated children and adults (aged 2-47 years) were used for quantitative and qualitative detection of HBsAb by ELISA.Three hundred and sixty serum samples representing undetectable or low or high HBsAb were screened for markers of active HBV infection (HBsAg,HBcAb (IgG) and HBeAb by ELISA,plus HBsAg by AxSYM) and HBV-DNA genotyping by nested multiplex PCR and by DNA sequencing.RESULTS:It was found that 65% of children aged 2-4 years,and 20.5% aged 4-13 years,as well as 45% adults were good responders to HBV vaccination mounting protective level HBsAb.Poor responders were 28%,59.5% and 34%,and non-responders were 7%,20% and 21% respectively,in the three studied groups.Markers of asymptomatic HBV infections were HBsAg detected by ELISA in 2.5% vs 11.39% by AxSYM.Other markers were HBcAb (IgG) in 1.38%,HBeAb in 0.83%,and HBV-DNA in 7.8%.All had HBV genotype E infection.CONCLUSION:It is concluded that HBV vaccine is efficient in controlling HBV infection among children and adults.The vaccine breakthrough infection was by HBV genotype E.A booster dose of vaccine is recommended,probably four years after initial vaccination.
基金Supported by the Major Project Fund of Jilin Provincial Science and Technology Department,China(No.20082123)Province-university Union Fund of Jilin Province,China(No.20082011)
文摘An improved allele-specific PCR（AS-PCR） approach was applied to investigating -55C/T polymorphism in promoter region of the uncoupling protein 3（UCP3）gene. AS-PCR is a competitive PCR method which is based on positioning the 3＇ base of a PCR primer to match one single nucleotide polymorphism（SNP） allele and accurately extend only the correctly matched primer. But it is limited in use because of its poor specificity. In this study, we improved the specificity of AS-PCR by introducing additional mismatch at the penultimate base of 3＇ end of AS-PCR primer in combination with decreasing the level of dNTP in the reaction mixture. Sensitivity, specificity and reliability of this method were assessed for both simple plasmid model and complex human genomic SNP targets. The -55C/T（rs1800849） polymorphisrn of the UCP3 gene was analyzed via this AS-PCR and restriction fragment length polymorphism（RFLP）, the latter was used as a gold standard. The results suggest that the increase in AS-PCR discrimination with this method should facilitate the use of this simple, rapid, and inexpensive technique for SNP genotyping application.
基金partially supported by grants from the National Natural Science Foundation of China(Nos.81472871 and31230046)the Natural Science Foundation of Beijing(No.7132073)the State Key Laboratory of Molecular Developmental Biology of China(No.2013-MDB-KF-03)
文摘Oculocutaneous albinism（OCA） is an autosomal recessive disorder characterized by hypopigmentation in eyes,hair and skin,accompanied with vision loss.Currently,six genes have been identified as causative genes for non-syndromic OCA（OCA-1w4,6,7）,and ten genes for syndromic OCA（HPS-1e9,CHS-1）.Genetic counseling of 51 Chinese OCA families（39 OCA-1 with mutations in the TYR gene,6 OCA-2 with mutations in the OCA2 gene,4 OCA-4 with mutations in the SLC45A2 gene,1 HPS-1（Hermanskye Pudlak syndrome-1） with mutation in the HPS1 gene,and 1 mixed OCA-1 and OCA-4） led us to perform the prenatal genetic testing of OCA using amniotic fluid cells through the implementation of our optimized strategy.In our cohort,eleven previously unidentified alleles（PUAs）（5 in TYR,2 in OCA2,and 4 in SLC45A2） were found.Three missense PUAs（p.C112 R,p.H363 R and p.G379 V of TYR） and one in-frame deletional PUA（p.S222 del of SLC24A5） led to fetuses with OCA when co-inherited with other disease causative alleles.Three PUAs（p.P152 H and p.W272 X of TYR,p.A486 T of SLC24A5） identified in the OCA probands did not co-transmit with known pathological alleles and thus gave rise to unaffected fetuses.Four PUAs（p.Q83 X and p.A658 T of TYR,p.G161 R and p.G366 R of SLC24A5） did not transmit to the unaffected fetuses.In addition,the in vitro transfection assays showed that the p.S192 Y variant of TYR produced less pigment compared to the wild-type allele.A fetus with a digenic carrier of OCA-1 and OCA-4 was unaffected.In combination with functional assays,the family inheritance pattern is useful for the evaluation of pathogenicity of PUAs and genetic counseling of OCA.
文摘We have developed a novel dual enzyme chemistry called rhAmp®SNP genotyping based on RNase H2-dependent PCR (rhPCR) that provides high signal and specificity for SNP analysis. rhAmp SNP genotyping combines a unique two-enzyme system with 3’ end blocked DNA-RNA hybrid primers to interrogate SNP loci. Activation of the blocked primers occurs upon hybridization to its perfectly matched target, which eliminates or greatly reduces primer dimers. A thermostable hot-start RNase H2 cleaves the primer immediately 5’ of the ribose sugar, releasing the blocking group and allowing primer extension. PCR specificity is further improved with the use of a mutant Taq DNA polymerase, resulting in improved allelic discrimination. Signal generation is obtained using a universal reporter system which requires only two reporter probes for any bi-allelic SNP. 1000 randomly selected SNPs were chosen to validate the 95% design rate of the design pipeline. A subsampling of 130 human SNP targets was tested and achieved a 98% call rate, and 99% call accuracy. rhAmp SNP genotyping assays are compatible with various qPCR instruments including QuantStudioTM 7 Flex, CFX384TM, IntelliQube®, and Biomark HDTM. In comparison to TaqMan®, rhAmp SNP genotyping assays show higher signal (Rn) and greater cluster separation, resulting in more reliable SNP genotyping performance. The rhAmp SNP genotyping solution is suited for high-throughput SNP genotyping applications in humans and plants.
基金supported by the Genomic Selection in PlantsAnimals(GenSAP)research project financed by the Danish Council of Strategic Research(Aarhus,Denmark)the scholarship provided by the China Scholarship Council(CSC)
文摘Background:Genotyping by sequencing(GBS)is a robust method to genotype markers.Many factors can influence the genotyping quality.One is that heterozygous genotypes could be wrongly genotyped as homozygotes,dependent on the genotyping depths.In this study,a method correcting this type of genotyping error was demonstrated.The efficiency of this correction method and its effect on genomic prediction were assessed using simulated data of livestock populations.Results:Chip array(Chip)and four depths of GBS data was simulated.After quality control(call rate≥0.8 and MAF≥0.01),the remaining number of Chip and GBS SNPs were both approximately 7,000,averaged over 10 replicates.GBS genotypes were corrected with the proposed method.The reliability of genomic prediction was calculated using GBS,corrected GBS(GBSc),true genotypes for the GBS loci(GBSr)and Chip data.The results showed that GBSc had higher rates of correct genotype calls and higher correlations with true genotypes than GBS.For genomic prediction,using Chip data resulted in the highest reliability.As the depth increased to 10,the prediction reliabilities using GBS and GBSc data approached those using true GBS data.The reliabilities of genomic prediction using GBSc data were 0.604,0.672,0.684 and 0.704 after genomic correction,with the improved values of 0.013,0.009,0.006 and 0.001 at depth=2,4,5 and 10,respectively.Conclusions:The current study showed that a correction method for GBS data increased the genotype accuracies and,consequently,improved genomic predictions.These results suggest that a correction of GBS genotype is necessary,especially for the GBS data with low depths.
基金supported by the National Natural Science Foundation of China (Grant No. 40830854)the National Basic Research Program of China (Grant No.2011CB403606)
文摘Anchovy （Engraulis aponicus）, a small pelagic fish and food of other economic fishes, is a key species in the Yellow Sea ecosystem. Understanding the mechanisms of its recruitment and biomass variation is important for the prediction and management of fishery resources. Coupled with a hydrodynamic model （POM） and a lower trophic level ecosystem model （NEMURO）, an individual-based model of anchovy is developed to study the influence of physical environment on anchovy＇s biomass variation, Seasonal variations of circulation, water temperature and mix-layer depth from POM are used as external forcing for NEMURO and the anchovy model. Biomasses of large zooplankton and predatory zooplankton which anchovy feeds on are output from NEMURO and are controlled by the consumption of anchovy on them. Survival fitness theory related to temperature and food is used to determine the swimming action of anchovy in the model. The simulation results agree well with observations and elucidate the influence of temperature in over-wintering migration and food in feeding migration.
文摘Common variants explain little of the variance of most common disease, prompting large-scale sequencing studies to understand the contribution of rare variants to these diseases. Imputation of rare variants from genome-wide genotypic arrays offers a cost-efficient strategy to achieve necessary sample sizes required for adequate statistical power. To estimate the performance of imputation of rare variants, we imputed 153 individuals, each of whom was genotyped on 3 different genotype arrays including 317k, 610k and 1 million single nucleotide polymorphisms （SNPs）, to two different reference panels： HapMap2 and 1000 Genomes pilot March 2010 release （1KGpilot） by using IMPUTE version 2. We found that more than 94% and 84% of all SNPs yield acceptable accuracy （info 〉 0.4） in HapMap2 and 1KGpilot-based imputation, respectively. For rare variants （minor allele frequency （MAF） 〈5%）, the proportion of well- imputed SNPs increased as the MAF increased from 0.3% to 5% across all 3 genome-wide association study （GWAS） datasets. The proportion of well-imputed SNPs was 69%, 60% and 49% for SNPs with a MAF from 0.3% to 5% for 1M, 610k and 317k, respectively. None of the very rare variants （MAF 〈 0.3%） were well imputed. We conclude that the imputation accuracy of rare variants increases with higher density of genome-wide genotyping arrays when the size of the reference panel is small. Variants with lower MAF are more difficult to impute. These findings have important implications in the design and replication of large-scale sequencing studies.
基金This study was funded by Agri-Food and Agriculture Canada(Project AAFC J0000–75)
文摘The Genome Analysis Toolkit(GATK) is a popular set of programs for discovering and genotyping variants from next-generation sequencing data.The current GATK recommendation for RNA sequencing(RNA-seq) is to perform variant calling from individual samples,with the drawback that only variable positions are reported.Versions 3.0 and above of GATK offer the possibility of calling DNA variants on cohorts of samples using the HaplotypeCaller algorithm in Genomic Variant Call Format(GVCF) mode.Using this approach,variants are called individually on each sample,generating one GVCF file per sample that lists genotype likelihoods and their genome annotations.In a second step,variants are called from the GVCF files through a joint genotyping analysis.This strategy is more flexible and reduces computational challenges in comparison to the traditional joint discovery workflow.Using a GVCF workflow for mining SNP in RNA-seq data provides substantial advantages,including reporting homozygous genotypes for the reference allele as well as missing data.Taking advantage of RNA-seq data derived from primary macrophages isolated from 50 cows,the GATK joint genotyping method for calling variants on RNA-seq data was validated by comparing this approach to a so-called "per-sample" method.In addition,pair-wise comparisons of the two methods were performed to evaluate their respective sensitivity,precision and accuracy using DNA genotypes from a companion study including the same 50 cows genotyped using either genotyping-by-sequencing or with the Bovine SNP50 Beadchip(imputed to the Bovine high density).Results indicate that both approaches are very close in their capacity of detecting reference variants and that the joint genotyping method is more sensitive than the per-sample method.Given that the joint genotyping method is more flexible and technically easier,we recommend this approach for variant calling in RNA-seq experiments.
基金supported by the project "Transmission Mode of Tuberculosis" (2008ZX100/03-010-02)"Warning Mode of Tuberculosis" (2008ZX10003-008) of the National Key Programme of Mega Infectious Diseasesupported by the project "Mycobacterium tuberculosis genome SNP analysis and research on the origin of the Beijing family strains" (2011SKLID208) of State Key Laboratory for Infectious Disease Prevention and Control
文摘Objective To evaluate four candidate variable number tandem repeat （VNTR） loci for genotyping Mycobacterium tuberculosis complex strains. Methods Genomic sequences for two M. tuberculosis strains （CCDC5079 and CCDC5180） were generated, and using published sequence data, four candidate VNTR loci were identified. The VNTRs were used to genotype 225 Chinese clinical M. tuberculosis complex strains. The discriminatory power of the VNTRs was evaluated using BioNumerics 5.0 software. Results The Hunter-Gaston Index （HGI） for BJ1, BJ2, BJ3, and BJ4 loci was 0.634, 0.917, 0.697, and 0.910, respectively. Combining all four loci gave an HGI value of 0.995, thus confirming that the genotyping had good discriminatory power. The HGI values for BJ1, BJ2, BJ3, and BJ4, obtained from Beijing family strain genotyping, were 0.447, 0.878, 0.315, and 0.850, respectively. Combining all four loci produced an HGI value of 0.988 for genotyping the Beijing family strains. We observed unique patterns for M. boris and M. africanum strains from the four loci. Conclusion We have shown that the four VNTR loci can be successfully used for genotyping M. tuberculosis complex strains. Notably, these new loci may provide additional information about Chinese M. tuberculosis isolates than that currently afforded by established VNTR loci typing.
