25 results on '"Ji AQ"'
Search Results
2. The effect of EDARV370A on facial and ear morphologies in Uyghur population
- Author
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Li, Y, Zhao, WT, Li, D, Tao, XM, Xiong, ZY, Liu, J, Zhang, W, Liu, HB, Ji, AQ, Tang, K, Liu, Fan, Li, C X, and Genetic Identification
- Published
- 2018
3. Improved understanding of sequence polymorphisms at 42 Y chromosome short tandem repeats for the Chinese Han population.
- Author
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Miao L, Liu S, Pan KP, Jiao RL, Zhang Q, Xu TY, Tong SY, Kang KL, Zhao J, Zhang C, Wang KD, Ji AQ, Wu J, and Wang L
- Subjects
- Humans, Male, China, DNA Fingerprinting, East Asian People genetics, Polymerase Chain Reaction, Sequence Analysis, DNA, Chromosomes, Human, Y, Gene Frequency, Genetics, Population, Microsatellite Repeats, Polymorphism, Genetic
- Abstract
Y-chromosome short tandem repeat (Y-STR) is an important type of genetic markers in the human genome, widely used in molecular anthropology and forensic genetics. However, most Y-STR studies has been focused on the length-based variations resulting from differences in the number of repeat units. Less attention was paid to sequence-based Y-STR variations. Consequently, sequence-based variation characteristics of Y-STRs in Chinese populations remain insufficiently studied. In this study, targeted sequencing of 42 Y-STR loci was performed for 331 Chinese Han males (with an average sequencing depth of 612 ×), unveiling a total of 387 sequence allele types and their frequencies in the population. Repeat pattern variations were observed in seven loci containing multiple repeat units. Across all sequenced repeat and flanking regions, 46 single-nucleotide substitutions and insertion/deletion variations were identified, including 13 mutations not recorded in the dbSNP database. Twenty-seven previously unreported sequence-based alleles were identified. Additionally, differences in Y-STRs between the Chinese Han population and three American populations (African Americans, Caucasians, and Hispanics) were revealed from sequence-based data analysis. In summary, this study provides a detailed summary of the sequence features of 42 Y-STRs in the Chinese Han population, improving our understanding of Y-STRs and providing basic data of sequence variations for the application of Y-STRs., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)
- Published
- 2025
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4. Developmental validation of the STRSeqTyper122 kit for massively parallel sequencing of forensic STRs.
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Guo LL, Yuan JH, Zhang C, Zhao J, Yao YR, Guo KL, Meng Y, Ji AQ, Kang KL, and Wang L
- Subjects
- Humans, Amelogenin genetics, Reproducibility of Results, Sequence Analysis, DNA methods, Genotype, Polymerase Chain Reaction, Species Specificity, Male, Animals, DNA Degradation, Necrotic, Electrophoresis, Capillary, Female, Microsatellite Repeats, High-Throughput Nucleotide Sequencing, DNA Fingerprinting methods
- Abstract
Massively parallel sequencing allows for integrated genotyping of different types of forensic markers, which reduces DNA consumption, simplifies experimental processes, and provides additional sequence-based genetic information. The STRseqTyper122 kit genotypes 63 autosomal STRs, 16 X-STRs, 42 Y-STRs, and the Amelogenin locus. Amplicon sizes of 117 loci were below 300 bp. In this study, MiSeq FGx sequencing metrics for STRseqTyper122 were presented. The genotyping accuracy of this kit was examined by comparing to certified genotypes of NIST standard reference materials and results from five capillary electrophoresis-based kits. The sensitivity of STRseqTyper122 reached 125 pg, and > 80% of the loci were correctly called with 62.5 pg and 31.25 pg input genomic DNA. Repeatability, species specificity, and tolerance for DNA degradation and PCR inhibitors of this kit were also evaluated. STRseqTyper122 demonstrated reliable performance with routine case-work samples and provided a powerful tool for forensic applications., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)
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- 2024
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5. Boosting 2000-Fold Hypergolic Ignition Rate of Carborane by Substitutes Migration in Metal Clusters.
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Huang JH, Ji AQ, Wang ZY, Wang QY, and Zang SQ
- Abstract
Hypergolic propellants rely on fuel and oxidizer that spontaneously ignite upon contact, which fulfill a wide variety of mission roles in launch vehicles and spacecraft. Energy-rich carboranes are promising hypergolic fuels, but triggering their energy release is quite difficult because of their ultrastable aromatic cage structure. To steer the development of carborane-based high-performance hypergolic material, carboranylthiolated compounds integrated with atomically precise copper clusters are presented, yielding two distinct isomers, Cu
14B-S and Cu14C-S , both possessing similar ligands and core structures. With the migration of thiolate groups from carbon atoms to boron atoms, the ignition delay (ID) time shortened from 6870 to 3 ms when contacted with environmentally benign oxidizer high-test peroxide (HTP, with a H2 O2 concentration of 90%). The extraordinarily short ignition ID time of Cu14B-S is ranking among the best of HTP-active hypergolic materials. The experimental and theoretical findings reveal that benefitting from the migration of thiolate groups, Cu14B-S , characterized by an electron-rich metal kernel, displays enhanced reducibility and superior charge transfer efficiency. This results in exceptional activation rates with HTP, consequently inducing carborane combustion and the simultaneous release of energy. This fundamental investigation shed light on the development of advanced green hypergolic propulsion systems., (© 2024 The Authors. Advanced Science published by Wiley‐VCH GmbH.)- Published
- 2024
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6. Developmental validation of a high-resolution panel genotyping 639 Y-chromosome SNP and InDel markers and its evolutionary features in Chinese populations.
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Zhao GB, Miao L, Wang M, Yuan JH, Wei LH, Feng YS, Zhao J, Kang KL, Zhang C, Ji AQ, He G, and Wang L
- Subjects
- Humans, Genotype, Reproducibility of Results, Genetics, Population, Haplotypes, Chromosomes, Human, Y genetics, DNA, Polymorphism, Single Nucleotide, East Asian People
- Abstract
Uniparental-inherited haploid genetic marker of Y-chromosome single nucleotide polymorphisms (Y-SNP) have the power to provide a deep understanding of the human evolutionary past, forensic pedigree, and bio-geographical ancestry information. Several international cross-continental or regional Y-panels instead of Y-whole sequencing have recently been developed to promote Y-tools in forensic practice. However, panels based on next-generation sequencing (NGS) explicitly developed for Chinese populations are insufficient to represent the Chinese Y-chromosome genetic diversity and complex population structures, especially for Chinese-predominant haplogroup O. We developed and validated a 639-plex panel including 633 Y-SNPs and 6 Y-Insertion/deletions, which covered 573 Y haplogroups on the Y-DNA haplogroup tree. In this panel, subgroups from haplogroup O accounted for 64.4% of total inferable haplogroups. We reported the sequencing metrics of 354 libraries sequenced with this panel, with the average sequencing depth among 226 individuals being 3,741×. We illuminated the high level of concordance, accuracy, reproducibility, and specificity of the 639-plex panel and found that 610 loci were genotyped with as little as 0.03 ng of genomic DNA in the sensitivity test. 94.05% of the 639 loci were detectable in male-female mixed DNA samples with a mix ratio of 1:500. Nearly all of the loci were genotyped correctly when no more than 25 ng/μL tannic acid, 20 ng/μL humic acid, or 37.5 μM hematin was added to the amplification mixture. More than 80% of genotypes were obtained from degraded DNA samples with a degradation index of 11.76. Individuals from the same pedigree shared identical genotypes in 11 male pedigrees. Finally, we presented the complex evolutionary history of 183 northern Chinese Hans and six other Chinese populations, and found multiple founding lineages that contributed to the northern Han Chinese gene pool. The 639-plex panel proved an efficient tool for Chinese paternal studies and forensic applications., (© 2023. BioMed Central Ltd., part of Springer Nature.)
- Published
- 2023
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7. Application of Duplex Droplet Digital PCR Detection of miR-888 and miR-891a in Semen Identification.
- Author
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Wei SX, Chen HX, Hu S, Zhao YX, Shi HX, Wang Z, Li W, Ji AQ, and Sun QF
- Subjects
- Female, Humans, Real-Time Polymerase Chain Reaction methods, Saliva chemistry, Semen chemistry, Male, Body Fluids chemistry, MicroRNAs analysis
- Abstract
Objectives: To establish a system for simultaneous detection of miR-888 and miR-891a by droplet digital PCR (ddPCR), and to evaluate its application value in semen identification., Methods: The hydrolysis probes with different fluorescence modified reporter groups were designed to realize the detection of miR-888 and miR-891a by duplex ddPCR. A total of 75 samples of 5 body fluids (including peripheral blood, menstrual blood, semen, saliva and vaginal secretion) were detected. The difference analysis was conducted by Mann-Whitney U test. The semen differentiation ability of miR-888 and miR-891a was evaluated by ROC curve analysis and the optimal cut-off value was obtained., Results: There was no significant difference between the dual-plex assay and the single assay in this system. The detection sensitivity was up to 0.1 ng total RNA, and the intra- and inter-batch coefficients of variation were less than 15%. The expression levels of miR-888 and miR-891a detected by duplex ddPCR in semen were both higher than those in other body fluids. ROC curve analysis showed that the AUC of miR-888 was 0.976, the optimal cut-off value was 2.250 copies/μL, and the discrimination accuracy was 97.33%; the AUC of miR-891a was 1.000, the optimal cut-off value was 1.100 copies/μL, and the discrimination accuracy was 100%., Conclusions: In this study, a method for detection of miR-888 and miR-891a by duplex ddPCR was successfully established. The system has good stability and repeatability and can be used for semen identification. Both miR-888 and miR-891a have high ability to identify semen, and the discrimination accuracy of miR-891a is higher.
- Published
- 2022
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8. Evaluation of the MHSeqTyper47 kit for forensically challenging DNA samples.
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Feng YS, Zhang C, Chen QF, Wang Y, Kang KL, Zhao J, Ji AQ, Ye J, and Wang L
- Subjects
- Humans, Humic Substances analysis, Indigo Carmine, Microsatellite Repeats, DNA genetics, DNA analysis, Sequence Analysis, DNA, Polymorphism, Single Nucleotide, Heme, Tannins, DNA Fingerprinting methods, High-Throughput Nucleotide Sequencing methods
- Abstract
Microhaplotypes have been highly regarded for forensic mixture DNA deconvolution because they do not experience interference from stutters in the same way as short tandem repeat markers, and they tend to be more polymorphic than single nucleotide polymorphism markers. However, forensic microhaplotype kits have not been reported. The MHSeqTyper47 kit genotypes 47 microhaplotype loci. In this study, MiSeq FGx sequencing metrics for MHSeqTyper47 were presented, and the genotyping accuracy of this kit was examined. The sensitivity of MHSeqTyper47 reached 62.5 pg, and full genotyping results were obtained from degraded DNA samples with degradation indexes ≤ 3.00. Full genotypes were obtained in the presence of 100 ng/μL tannin, 50 μM heme, 25 ng/μL humic acid, and 1.25 μg/μL indigo dye. In DNA mixture studies, a minimum of 31 loci of the minor contributor were correctly genotyped at 1:99 or 99:1 mixing ratios, with the cumulative random matching probability of these loci reaching 4.54 × 10
-25 . Mixing ratios could be reliably predicted from two-donor DNA mixtures based on the loci with four called alleles. Taken together, these data showed that the MHSeqTyper47 kit was effective for forensically challenging DNA analysis., (Copyright © 2022 Elsevier B.V. All rights reserved.)- Published
- 2022
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9. Sequence polymorphisms of forensic Y-STRs revealed by a 68-plex in-house massively parallel sequencing panel.
- Author
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Yang KR, Miao L, Kang KL, Feng YS, Ji AQ, Zhang C, Guo LL, Gao Y, Wei MT, Ye J, Wu J, and Wang L
- Subjects
- Alleles, Chromosomes, Human, Y, Humans, Microsatellite Repeats, Polymorphism, Single Nucleotide, DNA Fingerprinting, High-Throughput Nucleotide Sequencing methods
- Abstract
Sequence polymorphisms of Y chromosome short tandem repeat (Y-STR) markers can be unveiled using next generation sequencing (NGS). Compared to capillary electrophoresis, NGS has the advantage of distinguishing between some alleles of the same length. Here, a 68-plex in-house panel covering 67 Y-STR loci and the sex determinant Amelogenin locus, was developed. The accuracy of this panel was 100% concordant with three standard reference samples. The sensitive was as low as 250 pg. A total of 466 length-based alleles, 806 sequence-based alleles, and 149 haplotypes were observed across 149 Chinese Han individuals. The total haplotype diversity and discrimination capacity was 1.0000 in detected samples. The DYS710 locus possessed the highest diversity by sequence among these Y-STRs, with 109 sequence-based alleles observed. Micro-variant alleles with the same length were observed in 39 Y-STR loci, with their sequence variations mainly attributable to repeat pattern variations. While the number of sequence-based alleles identified for DYS447, DYS449, DYS710, DYS720 and DYF387S1a/b was approximately three times that of their length-based alleles, flanking sequence variations were observed in 18 alleles. In addition, 201 sequence-based alleles in 42 loci were newly discovered. This significantly expanded the knowledge of human Y-STR sequence polymorphisms. Collectively, the 68-plex panel provided reliable Y-STR results as well as higher resolution for paternal lineage analysis., (Copyright © 2022 Elsevier B.V. All rights reserved.)
- Published
- 2022
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10. Screening of highly discriminative microhaplotype markers for individual identification and mixture deconvolution in East Asian populations.
- Author
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Yu WS, Feng YS, Kang KL, Zhang C, Ji AQ, Ye J, and Wang L
- Subjects
- DNA Fingerprinting methods, Gene Frequency, Genetics, Population, Haplotypes, Humans, Microsatellite Repeats, Polymorphism, Single Nucleotide, Forensic Genetics methods, High-Throughput Nucleotide Sequencing methods
- Abstract
Microhaplotypes are forensic genetic markers that combine single nucleotide polymorphisms in close proximity to one another. Highly discriminative microhaplotype markers could be superior to short tandem repeats (STRs) in DNA mixture deconvolution investigations because they are not interfered by stutters. In this study, the effective number of alleles (A
e ) and discrimination power values of microhaplotypes and STRs were compared. It was found that current microhaplotypes are not as discriminative as commonly used forensic STRs. Effective screening of highly discriminative microhaplotype markers were consequently conducted for East Asian populations. To satisfy different forensic application needs, four sets of microhaplotypes with Ae values ≥ 4 were screened for under different conditions that included marker length and physical distances between markers. While the four sets contained 703, 301, 337, and 190 microhaplotypes, their average Ae values reached 5.38, 6.30, 7.39, and 5.61, respectively. The microhaplotype group containing 301 markers (maximum length of 200 bp and separated by ≥ 5 million bases) was further investigated. The results showed that none of the 301 loci were exactly the same as those previously reported, while seven loci partially overlapped with known markers. While Ae values of 45 loci were ≥ 8, the Ae value of the mh17WL-008 locus reached a maximum of 93.57. Further analysis showed that the newly identified microhaplotype markers were also highly polymorphic in African, American, European, and South Asian populations., (Copyright © 2022 Elsevier B.V. All rights reserved.)- Published
- 2022
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11. Allelic diversity and forensic estimations of the Beijing Hans: Comparative data on sequence-based and length-based STRs.
- Author
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Chen QF, Kang KL, Song JJ, Zhang C, Yu ZL, Zhao GB, Wu H, Ji AQ, Ye J, and Wang L
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- China, DNA Fingerprinting, Genetics, Population, High-Throughput Nucleotide Sequencing, Humans, Polymerase Chain Reaction, Sequence Analysis, DNA, Alleles, Ethnicity genetics, Genetic Variation, Microsatellite Repeats
- Abstract
Short tandem repeat (STR) profiling is routinely used in forensic genetics. At present, STR analysis is mainly performed by capillary electrophoresis (CE). However, due to limitations associated with the CE method, STR genotyping has been limited to length polymorphisms only. Because next generation sequencing (NGS) is capable of providing full resolution STR data at the sequence variation level, the individual identification capability of forensic STR loci could be significantly improved. Here we present sequence-based STR data for the Beijing Han population in which 291 individuals were screened for 23 commonly used forensic STRs using the SeqTypeR24 CASE kit on an Ion PGM platform. In total, 234 length-based alleles and 356 sequence-based alleles, which included 22 novel core repeat sequences, were observed. The sequence-based matching probability and power of discrimination were superior to the length-based numbers for 16 loci bearing micro-variant alleles. Combined matching probability reached 8.2 × 10
-29 for 23 STR loci at the sequence level. This was two orders of magnitude higher than the parameters at length level and provides a data base for sequence-based STR casework applications., (Copyright © 2020 Elsevier B.V. All rights reserved.)- Published
- 2021
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12. Massively parallel sequencing of STRs using a 29-plex panel reveals stutter sequence characteristics.
- Author
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Wu H, Ji AC, Liu YC, Kang KL, Zhang C, Li ZW, Ji AQ, Ye J, Nie SJ, and Wang L
- Subjects
- Asian People genetics, China, Humans, Multiplex Polymerase Chain Reaction, Forensic Genetics methods, High-Throughput Nucleotide Sequencing methods, Microsatellite Repeats genetics, Sequence Analysis, DNA methods
- Abstract
Massively parallel sequencing of forensic STRs simultaneously provides length-based genotypes and core repeat sequences as well as flanking sequence variations. Here, we report primer sequences and concentrations of a next-generation sequencing (NGS)-based in-house panel covering 28 autosomal STR loci (CSF1PO, D1GATA113, D1S1627, D1S1656, D1S1677, D2S441, D2S1776, D3S3053, D5S818, D6S474, D6S1017, D6S1043, D8S1179, D9S2157, D10S1435, D11S4463, D13S317, D14S1434, D16S539, D18S51, D18S853, D20S482, D20S1082, D22S1045, FGA, TH01, TPOX, and vWA) and the sex determinant locus Amelogenin. Preliminary evaluation experiments showed that the panel yielded intralocus- and interlocus-balanced sequencing data with a sensitivity as low as 62.5 pg input DNA. A total of 203 individuals from Yunnan Bai population were sequenced with this panel. Comparative forensic genetic analyses showed that sequence-based matching probability of this 29-plex panel reached 2.37 × 10
-29 , which was 23 times lower than the length-based data. Compound stutter sequences of eight STRs were compared with parental alleles. For seven loci, repeat motif insertions or deletions occurred in the longest uninterrupted repeat sequences (LUS). However, LUS and non-LUS stutters co-existed in the locus D6S474 with different sequencing depth ratios. These results supplemented our current knowledge of forensic STR stutters, and provided a sound basis for DNA mixture deconvolution., (© 2020 Wiley-VCH GmbH.)- Published
- 2020
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13. Identification of Peripheral Blood and Menstrual Blood Based on the Expression Level of MicroRNAs and Discriminant Analysis.
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He HX, Ji AQ, Han N, Zhao YX, Hu S, Kong QL, Liu Y, and Sun QF
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- Discriminant Analysis, Female, Forensic Genetics, Semen, Body Fluids, MicroRNAs genetics
- Abstract
Abstract: Objective To construct a discriminant analysis model based on the differential expression of multiple microRNAs (miRNAs) in two kinds of blood samples (peripheral blood and menstrual blood) and three non-blood samples (saliva, semen and vaginal secretion), to form an identification solution for peripheral blood and menstrual blood. Methods Six kinds of miRNA (miR-451a, miR-144-3p, miR-144-5p, miR-214-3p, miR-203-3p and miR-205-5p) were selected from literature, the samples of five kinds of body fluids commonly seen in forensic practice (peripheral blood, menstrual blood, saliva, semen, vaginal secretion) were collected, then the samples were divided into training set and testing set and detected by SYBR Green real-time qPCR. A discriminant analysis model was set up based on the expression data of training set and the expression data of testing set was used to examine the accuracy of the model. Results A discriminant analysis statistical model that could distinguish blood samples from non-blood samples and distinguish peripheral blood samples from menstrual blood samples at the same time was successfully constructed. The identification accuracy of the model was over 99%. Conclusion This study provides a scientific and accurate identification strategy for forensic fluid identification of peripheral blood and menstrual blood samples and could be used in forensic practice., Competing Interests: The authors of this article and the planning committee members and staff have no relevant financial relationships with commercial interests to disclose., (Copyright© by the Editorial Department of Journal of Forensic Medicine.)
- Published
- 2020
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14. COVID-19 and early-stage lung cancer both featuring ground-glass opacities: a propensity score-matched study.
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Zhang YJ, Yang WJ, Liu D, Cao YQ, Zheng YY, Han YC, Jin RS, Han Y, Wang XY, Pan AS, Dai JY, Sun QF, Zhao FQ, Yang QY, Zhang JH, Liu SJ, Da Q, Guo W, Li CQ, Zhang WT, Wu H, Chen XS, Ji AQ, Xiang J, Chen K, Feng XJ, Zhang XF, Cao QQ, Qin L, Li J, Zhou M, Lu Y, Wang CF, Yan FH, Li HC, and Qu JM
- Abstract
Background: Radiological manifestations of coronavirus disease 2019 (COVID-19) featured ground-glass opacities (GGOs), especially in the early stage, which might create confusion in differential diagnosis with early lung cancer. We aimed to specify the radiological characteristics of COVID-19 and early lung cancer and to unveil the discrepancy between them., Methods: One hundred and fifty-seven COVID-19 patients and 374 early lung cancer patients from four hospitals in China were retrospectively enrolled. Epidemiological, clinical, radiological, and pathological characteristics were compared between the two groups using propensity score-matched (PSM) analysis., Results: COVID-19 patients had more distinct symptoms, tended to be younger (P<0.0001), male (P<0.0001), and had a higher body mass index (P=0.014). After 1:1 PSM, 121 matched pairs were identified. Regarding radiological characteristics, patients with a single lesion accounted for 17% in COVID-19 and 89% in lung cancer (P<0.0001). Most lesions were peripherally found in both groups. Lesions in COVID-19 involved more lobes (median 3.5 vs. 1; P<0.0001) and segments (median 6 vs. 1; P<0.0001) and tended to have multiple types (67%) with patchy form (54%). Early lung cancer was more likely to have a single type (92%) with oval form (66%). Also, COVID-19 and early lung cancer either had some distinctive features on computed tomography (CT) images., Conclusions: Both COVID-19 and early lung cancers showed GGOs, with similar but independent features. The imaging characteristics should be fully understood and combined with epidemiological history, pathogen detection, laboratory tests, short-term CT reexamination, and pathological results to aid differential diagnosis., Competing Interests: Conflicts of Interest: All authors have completed the ICMJE uniform disclosure form (available at http://dx.doi.org/10.21037/tlcr-20-892). Dr. YJZ reports grants from National Natural Science Foundation of China, during the conduct of the study. Dr. HCL reports grants from National Natural Science Foundation of China, grants from Shanghai Municipal Commission of Health and Family Planning Outstanding Academic Leaders Training Program, grants from Shanghai Municipal Education Commission - Gaofeng Clinical Medicine Grant, during the conduct of the study. The other authors have no conflicts of interest to declare., (2020 Translational Lung Cancer Research. All rights reserved.)
- Published
- 2020
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15. The ancestry inference of Chinese populations using 74-plex SNPs system.
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Liu Y, Sun CC, Ma M, Wang L, Zhao WT, Ma Q, Ji AQ, Liu J, and Li CX
- Subjects
- China, Gene Frequency, Genotype, Humans, Asian People genetics, Genetics, Population, Polymorphism, Single Nucleotide
- Abstract
A panel of ancestry informative SNPs (AISNPs) can be used to analyze the genetic components of a population and infer the ancestral origin of a DNA sample. Previously, we have selected a 74-AISNPs panel and used it to infer the ancestry of unknown individuals in the following ten geographical regions: Sub-Saharan Africa, North Africa, Europe, Pacific, Americas, Southwest Asia, South Asia, North Asia, East Asia and Southeast Asia. We have also established a 74-plex SNPs assay based on SEQUENOM system. In the present study, we genotyped 1371 individuals from 14 populations of China using this multiplex assay, and validated its ability to infer the ancestry in Chinese populations. Firstly, based on the reference database of 3628 individuals from 57 world populations, Structure and Heatmap were employed to evaluate the population differentiation capacity. The training data include 1654 individuals from 14 Chinese populations and 3 populations from 1K Genome, which are not included in the reference database. Then the likelihood ratio and ancestry components were analyzed for individual ancestry assignment using the 74-plex SNPs. The minimum amount of DNA required for a full genotype of the 74 SNPs is 1.5 ng, which is applicable for forensic analysis. The results demonstrate that this system can be used in differentiating the population from ten geographical regions. The ancestry inference accuracy for EUR/SAFR/AME population is 95.4%, 71.0% for East Asia and 66.4% for Southeast Asia respectively. The ancestry inference inclusive rate for EUR/SAFR/AME population is 1.06%, 17.9% for East Asia and 33.3% for Southeast Asia respectively. The results suggest that this method can be used in forensic investigations of criminal cases.
- Published
- 2020
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16. A 124-plex Microhaplotype Panel Based on Next-generation Sequencing Developed for Forensic Applications.
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Pang JB, Rao M, Chen QF, Ji AQ, Zhang C, Kang KL, Wu H, Ye J, Nie SJ, and Wang L
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- Alleles, Asian People genetics, DNA genetics, DNA Fingerprinting methods, Genotype, High-Throughput Nucleotide Sequencing methods, Humans, Linkage Disequilibrium genetics, Microsatellite Repeats genetics, Probability, Sequence Analysis, DNA methods, Forensic Genetics, Haplotypes genetics, Polymorphism, Single Nucleotide genetics
- Abstract
Microhaplotypes are an emerging type of forensic genetic marker that are expected to support multiple forensic applications. Here, we developed a 124-plex panel for microhaplotype genotyping based on next-generation sequencing (NGS). The panel yielded intralocus and interlocus balanced sequencing data with a high percentage of effective reads. A full genotype was determined with as little as 0.1 ng of input DNA. Parallel mixture experiments and in-depth comparative analyses were performed with capillary-electrophoresis-based short tandem repeat (STR) and NGS-based microhaplotype genotyping, and demonstrated that microhaplotypes are far superior to STRs for mixture deconvolution. DNA from Han Chinese individuals (n = 256) was sequenced with the 124-plex panel. In total, 514 alleles were observed, and the forensic genetic parameters were calculated. A comparison of the forensic parameters for the 20 microhaplotypes with the top A
e values in the 124-plex panel and 20 commonly used forensic STRs showed that these microhaplotypes were as effective as STRs in identifying individuals. A linkage disequilibrium analysis showed that 106 of the 124 microhaplotypes were independently hereditary, and the combined match probability for these 106 microhaplotypes was 5.23 × 10-66 . We conclude that this 124-plex microhaplotype panel is a powerful tool for forensic applications.- Published
- 2020
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17. [The effect of EDARV370A on facial and ear morphologies in Uyghur population].
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Li Y, Zhao WT, Li D, Tao XM, Xiong ZY, Liu J, Zhang W, Liu HB, Ji AQ, Tang K, Liu F, and Li CX
- Subjects
- Adolescent, Adult, Alleles, Asian People ethnology, China ethnology, Ear growth & development, Edar Receptor metabolism, Female, Humans, Male, Maxillofacial Development, Middle Aged, Phenotype, Young Adult, Asian People genetics, Ear anatomy & histology, Edar Receptor genetics, Face anatomy & histology, Mutation, Missense
- Abstract
The ectodysplasinA receptor gene (EDAR) plays an important role in the development of ectoderm. The derived G allele of its key missense variant EDARV370A is prevalent in East Asians and Americans, but rare in Africans and Europeans. This leads to distinct ectodermal-derived phenotypes between different continental groups, such as the straighter and thicker hair, more eccrine sweat glands, feminine smaller breasts, shovel incisors characteristic of East Asians. At present, we know little about the association between EDARV370A and facial and ear morphology characteristics. To better understand the effect of EDARV370A on craniofacial phenotypes, we systematically examined the association between EDARV370A and 136 facial quantitative phenotypes, one chin ordinal phenotype and six ear ordinal phenotypes in 715 Uyghurs. The quantitative phenotypes were derived by applying our automated landmark annotation method to facial 3D photos and the ordinal phenotypes were manually graded from facial 2D photos. The analysis identified significant association (P<0.05 after multiple testing correction) between EDARV370A and eight facial phenotypes, one chin phenotype and three ear morphology phenotypes. Our study thus elucidated the pleotropic effect of EDARV370A on craniofacial phenotypes in a European-Asian admixed Uyghur population.
- Published
- 2018
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18. Massively Parallel Sequencing of Forensic STRs Using the Ion Chef™ and the Ion S5™ XL Systems.
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Wang L, Chen M, Wu B, Liu YC, Zhang GF, Jiang L, Xu XL, Zhao XC, Ji AQ, and Ye J
- Subjects
- Alleles, DNA Fingerprinting, Forensic Genetics, Genotype, Humans, Reproducibility of Results, High-Throughput Nucleotide Sequencing instrumentation, Microsatellite Repeats, Sequence Analysis, DNA
- Abstract
Next-generation sequencing (NGS) has been used to genotype forensic short tandem repeat (STR) markers for individual identification and kinship analysis. STR data from several NGS platforms have been published, but forensic application trials using the Ion S5™ XL system have not been reported. In this work, we report sensitivity, reproducibility, mixture, simulated degradation, and casework sample data on the Ion Chef™ and S5™ XL systems using an early access 25-plex panel. Sensitivity experiments showed that over 97% of the alleles were detectable with down to 62 pg input of genomic DNA. In mixture studies, alleles from minor contributors were correctly assigned at 1:9 and 9:1 ratios. NGS successfully gave 12 full genotype results from 13 challenging casework samples, compared with five full results using the CE platform. In conclusion, the Ion Chef™ and the Ion S5™ XL systems provided an alternative and promising approach for forensic STR genotyping., (© 2018 American Academy of Forensic Sciences.)
- Published
- 2018
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19. Optimization and validation of analysis method based on 27-plex SNP panel for ancestry inference.
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Jiang L, Sun QF, Ma Q, Zhao WT, Liu J, Zhao L, Ji AQ, and Li CX
- Subjects
- Forensic Genetics, Humans, Genetics, Population, Polymorphism, Single Nucleotide
- Abstract
Anthropology generally divides the individuals into the East Asian Mongolia race, European Caucasian race and African Nigro race. The 27-plex single nucleotide polymorphism (SNP) panel for ancestry information has been established to differentiate samples from East Asian, European, African and admixture populations of East Asian and European origin by genotyping and ancestry inference. To infer ancestry for unknown individuals, we established an optimized analysis pipeline based on the likelihood ratio, ancestry component and individual ancestry assignment. Four samples from East Asian, European, African and admixture populations of East Asian and European origin were tested using the optimized analysis pipeline. Cross validation within basic referential database and validation of 1 010 test samples were both used to evaluate the inference process. The results showed that accuracy of the method was higher than 99% in East Asia, Europe, Africa and admixture populations. The inference method can characterize the ancestry information of DNA donors, and has important practical application values in the field of human molecular and forensic genetics.
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- 2017
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20. Mucosal cell isolation and analysis from cellular mixtures of three contributors.
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Xu C, Feng L, Yang F, Jia J, Ji AQ, Hu L, and Li CX
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- Blood, Cell Differentiation, Homicide, Humans, Polymerase Chain Reaction, Tobacco Products, Cell Separation, DNA isolation & purification, DNA Fingerprinting methods, Mouth Mucosa cytology
- Abstract
In forensic genetic analyses, mixtures of various biological materials are common samples. Micromanipulation, which is performed based on differences in cellular morphology, is an effective method for the isolation of cells from mixtures. In this study, mucosal cell was isolated from somatic cellular mixtures (blood and saliva) based on micromanipulation and a low volume-PCR (LV-PCR) platform. One hundred and twenty-six parallel LV-PCR processes were performed using an Identifiler(®) kit, with 107 reactions yielding single-source DNA profiles. Among them, 54 full profiles (50%) and 37 partial profiles (13-15 loci) were obtained. Based on the above method, we obtained a single-source DNA profile from a cigarette butt contaminated by two victims' blood in a murder case. The generated genotype was used to query a DNA database, and a perfect match was found., (© 2015 American Academy of Forensic Sciences.)
- Published
- 2015
- Full Text
- View/download PDF
21. Effects of early life exposure to ultraviolet C radiation on mitochondrial DNA content, transcription, ATP production, and oxygen consumption in developing Caenorhabditis elegans.
- Author
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Leung MC, Rooney JP, Ryde IT, Bernal AJ, Bess AS, Crocker TL, Ji AQ, and Meyer JN
- Subjects
- Adenosine Triphosphate metabolism, Animals, Caenorhabditis elegans genetics, Caenorhabditis elegans metabolism, DNA Copy Number Variations, DNA Damage, Gene Expression Profiling, Oligonucleotide Array Sequence Analysis, Oxygen Consumption, Transcription, Genetic radiation effects, Caenorhabditis elegans radiation effects, DNA, Mitochondrial radiation effects, Ultraviolet Rays
- Abstract
Background: Mitochondrial DNA (mtDNA) is present in multiple copies per cell and undergoes dramatic amplification during development. The impacts of mtDNA damage incurred early in development are not well understood, especially in the case of types of mtDNA damage that are irreparable, such as ultraviolet C radiation (UVC)-induced photodimers., Methods: We exposed first larval stage nematodes to UVC using a protocol that results in accumulated mtDNA damage but permits nuclear DNA (nDNA) repair. We then measured the transcriptional response, as well as oxygen consumption, ATP levels, and mtDNA copy number through adulthood., Results: Although the mtDNA damage persisted to the fourth larval stage, we observed only a relatively minor ~40% decrease in mtDNA copy number. Transcriptomic analysis suggested an inhibition of aerobic metabolism and developmental processes; mRNA levels for mtDNA-encoded genes were reduced ~50% at 3 hours post-treatment, but recovered and, in some cases, were upregulated at 24 and 48 hours post-exposure. The mtDNA polymerase γ was also induced ~8-fold at 48 hours post-exposure. Moreover, ATP levels and oxygen consumption were reduced in response to UVC exposure, with marked reductions of ~50% at the later larval stages., Conclusions: These results support the hypothesis that early life exposure to mitochondrial genotoxicants could result in mitochondrial dysfunction at later stages of life, thereby highlighting the potential health hazards of time-delayed effects of these genotoxicants in the environment.
- Published
- 2013
- Full Text
- View/download PDF
22. New cell separation technique for the isolation and analysis of cells from biological mixtures in forensic caseworks.
- Author
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Li CX, Wang GQ, Li WS, Huang JP, Ji AQ, and Hu L
- Subjects
- Cell Separation instrumentation, Crime, DNA analysis, Electrophoresis, Forensic Sciences instrumentation, Genetic Markers, Genotype, Humans, Cell Separation methods, Forensic Sciences methods, Homicide statistics & numerical data, Microsatellite Repeats genetics, Rape statistics & numerical data
- Abstract
Aim: To isolate mucosal cells of the perpetrator in a sexual assault case from a complex mixture of his mucosal cells and the victim's skin by micromanipulation prior to genomic analysis., Methods: To capture and analyze mucosal cells we used the micromanipulation with on-chip low volume polymerase chain reaction (LV-PCR). Consensus DNA profiles were generated from 5 replicate experiments., Results and Conclusions: We validated the use of micromanipulation with on-chip LV-PCR for genomic analysis of complex biological mixtures in a fatal rape case. The perpetrator's mucosal cells were captured from nipple swabs of the victim, and a single-source DNA profile was generated from cell mixtures. These data suggest that micromanipulation with on-chip LV-PCR is an effective forensic tool for the analysis of specific cells from complex samples.
- Published
- 2011
- Full Text
- View/download PDF
23. DNA profiling of spermatozoa by laser capture microdissection and low volume-PCR.
- Author
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Li CX, Han JP, Ren WY, Ji AQ, Xu XL, and Hu L
- Subjects
- Cell Separation, Female, Genetic Loci genetics, Genotype, Haploidy, Humans, Lab-On-A-Chip Devices, Male, Rape, Specimen Handling, Spermatozoa cytology, Tandem Repeat Sequences genetics, DNA Fingerprinting methods, Laser Capture Microdissection methods, Polymerase Chain Reaction methods, Spermatozoa metabolism
- Abstract
Genetic profiling of sperm from complex biological mixtures such as sexual assault casework samples requires isolation of a pure sperm population and the ability to analyze low abundant samples. Current standard procedure for sperm isolation includes preferential lysis of epithelial contaminants followed by collection of intact sperm by centrifugation. While effective for samples where sperm are abundant, this method is less effective when samples contain few spermatozoa. Laser capture microdissection (LCM) is a proven method for the isolation of cells biological mixtures, even when found in low abundance. Here, we demonstrate the efficacy of LCM coupled with on-chip low volume PCR (LV-PCR) for the isolation and genotyping of low abundance sperm samples. Our results indicate that this method can obtain complete profiles (13-16 loci) from as few as 15 sperm cells with 80% reproducibility, whereas at least 40 sperm cells are required to profile 13-16 loci by standard 'in-tube' PCR. Further, LCM and LV-PCR of a sexual assault casework sample generated a DNA genotype that was consistent with that of the suspect. This method was unable, however, to analyze a casework sample from a gang rape case in which two or more sperm contributors were in a mixed population. The results indicate that LCM and LV-PCR is sensitive and effective for genotyping sperm from sperm/epithelial cell mixtures when epithelial lysis may be insufficient due to low abundance of sperm; LCM and LV-PCR, however, failed in a casework sample when spermatozoa from multiple donors was present, indicating that further study is necessitated.
- Published
- 2011
- Full Text
- View/download PDF
24. [Transient therapeutic effect and safety of superficial needling therapy for treatment of periarthritis of shoulder].
- Author
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Lu J, Sun JH, Fu ZH, Yuan JH, Li J, and Ji AQ
- Subjects
- Acupuncture Therapy adverse effects, Adult, Aged, Female, Humans, Male, Middle Aged, Range of Motion, Articular, Acupuncture Therapy methods, Periarthritis therapy, Shoulder Joint, Shoulder Pain therapy
- Abstract
Objective: To scientifically assess effectiveness and safety of mono-use fu-needle., Methods: Sixty cases of periarthritis of shoulder were randomly divided into a fu-needle group and a routine acupuncture group. The fu-needle group were treated with fu-needle, and the routine acupuncture group were treated with a needle of 0.38 mm in diameter and 40 mm in length. The articular mobility of the most limited direction, soft tissue pain self-rating score and self-rating score of shoulder tenderness before and after treatment, stabbing times and degree at inserting the needle, scattering and during retention of the needle, and bleeding at withdrawing the needle were compared in the two groups., Results: The fu-needle group was better than the routine acupuncture group in improvement of mobility-related pain, tenderness, and the articular mobility of the most limited direction, indicating that the transient effect in the fu-needle group was better than the routine acupuncture group, and the stabbing times and degree at insertion of the needle were less than the routine acupuncture group. And there was no significant difference between the two groups in stabbing times and degree at scattering and retaining the needle and bleeding times in withdrawing the needle., Conclusion: The superficial needling therapy with mono-use fu-needle is more effective and more safe than the routine acupuncture for treatment of periarthritis of shoulder.
- Published
- 2008
25. [Study of DNA identification in burned bones].
- Author
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Ye J, Ji AQ, and Zhao XC
- Subjects
- Burns metabolism, Cetrimonium Compounds, Female, Humans, Male, Polymerase Chain Reaction methods, Sensitivity and Specificity, Tandem Repeat Sequences, Time Factors, Bone and Bones chemistry, DNA isolation & purification, DNA Fingerprinting methods, Forensic Medicine methods
- Abstract
Objective: For the purpose of solving a problems of DNA testing of burned bones., Methods: We present a novel strategy to obtain DNA from burned bones based on the use of cetyltrimethylammonium bromide (CTAB) lysis buffer and isoamyl alcohol-chlorophorm extraction with subsequent DNA purification using the DNA IQ System., Results: The methods were found to be effective in removing the PCR inhibitors from the burned bone. Then the extracted DNA was successfully genotyped by using the florescence labeling STR multiplex method., Conclusion: The results of this research will assist forensic scientists in the identification of DNA from victims whose bodies underwent significant trauma or burning, precluding the utilization of traditional forensic DNA identification techniques.
- Published
- 2004
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