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Guo F, Jing G, Lang Y, Liu Z, Yu S. Simultaneous sequencing of 102 Y-STRs on Ion Torrent ™ GeneStudio ™ S5 System. Forensic Sci Int Genet 2024; 71:103059. [PMID: 38749212 DOI: 10.1016/j.fsigen.2024.103059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 05/02/2024] [Accepted: 05/05/2024] [Indexed: 06/18/2024]
Abstract
The Precision ID NGS System from Thermo Fisher Scientific is a mainstream next-generation sequencing (NGS) platform used in forensic laboratories to detect almost all commonly used forensic markers, except for Y-chromosomal short tandem repeats (Y-STRs). This study aimed to: 1) develop a Y-STR panel compatible with the automatic workflow of the NGS system using Ion AmpliSeq Technology, 2) evaluate the panel performance following the SWGDAM guidelines, and 3) explore the possibility of using a combination workflow to detect autosomal STRs and Y-STRs (AY-STR NGS workflow). The GrandFiler Y-STR Panel was successfully designed using the 'separating' and 'merging' strategies, including 102 Y-STRs and Amelogenin with an average amplicon length of 133 bp. It is a mega Y-STR multiplex system in which up to 16 samples can be sequenced simultaneously on an Ion 530 ™ Chip. Developmental validation studies of the performance of the NGS platform, species specificity, reproducibility, concordance, sensitivity, degraded samples, case-type samples, and mixtures were conducted to unequivocally determine whether the GrandFiler Y-STR Panel is suitable for real scenarios. The newly developed Y-STR panel showed compelling run metrics and NGS performance, including 92.47% bases with ≥ Q20, 91.80% effective reads, 2106 × depth of coverage (DoC), and 97.09% inter-locus balance. Additionally, it showed high specificity for human males and 99.40% methodological and bioinformatical concordance, generated complete profiles at ≥ 0.1 ng input DNA, and recovered more genetic information from severely degraded and diverse case samples. Although the outcome when used on mixtures was not as expected, more genetic information was obtained compared to that from capillary electrophoresis (CE) methods. The AY-STR NGS workflow was established by combining the GrandFiler Y-STR Panel with the Precision ID GlobalFiler ™ NGS STR Panel v2 at a 2:1 concentration ratio. The combination workflow on NGS performance, reproducibility, concordance, and sensitivity was as stable as the single Y-STR NGS workflow, providing more options for forensic scientists when dealing with different case scenarios. Overall, the GrandFiler Y-STR Panel was confirmed as the first to effectively detect a large number of Y-STR markers on the Precision ID NGS System, which is compatible with 51 Y-STRs in commercial CE kits and 51 Y-STRs in commercial NGS kits and the STRBase. The panel is as robust, reliable, and sensitive as current CE/NGS kits, and is suitable for solving real cases, especially for severely degraded samples (degradation index > 10).
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Affiliation(s)
- Fei Guo
- Shenyang Medical College, Shenyang, Liaoning 110034, PR China; Key Laboratory of Human Ethnic Specificity and Phenomics of Critical Illness in Liaoning Province, Shenyang, Liaoning 110034, PR China; Key Laboratory of Phenomics in Shenyang City, Shenyang, Liaoning 110034, PR China.
| | - Guangxin Jing
- Heyuan Public Security Forensic Science Center, Heyuan, Guangdong 517000, PR China
| | - Yubo Lang
- School of Public Security Information Technology and Intelligence, Criminal Investigation Police University of China, Shenyang, Liaoning 110854, PR China
| | - Ze Liu
- DNA Laboratory of Forensic Science Center, Shenyang Public Security Bureau, Shenyang, Liaoning 110002, PR China
| | - Shaobo Yu
- DNA Laboratory of Forensic Science Center, Shenyang Public Security Bureau, Shenyang, Liaoning 110002, PR China.
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2
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Fu D, Adnan A, Yao J, Aldayan NH, Wang CC, Hongyi C. Unraveling the paternal genetic structure and forensic traits of the Hui population in Liaoning Province, China using Y-chromosome analysis. BMC Genomics 2023; 24:691. [PMID: 37978341 PMCID: PMC10655310 DOI: 10.1186/s12864-023-09774-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 10/30/2023] [Indexed: 11/19/2023] Open
Abstract
The Hui people are the second-largest ethnic minority in China, and they are distributed throughout the country. A previous study explored the paternal genetic structure of the Hui population in nine different regions of China, but it overlooked the Liaoning province. In this study, we examined the paternal genetic makeup and forensic traits of the Hui population in Liaoning province by analyzing 157 Y-chromosome single nucleotide polymorphisms (Y-SNPs) and 26 short tandem repeats (Y-STRs). We successfully genotyped 282 unrelated male individuals from the Hui population of Liaoning province using the SNaPshot® single base extension assay and Goldeneye™ Y26 system kit (PEOPLESPOT R&D, Beijing, China). The results revealed high haplotypic diversity (0.9998) and identified 46 terminal haplogroups for the Hui population. Additional analyses, such as heat maps, principal component analysis (PCA), genetic distance (FST), Multidimensional scaling (MDS) analysis, and median-joining network (MJ) analysis, showed that the Hui population could be classified into three groups: Northwest Hui populations (NWH), including Liaoning, Xinjiang, Qinghai, Gansu, Ningxia, Shaanxi, and Henan; Hui populations from Sichuan and Shandong (SSH); and Yunnan Hui populations (YNH). Pairwise genetic distance (Rst) comparisons with other Chinese populations revealed that the Hui population displayed genetic affinity with the Han population. The comprehensive understanding of the Hui population in Liaoning province, explored by Y-SNPs and Y-STRs, can be utilized to interpret their genetic structure and enhance the accuracy of forensic databases.
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Affiliation(s)
- Dazhi Fu
- First Affiliated Hospital of China Medical University, 155 Heping District, Shenyang, 110001, China
| | - Atif Adnan
- Department of Forensic Sciences, Collage of Criminal Justice, Naif Arab University for Security Sciences, Riyadh, Saudi Arabia.
| | - Jun Yao
- Department of Forensic Biology and Genetics, School of Forensic Medicine, China Medical University, Shenyang, 110001, China
| | - Noura H Aldayan
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam Ibn Abdulaziz University, Al-Kharj, 16273, Saudi Arabia
| | - Chuan-Chao Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, Fujian, People's Republic of China.
| | - Cao Hongyi
- First Affiliated Hospital of China Medical University, 155 Heping District, Shenyang, 110001, China.
- Department of Pathology, School of Basic Medical Sciences, China Medical University, Shenyang, 110001, China.
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Liu Z, Long G, Lang Y, Liu D, Zhang B, Yu S, Guo F. Sequence-based mutation patterns at 41 Y chromosomal STRs in 2 548 father-son pairs. Forensic Sci Res 2023; 8:152-162. [PMID: 37621447 PMCID: PMC10445670 DOI: 10.1093/fsr/owad016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 06/16/2023] [Indexed: 08/26/2023] Open
Abstract
A total of 2 548 unrelated healthy father-son pairs from a Northern Han Chinese population were genotyped at 41 Y chromosomal short tandem repeat (Y-STRs) including DYS19, DYS388, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS444, DYS447, DYS448, DYS449, DYS456, DYS458, DYS460, DYS481, DYS518, DYS522, DYS549, DYS533, DYS557, DYS570, DYS576, DYS593, DYS596, DYS627, DYS635, DYS643, DYS645, Y-GATA-H4, DYF387S1a/b, DYF404S1a/b, DYS385a/b, and DYS527a/b. In 2 548 father samples, 2 387 unique haplotypes were detected with the haplotype diversity and discrimination capacity values of 0.999 956 608 and 0.96 741 007. The average gene diversity (GD) value was 0.6934 with a range from 0.1051 at DYS645 to 0.9657 at DYS385a/b. When comparing alleles at 24 overlapped Y-STRs between the ForenSeq™ deoxyribonucleic acid (DNA) Signature Prep Kit on the MiSeq FGx® Forensic Genomics System and the Goldeneye® DNA ID Y Plus Kit on the Applied Biosystems™ 3730 DNA Analyzer from 308 father samples in mutational pairs, 258 alleles were detected by massively parallel sequencing (MPS) typing including 156 length-based alleles that could be obtained by capillary electrophoresis (CE) typing, 95 repeat region (RR) variant alleles and seven flanking region variant alleles. Hereof, we found 16 novel RR variant alleles and firstly identified two SNPs (rs2016239814 at DYS19 and rs2089968964 at DYS448) and one 4-bp deletion (rs2053269960 at DYS439) that had been validated by the Database of Short Genetic Variation. Sanger sequencing or MPS was employed to confirm 356 mutations from 104 468 allele transfers generated from CE, where 96.63% resulted in one-step mutations, 2.25% in two-step, and 1.12% in multi-step, and the overall ratio of repeat gains versus losses was balanced (173 gains vs. 183 losses). In 308 father-son pairs, 268 pairs occurred mutations at a single locus, 33 pairs at two loci, six pairs at three loci, and one pair at four loci. The average Y-STR mutation rate at 41 Y-STRs was ⁓3.4 × 10-3 (95% confidence intervals: 3.1 × 10-3-3.8 × 10-3). The mutation rates at DYS576 and DYS627 were higher than 1 × 10-2 in Northern Han Chinese, whilst the mutation rates at DYF387S1a/b, DYF404S1a/b, DYS449, DYS518, and DYS570 were lower than initially defined. In this study, the classical molecular factors (the longer STR region, the more complex motif and the order father) were confirmed to drive Y-STR mutation rates increased, but the length of repeat unit did not conform to the convention. Lastly, the interactive graphical and installable StatsY was developed to facilitate forensic scientists to automatically calculate allele and haplotype frequencies, forensic parameters, and mutation rates at Y-STRs. Key points 308 of 2 548 father-son pairs from Northern Han Chinese occurred at least one mutation(s) across 41 Y-STRs.Sanger sequencing or MPS was employed to confirm those mutations generated from CE.The longer STR region, the more complex motif and the order father drove Y-STR mutation rates increased.StatsY was developed to calculate allele and haplotype frequencies, forensic parameters and mutation rates at Y-STRs.
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Affiliation(s)
- Ze Liu
- DNA Laboratory of Forensic Science Center, Shenyang Public Security Bureau, Shenyang, China
| | - Guannan Long
- DNA Laboratory of Forensic Science Center, Shenyang Public Security Bureau, Shenyang, China
| | - Yubo Lang
- School of Public Security Information Technology and Intelligence, Criminal Investigation Police University of China, Shenyang, China
| | - Dahua Liu
- Department of Forensic Medicine, Jinzhou Medical University, Jinzhou, China
| | - Biao Zhang
- DNA Laboratory of Forensic Science Center, Shenyang Public Security Bureau, Shenyang, China
| | - Shaobo Yu
- DNA Laboratory of Forensic Science Center, Shenyang Public Security Bureau, Shenyang, China
| | - Fei Guo
- School of Forensic Science and Technology, Criminal Investigation Police University of China, Shenyang, China
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Zhou Y, Cui W, Wu B, Zhu B. Development and validation of a new multiplex Y-STR panel designed to increase the power of discrimination. Electrophoresis 2022; 43:1899-1910. [PMID: 35856743 DOI: 10.1002/elps.202100313] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 03/28/2022] [Accepted: 07/08/2022] [Indexed: 12/14/2022]
Abstract
In an attempt to increase the discrimination capacity (DC) and reduce the adventitious match probability, a 6-dye multiplex Y-chromosomal short tandem repeat (Y-STR) panel named Y34plex was constructed that combined 25 Y-chromosomal markers (DYS456, DYS627, DYS390, DYS570, DYS635, DYS385a/b, DYS448, DYS437, DYS533, DYS449, DYS481, DYS392, DYS391, DYS389I, DYS460, YGATAH4, DYS438, DYS389II, DYS19, DYS458, DYF387S1a/b, DYS439, DYS393, DYS576, and DYS518) in widely used commercial kits, with nine highly polymorphic Y-STR loci (DYS557, DYS527a/b, DYS593, DYS444, DYS596, DYS643, DYS447, DYS549, and DYS645). The Y34plex is a promising type system to distinguish both unrelated and related male individuals due to the incorporation of rapidly mutated Y-STR loci. A validation study of the Y34plex was performed and followed the guidelines of the Scientific Working Group on DNA analysis methods. Results show that full Y-STR profiles were obtained from male/female DNA mixtures with 125 pg of male DNA in the presence of 50 ng of female DNA. The ability to tolerate polymerase chain reaction inhibitors commonly contained in forensic casework samples demonstrated the applicability and robustness of the Y34plex. Compared with the Yfiler Plus kit, the novel panel showed an increased power of discrimination in Chinese Wuxi Han population (n = 434). The overall haplotype diversity of the Y34plex was 0.999606, whereas DC value was 0.956221, which is suitable for use on forensic paternal investigation.
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Affiliation(s)
- Yongsong Zhou
- Shenzhen Stomatology Hospital (Pingshan), Southern Medical University, Shenzhen, P. R. China.,Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Wei Cui
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Buling Wu
- Shenzhen Stomatology Hospital (Pingshan), Southern Medical University, Shenzhen, P. R. China
| | - Bofeng Zhu
- Shenzhen Stomatology Hospital (Pingshan), Southern Medical University, Shenzhen, P. R. China.,Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China.,Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, P. R. China
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5
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Adnan A, Rakha A, Nazir S, Alghafri R, Hassan Q, Wang CC, Lu J. Forensic features and genetic legacy of the Baloch population of Pakistan and the Hazara population across Durand line revealed by Y-chromosomal STRs. Int J Legal Med 2021; 135:1777-1784. [PMID: 33818632 DOI: 10.1007/s00414-021-02591-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 03/26/2021] [Indexed: 11/27/2022]
Abstract
The Hazara population across Durand line has experienced extensive interaction with Central Asian and East Asian populations. Hazara individuals have typical Mongolian facial appearances and they called themselves descendants of Genghis Khan's army. The people who speak the Balochi language are called Baloch. Previously, a worldwide analysis of Y-chromosomal haplotype diversity for rapidly mutating (RM) Y-STRs and with PowerPlex Y23 System (Promega Corporation Madison, USA) kit was created with collaborative efforts, but Baloch and Hazara population from Pakistan and Hazara population from Afghanistan were missing. In the current study, Yfiler Plus PCR Amplification Kit loci were examined in 260 unrelated Hazara individuals from Afghanistan, 153 Hazara individuals, and 111 Balochi individuals from Baluchistan Pakistan. For the Hazara population from Afghanistan and Pakistan overall, 380 different haplotypes were observed on these 27 Y-STR loci, gene diversities ranged from 0.51288 (DYS389I) to 0.9257 (DYF387S1), and haplotype diversity was 0.9992. For the Baloch population, every individual was unique at 27 Y-STR loci; gene diversity ranged from 0.5718 (DYS460) to 0.9371(DYF387S1). Twelve haplotypes were shared between 178 individuals, while only two haplotypes among these twelve were shared between 87 individuals in Hazara populations. Rst and Fst pairwise genetic distance analyses, multidimensional scaling plot, neighbor-joining tree, linear discriminatory analysis, and median-joining network were performed, which shed light on the history of Hazara and Baloch populations. The results of our study showed that the Yfiler Plus PCR Amplification Kit marker set provided substantially stronger discriminatory power in the Baloch population of Pakistan and the Hazara population across the Durand line.
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Affiliation(s)
- Atif Adnan
- Department of Human Anatomy, School of Basic Medicine, China Medical University, Shenyang, Liaoning, 110122, People's Republic of China.
| | - Allah Rakha
- Department of Forensic Sciences, University of Health Sciences Lahore, Lahore, 54600, Pakistan
| | - Shahid Nazir
- Department of Forensic Sciences, University of Health Sciences Lahore, Lahore, 54600, Pakistan
| | - Rashed Alghafri
- General Department of Forensic Sciences and Criminology, Dubai Police General Head Quarters, Dubai, United Arab Emirates
| | - Qudsia Hassan
- Department of Forensic Medicine & Toxicology, Ziauddin Medical College Clifton, Karachi, Pakistan
| | - Chuan-Chao Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, 361005, People's Republic of China
| | - Jie Lu
- Department of Human Anatomy, School of Basic Medicine, China Medical University, Shenyang, Liaoning, 110122, People's Republic of China.
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6
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Zhao Y, Yao X, Li Y, Chen C, Guo D, Jiao Z, Yang Z, Yu Z, Ma W, Zhang Q. Developmental validation of the Microreader™ Y Prime Plus ID System: An advanced Y-STR 38-plex system for forensic applications. Sci Justice 2021; 61:260-270. [PMID: 33985674 DOI: 10.1016/j.scijus.2021.01.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 12/24/2020] [Accepted: 01/23/2021] [Indexed: 11/16/2022]
Abstract
Y-STR is widely used in sexual assaults and familial searches of suspects. Here, we reported a novel 38-plex STR genotyping system designed for forensic applications. Microreader™ Y Prime Plus ID System (YPP) amplifies 38 loci in one reaction, including 29 loci from commonly used Yfiler® Plus PCR Amplification Kit & PowerPlex® Y23 System (DYS393, DYS570, DYS19, DYS392, DYS549, Y GATA H4, DYS460, DYS458, DYS481, DYS635, DYS448, DYS533, DYS449, DYS456, DYS389I, DYS390, DYS389Ⅱ, DYS438, DYS391, DYS439, DYS437, DYS385a/b, DYS643, DYS518, DYS576, DYF387S1a/b, and DYS627), 6 commonly used loci for the Y-STR database (DYS444, DYS447, DYS596, DYF404a/b, DYS527a/b, DYS557) and one Y-indel specific for the Chinese population. YPP is designed for different types of samples, such as blood card and swabs. In this work, YPP was validated following SWGDAM guidelines (2016) and guidelines from Ministry of Public Security of the People's Republic of China, including PCR-based, sensitivity, accuracy and precision, mixture, stability and inhibitor, and species specificity. The results indicate that the Microreader™ Y Prime Plus ID System is a powerful identification kit designed for forensic databases.
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Affiliation(s)
- Yi Zhao
- Forensic Science Service of the Beijing Public Security Bureau, 100192 Beijing, China
| | - Xiaojuan Yao
- Forensic Science Service of the Xinzhou Public Security Bureau, 034000 Shanxi, China
| | - Yifan Li
- Beijing Microread Genetics, 100045 Beijing, China
| | - Chengjian Chen
- Forensic Science Service of the Beijing Public Security Bureau, 100192 Beijing, China
| | - Dan Guo
- Beijing Microread Genetics, 100045 Beijing, China
| | - Zhangping Jiao
- Forensic Science Service of the Beijing Public Security Bureau, 100192 Beijing, China
| | - Zhipan Yang
- Beijing Microread Genetics, 100045 Beijing, China
| | - Zailiang Yu
- Beijing Microread Genetics, 100045 Beijing, China.
| | - Wanshan Ma
- Suzhou Microread Genetics, 215163 Suzhou, China.
| | - Qingxia Zhang
- Forensic Science Service of the Beijing Public Security Bureau, 100192 Beijing, China.
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Mateen RM, Sabar MF, Hussain S, Parveen R, Hussain M. Familial DNA analysis and criminal investigation: Usage, downsides and privacy concerns. Forensic Sci Int 2020; 318:110576. [PMID: 33234348 DOI: 10.1016/j.forsciint.2020.110576] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/07/2020] [Accepted: 11/01/2020] [Indexed: 02/08/2023]
Abstract
Since the discovery of Deoxyribonucleic acid (DNA) capability in forensic investigation, it has been an important part of the criminal justice system. In most criminal cases DNA profile originating from evidence sample collected from the crime scene is compared with the DNA profile from the reference sample. However, when a reference sample is not available for comparison, familial DNA analysis can provide important investigation leads in a criminal investigation process by identifying an individual. Moreover, this analysis is also proving effective in the identification of ethnicity and ancestry of an individual. A number of different methodologies and software are being used for familial DNA analysis. This review describes the importance of familial DNA analysis, methodologies used for familial DNA searching and identification, and its advantages in forensic. Moreover, ethical, legal and social issues associated with familial DNA analysis have also been discussed along with future directions for the proper implementation of this technology.
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Affiliation(s)
- Rana Muhammad Mateen
- Center for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan.
| | | | - Safdar Hussain
- Center for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan.
| | - Rukhsana Parveen
- Center for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan.
| | - Manzoor Hussain
- Center for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan.
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Oldoni F, Podini D. Forensic molecular biomarkers for mixture analysis. Forensic Sci Int Genet 2019; 41:107-119. [DOI: 10.1016/j.fsigen.2019.04.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 03/06/2019] [Accepted: 04/17/2019] [Indexed: 01/10/2023]
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9
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A comprehensive mutation study in wide deep-rooted R1b Serbian pedigree: mutation rates and male relative differentiation capacity of 36 Y-STR markers. Forensic Sci Int Genet 2019; 41:137-144. [DOI: 10.1016/j.fsigen.2019.04.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 04/05/2019] [Accepted: 04/29/2019] [Indexed: 11/23/2022]
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10
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Khan K, Siddiqi MH, Abbas M, Almas M, Idrees M. Forensic applications of Y chromosomal properties. Leg Med (Tokyo) 2017; 26:86-91. [DOI: 10.1016/j.legalmed.2017.04.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 04/08/2017] [Accepted: 04/15/2017] [Indexed: 01/17/2023]
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Kayser M. Forensic use of Y-chromosome DNA: a general overview. Hum Genet 2017; 136:621-635. [PMID: 28315050 PMCID: PMC5418305 DOI: 10.1007/s00439-017-1776-9] [Citation(s) in RCA: 185] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Accepted: 03/08/2017] [Indexed: 11/19/2022]
Abstract
The male-specific part of the human Y chromosome is widely used in forensic DNA analysis, particularly in cases where standard autosomal DNA profiling is not informative. A Y-chromosomal gene fragment is applied for inferring the biological sex of a crime scene trace donor. Haplotypes composed of Y-chromosomal short tandem repeat polymorphisms (Y-STRs) are used to characterise paternal lineages of unknown male trace donors, especially suitable when males and females have contributed to the same trace, such as in sexual assault cases. Y-STR haplotyping applied in crime scene investigation can (i) exclude male suspects from involvement in crime, (ii) identify the paternal lineage of male perpetrators, (iii) highlight multiple male contributors to a trace, and (iv) provide investigative leads for finding unknown male perpetrators. Y-STR haplotype analysis is employed in paternity disputes of male offspring and other types of paternal kinship testing, including historical cases, as well as in special cases of missing person and disaster victim identification involving men. Y-chromosome polymorphisms are applied for inferring the paternal bio-geographic ancestry of unknown trace donors or missing persons, in cases where autosomal DNA profiling is uninformative. In this overview, all different forensic applications of Y-chromosome DNA are described. To illustrate the necessity of forensic Y-chromosome analysis, the investigation of a prominent murder case is described, which initiated two changes in national forensic DNA legislation both covering Y-chromosome use, and was finally solved via an innovative Y-STR dragnet involving thousands of volunteers after 14 years. Finally, expectations for the future of forensic Y-chromosome DNA analysis are discussed.
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Affiliation(s)
- Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, PO Box 2040, 3000 CA, Rotterdam, The Netherlands.
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12
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Adnan A, Ralf A, Rakha A, Kousouri N, Kayser M. Improving empirical evidence on differentiating closely related men with RM Y-STRs: A comprehensive pedigree study from Pakistan. Forensic Sci Int Genet 2016; 25:45-51. [DOI: 10.1016/j.fsigen.2016.07.005] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 06/07/2016] [Accepted: 07/07/2016] [Indexed: 11/17/2022]
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13
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Turrina S, Caratti S, Ferrian M, De Leo D. Are rapidly mutating Y-short tandem repeats useful to resolve a lineage? Expanding mutability data on distant male relationships. Transfusion 2015; 56:533-8. [DOI: 10.1111/trf.13368] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 07/24/2015] [Accepted: 08/31/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Stefania Turrina
- Department of Public Health and Community Medicine; Institute of Legal Medicine, Forensic Genetic Laboratory, University of Verona; Verona Italy
| | - Stefano Caratti
- Department of Public Health and Community Medicine; Institute of Legal Medicine, Forensic Genetic Laboratory, University of Verona; Verona Italy
| | - Melissa Ferrian
- Department of Public Health and Community Medicine; Institute of Legal Medicine, Forensic Genetic Laboratory, University of Verona; Verona Italy
| | - Domenico De Leo
- Department of Public Health and Community Medicine; Institute of Legal Medicine, Forensic Genetic Laboratory, University of Verona; Verona Italy
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14
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Abstract
Determing the sex of a give DNA sample can provide criminal investigators with useful intelligence and can aid the identification of missing persons and disaster victims. Polymerase chain reaction-based systems that amplify regions of the am elogenin gene have become the method of choice for sex determination of biological samples. This system can, however, result in false female sex designation when mutations affect primer binding sites of the Y homolog of this target sequence, causing drop out of the Y amplification product. Erroneous sex determination could have drastic consequences when applied to forensic situations by misdirecting investigators or hindering the identification of deceased individuals. Current methods of sex determination are described and possible alternative approaches to avoid errors are discussed.
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Affiliation(s)
- Eleanor A M Graham
- Forensic Pathology Unit, University of Leicester, Robert Kilpatrick Building Leicester Royal Infirmary, LE2 7LX, Leicester, UK,
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15
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Ballantyne KN, Keerl V, Wollstein A, Choi Y, Zuniga SB, Ralf A, Vermeulen M, de Knijff P, Kayser M. A new future of forensic Y-chromosome analysis: Rapidly mutating Y-STRs for differentiating male relatives and paternal lineages. Forensic Sci Int Genet 2012; 6:208-18. [DOI: 10.1016/j.fsigen.2011.04.017] [Citation(s) in RCA: 148] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2011] [Revised: 04/08/2011] [Accepted: 04/27/2011] [Indexed: 10/18/2022]
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16
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Hanson E, Maybruck JL, Ballantyne J, Fuerst PA. Performance evaluation and optimization of multiplex PCRs for the highly discriminating OSU 10-locus set Y-STRs. J Forensic Sci 2011; 57:52-9. [PMID: 21939439 DOI: 10.1111/j.1556-4029.2011.01910.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In a previous study, a new set of Y-chromosome short tandem repeats, the OSU 10-locus set (MPM1 and MPM2), was shown to have a higher discrimination power when evaluated against the 10 SWGDAM loci on a common population panel. Here, we describe the optimization of the multiplex reactions using dye-labeled primers followed by performance evaluations. The loci exhibited high precision, human male specificity, reliability in different body fluids, high sensitivity, stability, and the ability to amplify nonprobative casework and mixture samples. Stutter for the all of the loci, with the exception of the highly polymorphic locus DYS688, was similar to that observed for autosomal loci. The results of the performance evaluations reinforced the utility of these loci.
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Affiliation(s)
- Erin Hanson
- Graduate Program in Biomolecular Science, University of Central Florida, Orlando, FL 32816-2366, USA
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17
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Batini C, Ferri G, Destro-Bisol G, Brisighelli F, Luiselli D, Sanchez-Diz P, Rocha J, Simonson T, Brehm A, Montano V, Elwali NE, Spedini G, D'Amato ME, Myres N, Ebbesen P, Comas D, Capelli C. Signatures of the Preagricultural Peopling Processes in Sub-Saharan Africa as Revealed by the Phylogeography of Early Y Chromosome Lineages. Mol Biol Evol 2011; 28:2603-13. [DOI: 10.1093/molbev/msr089] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
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18
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van Oven M, Vermeulen M, Kayser M. Multiplex genotyping system for efficient inference of matrilineal genetic ancestry with continental resolution. INVESTIGATIVE GENETICS 2011; 2:6. [PMID: 21429198 PMCID: PMC3078086 DOI: 10.1186/2041-2223-2-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Accepted: 03/23/2011] [Indexed: 12/17/2022]
Abstract
Background In recent years, phylogeographic studies have produced detailed knowledge on the worldwide distribution of mitochondrial DNA (mtDNA) variants, linking specific clades of the mtDNA phylogeny with certain geographic areas. However, a multiplex genotyping system for the detection of the mtDNA haplogroups of major continental distribution that would be desirable for efficient DNA-based bio-geographic ancestry testing in various applications is still missing. Results Three multiplex genotyping assays, based on single-base primer extension technology, were developed targeting a total of 36 coding-region mtDNA variants that together differentiate 43 matrilineal haplo-/paragroups. These include the major diagnostic haplogroups for Africa, Western Eurasia, Eastern Eurasia and Native America. The assays show high sensitivity with respect to the amount of template DNA: successful amplification could still be obtained when using as little as 4 pg of genomic DNA and the technology is suitable for medium-throughput analyses. Conclusions We introduce an efficient and sensitive multiplex genotyping system for bio-geographic ancestry inference from mtDNA that provides resolution on the continental level. The method can be applied in forensics, to aid tracing unknown suspects, as well as in population studies, genealogy and personal ancestry testing. For more complete inferences of overall bio-geographic ancestry from DNA, the mtDNA system provided here can be combined with multiplex systems for suitable autosomal and, in the case of males, Y-chromosomal ancestry-sensitive DNA markers.
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Affiliation(s)
- Mannis van Oven
- Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands.
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19
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Giardina E, Spinella A, Novelli G. Past, present and future of forensic DNA typing. Nanomedicine (Lond) 2011; 6:257-70. [DOI: 10.2217/nnm.10.160] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Recent advances in our ability to dissect the human genome and the availability of platforms for genome-wide analysis and whole-genome sequencing are expected to develop new tools for both biomedical and forensic DNA analyses. Nowadays, we can individualize single cells left at the crime scene or analyze ancient human remains. Here, we provide a general view on the past, current and likely future directions of forensic DNA analysis.
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Affiliation(s)
| | - Aldo Spinella
- Direzione Centrale Anticrimine, Servizio di Polizia Scientifica, Rome, Italy
| | - Giuseppe Novelli
- Centre of Excellence for Genomic Risk Assessment in Multifactorial & Complex Diseases, School of Medicine, University of Rome Tor Vergata, Via Montpellier, 1–00133 Rome, Italy
- Division of Cardiovascular Medicine, Department of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA
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20
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Diegoli TM, Coble MD. Development and characterization of two mini-X chromosomal short tandem repeat multiplexes. Forensic Sci Int Genet 2010; 5:415-21. [PMID: 20943451 DOI: 10.1016/j.fsigen.2010.08.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2010] [Revised: 08/27/2010] [Accepted: 08/30/2010] [Indexed: 10/19/2022]
Abstract
This study presents the development and characterization of two X chromosomal short tandem repeat (STR) multiplexes utilizing reduced-size amplicons (less than 200 base pairs) for identity and kinship testing with degraded DNA. Approximately 1360 samples across 4 U.S. population groups were typed for 15 X chromosomal STR markers: DXS6789, DXS7130, DXS9902, GATA31E08, DXS7424, GATA165B12, DXS101, DXS6795, GATA172D05, DXS10147, DXS8378, DXS7132, DXS6803, HPRTB, and DXS7423. A high degree of polymorphism was observed for each marker and both multiplexes were sensitive down to 200pg of pristine DNA. The two proposed multiplexes are suitable for forensic use, and show potential for improved analysis of compromised bone samples.
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Affiliation(s)
- Toni M Diegoli
- Armed Forces DNA Identification Laboratory, Research Section, 1413 Research Blvd., Suite 101, Rockville, MD 20850, USA.
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21
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Budowle B, Onorato AJ, Callaghan TF, Manna AD, Gross AM, Guerrieri RA, Luttman JC, McClure DL. Mixture Interpretation: Defining the Relevant Features for Guidelines for the Assessment of Mixed DNA Profiles in Forensic Casework. J Forensic Sci 2009; 54:810-21. [DOI: 10.1111/j.1556-4029.2009.01046.x] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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22
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Development of a genotyping method for potato scab pathogens based on multiplex PCR. Biosci Biotechnol Biochem 2008; 72:2324-34. [PMID: 18776692 DOI: 10.1271/bbb.80234] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Scab disease significantly damages potato and other root crops. Streptomyces scabiei, S. acidiscabiei, and S. turgidiscabiei are the best-known causal agents of this disease. We have developed a novel genotyping method for these potato scab pathogens using multiplex PCR, whose benefits include rapid and easy detection of multiple species. We designed a species-specific primer set (6 primers, 3 pairs) for the 16S rRNA genes and 16S-23S ITS regions of these potato scab pathogens. The specificity of the primer set was confirmed by testing 18 strains containing potato scab pathogens, other Streptomyces species, and strains of other genera. The application of the developed method to potato field soil and potato tissue samples resulted in the clear detection and identification of pathogens. Since this method is applicable to a large number of environmental samples, it is expected to be useful for a high-throughput analysis of soil and plant tissues of scab disease.
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23
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Hudlow WR, Chong MD, Swango KL, Timken MD, Buoncristiani MR. A quadruplex real-time qPCR assay for the simultaneous assessment of total human DNA, human male DNA, DNA degradation and the presence of PCR inhibitors in forensic samples: A diagnostic tool for STR typing. Forensic Sci Int Genet 2008; 2:108-25. [DOI: 10.1016/j.fsigen.2007.09.001] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2007] [Revised: 08/14/2007] [Accepted: 09/20/2007] [Indexed: 11/24/2022]
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24
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Mizuno N, Nakahara H, Sekiguchi K, Yoshida K, Nakano M, Kasai K. 16 Y chromosomal STR haplotypes in Japanese. Forensic Sci Int 2008; 174:71-6. [PMID: 17350780 DOI: 10.1016/j.forsciint.2007.01.032] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2006] [Revised: 01/04/2007] [Accepted: 01/05/2007] [Indexed: 11/19/2022]
Abstract
A total of 1079 Japanese males were typed for the following 16 Y chromosomal short tandem repeat (Y-STR) markers: DYS456, DYS389I, DYS390, DYS389II, DYS458, DYS19, DYS385, DYS393, DYS391, DYS439, DYS635, DYS392, Y GATA H4, DYS437, DYS438 and DYS448 using an AmpFlSTR(R) Yfiler PCR Amplification kit (Applied Biosystems). A total of 950 haplotypes for the 16 Y-STR markers were detected and, of these, 886 haplotypes were unique. The most frequent haplotype was found in 22 Japanese males. The haplotype diversity was 0.9992, indicating a high potential for differentiating between male individuals. There were 10 haplotypes with no allele detected at the DYS448 marker. Thus, the presence of such atypical haplotypes should be noted, when DNA typing results obtained from degraded DNA samples and/or DNA mixture samples from more than one male individual are being interpreted.
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Affiliation(s)
- Natsuko Mizuno
- Fourth Biology Section, Department of First Forensic Science, National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa, Chiba 277-0882, Japan.
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25
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Capelli C, Brisighelli F, Scarnicci F, Blanco-Verea A, Brion M, Pascali VL. Phylogenetic evidence for multiple independent duplication events at the DYS19 locus. Forensic Sci Int Genet 2007; 1:287-90. [PMID: 19083776 DOI: 10.1016/j.fsigen.2007.06.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2007] [Revised: 05/10/2007] [Accepted: 06/01/2007] [Indexed: 11/19/2022]
Abstract
Duplication events at Y chromosome STR loci have been repeatedly described in human populations. DYS19 is probably the best known example and it exhibits duplicate state in individuals from all continents. Despite the large amount of available data, evolutionary relationship between DYS19 duplication-bearing chromosomes has not been so far investigated. We address the genealogical correlation among such chromosomes by analysing newly identified DYS19 duplicated Y chromosomes by SNP genotyping and microsatellite-based network analysis. SNP and network analysis show that DYS19 duplicated Y chromosomes associate with different Y chromosome lineages. These results indicate that DYS19 duplication occurred more than once during human evolution.
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Affiliation(s)
- Cristian Capelli
- Department of Zoology, University of Oxford, Tinbergen Building, South Parks Road, OX1 3PS Oxford, UK.
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26
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Wegrzyn P, Jura J, Kupiec T, Piekoszewski W, Władyka B, Zarebski A, Koj A. A search for genes modulated by interleukin-6 alone or with interleukin-1beta in HepG2 cells using differential display analysis. Biochim Biophys Acta Mol Basis Dis 2005; 1762:319-28. [PMID: 16338121 DOI: 10.1016/j.bbadis.2005.11.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2005] [Revised: 10/11/2005] [Accepted: 11/01/2005] [Indexed: 10/25/2022]
Abstract
Interleukin-1 and interleukin-6 are principal cytokines involved in regulation of expression of acute-phase proteins. In the joint action of both cytokines IL-1 can suppress or enhance the IL-6-dependent induction of gene expression. Here, we report changes in the transcriptome profile of HepG2 cells exposed to IL-6 alone, or IL-1 and IL-6. Cytokine-responsive genes were identified by differential display analysis. Validation of observed changes in the transcript level was carried out using the slot blot method. Out of 88 cDNA species modulated by IL-6, only 38 represent different known genes whereas 18 clones match genomic clones in NCBI data with hypothetical cDNA sequences (the remaining 32 clones showed no homology with the database or represented several clones of the same gene). In the experiments with HepG2 cells prestimulated for 3 h with IL-1 and then stimulated with IL-6, 43 cDNA fragments were amplified. Twenty-three of them represent known genes while 10 clones have inserts matching hypothetical cDNA sequences in NCBI data. The identified transcripts modulated by IL-6 or both cytokines in HepG2 cells code for intracellular proteins of various function. The largest groups represent genes engaged in metabolism, protein synthesis and signaling pathways. Among all genes identified as differentially regulated under stimulation by IL-6, or IL-1/IL-6, six were detected in both types of stimulation. None of the typical genes coding for plasma acute phase proteins was identified in our experiments. This indicates that differential display cannot be used to characterize the profile of a given transcriptome. On the other hand, it is a useful technique for detection of new genes responding to IL-6 alone or IL-6 in combination with IL-1.
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Affiliation(s)
- Paulina Wegrzyn
- Department of Cell Biochemistry, Faculty of Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
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